Author Archives: Francis Hittinger

About Francis Hittinger

Ph.D. candidate in the Department of Italian and Institute for Comparative Literature and Society, Columbia University. Digital Humanities Fellow, Columbia University Digital Humanities Center.

Sente for PDF Management on the Mac and iPad (4): Reading/Annotation in Sente and Power Note Taking ($$tagging$$) with Sente Assistant

This is the seventh post in the series Digital Workflows for Academic Research on the Mac for the Columbia Libraries Digital Humanities Center.


SENTEANNOTATIONHEADERSYNC

In my previous installments on Sente, Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs, Sente for PDF Management on the Mac and iPad (2): Capturing and Organizing PDFs, Metadata, Tagging, Statuses, and Sente for PDF Management on the Mac and iPad (3): Quick Add, Zotero Workflow, and Automated (Re)searching, I demonstrated the lion-share of Sente’s powerful PDF and reference retrieval and organizational features and got you on the path to setting up your own efficient, and customized library for your academic workflow needs. Before that, in the second post, PDF Chaos? Digital Workflow Basics, I discussed some best practices for staging, splitting, OCRing and setting up your Sente library.

I’d like to thank guest contributor Daniel Wessel for his insightful and comprehensive (re)introduction to the methodology and practice of outlining in scientific writing, Using Content Outlines and Circus Ponies Notebooks for Writing Articles and Theses, which features as the sixth installment of the present Digital Workflows for Academic Research on the Mac and is also viewable on our Butler Library Blog. His contribution is especially valuable and salient to the present post, and I have written this post and planned the next one–which will cover OPML, Text, and Hierarchical Structure: Moving Data between Sente, DEVONThink, CPN, Scrivener and other applications (where I’ll show you how the annotation and reference information in your personal, intertextual archive you’ve built up can be exported–using third part scripts and apps–through OPML/ RTF, and RTFD to a host of different mind map and database applications, plus writing and outlining platforms for such content outlines etc.), also with his post in mind: not only should the three posts be thought of together, but in fact, they basically constitute the peak of the series’ aspiration; namely, helping you move from tools to streamlined processes and well thought out (traditional and hybrid) methodologies which actually allow you to translate your research into realized products: theses, articles, conference papers, and sharable presentations.

The annotation functionality of Sente is its most amazing feature, in my opinion, because it allows you to read and annotate your PDFs–save quotes, make comments, and highlight–and keep them organized and synchronized on your desktop Mac and iPad–and now iPhone (as I was writing this post the new iOS version of Sente was released) through the cloud! Sente is now a one stop solution for you to keep your literature and research at hand at all times. I will also discuss what I call “power note taking,” because Sente operates on a Rich and Plaintext model such that you can easily combine it with a custom tagging system for individual notes–not just references–and even write your individual annotations on captured text in MultiMarkdown first, thus allowing you to tag, use MM syntax, and maintain the integrity of citation keys (for cite and scan). “Power note taking” thus represents making the most of all the tools in the digital humanist tool box for optimizing its use while avoiding any of your hard work being trapped in a single application. By the end of your post I think you’ll be convinced of Sente’s note taking prowess and superiority over Zotero for multiple reasons, not least since it does not yet embed annotations in PDFs, still requires the use of an external editor, and doesn’t take advantage of the simulated book that the iPad and iPhone afford.

The Centrality of Note Taking in Academic Thinking and Research

Note taking is one of the most important and fundamental practices in academic research. Not only does it help you to record, capture, and the collect ideas of others, but the benefits of dialectical thinking truly spring from annotating texts while reading them. The practice and habit of annotation for the majority of academic readers–whether on a separate sheet of paper, sticky notes, subject notebooks, in margins of a book, or in an index-card system of cross-references like Luhmann’s infamous and innovative Zettelkasten, ends up being one’s personal archive of thought and the wellspring for creative intellectual endeavors on the page. Thus note taking is not merely something we do to index and keep track of the ideas of others, but it is an important, deep-seated practice for most academic researchers that ought to be systematized as a kind of extended memory that will serve a lifetime of intellectual work.

Indeed, Luhmann, as the Taking Note Blog points out,

described his system as his secondary memory (Zweitgedächtnis), alter ego, or his reading memory or (Lesegedächtnis). Luhmann’s notecard system is different from that of others because of the way he organized the information, intending it not just for the next paper or the next book, as most other researchers did, but for a life-time of working and publishing. He thus rejected the mere alphabetical organisation of the material just as much as the systematic arrangement in accordance with fixed categories, like that of the Dewey Decimal System, for instance. Instead, he opted for an approach that was “thematically unlimited,” or is limited only insofar as it limits itself.

While there is an app that attempts to replicate the paper Zettelkasten system digitally, there is no doubt that annotation practices have a wide range of complexity and idiosyncrasy such that Zettelkasten wouldn’t work for everyone anyway, and furthermore that they all have varying degrees of adaptability in new media contexts. In any case, most mainstream annotation and reading practices have been made newly complicated on several levels by the realities of and challenges to traditional reading and writing practices in academia and our society–between digital and analog, screen and page, biological and artificial intelligence, political-economic and liberal-arts/humanistic valuations, and a panapoloy of apps, devices, and interfaces. But understanding the dynamics of what is possible with the hybridized nature of the print and print-like form with technology such as iPads, iPhones, Macs and Web 2.0 when applied to evolving traditional, “philologocentric” (if I may) annotation techniques is an advance for the digital humanities in the right direction.

Not only that, but it is really about how the scholar and researcher link together, conceive of, and think about information. Text, in its jump to the cooler hybridized media forms, is still fundamentally hot as a practice, though the text straddles the two domains, and the speed and increased access to text across media means an inherent blending and evolution of hot and cool (I use the McLuhan language playfully, but there is an obvious truth to it. See this and this too, by David Bobbitt on Teaching McLuhan–“…we misconstrue McLuhan’s “hot” versus “cool” distinction when we try to force these terms into static definitions,” for more).

Screen Shot 2014-05-29 at 12.15.21 PM

Bridging this is still of key importance.

In fact, it seems this was the motivation behind Ted Nelson’s Xanadu, now released fully after 54 years, which has been thought of as one of the key experiments in hypertext that was a parallel conceptual driver of the world wide web, though Nelson doesn’t quite see it that way. Nelson himself characterized Xanadu as “proposing an entire form of literature where links do not break as versions change; where documents may be closely compared side by side and closely annotated; where it is possible to see the origins of every quotation; and in which there is a valid copyright system– a literary, legal and business arrangement– for frictionless, non-negotiated quotation at any time and in any amount.” 

Xanadu Screenshot

Xanadu.com

Moerover, Nelson’s Xanadu vision approximates my own aims here in Digital Workflows with PDFs. As the Xandau concept states:

We foresaw in 1960 that all document work would migrate to the interactive computer screen, so we could write in new ways– – paper enforces sequence– we could escape that! – paper documents can’t be connected– we could escape that! – this means a different form of writing – this means a different form of publishing – this means a different document format, to send people and to archive. We screwed up in the 1980s, and missed our chance to be world wide hypertext (the Web got that niche). However, we can still compete with PDF, which simulates paper, by showing text connections.

While I think PDF is the future and the now, Lehmann’s Zettelkasten and Nelson’s Xandau are harbingers of what is already now possible in a well-thought-out workflow using a suite of professional apps, devices, and good practices.

A key part of that, is thinking through a system of note taking and annotation that allows us to efficiently bridge the gap between digital and analog worlds without wasting time and throwing out traditional best practices of reading and annotation with the “bath water.” How do we translate these traditional modes of reading and annotation from this Changing Practices to the realities of the cloud, multiple devices, and a deluge of electronic practices and receptacles of information? Information Deluge What is(n’t) digital humanities (and why it matters)?

Credit: Digital Humanities Manifesto 2.0

Credit: Digital Humanities Manifesto 2.0

I want to think about this in a bit more depth, and in terms of the Digital Humanities. In the first post, Introducing Digital Workflows for Academic Research on the Mac I wrote that in the world of Web 2.0, there are tools and apps galore, vast databases of digitized books, articles, shared information, websites, etc. The collection and review of information involves vastly greater quantities of text and also new kinds of media and other crucial information available through the internet which offer incredibly expanded possibilities for research. However, the repository of history and the human sciences not only still predominantly exists on paper and in the library stacks–how many times have you had to scan something in the Digital Humanities Center? raise your hands–but the reality of contemporary research involves a mixture of digital and analog materials and hybridized practices not all of which are equal: a confusing complex in which we–the biological and rational creatures–must work between machines and digital media and yet still adhere to the rightly rigorous demands of linear information presentation and scholastic conventions in the production of papers, articles, and dissertations.

In other words, when it comes to how we think with text (read and work with text) we are talking about an ancient and basic part of the scientific process (note taking and annotation), and thus we are really talking not only talking about how to adapt, but also how to evolve a key and long standing scholarly practice of textual work which inherently involves negotiating convergent practices.  Indeed, this is essentially what Presner and Schnapp argue in the Digital Humanities Manifesto 2.0–in an oft cited passage:

Digital Humanities is not a unified field but an array of convergent practices that explore a universe in which: a) print is no longer the exclusive or the normative medium in which knowledge is produced and/or disseminated; instead, print finds itself absorbed into new, multimedia configurations; and b) digital tools, techniques, and media have altered the production and dissemination of knowledge in the arts, human and social sciences. The Digital Humanities seeks to play an inaugural role with respect to a world in which, no longer the sole producers, stewards, and disseminators of knowledge or culture, universities are called upon to shape natively digital models of scholarly discourse for the newly emergent public spheres of the present era (the www, the blogosphere, digital libraries, etc.), to model excellence and innovation in these domains, and to facilitate the formation of networks of knowledge production, exchange, and dissemination that are, at once, global and local.

What I propose here in the Sente workflow for annotation really goes to the core of negotiating these convergent practices. While some utterly ill-conceived and poorly thoughtout news bites out there (like this piece in the New Republic) continute to herald the collapse of the humanities because no one supposedly reads books anymore in print (to be specific, the author somehow thinks that print qua paper is fundamentally different from print qua screen: “only wealthy institutions will be able to afford the luxury of faculty devoted to studying written and printed text…The change isn’t necessarily an evil to be decried but simply reflects how most people now generate and read narratives and textthey do it on digitally based multimedia platforms”), others trumpet the use of iPads and digital forms of print–and electronic annotation, as a fundamental revolution as if it has nothing to do with its analog counterpart, clearly missing the point. As expensive as iPads and iPhones may be, they are now “market center” and as popular as the newspaper used to be. I support a reasoned, populist approach to turning the idea of the exclusivity of the humanities (and contorted unsound evaluative categories of evaluating humanistic inquiry) on its head, come on folks!

The other problem is that there is a legitimate claim in the digital humantnies that in these convergent practices print and print like articles no longer constitute the only form of scholarship. Many contemporary professional scholars are not exclusively generating the ‘linear’ outputs–in other words, many people in academia are now producing unprintable digital scholarship. (Though for me, any idea will have to be communicable and sharable in some sort of linguistic way that resembles print, gasp!– language–at some point, or else consists of a (hermetic) futurism/avant-garde). The question is how does this kind of workflow change or work with this reality of new forms of scholarship? The question is well put because if non-printable scholarship is the real trajectory of the Digital Humanities, it could be argued that print-enabling energies should be spent on a more minimalist-coding based workflow approach that–I wager–will also help prepare scholars for more coding and data driven forms of scholarship that diverge from the written page.

lexoriter

https://github.com/dhcolumbia/pandoc-workflow/blob/master/main.md

The more coding-based adherents of DH support this excellent technology stack called Sustainable Authorship in Plain Text Using Pandoc and Markdown which is solid combination of already-made graphic interfaces, script libraries and coding for the creation of “linear” print and print-like forms. This approach’s most “consumer” component would be Zotero, which it combines with Pandoc and Markdown. But simplicity is its key appeal (it is an app, a package and coding)–though it is strikingly scholastic (and terminal-text based) and may feel for the outsider and like learning Latin. Its adherents believe the learning for it is extremely efficient, and that its open and interoperable approach is equatable to the learning curves associated with a stack of apps with higher pay off at the end. My point is that in many ways this coding based approach to the DH is almost as “hot” as the analog practices that preceded it, and that annotation gets to the heart of where “convergent” practices can not only intersect but combine a Sustainable Authorship in Plaintext Approach with great applications and graphical interfaces for different functions and processes (also on amazing interactive devices like iPads and iPhones). I hope that you will see by the end of this article that there is a great advantage to extending and hybridizing this sort of stack within a Sente workflow and seeing how a Plaintext-Pandoc-Markdown (MultiMarkdown approach) can evolve within a WYSIWYG consumer tablet-smartphone-laptop setting, in this case involving a fairly normative, but powerful and serious platform that allows non-coders the ability to do serious work: reaching a market of coders, pre-coders, non-coders, professional and amateur scholars across the spectrum of possibility. Sente Library on iPadThe note-taking and later OPML-Plaintext hybrid workflow I propose here also does allow users to break free from apps that black box their work because the data is ultimately fungible as text (no data islands–provided one has understanding of how the file formats and processes work together), while on the other hand allowing one to move between and in and out of good, professional applications such as Sente, Scrivener, and DEVONthink which thus additionally allow intelligent users a great deal more power and flexibility–a dynamism which only increases exponentially when combined with the more coding based Markdown-Pandoc workflow. Scrivener and DEVONthink now offer full support for Markdown and MultiMarkdown and one can easily migrate plaintext fruitfully between these various applications.

Analog Annotation and Reading 

Sessa 1578 Dante Commentary with Renaissance Reader's Annotations. Credit: www.italnet.nd.edu/

Sessa 1578 Dante Commentary with Renaissance Reader’s Annotations. Credit: www.italnet.nd.edu/

Now that we’ve established that bridging and evolving textual practices between the hot and cool media and practices is really an important function of the digital humanities, there is a great deal of value to figuring out how to do traditional annotations, like making marginal and keyword annotations in texts; to make them actually work out in the digital medium by thinking about how it has been done since time immemorial.

In fact, my feeling on this is that the convergence of digital tools and traditional practices actually improves the traditional organization and doing of research in the analog mode in many myriad ways. Let’s take this example, a page from Dante Alighieri’s Convivio that I have annotated for my dissertation, which exemplifies the highly personal and individual “hot” medium analog experience of textual scholarship and reading in terms of “annotating” and an old school version what we now call #tagging. It also exemplifies its limitations in comparison to what computers can do.

Annotated Book

Alighieri, Dante. 1993. Convivio. Ed. Giorgio Inglese. Milano: Rizzoli

Having spent a lot of time with academics, this is more or less a classic example of how many scholars read books (some I know keep their annotations separate, but in that case would somewhat mirror their response to the text outside of it but still with it). What can we say about the defects of analog annotating?

  1. The analog annotations are locked in analog practices. When you make annotations directly on the pages, you have to have an external apparatus or filling system or cards, or index to your own highlights and quotes.
  2. The analog annotations are not searchable.
  3. Underlines are not actual records of quoted material. Underlines are ambiguous as to the meaning of the underlined text.
  4. The tags and keywords (keywords and words, as in my example, like “princes” are effectively tags) that go next to analog quotations are often times something you forget unless you immediately pair it with an explanation and commentary in a notecard or separate sheet of paper.
  5. There is little physical space for elongated commentary in marginal spaces which makes it really difficult to really comment there meaningfully whilst thinking and reading. Hence the popularity of speaking of “marginalized” literature as a metaphor for something sidelined next to a dominant and canonical text/authority. (Medievalists in the house: think scripture, Glossa Ordinaria, Corpus Iuris Canonici, Latin auctores, etc. etc.)
  6. If you have annotated a whole book, with marginal notes, underlined key quotes, and marginal keywords, some of which are cross-references, when you are working on a larger project, these analog annotations and cross-references are unable to speak to each other. Here we go to Ted Nelson’s Xanadu vision and Lehmann’s analog solution. Cross-referencing is literally like “See above p. whatever” cross referencing–hated because they are easy to break in publishing (when pagination gets off or material added or adapted)–but when we marginally annotate we hardly ever do this. Wikilinks and hyperlinks, or digital references would be great! This is why indexes were so important for evolved pre-digital print culture.
  7. When it’s intertextual, i.e. between ideas or facts or proper nouns in other works, authors or texts, if we wanted to make use of these marginal annotations, we’d really need to start manually re-hashing all of them and quickly assembling an outline before we forget why they are important, or what exactly the intertext is.

When this is migrated to the digital medium, it offers multiple improvements. The rest of this post will address how Sente and Sente assistant help us evolve all of this!

