Academic Workflow

Discussion in 'Mac Apps and Mac App Store' started by skaertus, Apr 23, 2014.

  1. skaertus macrumors 68030

    skaertus

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    #1
    Last year I finished my PhD thesis. However, I am not entirely sure that I used the most efficient workflow for academic research. I wanted to go risk-free, as I had a tight deadline and nothing could go wrong. I worked on a Windows environment, and I used Microsoft Word 2010 (the 2013 version had not yet shipped at the time) for outlining and writing, Endnote (for citations), Adobe Reader (for PDF reading) and a combination of dtSearch, Qiqqa and Archivarius (for PDF search). Not the best workflow, perhaps, but I decided to play safe with Word + Endnote.

    Now, I am on a Mac, and I would like to streamline my workflow. I am tending to use the following applications, and I would like to know if you would suggest any alternatives or if you would recommend me to take a second look on any software I may have overlooked. I would like to know what do you use.

    DevonThink Pro Office for PDF indexing and searching. It has a clunkly interface, and may be overkill for the task, but it is fast, searches all my documents and organize the results. Plus, it highlights all the searches. And also has OCR for those PDFs that contain only images. I found it to be good. I tried Together, which has a very nice interface, but it could not organize well the results nor highlight them. Yojimbo highlights the search results, but cannot display them hierarchically. Ditto for EagleFiler.

    Skim for annotating PDFs. Although I think Preview or Adobe Reader are also up to the task, and I don't see much difference between them for this. Is there any?

    Circus Ponies Notebook for taking notes, collecting information and basic outlining. It may be a little outdated (the version 3.0 dates back from 2008), but looked and felt nice. In addition, it can hyperlink to other sections of the document, which is nice. I also tried OmniOutliner Pro, which is in version 4.0 now, and has a better interface, but, although I feel it is a very competent outliner, it may not be so good at taking notes. I may be wrong, though, and may be skipping a brand new and fully-featured piece of software in exchange for some old and outdated software. There is also Microsoft OneNote, but I felt it underpowered compared to the Windows version.

    Scrivener for writing. It looks and feels like a very competent piece of software for academic and structured writing. The draft view is very useful, and I can see all footnotes at once (and not only those that fit on the page). It is awkward not knowing how the page will look like in the end, but I will have to get accostumed with that. Microsoft Word would be my second choice. It is very fully-featured, but Microsoft seems to constantly neglect the Mac, as the Windows version is far superior and there are no signs of release of the next version. LibreOffice Writer and OpenOffice Writer seem like cheap Word alternatives and I rather prefer to use the original. Mellel is nice and solid, especially for academic work, but is bad for converting files to Microsoft Word format (which is the standard that I must use). Plus, its interface does not help and seems to be clunky. Nisus Writer Pro is good, but, again, to use a Word replacement, I would rather go with Word itself. I see no reason for using Nisus instead of Word. Apple Pages is OK and has a very nice interface, but it lacks features and does not even support cross-references.

    Sente for citations. I need to cite in footnotes in my field of research and Sente seems to support that. In addition, I found the interface to be good and the system of citations to be straightforward (a "cite" button inside the program). I tried Papers which is on a very criticized version 3.0, and the interface is also very good. However, the system of Magic Citations, although beautifully designed, seems to get in the way of doing things. (Why is so many people complaining about Papers?) Bookends is also nice, but it does not have exactly the best interface nor the best citation system in the world. Endnote integrates well with Word, but the system seems outdated. Zotero is nice, although it does not have the best interface; the citations seem to work well with Word, but not with too many programs. I have yet to figure out Mendeley and BibDesk, but I guess neither of them will be as good and streamlined as the others.

    Microsoft Word for final review of the draft. I could use Apple Pages or Nisus Writer Pro or LibreOffice Writer. However, as I will have to send the article on Word format to any publisher, or share in Word format with anyone else, I would prefer to go with the original.

    So, what do you think? Anything missing? Agree or disagree?
     
  2. expertmonk macrumors newbie

    Joined:
    Feb 23, 2011
    #2
    I think you've got a bit too much going on there. With Sente, Devonthink, Scrivener, and pandoc you'll have about all you need. Maybe a mindmapper that can export OPML and omnioutliner in the mix too. Sente notes can be exported to devonthink via Rob Trew's scripts: https://github.com/RobTrew/tree-tools/tree/master/DevonThink scripts

    Then you can pull those notes into your research folder in scrivener to write your paper. Export plain text from scrivener, scan using sepp for sente citations https://github.com/smirarab/sepp, then use pandoc to convert to pdf, latex, docx, or whatever you need.
     
  3. skaertus thread starter macrumors 68030

    skaertus

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    #3
    Thank you for the feedback.

    I am not sure I like MindMappers... I have tried them before, but I do not think they really help me.

    I saw this Sente to DevonThink script and it looks really neat, although I have not yet tested it.

    How do I pull the notes to my research folder in Scrivener? Do I have to copy and paste one by one? It would be counter productive. In the ideal world, I would prefer some sort of link to each note in the PDF file, but I do not know if that is possible. I know I can add an entire PDF to Circus Ponies Notebook, and link a note to a specific page of the PDF where a note is, but I do not know any other way of doing it.
     
  4. onekerato macrumors regular

    Joined:
    Jun 6, 2011
    #4
    I wrote an app, PDFoo, to create URLs to content inside PDFs. It can link to a page, or specific point on the page, or a table-of-contents (TOC) entry. Or you can export annotations in the PDF with a pdfoo:// URL attached to each of them. Clicking the URL opens up the PDF in PDFoo app to the correct location.
     
  5. skaertus thread starter macrumors 68030

    skaertus

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    #5
    Thanks. It looks like what I need. I will take a look at it.
     
  6. metanoiac macrumors member

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    Jan 21, 2012
    #6
    It looks like you have already come to a good workflow for yourself, and the apps you list seem to be a quite thorough survey of the academic apps landscape. I tend to echo a previous comment that you maybe have too much going on (e.g., why not also use Sente to organize and read your PDFs instead of Skim?), and if you are looking for a good, simple and fast mindmapping app, I highly recommend Mindnode. It is really bare bones, which I like more than the overblown alternatives out there. Plus it nicely links with an iPad companion app, which brings me to my next point:

    Overall, my biggest concern in my workflow is to have it working across different machines (e.g., replacing the Mac) and, more importantly, integrating data across the Mac and iPad.

    I used to