Annotations in Sente for Mac

I’ll demonstrate the annotations in the iOS Sente below, but let’s get started in the desktop Sente. If you’d like to see any of this in action, you can check out the official video on the website of Third Street Software or Dan LaSota’s Youtube video. To annotate a pdf attachment simply open the attachment by double clicking it in the library window. You can also access the attachment pane by clicking the reference and pressing command + option + G (⌘+ ⌥+ G).   In the attachment pane, above the displayed PDF file, you will note two icons (below).  annotationicons The “A” stands for text annotation, while the square frame allows you to take snapshot annotations (think about taking a snapshot picture of an image or portion of the PDF itself) by drawing the frame around the portion you wish to record. I’ll detail the snapshot function below. For now, let’s just examine the text annotation functions  (this should be active by default): all you have to do is click and highlight the text, which will bring up the annotation panel selector. Click Annotate Tis the question, highlight, comment, or quote? Obviously you can copy if you want to put the quote on the clipboard immediately. I think highlighting and commenting can serve a function, but my preference is to use the “quote” function almost all the time. This is because the highlight function merely highlights the text (like underlining it is only of momentary cognitive-reading value, being active in reading or marking something is important) , and the comment function makes a blank note. This will be more apparent when you try it out. 2014-05-16_15-49-08Generally, though, the quote function is the best because as you are reading you can highlight salient quotes, you can select whatever color you’d like, and when you press the “quote” button, Sente will automatically snag the exact text into the notes panel, and add it to a running list of notes associated with the particular PDF in the reference. This is alas, the “notes” tab within the reference editor. 2014-06-05_14-38-42 In the example, pictured here (above), I’ve taken several annotations to exemplify this feature. A few things to “note”:

  1. The default “quote” function will snag the selected text, highlight it on the PDF, and Sente, as circled above, will also place a sticky note icon (similar to Acrobat’s note icon) right next to your annotated text.
  2. Sente will generate the note title from the first sentence of the text you highlight.  I highly recommend that you title your note based on a summary or key point of the cited text–this will serve you greatly later when you start exporting your notes for content outlines.
  3. 2014-06-05_14-01-30The quoted text will appear under the title and a “comment” field will be left blank. Some people may want to simply quote the text and leave the comment field blank, others (and different people in different circumstances) will want to immediately comment. Below I’ll explain why I have so many phrases in $$tag$$ marks, but for now, the salient point is that I think it’s important to always put your comments in immediately. This function is great because traditional scholarship is reading and responding to ideas, and Sente’s quote/comment annotation function allows you to collect ideas and immediately capture your own responses.
  4. Moreover, tying your comments to the reference and with the quoted text and page number–besides obviously assisting in the beauty of dialectical thinking–allows you to avoid the sin of plagiarism! In his post on Content Outlines, Daniel wrote about how important it is that an “information unit… be tagged with the source. This requirement is crucial to correctly refer to the source when you write the text. Otherwise you can (and likely will) be found out as plagiarist (give Google a few years more). And whether deliberate or not, that time-bomb will impede or even destroy your career.”  Using Sente’s annotation feature to free associate and think with your quoted texts allows you to streamline and bridge your research and bibliographical practices and bridge them with your writing and poetic practices, while making sure you always remember where you had an idea and whose idea it is attributable to, and what page you found it on. 
  5. As you see in the example, Sente will put the page number of the place where your quote is from in the PDF directly into the page number field in the note. This alone deserves a small discussion.

Page numbers–do it write!

I mentioned this in a previous post cursorily, and it has just come up again recently in the Sente forums: the issue of correct pagination. I participated extensively in that discussion already, so what I say here will be a brief distillation of that and I’ll leave it to you to think about. Depending on the PDF you are annotating, page 1 may very well be page xi of Latin front matter. Depending on the number of blank pages before the main text starts and the number of Roman Numeral pages of front matter (intro, preface, TOC etc.), likewise, page 20 of the PDF document could, in fact, be actual page 3 (or whatever) of the Arabic number pagination in the printed text of which the PDF is a facsimile. This divergence is a complicated part of the hybridization of textual scholarship between media and is very very difficult to automate software to read it correctly. The good news is that the newest version of iOS Sente has vastly improved automating it, but it’s still your responsibility to manually correct, if necessary. I suggest doing it first along with making the annotation. It would be hell to fix later.

Therefore: thou shalt always make sure when you add an annotation that the pagination matches the published official pagination and would withstand bibliographic scrutiny.

Sente does not always do it automatically–but does so much better than Zotero, for example. I say do it “write,” because the purpose of marking and saving quotations, especially those we have comments on, is imperative for effectively citing and remembering where you found your text and for avoiding plagiarism in future writing projects. If you don’t do it right the first time, you may end up with an embarrassing error later. This is a key piece of metadata–especially when you run cite and scan routines for formatting footnotes, citations, and bibliographies. If the page number is wrong (John Doe 2014@12) and it should actually be (John Doe 2014@xi), you will end up with an erroneous note.

Color coding?

Sente allows you to color your citations according to the standard panel of colors (below). I have mixed feelings about color coding. Drosophiliac has some thoughts about color coding in his post on An Academic Notetaking Workflow. I’ve tinkered with an adaptation of his ideas for color coding, below, but I think it will be more appealing to other people as I personally have tried this and decided that it was more distracting than helpful. I know some people are obsessed with color coding and will love this sort of scheme, and perhaps I’ll try it out again sometime.

  • Red – Summary
  • Orange – Important Methodological or Theoretical Information
  • Yellow – Key Information (historical/factual/topical)
  • Green – References (to other background info, papers, specific citations to follow up on)
  • Cyan – Hypotheses and interpretations
  • Magenta – Intertexts, connections to other texts, conntections to my own projects/ideas, questions for further research

You can choose whatever you want, but should probably stick to the deafault color palette above and consistently retain labels.

Snapshot and Image Annotations

In Sente, you can also take “snapshot” annotations. This is especially helpful if you want to capture an image or or a table or figure in a PDF, for example, that does not at all translate into OCR, and is hence not really annotatable based on the document’s OCR information. 2014-06-10_11-24-10 For example, say you want to note and comment on an Image, or simply want to use it later and remix it. Just click the Square box in the annotation panel. Draw a box around the object, and click “Snapshot.” 2014-06-10_11-24-35 The “snapshot” now appears as an individual note in the notes pane. There’s nothing more to it.

Sente for iPad and iPhone: Setup and Interface Sente in AppStore

The exciting news is that while writing this post I had the opportunity to beta test the new version of Sente, which has now been expanded to work on iOS generally–to put it on your iPhone and/or iPad– get it in the App Store. Here I will quickly walk you through the features, which should be familiar to you from what I’ve already said about desktop Sente. Generally, the new Sente iOS interface offers seamless synchronization and functionality with your synchronized libraries. I tend to read just as much on my iPhone as I do on my iPad, and I’m just thrilled that everything now syncs on my phone too.  (In fact, there’s something of a phone device zombie-ism around, we are all walking around constantly glued to our devices, especially iPhones and Androids. Perhaps the addiction to devices is not a good thing, but I’ll leave you to be the judge of that). First things first. When you install a library, it will download from your cloud account. IMG_0082 The next box will ask you to decided to download all or download attachments ad hoc: IMG_0083 What you choose here should really depend on how big your iPad storage is. I invested in a 128gb capacity iPad, so I could automatically download all my attachments, but on my iPhone, which is limited to 16gb, I do download on demand, also because I have data service on the iPhone, but not on the iPad. The Sente Library screen will now pop up and your references will be installed from the cloud. IMG_0085 I won’t try to explicate this because I have already gone over the functions, such as Smart Collections, Ratings, Status etc. in the previous posts. It should just be noted that you can navigate your library that way as well as via your Quick Tag ontologies from the Desktop Sente in the iOS version too once everything has synchronized. Once your references have synchronized (and if you chose automatic sync with a very large library, you may need to give it some good time to sync), you can access your references by Pressing on the file folder icon –here “25 References in Library”– and it will open the list.

iOS Sente: Downloading Attachments

If you’ve chosen not to download automatically, you need to press the triangle button on your reference, or navigate to the “File” tab and select to download the reference from the cloud sync. IMG_0385 iOS Sente: Reference Pane

Here I will show you reference editor interface first, and later the reading and annotation interface. By way of example here is a reference with an attachment I read and annotated for this post. I’ve downloaded the attachment, so let’s get started by familiarizing ourselves with the  reference pane. iOS Sente Reference 1 There are four menus you can access here. “Reference” is the initial window, and is basically the iOS equivalent of the reference editor in the desktop version. Pressing “edit” will allow you to modify and correct the metadata of your reference, as usual. Likewise, you see that whatever statuses you setup in your library have synced here too, and you can also assign a rating.  Pressing “Tags” will allow you to add or modify tags to your reference. iOS Sente Tags Pressing the “File” menu will display the auto link options for the reference, iOS Sente Reference File Tab Here, for example, clicking the “Google Scholar” Autolink, will open the iOS Sente browser (for the record, I won’t discuss it here but you can also do target browsing and file downloading in the iOS Sente browser in a way that is similar to the desktop version). Here we see the “Google Scholar” page of similar articles. Clicking on any of the entries will allow you to enter targeted browsing mode and save new references and PDFs. IMG_0115 In any case, as I was saying before, besides the auto links, you can also open the attachment from within the reference pane: pressing “open file” will open the PDF in Sente’s reading interface. iOS Sente Reading Interface 1 You can also access the reading interface of an attachment by pressing on the icon of the PDF in the library pane, provided it’s already been downloaded. As you see, I’ve already annotated this some, but how does the digital annotation and reading work?

Sente for iPad and iPhone: Reading and Annotation

Once we tap the PDF attachment, we enter the reading mode on the iPad–which will be intuitive for almost everyone who has used a tablet at this point. You will see thumbnail previews of specific pages on the bottom of the screen. To move ahead within the document you can tap forward pages on the thumbnails, or swipe from right to left with your fingers to move between pages like turing pages of a book. Moreover, the orientation will change on the iPad and iPhone depending on whether your are holding the device vertically or horizontally. You can also zoom in a quite crisp resolution to specific sides or parts of the PDF within the Sente reader depending on what’s comfortable for your own eyes. So reading down the page I find a quote I’d like to remember. iOS Sente makes this a piece of cake. IMG_0060 Using either a stylus of choice, or my finger, I simply highlight the text i’d like (dragging the two selector dots around the text) and the annotation menu comes up. It includes the same options that the desktop version does. In this case the quote actually wraps into the next column (this is not a problem on other non-column set PDFS) setting, so to capture the whole sentence or paragraph I copy the rest of the portion on the next column first, then press quote on the selected text and go back in and am ready to paste it in my reference. IMG_0062 Note that the actual page 82 matches the page number printed in the digital text. You will always want to make sure the page numbers match. I discussed this already, and the new iOS version of Sente has made some great improvements in this arena, but as a good practice, as with all metadata, it is worth making sure it’s right the first time. Reading through the text I can zoom in close to the text easily, Sente puts a little icon next to my highlighted text, there is no pixelation: IMG_0066Here is what that annotation looks like in the annotation editor: IMG_0065 On the iPhone:IMG_0352 Serious Sente annotators will want a durable bluetooth keyboard/case combo. I use this Belkin case keyboard combo with my iPad air. It’s about $100, but why not get the most of your iPad investment? 71HxxcRO26L._SL1500_   I think having the keyboard option handy makes taking annotations on the train or bus a breeze. There are a myriad of styli out there, I don’t think it matters which one you pick, but I personally like one that feels like a real pen or pencil. The physical feedback or at least nostalgia for the traditional reading and writing practice feels really really good as an iPad (which inadvertently weights about as much as a slim scholarly hardback) digital humanist. There’s just something about holding the stylus and reading the text like an old book that I like, call it philology I guess.

Browsing Bookmarks and Annotations

Once I’ve annotated everything, I can browse my annotations and bookmarks. Click the Book icon at the top of the window in reading mode: IMG_0100 Here we can see the pages I’ve bookmarked. Press the plus button to add a new bookmark, and “edit” to edit them. IMG_0099 Going back to the reference pane, you can also view your notes and access them from the “notes” tab–and again–this time on my iPhone, not iPad. The joy, everything is synchronized! iPhone Notes Pane Otherwise, Sente’s iOS interface really allows you a lot of flexibility in browsing your documents, quotes, comments, annotations and highlights. You can view everything as a gallery of thumbnails. Sente iOS Gallery Annotations The Book icon will open a tab that contains tabs. The bookmarks and annotation tabs will take you back to your individual annotations or bookmarked pages embedded in the PDF through the Sente browser. But I like the outline tab as well because it translates and enhances the traditional table of contents function. If your PDF has the table of contents metadata built in Sente will allow you to navigate the document (book, really) by the outline TOC. IMG_0113

Searching in iOS Sente 

Another great function is the OCR search functionality. The Search Icon, with magnifying glass was added in an update 6.81 after I took the above screen shots, but was really present the whole time as well in the previous version and in the initial 6.8 iOS release via the action menu (I only mention it to make sure there’s not confusion about why it was missing in some of the other screen shots). iOS Sente Search Organizing Creativity This function is really great and enhances the reading and note taking functionality of the traditional linear printed text when translated into OCR text and made fungible on the iPad device. You suddenly have something that works like an enhanced e-text. If you want, for example, to read and annotate based on certain keywords, or tag pages based on those keywords, bookmark based on key words, Sente’s got you covered here too.  As you can see Sente will find all the instances of the search string, and allow you to navigate to the pages where it is found. It will also, as in the example (above) highlight them, in this case, the instances of “Sente” in Daniel Wessel’s book Organizing Creativity.  Obviously, other PDF readers and software have this function too, but the complex of functions under one roof, here geared towards the nuts and bolts of academic research and reference management is the key and crowning part here, and the ability of searching the PDF for OCRed text that allows you to dynamically to create and manage your own archive of metadata that pairs with your own research database.

Emailing Notes and Attachments in iOS Sente 

By this point you’re probably thinking “this is great, but how do I manage and organize all these individual citations?” You can enter your annotations in the reference pane and can always opt to send them to yourself. IMG_0383 Once you make your choice, press send and Sente will automate the process and open a new email for your in apple mail.

Power Note Taking with Sente Assistant

But what about making use of your many annotations as a personal archive? How to deploy them and find particular annotations? Since Sente still doesn’t yet allow you to tag individual notes, but only references, the Sente community has created it’s own solution to this. Many of you have by now noticed the many $$tagged$$ strings I put into my individual comments. I put them there as the digital equivalents of keyword or sticky tags or marginal key words in the margins of texts. This allows me, using the tag characters $$string string$$ along with Sente Assistant to start generating a tag index within my Sente library. Screen Shot 2014-05-23 at 11.20.56 AM In my opinion, Sente Assistant is perhaps one of the crowning examples of what kinds of practical things can occur from a determined user group dedicated to finding solutions to creating more functionality in already great software. Sente assistant is an amazing commercial-free companion application to Sente written by M. Roberts and inspired by Dana Leighton’s script, which I will discuss in the post on OPML–where I will continue showing you other applications of how to move reference and note information out of Sente into other applications as part of a complete workflow. No doubt some of these features are things I’m sure Sente’s development team are going to natively include in future releases of the software, but for now, Sente Assistant’s features add significantly to the already amazing functionalities of the iOS and OS X Mavericks suite.

Running Sente Assistant on your synchronized Sente libraries, all your notes and references become instantly accessible as a personal archive. The Sente Assistant allows you to:

  • Browse your Sente notes, sorted by their correct position on the source page
  • Perform keyword, wildcard, or tag searches of your notes
  • Search the references you select in Sente, or across all notes in your Library
  • Generate an index of all tagged notes
  • Identify duplicate references in your library
  • Save your filtered notes or search results in a single RTF, HTML, PDF, ODT, DOC, DOCX, or TXT file
  • Customize the presentation of your notes in the Assistant

Download Sente Assistant (the thread for the application is found here). The most recent version is .68, and can be downloaded here. Once you download the package, click to unzip it, and navigate to the folder. I recommend reading the entire “Read Me,” though I will repeat some of the things here. To install the Assistant, unzip the file and place the entire Sente Assistant folder inside your Applications folder. All the pieces needed by the Assistant are contained within this one folder. To use Sente Assistant drag it to your applications folder. Sente Assistant Folder I’d also drag the Sente Assistant app into your dock bar, so you can easily click on it. Now, once that is done, you need to click the Icon “Sente Assistant”–which also is an application in the task manager called “Visual Works”, open Safari, and navigate to

http://localhost:8008/senteAssistant.ssp

You will want to make a bookmark for this in your browser.

Sente Assistant Interface

Remember you have to have a Sente Library active. When your library is active Sente Assistant presents you several different options for visualizing your data. Notes and summary shows you the totality of your archive, in order of reference, as dialectic of your thoughts with other authors’ texts and intertexts. Screen Shot 2014-06-12 at 1.12.35 PM You can also save all your notes into an RTF file. Screen Shot 2014-06-09 at 2.19.41 PM Tagging Individual Notes and the Sente Assistant Tag Cloud

Sente Assistant’s preferences allow you to customize the color and textual aesthetics etc. as you’d like. Here the really important thing is how to configure your tags. I offer you something that I’ve experimented with and that think works well for several purposes. 2014-06-09_13-47-39By default, the tag format uses a hash mark (e.g., #Sente), but you can make your own custom format from the “Preferences” pane. The tag pattern you set on this page is used to generate the tag index. If you use the hash mark or another single character, your tags cannot include spaces; however, if you use curly brackets or some other characters at the beginning and ending of the tag pattern, your tags can be strings that include spaces, hyphens, or other non-alphanumeric characters. For the tag markers, only non-alphanumeric characters are recognized for tags, with the exception of a few reserved characters used by the SQLite database (e.g., single quote, underscrore, percent sign, and ampersand). To save this configuration make sure Sente is closed, and then “quit” Sente Assistant. When you quit and re-open, you have to restart Safari and the Visual Works application (this is documented in the Sente Assistant) PDF manual. iPhone Notes Pane Thus the point is that using the familiar #hashtag we are all familiar with from Twitter, it is possible to tag individual notes, but I’ve tested several combinations, and I find the most reliable tagging regime here is to use $$tag tag$$ because it lets you make both one word and multiword tags that do not interfere with other characters in the system or SQLite database, and these tags do not interfere with plain text syntax that might be useful to those who routinely use Markdown and Multimarkdown to write. The result of these $$tags$$ in my notes can be seenin the list view, when you go to Sente Assistant’s “Tag Index”–accessible from a drop box menu in the interface. Screen Shot 2014-06-09 at 2.00.09 PM The plain text $$tags$$ are all indexed and hyperlinked now: Sente Assistant Tag Index When you click on the tags within the assistant, it will take you to all the references which include the tag in that library (also keep in mind since it’s plain text embedded within the reference) you can move these across libraries and keep the tags. Sente Assistant will always interpret them.

In the next section I talk about using Markdown and Multimarkdown in notes, but $$tagging$$ with dollar signs in my Sente annotations translates into beautiful tag clouds. If you employed this over hundreds or even thousands of your own comments and notes in your Sente reference and annotation database, the sky would be the limit for harnessing the power of your personal thought archive. There are ways this can be amplified using a Wiki or DEVONthink that cannot be discussed here fully, but Sente Assistant allows this tagging, tag clouding and searching not just of all notes, but of individual notes.

This is something different for now from the Ulysses III kind of tagging using Openmeta tags, see Macademic on this, and I think that ultimately if you get DEVONthink in the mix you are all set in searching metadata. Anyway, I like this kind of tagging because it combines the best of WYSIWYG interfacing, plain text scholarship stacks, and the enhancements of digital text and tablet computing.

Idea: MultiMarkdown inside individual annotations

For those of you who use MultiMarkdown, you will probably like where I’m going with this. If you’re not familiar with MultiMarkdown, it is a derivative of Markdown and facilities easy formatting for writing hassle-free with plain text. Here’s a syntax guide for the uninitiated. The custom tags feature is great because whether you want to write in an outliner, mind map, or word processor, but desire to retain non-interference with other syntaxes, like MultiMarkdown, you could use your tag custom option and make dollar sign $$abc$$ for the tags to insert in the annotations to quoted passages.

This is great because that wouldn’t interfere with either with normal (John Done 2014@page number(s)) in texts–important for Citation Keys used in Cite-Scan functions (to be discussed perhaps in a different setting) or other identifiers with brackets in exported notes that I end up using in a body paragraph. Here’s an example I made in MultiMarkdown Composer: MultiMarkDown Composer Example So if you’re not familiar with MultiMarkdown, to summarize: if I have a note with several tags in the comments, like $$tag one$$ $$economics$$ $$aristotle$$ $$food$$, and I export the notes into a text I’m writing –and they inadvertently end up in the editor or I keep them in a note or comment to remind myself of topics etc. in the tags as mental cue of whatever I want– I don’t have to worry about interference with (Author Year@ pages) citation tags from Sente, the “# “used by MultiMarkdown for headings, or even the other bracketed [^abc xyc cdefg] syntax for footnotes. In the end (as in the above example) you can annotate directly when doing the commentary on the text if you wish something like [^See (Kaye 2007@22-25)], which generates a footnote with the scan citation i’ve chosen.  It doesn’t mess up citations [#] with page number, ex. cite a fake book.[p. 43][#fake] [#fake]: (john doe 2000@44)- etc. The tags, moreover, are rendered by MM like this: \[ tag \[.

Some people might not like this, but you can easily delete the junk when you edit your paper, or simply find replace and delete all of them when ready, and at the least it will be a reminder to you that you had tagged a key piece of information there and perhaps you should make sure you don’t need to consult the tag cloud for more information there anyway. At the moment, these tags do not coincide with Openmeta tags, but if you put them into DEVONthink they should be indexed anyway.

Help, I need to take notes on a real print book!

box-ip6-support

Iris Pen Express 6 for Mac

Get a scan Pen! I personally use an older model IRISPen express 6, but have also become familiar with a newer generation Product called WorldPenScan, Made by PenPower Inc. I have not tested it, but I have used the IRISPen Express 6, and it works for me in English, Italian, and German with about 90% accuracy–meaning that if you learn to calibrate and use it correctly, as well as hold it well and not scan two lines of text you can get pretty good accuracy of OCRing text on the fly. In any case, the point is that you can and will want to scan quotes into your Sente library sometimes without having to physically scan the book and there’s no reason why you can’t do it into a blank note in Sente–this will also sync into your library.

Doing so is self-explanatory. Get a scan pen, scan the paragraph or lines: IMG_0358   In this example, I scanned a few lines from MacKinnon’s book, which needs a bit of manual correcting. Also, don’t forget to put in the proper page number, so that you don’t improperly cite it, if you end up doing so. Screen Shot 2014-06-09 at 2.09.58 PM

Daniel Wessel: Using Content Outlines and Circus Ponies Notebooks for Writing Articles and Theses

daniel-wessel

This is the sixth post in the series Digital Workflows for Academic Research on the Mac for the Columbia Libraries Digital Humanities Center. It is written by guest contributor Dr. Daniel Wessel. Daniel is a scientist at a research institute in Tuebingen, and holds a research doctorate in Psychology from the University of Tuebingen (Eberhard-Karls-Universität Tübingen), Germany. During his dissertation thesis on supporting interest and learning with mobile devices, he became interested in ways to organize creativity in art and science (including writing a thesis).  This interest turned into a blog and a freely available eBook, Organizing Creativity (http://organizingcreativity.com). 


There is no way around it. At one point, all writers face the task of collecting and organizing all their ideas and evidence to produce a coherent written text. And academic texts usually contain a lot of complex information. Putting this information into a coherent structure can be overwhelming and seem like an insurmountable task.

However, there are different ways to facilitate this task. Scientific writing is a craft — it works by using tools on the materials you have. And the tool I highly recommend for scientific writing is a content outline.

In this text, I’ll describe content outlines, their advantages and possible disadvantages, how to create them, and using an outliner application for working with them (with Circus Ponies Notebook as example application).

Content Outlines

Content outlines are different from simple structural outlines of a text, e.g., the Introduction, Methods, Results and Discussion structure for articles, or Introduction, Main Part, Conclusion structure for essays. They are also different from to do lists (e.g., what you want to read for the text) or mere place-holders (e.g., to what you want to refer at which part of the text, like “something about x here”). 

Instead, a content outline contains all the information that is used in the final text in a flexible, self-contained structure. In other words, in a content outline, you write down everything you want to use in the text, but in short information units you can easily move around. 

Every information unit in the content outline must fulfill the following two characteristics:

  1. Independent Units: The information unit must be understood on its own. This requirement essentially means short texts, almost like bullet points on a slide, but still understandable. It allows changes in the order of the information when you create a coherent structure or narrative. You grab it and move it around and can still make sense of it.
  2. Source Information: Each information unit must be tagged with the source. This requirement is crucial to correctly refer to the source when you write the text. Otherwise you can (and likely will) be found out as plagiarist (give Google a few years more). And whether deliberate or not, that time-bomb will impede or even destroy your career.

outline_sketchThe outline itself is usually not only linear, but also hierarchical, i.e., it contains groupings of information (see sketch on the right). This mirrors the later text, as text are usually linear. But texts also contain groupings or hierarchies of information. For example, you give an overview, then go into the details. Or vice versa, you group small pieces of information into summaries. Grouping information units is crucial: Unless you aggregate information, you risk get lost in the details, of losing sight of the wood in all the trees.

In a content outline, you create this hierarchical structure by indenting information, often multiple times. This indentation gives you a visual structure and allows you to refer back to the concrete information that is the basis of, e.g., a summary. Nothing gets lost, but everything is easy to find. And it can be easily changed later on. Prior to writing you can decide in which depth (“indent level”) you want to use the information for your text.

With a content outline, you focus on getting the information down first (the bones of the text). Writing can support thinking and you should think when you externalize and collect the information in a content outline. This allows you to see which information you have available, and to group and sort it into a coherent structure. But you don’t write actual paragraphs (the “flesh” of the text). Because when you write paragraphs, the sentences stick to each other (“thus …”, “therefore …”, or merely by their implicit order). Yes, you want the text to flow from sentence to sentence, but only when you are sure that this is the order in which you want to provide the information — i.e., in the final text.

While the rough position of the material is usually determined by the structure (e.g., your analyses go into the results section, your interpretation into the discussion section), you need the flexibility to reorder information within these sections. After all, you are not putting down facts one after the other like a robot. You argue in your writing, you are writing to make a point, to show a finding, and show why it matters or should matter to the reader. As objective and as truthful as possible. But you argue, and finding that structure to organize your information into a convincing narrative is hard. Trying to create or improve this narrative when you have already written a lot of text is tedious and wastes a lot of time and effort. You have to unravel your text again and again, like Sisyphus stuck in editing hell.

Note that the information you collect in a content outline can be anything that is relevant for your text, e.g., structure information of the text (e.g., “Introduction”, “Methods”, …), summaries of studies you have read, models of theories, notes on how you conducted your studies, result tables, diagrams from analyses, notes about your interpretations of results, conclusions, etc. Nearly everything has its place somewhere in the content outline. Whether it goes into the final text is another question which you can decide later. But externalize it — and keep it flexible.

Advantages of Content Outlines

In my experience, a content outline is the best mixture of a) having information to create a structure and think about what you want to say, and b) keeping the flexibility to actually implement the structure you come up with. 

Treating your material as information units that are understandable on their own, refer back to the source information, and can be freely reordered and grouped, essentially turns writing your text into building with Lego(TM) bricks. You can build your thesis or article with these bricks, allowing you to easily deal with the information you have and change the order until you get to a narrative that works. You can also “weigh” each stone for its quality and group them into “prefabricated” parts. 

Additionally, these are some of the advantages of externalizing all the information you need for the text in a content outline:

  • You can discover contradictions and gaps: Using content outlines allows you to see contradictions and discover gaps in your arguments. Humans have a high capability for holding contradictory thoughts. If you never thought about the two distant aspects of your text together, you might miss a contradiction. Externalizing your thoughts early prevents you from stumbling upon them when you have already written a lot of — suddenly questionable — text.
  • You are less likely to forget anything: There are a lot of things you have to consider for a good scientific text. You cannot hold everything in your mind — and if you did, there wouldn’t be much capacity for anything else.
  • You have a guide for writing: During the actual writing process, it provides you with the necessary information to write a good first draft “in one go”. You do not need to look up information or do additional analyses, which interrupts the writing flow.
  • You can focus on other things: You do not have to keep all the information or the sequence of the text in mind (virtually impossible), thus it reduces the mental effort to remember information. You can use the available resources to focus on the quality aspects of scientific writing (e.g., precision and clarity).

Once you have ordered the information in the right sequence, writing can become a breeze: The logical structure is clear to see and guides the writing process. For example, when my content outline (27k+ cells/1338 outline pages/320k words) of my dissertation was finished, I was able to write the thesis document (250 pages, 71k words) in a month.

Challenges of Content Outlines

No tool is perfect, not for every task and not for every person. There are (at least) three important caveats to consider when using content outlines:

  1. There is no guarantee that the content outline “works” until you have written the text. While you can gauge the text by “reading” the content outline — you essentially have talking points — there still is a gap between the content outline and the final text. Still, with some experience, you can learn “read” the content outline fairly well to get an idea whether it works or not.
  2. A content outlines puts a lot of work in finding the right structure before starting to write actual text. Keeping the structure flexible yet having all information available avoids editing hell … but it takes a long time until you have text to show for. It’s risky if it fails. While fewer revisions might be needed, do not underestimate the final writing task (being able to type with 10 fingers is really helpful here). Also, given that much of the writing happens “in one go”, be sure you know the requirements of the text that is expected from you. A good recommendation is to write a two page writing sample based on the content outline first and give it to your supervisor for a feedback. Identify the kind of mistakes you make and keep a reminder in sight while writing the final text.
  3. Given that you write the actual text relatively late, so there is little to share with an adviser. Whereas it contains all the information in the right sequence, a content outline is very hard for others to understand. A bit like giving someone index cards with talking points and asking them to do a presentation. It would not go well. Thus, you cannot simply give the content outline to your adviser to discuss your work. However, you can either type a short summary (the hierarchical structure of the content outlines makes this easy), or verbally discuss the structure. After all, the content outline does give you the necessary talking points. The content outline is also a good basis to create presentations for colloquiums, conference submissions, etc. After all, the information is available small information units to pick and chose from.

Creating a Content Outline

If you want to use a content outline for your text, try the following steps (and have a look at the tool suggestion in the next section):

  1. Create a structure outline first. Most texts have clear structural requirements (e.g., Introduction, Method, …). Start with this structural information, as it is the highest-level structure for the content outline. Make it stand out via highlighting, bold, etc.
  2. Collect all your information in the content outline. When writing, take care to:
    • Use short notes, not full sentences for the cell content: Avoid using “connections” like “therefore”, “thus”, “this means”, etc. They connect sentences and “glue” them together and you cannot resort them easily.
    • Use square brackets […] to add context information when needed: For example, what does “this” stand for, or “these points”? Even more important: Always make sure you keep your notes in line with the direction the author argued for! Imagine you write down points “for position x” an author has mentioned. But the author overall argues strongly “against x”. In these cases it’s important that you don’t cite the author later as arguing “for x”, even if this person conceded that there are arguments it. Authors take a very dim view on being misrepresented — for good reasons. It’s essentially quote-mining.
    • Always use tags or square brackets to denote the source information: Yes, you might never write in this characteristic style now, but the text you have to write likely has the same style requirements. And once you have written text of your own in that style, it will be very hard to differentiate between text you found and text you have written. In time you might even naturally write in that characteristic style (welcome to the community). This is particularly relevant for a PhD theses which takes years to write. Trust me on this, after a few years, you will have no idea where that information did come from. And plagiarism, intentionally or accidental, damages or ends careers.
    • Within an information unit, clearly differentiate between your own notes and cited text: Related to the previous point, use quotation marks if you mix cited text with your own notes. Alternatively, if you cite a lot and suddenly write your own notes, use something like “myNote:” or square brackets […] for your own notes.
    • Be careful if the cited text refers to another text: Authors frequently refer to other sources. If they use a verbatim quote, use something like “INQUOTE:” to make clear that it is not the authors who say this, but the people they cite. If they summarize other texts, preserve the information that this is a summary by the authors of another work. Never ever simply take their citation or summary as if you had read the cited text. If you would do this, you blindly trust the authors that their citation of the other text is correct. Even worse, when authors cite other authors, they carefully select what they cite or how they summarize a paper. You have to, as you cannot cite everything and condensing naturally reduces the amount of information. But this selection or summary might bias or misrepresent the work. So in adopting a citation other authors make, you not only take their verbatim quote or summary, you also adopt their point of view. And unless you know the original text, you have no way of knowing whether you actually agree with their take on the cited work. For a striking example in everyday life, look at a controversial topic in the news and compare it to the original sources.
    • Don’t depend on, but use, inspiration: If you get inspired and come up with good sentences or ways to explain complex issues in simple ways, by all means, write them down as well. Keeping something to write handy and write them down helps, as ideas frequently come at inopportune moments. It does not matter on which medium you capture, it all ends up in the content outline anyway. While the information units are bones, sometimes a paragraph or too can be helpful as well or treated as one unit. It’s stupid to depend on inspiration, but even more so not to use it when it presents itself. And you can always split sentences into smaller information units (and frequently, you should).
    • Create a hierarchical structure by aggregating information when needed: If possible, group information and write informative summaries above the grouped information. Don’t just name the content, summarize it in your own words. For example, instead of writing that the indented information deals with “arguments for x”, write a short summary of the arguments or reduce them to one or two words each. It will be a simplification, but putting the content in your own words will help you understand it. Later you can look at the summarized information to focus on the big picture or look at the indented information to dive into the details.
  3. Continue to collect the information until you have created the whole content outline. It might seem like a good idea to go in sections, e.g., first create a content outline for the introduction, then write the “final” text for the introduction, then create the content outline for the methods, etc. However, until you know what you want and can say, it makes little sense to write an introduction (or any other part of the text). Get the bones of the whole text before you start adding flesh — otherwise you might be creating a monster.
  4. Check the content. In particular:
    • Go through the whole content outline to ensure you have everything you need for the final text: Compare, e.g., the introduction with the conclusion to ensure that you have everything for an overarching frame. Check whether you have all the necessary analyses. All the figures, etc. pp. Look for gaps and contradictions.
    • Look at the aggregated information to make sure you know which story to tell: Yes, scientific writing must be objective and truthful, but it must also be understandable to the reader. And this requires some kind of narrative, ensuring the reader understands its importance and its findings. Create this narrative and write down a short preliminary abstract of your work. A couple of sentences, no more than half a page what your work is about. Focus on the story you tell, the information you provide. Make sure the reader understands the point of your work.
    • Re-“read” the content outline, one section after the other and make sure the information is in the right sequence: Treat it like telling someone the text. Not what it is about, but the actual content. If necessary, make notes what is important and what you need to remember while writing. Use another color for these notes. The point here is to ensure the clarity necessary to express your point when you start writing. To use an analogy, like “the more you sweat in training, the less you bleed in combat”, the more (easy) changes you make in the content outline, the less (excruciating) changes you have to make in the full text.
  5. Put the content outline next to your writing software and write down the text. The beauty of the content outline is that all information is visible and in the right order. In writing, the following things might be useful:
    • Re-read before you write: Before you write a section, check whether you still think the sequence makes sense. It will also remind you of the direction the writing will go.
    • Keep the depth in mind: While the content outline gives you guidance, you can make decisions on the fly, esp. regarding the depth you want to go into. Do you want to go further and further in the indentations (details, in depth) or stick to the surface? How much detail do you(r readers) need? As you can have summaries of summaries and so on, this gives you quite a bit of flexibility during writing. Best decide in advance how deep the text will be in different sections.
    • Keep attached to the lifeline (mostly): The content outline also serves as lifeline not to stray from your original narrative. If you have new ideas while writing, you might want to stop and think whether it makes sense to include them in your writing. The content outline shows you how the structure unfolds at the moment. Decide whether it makes sense to change it. Unless it’s a really important issue, I would normally recommend to capture the idea somewhere else and use it for another text. It might also fit into the “further studies” section of the work.
    • Mark (but don’t delete) which information units you have already used: Immediately after using it, mark the information as used. For example, by using checkboxes, striking the text through, etc. Just don’t delete it. In some cases, you realize that the text is going nowhere and want to start anew with this section. Then it’s helpful to still have the outline available. It’s also helpful to have a look at the x-ray version of the text, even if you have already added flesh, e.g., for a presentation or supervisor summary.

Using Outliner Applications

Theoretically, you could create a content outline on paper. Practically, when it comes to content outlines, digital tools shine. Digital tools give you the ability to quickly deal with a lot of information in a highly flexible manner. While you can use any program from a simple text editor to Word to MindMap Apps or the like, I would strongly suggest taking a look at an outliner

Outliners use “cells” to contain information. But unlike the cells in Excel or other spreadsheet programs, you can easily move the cells to re-arrange them. Even more practical, you create a hierarchical order by indenting cells below other cells. The indented cell becomes a child cell of the parent cell it is indented under. You can then collapse all child cells under the parent cell, leaving only the parent cell visible. This makes it easy to move the parent cell around (and with it, all not-visible child cells) until you want to expand the parent cell again to view its child cells. 

To give an example, have a look at the following video (animated gif, also as Video on YouTube):

outliner_animation

This function is extremely useful for dealing with lots of hierarchical information — which is the basis for every article or thesis. You can collapse information as needed to see only the big picture, compare, e.g., information in the introduction with the conclusion to ensure a consistent frame, put lots of statistical detail information in child cells and summaries in the parent cells to help you make sense of the data, and much more. 

There are a lot of different outliner programs. Personally I use Circus Ponies Notebook, which — unfortunately — is only available for the Mac (and iPad). But the Wikipedia entry has a list of outliners, including ones for Windows and Linux. In selecting an outliner, make sure you can export the data and that it is stable even when containing a lot of information. 

For an example of a good outliner, let’s look at Circus Ponies Notebook and why it works well for creating content outlines.

Outliner Example: Circus Ponies Notebook

Circus Ponies Notebook is an app for Mac OS X and the iPad (see figure below). I strongly recommend using the Mac version and not the iPad version. The Mac version is snappy and a joy to use. The iPad version is nice when you want to have your outline available, but a bit sluggish for actual work.

cpn4 As the name suggests, Circus Ponies Notebook (CPN) uses a notebook metaphor. The concept of a notebook is intuitively familiar and provides multiple ways to structure information. You can use different notebooks for different topics, and use dividers and different pages within a notebook. On each page you can write your information in outlines. 

For an article, using a single page to collect and sort all the information is probably best. For a thesis, at least in the beginning it can be helpful to use multiple pages (one for each major section, and perhaps other pages to plan studies and analyses). 

To facilitate work, CPN provides a lot of useful functionality.

  • Cells: Cells, the Lego(TM) bricks of your writing, can be assigned with priorities, stickies, keywords (= tags), and much more. They can easily be rearranged by clicking on the gray circle on the left of the cell (triangle if it’s a parent cell containing child cells) and dragging and dropping them.
  • Cell content: Cells can handle almost any data. You can directly write text in a cell — and you will likely do this a lot. Using text allows you to easily search for it. But you can also add files like Word or Pages documents, Excel files, PowerPoint presentations, videos, sound files, images, scripts, data files, etc. pp. If CPN recognizes the file, it shows, e.g. the image itself or the first page of a PDF file. If CPN does not recognize the file, it still imports it and shows you an icon of the file. Double click it and it opens in the respective application. I would not use CPN as document storage, but inserting the necessary images, statistical analyses, etc. and being able to easily move them around? Highly useful.
  • Different copy and paste options: You can paste text with and without formatting. You can also paste text as outline. Any paragraph break will start a new outliner cell. Note that if you copy and paste cells, depending on the copy and paste method you chose, keywords you have assigned to a cell will either be preserved or lost! Check the “Edit”, “Copy” and “Paste” options.
  • Navigation: There’s a content tab on the left, a Forward/Back Button similar to a browser in the toolbar, tabs can be assigned to dividers or pages, stickies (the red one in the picture) can used as bookmarks for pages or specific cells, and much more.
  • Multidex: CPN automatically creates an index of all used words, capitalized words, Numbers, Symbols, Internet Addresses, Highlighting, Keywords (= tags assigned to cells), stickers, attachments (= files, incl. images, added to the notebook), and more. Highly useful if you search for something.
  • Export as rtfd, Word, etc.: Given that CPN is not that widely used, you might need to get your outline in a different format if you want to share it. You can export the outline as webpage, rtfd, doc, and much more. Look at the export options, esp. the “Expand all Items before exporting” option. CPN can export what is current visible in your outline (e.g., collapsed cells will not be exported/printed), or expand all before exporting. Both have their uses, be sure you get what you want.

Looking at these features in context of content outlines, you can see why this program is so incredibly useful:

  • Cell hierarchy to deal with the content information: As written above, you can indent cells to order the information hierarchically and expand/collapse as needed.
  • Pasting Text as Outline to quickly import and reorder information: If you want to restructure a document, simply copy and paste it as outline. If you want to remove the formatting, copy and paste with match style first, then cut everything and paste it again as outline (on the page, not in a cell). Given that paragraph starts a new cell, you have the text neatly separated in cells by paragraph. This separation allows you to reorder the paragraphs quickly, create parent cells with summaries of the paragraph’s content, etc. You can split a cell into two by pressing ctr + RETURN. The cell is split at the cursor position. Very useful to split imported text into smaller units.
  • Keywords for source information: As you can assign keywords to cells, it’s very useful to use keywords for the source information. For example, if you use authorname_year (or authorname_authorname_year, etc.) to name and refer to your literature, you can use this as a tag. Want to know where the information in the cell is from? Display the keywords (cmd + k) and the information is there. Note that:
    • Length of source names: Using a short reference like authorname_year does not waste much screen space (you can manually change the width of the keyword margin). Use a, b, c, etc. for multiple works by the same author(s) in the same year.
    • Assigning Keywords/Tags: To assign keywords, write the author information, highlight it, and right-click on the highlighted text and chose “Assign as Keyword”. You can then click on any cell (gray circle/triangle) in the notebook to highlight the whole cell and right-click on the cell to select “Keywords”, “Add” and select the keyword. Even better, you can select multiple cells to assign the selected keyword to all these cells. If you enter a lot of information from the same source, it can help to create a new page, enter the information there, then select all cells and assign the keyword in one go.
    • Keywords for own notes: If you want to use keywords for your own notes as well (to ensure that you remember that these are your thoughts), consider using something like “0 your_name”. The keywords are sorted alphabetically and given that you probably assign this keyword a lot, it saves lots of scrolling. Personally, I do not tag my own thoughts — any cell without keyword (or source information in the text itself) is hopefully(?!) by me.
    • Keywords can vanish when using copy & paste: However, be careful when you copy and paste cells. Depending on the copy & paste option (CPN has several), keywords are either preserved or get removed. Check after pasting that the keyword is still there.
    • Keywords and Multidex: If you want to know where you have used which source, have a look at the Multidex. The keywords have a page there. Essentially an outliner page that lets you display this information as child cells of the used keywords.
  • Text formatting (when needed): You can easily change the font (notebook wide default with the Inspector, in the cell with cmd + t). However, best use one font only. Formatting should signal which information is important, not look “nice“. Bold, italics and text colors (via cmd + shift + c) can be helpful. Personally, I use orange as color for general reminders which information must be in which section and what must be clear to the reader after reading the section. I use red for personal notes to make it stand out within a lot of cited text.
  • Highlighted cells (to indicate their indent level): Given that you can indent the cells quickly and easily, it’s sometimes difficult to see which cells belong to which parent cells, or to see the indent level on which the cell is. Personally, I use cell highlighting for the highest levels. For example, in an article, cells with the structure information (Introduction, Methods, Results, Discussion) would be highlighted green (next indent levels would be blue, yellow, orange, red, purple — it’s the way I sorted my crayons as a child and the sequence makes sense to me). Using cell highlighting can provide useful visual information about the structure.
  • flexible_checkingCheckboxes during writing: You can easily assign checkboxes to the cells (select all, right-click on the cell, “Add a Status Checkbox”). These checkboxes are invaluable when writing. Mark which information you have used immediately after you have used it. If you are interrupted or stop for a while, you can quickly pick up where you left. Note that there is a setting in the CPN Preferences (cmd + ,) under the “Action Items” tab: “Change an item’s status to “completed” when all of its children are completed” I recommend deactivating this option. It allows you to tick off the checkboxes independent of the hierarchical structure the cells are in (see figure on the right). Otherwise, checking a parent cell will check all child cells, and when you checking the last child cell, the parent cell will be ticked off as well.

 

Caveats when using Circus Ponies Notebook

If you use CPN, there are (at least) two caveats you should know about.

  1. Keep old versions of backups: Doing Backups — early, often, saved on another medium, and stored in a safe location — is good advice in any case. With CPN, make sure to keep the old backups. CPN only loads the page you want to display, so if there ever is an error in saving the file, you might not immediately notice it, but only when you open that page. In case you cannot open a page anymore, you can then go back to prior versions (don’t use Mac’s Time Machine for it, if the disk is full, old backups will be overwritten).
  2. Careful with the search and replace function: The search and replace function (cmd + f) does not show you the settings unless you click on the magnifying glass. As search and replace uses or does not use case, and can relate to the page or the whole notebook, have a look at the search settings before you search and replace. Otherwise, you might affect more (or less) than you want. BTW, be especially careful when you import text and want to replace hyphenation by using search and replace. If the text contains numbers with negative values, the search and replace might replace the minus sign too. And in contrast to words with missing hyphenation this is much harder to spot while the consequences are much, much worse.

Final Recommendation

This was a short introduction to content outlines. Two final words of advice. 

First, tools do not work for everyone and tools are not a silver bullet. I (and others) find content outlines very useful, but they will not work for everyone and for every task. Also, CPN, no matter how powerful it is as an outliner, will not work for everyone. Try out whether it works for you, there’s a free 30 day trial version available. If it does not work for you, look for a different solution. And keep in mind that even the best tools cannot replace effort and persistence, they can only help you to to augment it. 

Second, if it works for you, consider using content outlines as long-term storage for your notes, not only for writing one particular text. Just imagine notebooks dealing with different subtopics, each containing pages with outlines of notes about the domain you work in. And all the cells include the source information as part of the outline cells — which are preserved when you copy these cells into an outline for another paper. You essentially have a box of sorted Lego(TM) bricks to work with. With the hierarchical structure of these outlines containing groupings of information units, you even have prefabricated parts which you can copy and paste into a new outline for a new text. In contrast to copying from a finished text, you only copy the bones, allowing you to add new flesh to it and thus avoiding verbatim self-plagiarism. Creating these Topic Notebooks can be extremely useful for long term work with a topic. 

In this text, I did not go into the details of how a text must be structured, as this depends on the particular discipline. It should work for any discipline which requires a written text, i.e. all. But if you want to know how the actual text must look like, ask your supervisor for an exceptionally well-written work. It might be hard to abstract from it, but it might give you an idea about the characteristic style that is required. If you want to have a short look at an actual content outline, you can see the first few hundred cells of my dissertation thesis outline on YouTube

I hope using a content outline can help you putting the complex information, which is the basis of your text, into a coherent structure. Without being overwhelmed by it. 

If you have questions, suggestions, and/or ideas, I’d like to hear them. Drop me a line. You can also contact me on my blog at http://organizingcreativity.com

Sente for PDF Management on the Mac and iPad (3): Quick Add, Zotero Workflow, and Automated (Re)searching

SENTEZOTEROIn the last post, Sente for PDF Management on the Mac and iPad (2): Capturing and Organizing PDFs, Metadata, Tagging, Statuses, I demonstrated Sente’s internal browser, further showed how to use its PDF and metadata capture modes, and concluded by exploring some of Sente’s organizational features, including ad hoc Tags, Hierarchical Quick Tags, Statuses (for process), and Star Ratings. This post continues demonstrating Sente’s organizational features, showing you how to use Smart Collections (similar to Smart Groups in DEVONthink), how to build bibliographies via Quick Add, how to import Zotero libraries and make Zotero’s Firefox capture functionality part of your Sente workflow, and how to automate searches using Sente’s SRU and Z39.50 plugin. This will be a shorter post, leading up to the next post, Sente for PDF Management on the Mac and iPad (4): Reading/Annotation in Sente and Power Note Taking ($$tagging$$) with Sente Assistant.

Other ways of adding files to build bibliographies: Quick Add

Lets get right to it. If you are merely looking to capture relevant books into your library on the fly as bibliographical references only, not attachments, Sente’s “Quick Add” tool is an easy way to add a reference to your library. This is an especially useful feature when you are doing research in a library, for example, and want to add a pile of print books you are consulting into you bibliography so that you don’t forget about them. In the next post on annotations, I’ll show you how you can also take quotes and annotations from print books digitally with a scan pen, into Sente while working with paper only texts (no PDF attachments). As an aside, you can always easily import references and bibliographies from Zotero or Endnote you have already made  using Sente (see below and the Sente manual for details).

Quick Add can be accessed from the gear shaped item in the Sente toolbar. Screen Shot 2014-04-29 at 1.18.22 PM

When you click on it, select “New Reference Using QuickAdd,” and the following box will appear, prompting you to enter the item’s DOI, Title, or ISBN.

Screen Shot 2014-04-29 at 1.18.40 PM

For purposes of demonstration, I own a paper copy of Laura MacKinnon’s Consent of the NetworkedThe Worldwide Struggle for Internet Freedom (2012) and I want to add it to my demo Sente DigitalWorkFlows library as a bibliographic item–so that I can include it in a formatted bibliography later.

Here I enter the ISBN number from the book:

mackinnon-consent-of-72-dpiIMG_0149

Once I enter the ISBN, we find the entry.

Screen Shot 2014-05-13 at 8.57.14 AM

In this case the reference and metadata come through almost flawlessly, requiring only minor changes. In general, often Quick Add will work just fine for searching by author name or title. If it doesn’t get an entry with good metadata, I’d recommend using the Sente browser and importing in the targeted mode from your preferred library catalog. 

Smart Collections 

Smart Collections, as we will see when I post on DEVONthink basics, work pretty much like DEVONthink’s Smart Groups. They will make sorting through your references and attachments by keyword fairly easy. Sente also facilitates the creation of arbitrarily complex smart collections–you can also use Boolean logic–which can also be nested as deeply as desired to create hierarchical trees. But you are already familiar with Smart Collections generally from the last post: statuses, ratings, Quick Tag Hierarchies, Author, Title, Year information etc. are already built-in Smart Collections.

Here I quickly demonstrate how to make a custom Smart Collection, for example, based on keyword.

To make a Smart Collection, click on the gear menu in Sente. I almost always opt to make a “Shared Smart Collection” so that it syncs across all my devices which use the library.

Screen Shot 2014-05-19 at 3.22.12 PM

I won’t dwell on this because I find it fairly straight forward: you can create search terms which will group your references and attachments based on the specific combinations of search terms located in your metadata.

Screen Shot 2014-05-19 at 3.20.38 PM

As you see in my example, Sente then groups automatically the references which match the keywords I search for. This can be very powerful over large libraries.

Here is a Smart Collection I made for the words “economy” and some of its Latin variations:

smartcollections

 

Using Zotero in Firefox

If you are familiar with this process, simply skip to the next section. If you’re not, then head over to Zotero.com and download the Zotero Firefox Plugin. Zotero functions best, I think, as a Firefox extension, and although there is a stand-alone Mac version, Sente imports from the Firefox Zotero. Moreover as this brief demonstration will show, people love Zotero for its easy (and magical) import of bulk references, metadata, and attachments (frequently, though not always, effective) from Firefox. A case in point: Zotero allows you to quickly vacuum up a list of references from Columbia’s CLIO electronic resources search.

If you’ve installed the plug-in (you need Firefox installed, obviously) and configured Zotero (I will leave this to you, as there is ample documentation), you can access Zotero either from the Firefox tools menu (FYI: in the newest update of Firefox you can also appears as a red “Z”) or, when you are on a page that contains possible references, such as Columbia’s CLIO, a blue book looking icon will appear in the URL bar. When you click on this button, particularly, it will prompt you to import the references you select and vacuum them into your library

capture-research-data.1252992817

 

 

 

As you see, Zotero can save you a lot of time if you want to bulk collect references.

Screen Shot 2014-05-19 at 3.29.01 PM

 

After selecting everything I want, once I click OK, it all accumulates in my Zotero library.

zotero

However, it needs to be said–as I said have repeatedly–that the metadata will still often require manual correction. This is a reason that for me, personally, I prefer the one by one import method of Sente because it allows me to manually correct the metadata the first time as I add them. But there are tradeoffs, I can also see the usefulness and benefits of bulk collection and why someone might not care about doing that the first time. In any case, I can see why many people might want to integrate Zotero’s bulk collection into a Sente workflow, or at lease have the prion to do so.

Importing Bulk-collection Zotero Libraries and Migrating its Data to Sente

So how to bring it into Sente? You should know that Sente is very versatile with imports of data and not just from Zotero. Sente documentation details how to import data from many other academic reference managers, also including EndNote, Mendeley, Papers, Bookends, Reference Manager and BibTeX. Sente supports import of a variety of other reference file formats as well. I include this mostly for those of you interested in integrating Zotero into your Sente workflow,  as well as for the reason that there are many people who might want to import Zotero libraries into Sente and Zotero is widely supported at Columbia and in the DHC.

My instructions are un-creatively gleaned and adapted from the Sente manual and serves mainly as a demonstration.

A Zotero library can be imported directly into Sente, without the need to first export the data from Zotero. Sente will import all reference data, including custom fields, and attachments. Sente also scans the references being imported for any duplicates and will report any detected duplicates.

To import the Zotero references directly into Sente, follow these steps:

  1. Make sure Firefox is completely shut down.
  2. Launch Sente and either open the library you want to use or create a new library.
  3. Select the File > Import command.
  4. In the file selector that appears, navigate to the folder containing the Zotero database (MAKE SURE IT IS NOT THE DIRECTORY FOR THE STAND ALONE APPLICATION, BUT THE FIREFOX ONE!). This directory can be found by clicking on the Show Data Directory button in the Advanced tab in Zotero preferences (accessed through the Zotero gear menu). The folder path should look something like (but not exactly like):                                                                    ~/Library/Application Support/Firefox/Profiles/nm9xpxow.default/zotero.

zoteroimport5. The correct folder will contain a file called zotero.sqlite. Select the folder that contains the sqlite database; do not select the database itself.

Click Open.

6. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click “Ok” when finished reviewing the report.

As we see (below), the references I collected from CLIO via Zotero come right into Sente perfectly… 

Zoterorefsimpoted

In fact, Zotero imports plenty of ad hoc tag metadata along with the references, and the Zotero references with attachments come through as well. Any notes you have taken in Zotero will also come through into Sente, making it easy for those of you who wish to transition to Sente or those of you who want to use both as part of an integrated workflow.

Also, upon Zotero import Sente’s duplicate filter (as sounds obvious) makes sure that you are not adding junk duplicate entries. Therefore, you can always update your library (or libraries) from Zotero into Sente without risking the need to manually delete duplicates. The only caveat to this is that I would reccommend making a special library in your Sente libraries called “Zotero Import.” This could be viewed as a staging area.

The logic is the following: since the metadata in Zotero will often need to be manually corrected anyway, and since you do not want to import from Zotero, correct the data, then overwrite your corrected metadata with duplicate imports (and hence incorrect the corrected metadata), you can always import references first, and then drag them to the appropriate Sente library you wish to use them in. That way if you update the references by importing again, any overwriting of already corrected references does not become a horror for you and waste of time. Alternatively, you could import all your Zotero items, correct them immediately, or label them “correct metadata later” before dragging them to the appropriate library.

You always can drag references between local and synced Sente libraries. When you do this, keep in mind that dragging a reference (or references) does not remove it (or them) from any library but will merely duplicate the reference inside the new library you drag it to. This is why I have a master library for all (or nearly all) my references and attachments and make new libraries for particular bibliographies and projects, as I have done during this series for the Digital Workflows demonstration with the “DigitalWorkflows” library.

As always, it’s up to you, and I recommend consistency. Zotero is great software and can be used effectively with Sente, but by now all my readers should be convinced that you can create big messes by irrationally depending on bulked automation or by being lax about the organization of your metadata and library structures. I only learned this lesson the hard way, stubborn as I am, after wishing that it would work itself out: it doesn’t. That’s why I came up with the Digital Workflows project: to offer you best practices and reasoned options for doing your best and having your mind free for thinking, not having duplicated (one correct/one incorrect) references and metadata mess up your day or conference bibliography. That said, Zotero bulk collect away friends!

Automated searches and source gathering using the Z39.50 Plugin

If you like to bulk collect references to make a tickler list for example of new items or just a specialized list of library resources that you’d like to filter through and maybe eventually consult, Sente’s automated search functions are amazing. Here i’ll show you quickly how to use the Z39.50/SRU plug in to automate your searches.

Ever heard of it? Z39.50 is an information retrieval standard supported by libraries and software vendors to access information resources independent of the database location or the hardware/software used. Its syntax is very complex and as Wikipedia informs us, “supports a number of actions, including search, retrieval, sort, and browse. Searches are expressed using attributes, typically from the bib-1 attribute set, which defines six attributes to be used in searches of information on the server computer: use, relation, position, structure, truncation, completeness. The syntax of the Z39.50 protocol allows for very complex queries.”

Sente provides a preconfigured list of mainly academic libraries (domestic and international) with Z39.50 servers, but you can also configure custom SRU/Z 39.50 servers, but on that see the Sente documentation.

To set up an automatic Z 39.50 search, go to “File” and click “New Search.”

In this example, I selected Columbia’s Z 39.50 “voyager.” I can either search for a keyword,

Screen Shot 2014-04-28 at 2.25.24 PM

or elect to do more complex searches, like the following:

Z39.50 Advanced Search

When I then execute the search, it will populate a list based on those search terms from the selected catalog. In this case I get 560 references. I can then sort them, drag them to my library, filter them further etc.

searchandautolinks

Also note in the picture above, that you can view several options of autolink pages for the selected references, but in general if available the Library of Congress or Google page for the reference will often automatically show up in the attachment pane when there is no attachment for the particular reference.

In any case, when you create a new search, it is placed under the “Searches” category in the source list, rather than directly in your main library. To add individual references from the search results into your library, you can drag them from the results onto the All References item in the source list. Alternatively, you can drag the entire search into the Local Collections entry in the source list and this will automatically add all of the search results to your library.

Searches can also be set up to run automatically, checking for new results. According to the Sente documentation, automatic searches are most useful for a data source like PubMed, which has good, built-in support for update queries. The disclaimer is that automatic functionality may  work for Z39.50 searches, but can cause performance problems for large searches.

Stay tuned for the next post on annotation in Sente for Mac and iPad.

 

Sente for PDF Management on the Mac and iPad (2): Capturing and Organizing PDFs, Metadata, Tagging, Statuses

In the first post on Sente,Sente 6 Logo Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs, I showed you how to make PDF and bibliographic libraries using Sente, and made some suggestions for how to set up your library bundles, namely so that they look like this. In previous posts, I introduced Digital Workflows for Academic Research for Mac, and discussed the basics of managing PDF chaos. In this post, I will continue exploring more of the main capturing functionalities of Sente, starting off by re-capping ways to add files and entries, demonstrate proper editing of metadata using a sample PDF, then showing you how to add items to libraries and capture PDFs in Sente’s internal browser. I will conclude this post with an introduction to some of Sente’s basic organization features: reference panel tags, hierarchical “quick tags,” star ratings, and statuses.

The next post–Sente for PDF Management on the Mac and iPad (3): Quick Add, Zotero Workflow, and Automated (Re)searching IMG_0249— will mostly conclude your understanding of Sente’s organizational features, then transition to a demonstration of how to use the software both for strictly building up bibliographies without attachments (i.e. for ad hoc projects, for re-assembling and modifying bibliographies for publication, etc.), and quick adding reference items. I will also show you how to import Endnote, Zotero, and other bibliography formats (i.e. BiBTeX). I will then briefly show how to use Sente’s automated search and research functions, like the Z39.50 and SRU plugin to automate research of hundreds of academic library catalogs, and explore how this can be used in conjunction with Sente’s “Smart Collections” feature.

It’s been a hiatus in posting, but there’s been a lot going on behind the scenes. For those of you interested in what’s currently planned and in production for the rest of the series, I’ve put together a tentative road map of posts to expect in the days and weeks ahead:

  • Caveat Emptor! Data, Privacy, Price, and Purpose in your Digital Workflow (or Sente vs. Mendeley vs. Zotero vs. and others)
  • Sente for PDF Management on the Mac and iPad (3): Quick Add, Zotero Workflow, and Automated (Re)searching
  • Sente for PDF Management on the Mac and iPad (4): Reading/Annotation in Sente at home and on the go, plus Power Note Taking (#tagging) with Sente Assistant
  • Sente for PDF Management on the Mac and iPad (5): Bibliography and Cite/Scan with Word/Mellel/Scrivener/Plain Text (Multimarkdown)
  • OPML, Rich Text, and Hierarchical Structure: Moving data between Sente, DEVONthink, Scrivener, and Outline/Mind Map Applications
  • DEVONthink (1): Introduction to Databases and Information Capture/Management
  • DEVONthink (2): Key Practical Applications and Uses within the Academic Digital Workflow

I have planned to conclude the series with a couple of posts on using Scrivener, as well as some discussion of ancillary apps for iPhone and iPad that make scanning and information capture easier, especially in bridging analog/print and digital media through applications like DEVONthink, Dropbox, and Evernote.

In any case, for those of you waiting for the iPad part of the Sente discussion, I have delayed it for two reasons:

Sente for iPhone1) First, because the Sente developers are on the cusp of releasing a version natively upgraded for the latest version of Apple iOS (iOS 7), pictured to the left. This is a significant upgrade, as the interface will be changing a bit and it will also include sync with an iPhone version of the Sente app.

2) Secondly, because the most useful features of the Sente iPad application– its annotation and reading interface–are most efficiently grasped after exploring the use and functionality of those same features on the desktop application. Moreover, as the iPad application has several of the same organizational features as the Mac desktop version (besides reading an annotation), I thought it would be better to finish that side of things first so that users are acclimated to it.

 

Re-cap: Adding PDF attachment references to Sente Libraries

We previously explored how to drag PDFs into the library and capture their metadata, pairing them to a reference inside your library. To re-cap: Sente has a built in automated feature that attempts to pair the metadata to references and attachments using the DOI (Digital Object Identifier) number, if possible, as I indicated previously. For those of us not predominantly using electronic scientific journals (and especially for those of us that have lots of ad hoc OCRed scans of various exceprted print books in our libraries), this does not usually work, and we will have to import the metadata ourselves.

I previously did discuss some of the drawbacks of various kinds of metadata, particularly from Google, and insisted that it is always worth while to double check the fields of your entries, and demonstrated some shortcomings. In general, I think the best way to add new items to Sente with generally good metadata information capture when the automatic DOI import does not work is to use either OCLC – Worldcat or some of Sente’s selected academic libraries. In Sente, Stanford University Libraries–for reasons unbeknownst to me (though I’m tempted to think its because of the latter’s location in Silicon Valley)–tends to have very clean import and population of metadata fields, while Worldcat can range from excellent to not so good.

Unknown-1Because Worldcat OCLC grew into accepted universal cataloging entity as a cooperative effort over a long period of time, some differences in metadata quality appear to stem from the fact that in OCLC, historically,  the initial (or master record) of a reference was created by the first library to submit the record for a particular reference or material. Later entries of this, for example, at subsequent institutions, libraries, and collections, would then “dock” their records on to the previous, master entry. Therefore, depending on the standards or cataloging quality of the original entry, and subsequent variations, then, Worldcat-OCLC data today ranges from very clean and comprehensive to sporadically not so clean. This is not meant to be a criticism of Worldcat, but just an explanation as to the genesis of the metadata and why there is some variation. That said, Worldcat-OCLC metadata tends to be the best and most comprehensive available, and as I continue to repeat, even under the best conditions, you will often have to develop a habit of “best metadata practices,” tailored not only to the kinds of bibliographies you want to generate and use in professional capacities (style, function, audience etc.), but to the level of standards of clean record keeping you want for yourself. Since Sente is also a bibliographic generator and citation management application, I urge you to think strategically as you enter your metadata about how the item would want to look in a real bibliography–this will save you time and pain later. No matter which software you use, this is a sine qua non of a good digital workflow!

Sente’s two metadata grabbing modes

To re-cap, then, and assuming you’ve OCRed your PDF using Acrobat or Abby Finereader, Sente has two metadata grabbing modes when you drag in a PDF into your library. One option is to highlight a portion of text and search for the selected text automatically in PubMed, Google Scholar, Google Books, US Library of Congress, or Worldcat. The other option, as shown below, will automatically copy the text selected and open the option you click. You will then have to manually paste (Command ⌘ + V) into the search box to find relevant targets to click and suck in metadata.

In this example, I’ve selected a PDF from a German/Italian translation project I had worked on. Now this is perfect example of a case in which getting the right metadata in your library still requires a lot of active thought and work. Sente, as with applications like Zotero, can give the impression of abracadabraism: it’s sort of true, but not really.

Screen Shot 2014-05-08 at 10.20.20 AM

In this example, I choose Worldcat.

Screen Shot 2014-05-08 at 10.20.55 AM

We see that the result initially is disappointing, albeit this is an arcane excerpt from a German published print volume. Now, what to do? Enter it manually? Alas, sometimes you’ll need to modify your search. Here I simply delete the word “Einleitung,” and search again. The window on the right is going to function like an internet browser window. You can ust click inside and delete the word “Einleitung” or add the author’s name. In my experience, sometimes you can find the record just by tinkering, which I do:

Screen Shot 2014-05-08 at 10.21.14 AM

When I click search again: bam, Worldcat finds my entry. I’m impressed!

Screen Shot 2014-05-08 at 10.21.34 AM

Once I click the target, which in Sente is the button for gathering the metadata on a particular entry, the software will now get it for me. I’m done right? Wrong.

Among other incomplete portions in this entry, in my bibliography this would have to be cited as a book chapter. To be it clear, a “book chapter” is a category meaningful, namely, for being a section or except from a larger work–it need not be a real “chapter”, but would be an item that would appear in your bibliography with cited pages and usually an section title with “in” in relation to a fuller citation. Like so (formatted for APA 6):

Hösle, V. (1990). Vico und die Idee der Kulturwissenschaft: Genese, Themen und Wirkungsgeschichte der ‘Scienza nuova’. In C. Jermann & V. Hösle (Eds.), Prinzipien einer neuen Wissenschaft über die gemeinsame Natur der Völker (pp. xxxi-ccxcii). Hamburg: Felix Meiner Verlag.

However, looking at the initial import there are several problems. I want to show you how to get from what the bib preview looks like below, which is incorrect, to something more correct, like above.

Screen-Shot-2014-05-08-at-10.22.20-AM

The preview window is so important because it lets you see how your bibliographical citation will look. I need to make some modifications, as the citation is clearly incorrect as it stands. I click the edit button in the top right corner.

Untitled

What to do? First, I change it from “Journal Article” to “Book Chapter.” Also, note here, that this particular PDF is excerpted from a series of pages “xxxi-ccxcii”, from volume one of a two volume publication. Depending on the citation style you are using, there could be variation (i.e. it may not require some of this information), but you want the data entered correctly, and so I fill this all in, based on my preference for and use of either APA or Chicago 15-16 AD or Notes/Bibliography. Here, I also know from working with this text that Christoph Jermann and Vittorio Hösle both edited and translated this volume. So, although Worldcat correctly populated the title of the article (in this case chapter/excerpt to be cited), it does not automatically populate this information. It also leaves out the number of volumes, the pages, publisher name, city of publication. Whew!

Also, Vittorio remains the author of the section/chapter, but since it is “in” the two volume published work Prinzipien einer neuen Wissenschaft über die gemeinsame Natur der Völker, we must manually populate this information. So, here I add Vittorio Hösle and Christoph Jermann as editors, by clicking on the arrow next to their names and selecting editor for each (this same function works if you are dealing with an editor or translator, or even editors and translators, which requires a manual set up category, or correction later). I also add the correct city of publication and publisher, and set it up so that our bibliography entries will be correct, regardless of the biblio style we opt for.

Screen Shot 2014-05-08 at 11.05.35 AM

Nota bene: In Sente, it’s important that you press enter after entering the name and middle name (or initial), if any, in the author first name box, such that the initial populates and visibly  goes into the parentheses as pictured above.

This is also important because  if you don’t enter the same exact author name every time or don’t make sure the initial appears next to the name in parentheses, then you may end up with duplicate entries for the same author because one has registered the name field correctly but the other has not. Don’t worry about this too much, but in case you notice an error in your bibliography, this might be why.

When I’m done, I click edit again and change the style to the one I want this time, APA 6, and  it’s finally formatted in the citation preview the way it should look, but note that Worldcat–a generally good source of metadata, did not automatically set this up, and does so perfectly with full automation only RARELY:

Screen Shot 2014-05-08 at 10.30.45 AM

Our citation will now be correct in when we use a citation key to cite this work or want to generate a complete correctly formatted bibliography.

Screen Shot 2014-05-08 at 11.33.48 AM

You can always access the “Bibliography Preview” from Sente’s “Window” menu.

Adding files using Sente’s Internal browser

Sente also has an internal browser that allows you to add PDFs to your library from internal databases you connect to through the institutional portal, or from any internet site. Here I’m going to show you how to use Sente to access and store your research from CLIO and accessible through the Columbia University Libraries.

The first thing to do is to set up a new bookmark for CLIO. To set up a bookmark in the Sente browser for Columbia’s CLIO, first go to “Web Book Marks Setup” in the left hand library setup bar.

Screen Shot 2014-04-29 at 1.45.13 PM

Click “New Bookmark,” add the URL, and make a label, “Columbia CLIO.” Click apply.

Screen Shot 2014-04-29 at 1.45.23 PM

We now see the Columbia CLIO portal in the bookmarks menu in Sente, along with other catalogs and resources. I add CLIO for Columbia because that’s where we will be able to log in with our institutional id to the subscription databases we use for our research at Butler. The rest of this will look very familiar. Click “Columbia CLIO” to launch a browser window. As you see in the picture (above) you can also open blank tabs:

Screen Shot 2014-04-29 at 1.45.34 PM

Screen Shot 2014-04-29 at 2.28.30 PM

Using CLIO as normal, I find an article I’d like to download:

Green, H. E. (2014). Facilitating Communities of Practice in Digital Humanities: Librarian Collaborations for Research and Training in Text Encoding. doi:10.1086/67533

When I click on the entry, I navigate to the page inside JSTOR/Chicago Journals:

Screen Shot 2014-05-08 at 1.18.19 PM

You have two places you might think you can get the PDF. Honestly sometimes it’s one or the other, sometimes (as in this case) clicking either of them works, or only one. Assuming you’ve signed in with your institutional credentials, you’ll be given the following JSTOR terms:

Screen-Shot-2014-05-08-at-1.20.56-PM

Once you click accept, Sente will automatically download the PDF and the following box will prompt you to either read the file or add the file to the library as a new reference. Sente is pretty good about automatically importing JSTOR references with the DOI.

Screen-Shot-2014-04-29-at-1.48.00-PM

Once you click “add” the metadata imports flawlessly this time, and you can read your PDF and check your entry.

What if the PDF downloaded in the Sente Browser Target Mode is not OCRed? Help!

Remember that if your PDF is not OCRed, you will need to find it in the library bundle and use Acrobat or DEVONthink to OCR the file (DEVONthink licenses the Abby Finereader software for its own OCR functionality). To find the file, and open it in an external reader and/or OCR it with Acrobat for example, and OCR it, and save it from its location in the library bundle. If you are unfamiliar with the bundle, go back and read my last post.

You can click on any reference and delete/modify attachments and find other information about it in the attachment menu–which can be found in the attachment pane, toggled by pressing Command + Option + G.

Click the drop down menu, “PDF.”

Screen Shot 2014-05-12 at 1.23.12 PM

Once you click “Reveal in Finder,” you can navigate to the file in the bundle,

Screen Shot 2014-05-12 at 1.24.33 PM

then manually open it up in Acrobat:

Screen Shot 2014-05-12 at 1.26.00 PM

 

 

Initial Organization of Added References (1): Statuses for Process

Screen Shot 2014-05-08 at 10.31.04 AMThere are three other places in the initial reference editing box where you can add your own sort of metadata to references in your library: statuses, star ratings, and tags.

The first one I want to discuss is the status box, which appears in the top left corner of the reference box, as shown here (Remember you can always open the reference editor by pressing Command (⌘) + G).  The default statuses are “Incomplete,” “To Be Read,” “Discuss Further,” “Done (Not Central),” and “Done.” As you see below, these statuses appear in on of the tabs of the library in the left column, and in the library setup, the “Statuses” category allows you to modify them.

Screen Shot 2014-05-08 at 1.41.56 PM

What I like most about the “Statuses” is that they allow a lot of versatility and customization for the user in terms of labeling things purely for process.

2014-05-08_13-56-02

Here are some suggested “New Statuses” I think could be helpful, but I merely demonstrate and leave it up to you. You could also use them to label content, by language or subject, for example, or even level of criticalness to your research, but that sort of thing is more for tags, stars, and quick tags. Statuses are great for labeling stages of process in reading, annotating, thinking, tagging etc.

2014-05-08_13-57-32

 

2014-05-08_14-00-13

Here I make a new status: “Clean Up Metadata Later.” I give it a Salmon color, and will use it when I know I need to go back to clean up the metadata for entries I don’t have time to do at the moment.

2014-05-08_14-20-57

I also make a category for “Core Dissertation Text,” a “Tickler List” of research materials I’d like to read someday, if ever, and I make a status for potential bibliographical entries without attachments that might require me to physically scan an excerpt for my research later. I could use this label to make sure I don’t forget to make those scans.

As we see below, this turns up in the status list to the left once I hit apply:

2014-05-08_14-21-31

And, as we see again below, when we click the status, Sente will then sort and display all the entries by that status.

2014-05-08_14-24-13

 

Initial Organization of Added References (2): Stars

Note, you can also give various titles and references a star rating. This is self-explanatory and works almost the same as the status function, except all you have to do is click the star rating in the top right corner of the reference editor when you’re ready to give it a rating. It requires no customization. The sorting mechanism is also on the left column of the library window. Screen Shot 2014-05-12 at 11.28.32 AM I like to do this only after I’ve read the book enough to have formed my opinion about it. I think it’s a great category of custom metadata because even if something is important scholarship in the field, if I severely dislike the argument or substance, over time and with many ratings, I can sort my whole library by things I like and dislike, and also learn interesting things about my own research and scholastic preferences.

 

Initial Organization of Added Files (3): Tags and Quicktags

Book Tags

What about all the tagging? This is a big topic that will have to be kept relatively short in relation to how long it could be.  This is an image I took of some of my own research books, and I like this image because it captures two ways of thinking about tagging. One way of thinking about tagging is for individual books. When I read and annotate–and we will think about this in the post on Sente for annotation–there is taking quotatings, marking pages, and even writing notes and comments in addition to key words in the margins of texts. I still have a habit of keeping stickies and Post-Its handy when I read print books, and no one will argue that it’s helpful when you need to remember key points of areas of a book you have read. Now, as this picture shows perfectly though, this concept can be applied to libraries of multiple texts, just as it can be applied to individual texts. One kind of annotation–the kind we will discuss in the later post–is centered on citing quotable text, pages, and making custom comments. These comments, as I will show you, can also be “tagged”, Twitter style with #hashtags, and you can build a tag cloud using Sente assistant to keep track of your tags of individual notes you have taken.

Let’s hold off on this for now, because the current topic, Sente’s “Quick Tag” hierarchy, is designed to tag references and draw inferences between possibly thousands of items in your master library collection, over a long period of time. Sente makes this easy by building in functionality for complex tagging ontologies. These tags, within a Quick Tag ontology, will autocomplete when you add tags to the reference editor, but not vice-versa. In other words, if you simply add tags to the tag window when you are adding or editing your reference (below), they will not automatically become part of your “Quick Tag” ontology.

Screen Shot 2014-05-12 at 2.21.16 PM

Screen Shot 2014-05-12 at 2.24.00 PMHowever, if you build up a “Quick Tag” ontology, those tags will auto-suggest and populate in the tagging window. To understand the basics of “Quick Tags,” which can be toggled by clicking the “Quick Tags” button on the main menu, I borrow the following efficient explanation from the Sente blog, lest I make a good explanation confusing:

1) In Sente 6, keywords are words or phrases attached to references by external data sources (PubMed, Web of Knowledge, JSTOR, etc.). Tags are words or phrases assigned to references by the Sente user.

2) In Sente 6, tags can either be created and assigned “on-the fly” by simply typing new values into the appropriate field in the reference editor, or assigned from the new QuickTag palette.

3) Tags in the QuickTag palette can be organized hierarchically. That is, one can organize QuickTags into categories that nest arbitrarily deep. Note that this is different from many tagging systems that do not permit nesting of tags.

For many people, it will be most efficient to work with tags using the QuickTag palette window. This window displays the entire hierarchy of QuickTags and shows which tags have been assigned to the currently selected reference(s). Toggling tags in this window will assign or remove a tag from the selected reference(s), which makes it easy to assign tags to many references at once.

In Sente 6, tags can be used in Smart Collection definitions and Sente automatically creates a hierarchy of built-in smart collections matching the QuickTag hierarchy, so you can easily see all the references that include any particular tag.

One thing to note about the QuickTag hierarchy is that if a reference is tagged with a tag several levels down in the hierarchy, it behaves as thought it is tagged with all of the parents of that tag. For example, if the QuickTag list included a category called “Bicycles” with sub-categories of “Mountain Bikes” and “Road Bikes”, any reference tagged with “Mountain Bikes” would be included whenever references tagged with “Bicycles” are displayed. And these “implied” tags are evaluated on-the-fly, so if you were to change the hierarchy, the new structure would be used when determining which references should be included.

The practical benefit of applying this tagging hierarchy over the long–term in your main Sente Library is obvious: you will eventually be able to draw connections between many different sources.

The best practice for tagging is to try to develop some basic tags in your QT ontology first, though this takes more work early on, and try to make these autopopulate the tags in the tag window of the reference editor. Here is an example of an ontology I made, which needs to be re-designed, but will give a general impression of what’s possible.

2014-05-08_14-33-32

To design or not to design a complex QT Ontology?

This has inspired some spirited discussions amongst Sente users, and the simple answer is that there is no one uniform sort of complex QT ontology, but many possible sorts, and moreover, that different users with different interests, fields, and methodologies, will make use of this in different ways. My main point here is to merely point you in the direction of those discussions which you can browse on the Sente forum: http://sente.tenderapp.com.

Stay tuned for future posts!

Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs

This post will focus on the business of capturing, categorizing, and organizing your PDFs in a coherent library using Sente for Mac.

Sente Loading Screen

If you followed my last post, PDF Chaos? Digital Workflow Basics, I discussed the chaos that can ensue without establishing a coherent filing system for PDF documents–and illustrated it with a chaotic demo library. I then walked through some “do’s and dont’s” of filenaming, splitting, and OCRing PDFs in a library staging inbox. Here we will start to  transform this disorganized library, and you will see how you can simplify and organize your PDF Chaos while also exploring how Sente can help you with the rest of your Academic Workflow.

So for the first post (of several) on Sente, I will focus chiefly on setting up libraries and introducing Sente’s key features. I assume you will have read my first post, Introducing Digital Workflows for Academic Research, and latest post where I give some basic principles for workflows with PDFs.

 Subsequent posts will explore:

  1. Annotation and notetaking on PDFs, including tagging, and also annotating with your iPad on the go.
  2. Sente’s automated research and document collecting capabilities; smart collections; bibliographic formatting; and other selected advanced functions.
  3. How to make use of Sente Assistant and some amazing free Apple Scripts to integrate the power of OPML into your workflow so that you can move your Sente annotations into Devonthink Pro Office, Scrivener, and other software, for writing.

But, why Sente?

Some people will argue that it is not worth paying for Sente when there is other software like Mendeley, for example, which does similar things for free. This is a complex issue,  which is not as simple as free or unfree–and similar can hide substantial difference. Since it cannot be discussed appropriately here, I will post a separate, companion piece on this issue, as it also offers the opportunity to discuss some key considerations about privacy and academic work, the pros and cons of paid versus unpaid software, and a more holistic view of the various trade-offs–including functionalities like social networking–that users should consider in selecting the core application component of their Digital Workflow among software like Sente, Papers, Mendeley, Zotero, and others.

For now, let’s just say it’s my opinion that Sente really shines over software like Zotero, for example, which does not offer an integrated cloud-based synchronization system for large PDF libraries and bibliographies along with a professional solution for serious annotation and idea collection during the review and thinking phase of your research. Again, with Devonthink, OPML scripts, and Sente Assistant, I’ll show you how you can use, search, tag, organize and analyze your collected quotes and comments from reading your PDFs, and even how to drop them into outlining software and use them as fungible material for your writing and production phase of work, but Sente itself is amazing as a one stop-shop tool. Sente’s versatility is what makes it so effective for maintaining control in the research process, leaving you ready to mold and create the research product you want, and is why I have chosen it as my staple workflow application.

In fact, according to President of Third Street Software, Inc. and Sente creator, Michael Cinkosky–with whom I’ve had the pleasure of discussing Sente and his long term goals for its development in some detail in preparing this and future posts–the name “Sente” derives from Japanese:

the name “Sente” is a Japanese term from the ancient game of Go. A player is said to have sente when they are controlling the direction of the game through the force of their moves. The other player is said to have gote (go-tay) because they have little choice but to respond passively to the player with sente. My goal with Sente was to help people feel more in control of their literature research and less like they were simply struggling to keep up.

As he elaborates, this vision of control drove the development of the software’s various features to where it is today:

My primary goal when I launched this company was to make it easier for people involved in research to acquire, organize and keep abreast of the literature most relevant to their research. I had already spent many years building software systems in support of scientific research (mostly biology) but I regularly heard complaints from users about how hard it was for them to stay current with the literature. All of the reference managers at the time were focused on formatting bibliographies, not on facilitating literature discovery and organization. I asked people what tools they were using to stay current with the literature, but they never had any. Programs like EndNote were (accurately, I think) seen as formatting tools, but not research tools.

So that is the main problem we have been focused on. For the first couple of years, we did not even do bibliography formatting, but people obviously want their reference manager to format bibliographies, so we eventually added this capability. But our primary focus was, and remains, on search, acquisition, organization, understanding, etc. Thus, we have devoted significant effort to features like: hierarchical tagging (what we call QuickTags); the ability to automatically capture quotations when highlighting text in a PDF; and transparent sync that lets you have your library up-to-date at all times, across all your Macs and iPads (and, soon, iPhones). We understand that people involved in academic research never really stop thinking about their research and they want to know they are not missing anything important in their field, and that once they find something, they don’t want to lose it. Our vision for Sente is that it be integral to the day-to-day activities of becoming, and remaining, an expert in each user’s chosen area of study.

I also asked Michael about how he sees Sente in relation to “free” tools like Mendeley, especially with regards to privacy and monetization, and he was kind enough to give me some details of his vision for the future of Sente. As I already said, I will discuss these issues in a later post.

Download Sente

Now, if you’re new to Sente, head on over to Third Street Software and download it, if not you might already know the basics covered here. The free license allows you a limited library, but the $59.99 academic license is completely worth it, giving you unlimited libraries and as much cloud synchronization space you need. If you’re not convinced, use the free version until you are.

Considerations before we begin

Sente is a powerful piece of software that includes many functions. The next few posts are merely designed to demonstrate what you can do with it in some elementary ways, but I insist that–as with anything else worthwhile–if you like what you see in trying it here, you will need to eventually spend some time reading the Sente manual, especially in regards to its more complex cite and scan features, the use and modification of citation styles, the integration of Sente with Microsoft Word, Scrivener, and Mellel, setting up autolinks etc. I realize that many people might balk at this initially because learning new software can often interfere with our work and involves an investment of precious time. But the truth is that Sente is such an amazing program because it combines several functions and processes that used to belong to multiple applications, streamlines them, and as such is worth spending some time (beyond reading these posts) to learn to use properly if you like what you see.

Capture and Organization

Sente’s first amazing feature is its easy interface for capturing PDFs and organizing them, which I focus on in this post, leaving aside its research collection functionalities for later.

Before we start bringing in our PDFs, let’s set it up. I argued previously that it is really important to have a consistent system of filing. David Allen reccomends an A-Z file, and I agree. Basically, I think every Sente library (which can be set up as a local or synced library) should be set-up with the Chicago Author-Date (or APA) system in mind–and I mean this conceptually: Sente will allow you to format your actual citations and bibliography in all of the standard styles, and thousands of others. All I mean is that we will set up the library so that when you add a PDF to Sente, it will be re-named, added to the library bundle, deleted in its previous location, and given a new name based on its Author-Date-Title.

Here is a demo library, DigitalWorkflows, I’ve made for this series.

Screen Shot 2014-04-15 at 11.12.14 AM

For now, I will let the user explore the greater interface. Let’s go immediately to “Library Setup,” and “Attachment Handling.”

Screen Shot 2014-04-14 at 3.15.05 PM

“Attachment Handling” is where you set up your library. “Attachment” handling because Sente is going to allow you to create a reference in your library and attach the document to that reference.

Screen Shot 2014-04-17 at 1.30.14 PM

While there is a separate panel of Sente Preferences, the library settings are mainly here. I reccommend the following settings (as pictured above)–but the good thing is that no matter what you choose for your file names and filing system, even if you have a thousand items and attachments, Sente will automatically re-name and re-file everything for you to fit your needs and whim, even if you change your mind later.

As I indicated, I model mine on the Chicago Manual of Style Author-Date model, which is very similar to APA bibliographic model, and in any case, makes perfect rational sense:  a folder for every Author (Last Name, fore name),  a folder for the Year/Date of works, and a folder for individual Titles (which is a good policy, especially if an author has more than one book or article published in the same year).

With Sente, when the file gets added to a library with this setup, the PDF is automatically renamed too. When we press apply, as the Sente box here shows, the software will now set up this structure for your library, and henceforth automatically move the files to the bundle, rename them, and delete the old files. Again, I advise selecting “file/renaming” instead of making a copy, because it makes little sense to have multiple versions of PDF files loose on your system outside of the library–unless under special circumstances.

Go ahead, press apply. Once you hit apply, you will receive a notification explaining your choice:

Screen Shot 2014-04-14 at 10.06.20 AM

Now, you may be wondering what “inside the library bundle” means. Where will Sente put my stuff? Sente stores files inside a closed library as a Sente library file, aka “bundle” (with a “.sente6lib” file extension), but don’t worry, that doesn’t mean you can’t access it. In fact, it just means that it keeps things filed for you automatically. The bundle is like a package containing all the references, attachments, and other information that comprises your entire library. Thus each library file is a bundle in this set up, and while you can set up libraries without bundles, this is not recommended, because it presents a hazard for breaking libraries and opens the door to losing data and inconsistencies. I make a master library for all my documents, and make new libraries including those and other files–or merely import Zotero or Endnote bibliographies as libraries–for different projects or with specific products in mind.

I want to show what things actually look like in your library bundle, so that you understand the rationality of the organizing principle Sente operates on, and so that you see concretely what the above pictured configuration looks like under the hood.

Library Bundle

To access the library bundle, navigate to the folder in which you keep the Sente library file (.sente6lib file), and right clicking “show package contents.” Here is what my “DigitalWorkflows.sente6lib” bundle looks lke. What we see is our author date framework, later we will index this structure to our Macintosh finder and spotlight, and DevonThink, but now just note that while Sente gives you a beautiful interface to experience your files and use them, it is also ordering them and keeping them safe as data not proprietarily locked in its system.

Screen Shot 2014-04-17 at 1.33.16 PM

So, now that we have our library set up, have made the settings to our liking, and understand the concept behind the library bundle, let’s add our PDFs.

Adding PDFs to Sente Libraries from your PDF inbox

So remembering our messy PDF inbox, let’s one by one add the files.  Remember the article I mentioned in the last post? Namely, 724707_1.pdf? Screen-Shot-2014-04-08-at-3.26.19-PM

Screen Shot 2014-04-16 at 1.19.59 PM

To add this file, simply drag it from the folder into the Library.  Sente will then then open up a “citation lookup” box.

Citation Lookup

Now since we OCRed the PDF before, everything in it is searchable, highlightable. This makes that essential part of the workflow worthwhile. Sente goes the rest of the way: simply highlight the title of the article, and right click (which we Mac users means control click). You now get a choice of citation look up.

Sente gives you two options, one is to automatically search for the selected text on Google Scholar, Google Books, Library of Congress, or WorldCat; the second option will allow you to copy the text and will then automatically open a search box in the selected catalog or database and let you manually paste it to search for it there.  I choose Google scholar for now:

Screen Shot 2014-04-16 at 1.20.46 PM

Once I highlight the title, control click it, and select “Google Scholar,” Sente now opens its targeted citation lookup mode. Voilà, here’s our reference!

Screen Shot 2014-04-16 at 1.20.57 PM

Screen Shot 2014-04-16 at 1.21.19 PMOn the right hand side, we see a reference box with targets. Upon clicking the target that matches, Sente pulls up the reference editor, which will allow us to edit the reference before adding it to the Library.

Screen Shot 2014-04-16 at 1.21.25 PM

An aside on precise and imprecise metadata 

Now, people should understand here that Sente merely gives you access to a wide variety of options for importing “metadata” about your document. I’ve found in my experience that Google metadata tends to be inconsistent and sometimes prone to errors in precision, because it seems that they build the metadata (I assume) often by scanning title and catalog pages, and having an algorithm make somewhat accurate guesses based on large pools of data about which pieces of information, that is–type of publication, author name, editor name, press, etc.– belong to the appropriate fields. Though it is almost always better to select Worldcat (OCLC) or an official academic library catalog for importing metadata, since Google is so pervasive I wanted to show that while it does work, it exemplifies some pitfalls that you should always look out for when adding metadata period.

Thou shalt always make sure your metadata is accurate the first time, and save hours and embarrassment later

Just as I have put so much emphasis on coherent filing, so too, we must put emphasis on precise metadata–not least because with every file you add, correct metadata will ensure you can actually simply just find things in your library. Depending on the database you import your information from, you will sometimes not populate your fields completely accurately. If you do not check to make sure that it looks good the first time, and that the data is correct, you will have to spend hours later correcting it all when you go to make your official bibliography, and use the cite and scan functions. In the worst case scenario, your bibliography will have embarrassing errors later if you have to use it but don’t have time to fix it when you do notice.

In other words, we still will need (and this is often the case, because full automation is somewhat of an absurd idea), to exercise rational intelligence in populating the fields. Sente does populate the fields correctly in so far as the data input to begin with in the originating database is correct.

As a general rule, Worldcat and academic libraries, like Stanford and University of Wisconsin work quite well within Sente. You can also target from Columbia’s CLIO, which I’ll show in a later post. The point is that since you want to treat this like your real, legitimate library–because it is as real and legitimate as a paper library–you want the information to match up as much as possible the first time.

Checking your entry

Screen Shot 2014-04-16 at 1.21.25 PM

Screen Shot 2014-04-16 at 1.24.22 PMLook at this example, does anything look off? First of all, in the original import of metadata, it says “conference proceedings.” In many ways, conference proceedings will function like journal articles, but I prefer in this case, based on the information available to me, to classify this as a journal article. Always check and make sure it’s the correct sort of publication, sometimes it is not, or will require you to decide long term if you care about making the difference between the books and conference proceedings category, or the difference between certain proceedings and stand-alone articles which proceed from said conference proceedings. My advice is merely to be consistent. Moreover, note that Google scholar has populated “7247, 724707” in the pages field. This is clearly not the pages, but is the volume data information for this database publication! (If you click “add new reference” in a hurry, you just added something you’ll need to correct later, or will inconveniently discover as an error). We now discover the origins and rationale of 724707_1.pdf as a file name.

Here I not only correct the data, but take the opportunity to add the DOI (digital object identifier), and also check to make sure there is nothing out of place. If the item is an edited volume with one or more editors qua authors (i.e. the volume’s editor is the primary citable contributor) , you can change the names to “editor” by clicking the drop down box, and then click the editor category, selecting “make editor primary contributor role.”

In the “preview” window, which I have set up to preview the citation according to my custom Chicago 16 Author Date bibliographic format rules–a slightly modified Chicago 15 AD–we see what the citation would look like in a bibliography. Once I fix things and click the edit button again, the updated citation will appear in the preview. Everything seems in place. Once we click “add reference,” we now see our document added to our library, and the PDF is readable in the reading window. If you use Sente on a synchronized iPad, this will automatically synchronize.

Screen Shot 2014-04-16 at 1.24.51 PM

Stay tuned on the next post on Sente, and in the meantime get started with your new library!

PDF Chaos? Digital Workflow Basics

Is PDF chaos on your mind? Is your Digital system insane in the membrane?

This is the second post of the series Digital Workflows for Academic Research on the Mac, and it’s, for lack of a better phrase, about taming your wild wild west world of unorganized PDFs, rogue USB drive sticks, and general lack of a organized digital system. You may not realize how much of a mess your digital world may be, and if you are a pristine PDF organizer already, offer your comments at the end of todays post on how you keep it all together–I’d like to encourage discussion on this since my way is not the only way. Here I offer some general principles. But first, let’s think to the old “analog” world of things.

If your desk looks like that, you may very well be a creative genius. You may very well be that person who can legitimately claim that “it looks messy, but there’s a method to the madness.” If your desk is always perfect, you’re likely to say, “what a mess! that is madness.” Now, even if such a pile is evidence of your genius; even if this pile did once contribute to a flourish of genius and a final product, in this current state of chaotic “pileness,” I hardly believe it would be any use to you now for future consultation without sorting, collating, and long term organizing. If you were ever to need these files again to generate new ideas, or for reference, you would need to sort through this pile of papers, notebooks, print outs, newspapers, and books again into some sort of filing system to make it serviceable it again for a project. Until that happened, and you need to restore order to the pile, the pile would literally be “on your mind.”

In fact, for David Allen, the Getting Things Done guru, “your mind is about having ideas not holding them,” and one of the first tasks he recommends in implementing his GTD system is for aspirants to stress-free productivity to physically account for every single object in their desk and home office space (check out his TED talk). For Allen, loose papers, and chaotic piles of reading material can constitute what he calls “open loops” that drain our mental focus and energy–and the small behaviors that rein them in can feel “awkward”, “unnatural,” and even “unnecessary.” They only cease to be overwhelming “open loops” when we put the things into buckets and containers, and consciously decide if they are important for a project, and then wheher or not they are actionable as a step in realizing that project. In Getting Things Done (2003, 13), Allen describes these generally in terms of “commitments,” but the general behaviors are worth mentioning for us in terms of PDF workflow basics–perhaps for us we could call them “reading, writing, and research commitments”:

Managing commitments well requires the implementation of some basic activities and behaviors: First of all, if it’s on your mind, your mind isn’t clear. Anything you consider unfinished in any way must be captured in a trusted system outside your mind, or what I call a collection bucket, that you know you’ll come back to regularly and sort through. Second, you must clarify exactly what your commitment is and decide what you have to do, if anything, to make progress toward fulfilling it. Third, once you’ve decided on all the actions you need to take, you must keep reminders of them organized in a system you review regularly.

For Allen, we are foolish to depend on our psyche as a system to manage the mess of projects and things of our creativity. If so we lose perspective and ability to put our focus on what we need; we lose both control and the stability we need to keep our attention on the processes and tasks necessary to accomplish (realize) our goals.

What system? You mean, like, an operating system?

From Wikipedia: Xerox Star workstation (1981) introduced the first GUI operating system

From Wikipedia: Xerox Star workstation (1981) introduced the first GUI operating system

Now since the whole development of the GUI (Graphical user interface) and WYSIWYG (What you see is what you get) interface back at the Xerox Parc research center, and even before that, Ivan Sutherland’s Sketchpad (1963)–which produced the concept behind the user interface we are so familiar with in the Microsoft Windows and Apple Macintosh operating systems–we have to remember that even leaving the whole problem of apps aside (see my previous post), the “operating system” was from the beginning entirely modeled off the the banality of “files,”  “folders,” and note “tags” of the analog office process of the pre-digital, “paper pushing” era. Indeed this is still a valid model for all productivity and workflow (see Merlin Mann’s 43 Folders), especially in academics. In his Laws of Media: The New Science (1992), Marshall McLuhan, pointed out that the new media technology as tool forms are always an extension of our body or sensual organs. As much as a “mouse” is a bodily input device, so the folder is a digital collection bucket. In this sense, the “file,” “folder,” and “tag” concept, which Macademic has recently blogged on, is still very much an old concept–despite the recent and beneficial craze about tagging–and highly relevant to what I say here about bringing order to PDF chaos: just as you would need to have a system for naming files, filing them, categorizing them, and “tagging” them in an analog system–and depend on it consistently every single time–so you need it in its digital equivalent, without looking at the computer as something that it’s not: a semi-autonomous, automatic thing managing machine. When computer technology appears to our consciousness as a quasi autonomous interface or interactive experience–as it often does with our proliferation of apps, devices, and “multimedia”–rather than an extension of our bodies, we easily default to the Google sirens and fall in the gadget trap. We can confuse the “medium” with the “message.” That is, we believe we don’t need to manage our files and apply extensive rational intelligence to it as we would in the paper world. The ability to “Google” or “Spotlight Search” documents creates an illusion or simulacrum of a system, but it is only an operating system, that is an apparatus of files, folders etc. in which a user must use it intelligently and rationally,  deploying its tools and structure in regards to process and product. We need to have a process and deliberate collection system.

PDF Workflow. Making it work.

Crystal_Clear_mimetype_pdf

So, it’s okay if you do not have your PDF situation under control, but often a bad PDF situation doesn’t look like it would if it were a real bungle of paper mess, and you can easily be deluded about how orderly things really are, especially given the predilection (I discussed above) we have for thinking we can always “Google” things back into our conscious realm of creativity.

Two years ago I found myself literally drowning in PDFs: PDFs I’d downloaded from JSTOR or other online databases–like Ebsco, PDF excerpts of monographs or chapters of serial publications I’d scanned and OCRed using Abby Finereader in the library for my research, complete PDF books from Google Books or Archive.org, and other forms of ebooks. I realized this chaos was the analog version of a paper mess all over the place (though it disappeared and was easy to hide and consider otherwise) that was interfering with my ability to remember, find, organize, think, and act on the ideas I wanted to develop in my papers and research. Let’s be honest: though the new amazing innovation of technology gave me greater access to obscenely useful quantities of information, I could hardly synthesize and keep my documents together in a way that actually helped me squeeze out a presentation or paper. I was miserable!

Since PDFs are the digital document standard, depending on the equipment used and the number of storage Media involved, it’s clear that you can accumulate a severity of PDF chaos in a short period of time even without much effort at all. Your digital workspace can begin, just by dint of not thinking of a system for Digital Workflows with PDFs, to turn into a big bunch of PDF research “open loops:” some scan stations, to make one example, prompt users to save their PDF files to USB sticks, send to email, or upload to Dropbox. If you’re like me, then you have normally done this on an ad hoc basis–lots of PDFs are somewhere in your Gmail inbox attached to messages, some of them are scattered in various folders of your computer, others here, there, and well, on three different USB sticks–one of which you may have left in a library terminal never to see again. This is further complicated by the fact that files you scan or download may have very diverse file names, some of them “PharosScan(1)” and others the random author or title descriptor you briefly entered in passing, and many simply random digits.

Often, downloading a file from the library begins with non-sensical filenames. For example, from the Columbia’s Library website, I find an article I’d like to download and read.

Screen-Shot-2014-04-08-at-2.57.20-PM-300x184What is the file name when I click to download it? Screen-Shot-2014-04-08-at-3.26.19-PM That’s not entirely helpful, and certainly not anything like PowleyEtAl.2009Enriching.PDF. I doubt I’d remember where it is or that I ever intended to look at it with this name. It’s also not helpful if I have multiple download locations for different browsers. Nor is it helpful if a PDF is not OCRed first, and yet I fail to OCR it, label, and file it immediately. In this case, it turns out my PDF is already OCRed. But if it were not, I’d need to open the document in Finereader or Adobe Acrobat Pro (Devonthink Pro Office, also has an OCR option, which we will discuss later).

Thou shalt always OCR your PDFs immediately

Every workflow needs to have a system for OCR scanning (optical character recognition), naming, and containing PDFs. Once you have your PDFs scanned, downloaded and OCRed, you also need to have a place where you keep, annotate, and use your PDFs and can name them according to the same parameters every single time (for example, author/date/title);  where they can be updated and stored coherently. It’s also important that they never disappear within the proprietary grasp of an application.

So to illustrate the point of (and the magnitude of the mess really depends on what system or lack thereof you have cultivated and how many files you have), I’ve assembled a smattering of PDF files from an old USB stick, and I will eventually show you, in the next post, how Sente can come to the rescue. The rest of this post will simply illustrate some considerations in preparing files for import into your permanent system. As you see, for this demonstration I’ve merely found and downloaded a couple of other files in an old USB stick back up I found on my desk. It perfectly illustrates my pre-workflow lack of a system.

How useful do you find all these random file names? Screen Shot 2014-04-11 at 2.55.57 PM Even if you don’t remember what the hell “filetmp_1389908321.pdf” is, Sente will not only help you remember, but will help you capture its bibliographic record, and allow you to set up a coherent library system for containing it.

But before we go there, let’s go ahead and OCR the files, if necessary. This is a must do, first of all, because it is impossible to effectively keyword search, read, annotate, and import the bibliographical information of un-OCRed PDFs, even leaving any applications aside. One of the greatest things about Sente is that it will allow you to almost instantly capture the correct bibliographic information of PDF documents from online databases, re-name, and file the PDFs for you into a usable library. Sure some other software does something similar, but I promise Sente gives you more power and control. In any case, even if you someday opt not to use Sente, OCRing your texts and renaming them is good practice. Now, also remembering our whole above discussion about folders and real files, you also need to create an ‘inbox’ for PDF documents  as part of your workflow (In a later post i’ll show you how Devonthink Pro Office lets you automatically import and OCR PDFs–and, additionally, create an intelligent and AI enhanced filing system).

Make a folder on your desktop or in your downloads folder where you’ll keep PDFs that need to be OCRed and then processed into Sente. I’ve called this now “To Add Sente,” in my example. Sente allows you to capture and download PDFs directly using its own browser, but you’ll want an inbox for “to add” files too since you will sometimes want to put them in different libraries or add them to Sente later, if needing OCRing, and if you’re not downloading them directly from a database.

If your PDF is not OCRed, I highly recommend using Acrobat Pro. The Academic license is only about $100, and it is well worth the cost.

OCR With Adobe Acrobat

Screen Shot 2014-04-10 at 11.35.13 AM Once in Acrobat, open your document. If the text does not highlight, or the text pasting comes out garbled, click Tools, then “text recognition.” Click “in this file.” Screen Shot 2014-04-10 at 11.38.39 AM For most needs, 300 dpi is the minimum acceptable on most grayscale texts, while 600 dpi is archive quality. Depending on the power of your CPU and the length of the documents, 600 dpi takes longer, but you will want to run it at 600 if your text has particularly small text and apparatus, in more than one language. Other software, like Abby Finereader on the PC offers options like 400, but since there’s no intermediate here, I usually choose 600. In the example, I select 600 dpi, and choose English as the language (Acrobat allows you to choose from a long list of languages!).

In my example folder, I’ve now OCRed this file. I’ve also checked that all my documents are OCRed. They are, but I come across a particular situation.

Thou shalt spilt your PDFs, and only then OCR them!

Here is a PDF (in German) that I worked from as translator of a monograph.

Screen Shot 2014-04-10 at 3.59.06 PM

The problem: every one page of the PDF is horizontal orientation, containing in two real book pages. We see the jump here from analog to digital though the scan medium, and the problems it can pose. Most people would find this annoying and think it doesn’t really matter. My opinion is that it does: if you don’t split the document, and re-OCR it you risk:

1) Garbling cited page numbers (John Sidiropoulos has thought about this a lot and it’s important). If you really use and annotate the document in the future, and you cite text on page two that might actually be either real page XXXII or page XXXIII, it’s better if each real page stands for only one page: pg. 2 PDF = XXXII, pg. 3 PDF = XXXIII. This cuts confusion. If you don’t split the PDF now, it is a real pain and gets in the way of your work later.

2) The second risk is that you copy a quote that spills across the entire horizontal page, so for every line of one paragraph on the right, you also get the adjacent line on the left. This is not always the case, but by golly, why bother with that kind of problem?!

It is essential for any workflow to split these dual-paged PDF files. A lot of scan stations automatically do this now, and Finereader does too in the DHC. But if you come across a PDF that is from before this was common, or otherwise find a scan like this, you just need to split it. When you want to cite the page of a PDF, no software will always perfectly number its pagination anyway. There may be a mismatch between the PDF page and the real page of the printed text, just split it so that you can be closer to solving this problem, and save extra confusion. We want things clean and für ewig, to invoke Goethe, which means something like “for all time” in German. Your PDF library is not an ad hoc matter, think about it like your real pristine print library–would want to use real printed books with messed up pagination? Not really.

You want to keep things clean and consistent.

Splitting a PDF

While Acrobat can also split PDFs, I recommend people do this task first always, and use a nifty freeware app called PDF scissors. 

Screen Shot 2014-04-10 at 3.31.37 PM   Open your file. Screen Shot 2014-04-10 at 4.02.05 PMChoose all together. It will then “stack” your file, and allow you to select “crop” into a single PDF. First though, you need to drag a rectangle around the borders of the pages. A safe place  to crop is outside the thick overlapped text. You will have to guess exactly where the center of the page is. Usually you will see a clearly darker line in the very center between pages, and in some cases this center is very clear because there is no text in it. Screen Shot 2014-04-10 at 4.09.05 PM Our new file is now clean, and ready! Once I save the file, here “singleeinleit,” and check it for accuracy, I should delete the double version! Why have a garbage file you might accidentally use then have to think, “where is my split file”? Screen Shot 2014-04-10 at 4.10.31 PM This file can then be OCRed in Acrobat and saved.

With all of our PDFs split and saved,  we are ready to build our Sente library.

In the next post of the series, Using Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs, I’ll show you how we can use Sente to automatically capture the correct bibliographic information of each PDF, automatically re-name and file each by author, date, and title in a permanent system, and how to index that library bundle for broader use within your operating system, while protecting its integrity.

Introducing Digital Workflows for Academic Research on the Mac

Annotating on Sente 6

This is the first, introductory post of what will be a series of posts for the Digital Humanities Center on the topic of Digital Workflows for Academic Research for Mac.

Digital workflows? What does that mean? Does this involve apps and nifty tools, hacks, and tutorials?

Yes. Good news for the huddled masses staring at their device and computer screens night and day, including the e-masses huddled in Butler library: of course this is about apps–plenty of apps. Apps for your iPhone, iPad, and Mac; web-based apps, cross-platform apps, I may even mention some PC apps. “There’s an app for that” is now quasi-proverbial (Thanks Apple!), and I promise to deliver here some great approaches—nifty tools, hacks, and tutorials—to help Columbia Mac users go from the phase of information collection and capture between print and digital media of academic research, to the analysis, annotation, and creativity phase of article and publication production, all while navigating the many questions and time-wasting puzzles that inadvertently arise between our Gmail inboxes, dozens, hundreds, or thousands of (either OCRed or unOCRed) PDFs, our own notes, web snippets, nuggets of data, bibliographic inanities, and the blinking cursor of the word processor in writing projects—before anything arrives at a publisher, conference, or your adviser’s desk (ahem, I mean, Gmail inbox) in the form of a reviewable piece of your own academic writing.

Why Mac? This series focuses nearly exclusively on Mac for two reasons:

Over the last ten years, along with Apple’s rising popularity, the Mac share of the higher and secondary education market is now at a saturation point that dwarfs its previous educator friendly reputation of the late 1980s and 1990s. According to some studies, as many as 60-70% of undergraduate and graduate students at major institutions use Mac exclusively—and also increasingly iOS devices (iPads and iPhones)—as their primary devices for school and study, as well as for recreation and personal use. While the Mac share of the market is still nowhere nearly as large as the PC, Mac users are beginning to predominate in education, engineering, and science. iPads are also becoming a serious learning tool.  Columbia’s academic Mac users are no exception.

Because of this, there is now an active community of software developers and innovators—including many students, faculty, and scientists at the institutional level—working together to make new tools and approaches for improving methods for “digital” academic research (for example, Macademic) in the humanities, sciences, and social sciences on the Mac platform. Many of the hottest applications and workflows for academic research now are clustering around the Mac. This is not to say that there are not great tools or there is no development being done in the PC/Wintel arena, but this year we decided that we wanted to help the sizable Columbia Mac student/faculty community by introducing them to the possibilities that they may not know of, as well as offer them some support for exploring digital workflows on the Mac at the Butler Digital Humanities center.

Annotating on Sente 6 for iPad

Annotating PDFs with Sente for iPad

The fact that there’s an app for that is a good thing, because writing and researching is hard work. Mac software like Sente 6 (with Sente Assistant), Devonthink Pro Office, Scrivener, OmniOutlinerNovamind 5 Pro, harnessed with the power of open-source Apple Scripts, a conceptual understanding of OPML architecture–and a demonstration of the general principles behind the practice of the digital workflow, which I hope to introduce (albeit not exhaustively) in the series–will present the user who wants to improve his or her digital process with real solutions for accomplishing efficient, organized, and research, while saving time and frustration, and  avoiding organizational catastrophes (which can delay or even undermine the realization of creative work) between iPhones, iPads and the Mac. For example, how to use Sente to annotate and read PDFs on the go on an iPad, keep them synchronized with cloud-based libraries, and how to use Mac Sente to import coupled bibliographical information with your PDF libraries cleanly and also export your organized annotations and quotations for use on your thesis or book projects.

I’ll offer some very tailored approaches I’ve discovered in the process of doing my own dissertation research and preparing this series as a Digital Humanities Intern this year. Daniel Wessel’s blog, and now book by the same title, Organizing Creativity, however, is a must-see for anyone who is ready to dive into the theoretical and highly detailed practical considerations of realizing creative work in the digital world generally, and has been a major influence on the approach I have developed (Thanks, Daniel!). The highly technical experiments in scripting on the Mac with various applications for academic research by John Sidiropoulos over at OrganoGnosi, moreover, have also been formative in developing this series, and offer a glimpse (for both expert users and novices) into the very many difficulties faced in trying to make and streamline a series of processes, like simply organizing and keeping PDFs, bibliographic information, and annotations together across applications, according to various needs.

But I will not cover every possible app and solution, nor pretend to, because the flip side of the there’s an app for that culture, is that the proliferation of tools and infrastructure for productivity offers little coherent and cogent guidance in the best tuned methodologies for actually accomplishing sharable, realized research.

Not only does new scientific research show that that true “multitasking” is a myth–yes, you know that checking your email, your Facebook, texting, reading a book for the first time and writing a term paper on it simultaneously does not really work out–but also that the value of the multiverse of e-and-iWhatevers which promise us shortcuts and “streamlining” of many tasks may not be as helpful as all the hullabaloo makes them appear, especially not when doing serious intellectual work. As Ryan Kalember pointed out recently over at Quartz (along with many, many others), perhaps “The biggest productivity killer is that there’s an app for that … and that … and that, too.” We are not only drowning in a panoply of devices, apps, and WiFi connections, but these rapid advances in technology –and the cultural mindsets and practices which follow–as represented by the app mentality, can contribute both to the illusion of productivity and careful goal-driven work, and at the very least raise serious questions about the app mindset in regard to tackling serious intellectual challenges.  

Katherine Xue, in an article on the app youth culture in Harvard Magazine, cites a recent book by Howard Gardner and Katie Davis, The App Generation:

“This is a generation that expects and wants to have applications,” says Gardner. Applications, more commonly known as apps, are shortcuts designed for accomplishing specific tasks. They’re ubiquitous, powerful, and strongly structured, and the authors argue that they’re changing the way we think. “Young people growing up in our time are not only immersed in apps,” they write, “they’ve come to think of the world as an ensemble of apps, to see their lives as a string of ordered apps, or perhaps, in many cases, a single, extended, cradle-to-grave app.” The app mindset, they say, motivates youth to seek direct, quick, easy solutions—the kinds of answers an app would provide—and to shy away from questions, whether large or small, when there’s no “app for that.”

Now, those born in the 1980s or earlier are likely to remember a world in which the entire stuff of academic research—that is, reading and writing—were, well, analog! Doing research, as it had been done, since perhaps the time of Gutenberg–or even earlier in the scholastic libraries of the Middle Ages–meant the following experience (which most graduate students and faculty who work in Butler should be familiar with): going to a physical library, handling dozens of real (often heavy) books, selecting them, and reading them. With pen and paper—or some other form of recording device like vellum (skin)—collecting, analyzing, capturing, recording, and synthesizing information both as quoted and cited from reading texts and from one’s own thoughts and reactions to the quotes, facts, narratives, and textual varia of other “authors” and “texts,” often over long periods of time and on a variety of projects or subject matter. Fast forward to the 20th century, post 1970s, and this perhaps included making “photocopies” of articles, snippets, or the title pages of references on the “Xerox machine” (hot 1980s technology!) or using an electric Microfilm or Microfiche reader to locate archival information or back periodicals. The general principle of organization involved custom systems of note cards, labels, binders with dividers, individual notebooks, etc. Usually some form of handwritten material and a series of sources, with comments, were organized at a desk and eventually, the researcher drafted a creative, new piece of research by hand or on a typewriter. 

A workflow for academic research from around 1984, until around 1996-2000, when the internet began to go mainstream, retained most of the above aspects, and might have been “digital” in so far as it operated on some sort of x86 silicon chip, and involved a “word processor” with bibliographic management software like Endnote. The former was little more than a more versatile typewriter, and the latter a translation, so to speak, of a card catalog model of bibliographic reference keeping to a digital medium. 

Enter Digital Workflows for Academic Research circa 2014. In the world of Web 2.0, there are tools and apps galore, vast databases of digitized books, articles, shared information, websites, etc. The collection of information involves vastly greater quantities of text and even new media of citable and crucial information available through the internet and offering incredible new possibilities for research. However, the repository of history and the human sciences not only still predominantly exists on paper and in the library stacks–how many times have you had to scan something in the Digital Humanities Center? raise your hands–but research now not only involves a mixture of digital and analog materials, but a confusing complex in which we–the biological and rational creatures–must work between machines and digital media and yet still adhere to the rightly rigorous demands of linear information presentation and scholastic conventions in the production of papers, articles, and dissertations. In short, little has changed about the craft of writing and doing scholarship, but much has changed which makes doing focused and productive scholarship more challenging when working between many sources of digital and analog information, and its “online” and “offline”–so to speak—synthesis by the “knowledge worker.”

Using OPML based outlining in Novamind Pro

Using OPML based outlining in Novamind Pro

The situation we face today generally requires students, writers, scholars and academics not only to employ research methodologies appropriate to their disciplines (or even interdisciplinary methods to answer questions which now transcend traditional spheres of academic expertise) but research methods and “workflows” which bridge what Marshall McLuhan, the visionary prophet of the 1960s, called the “hot” and “cold” media of today.

My series will not only offer some solutions to the above challenges for Mac users, but will also implicitly show how the older methods of research known to the pre-1990sbunch of us can benefit Millennial “app” scholars as much as the latter can benefit those of us seeking to integrate new technology into the old business of knowledge production. 

Stay tuned for a series of posts through the end of the spring semester on topics such as PDF management, outlining, syncing annotations to PDFs by quote, page number, and comment, searching your own tagged annotations in Sente and Sente assistant, building outlines and storing information for dissertations and books in Devonthink Pro Office, writing in Scrivener, OPML and outliners, and using your Mac and iPad for succeeding in your academic writing pursuits.

Academic Database with Devonthink Pro Office

Academic Database with Devonthink Pro Office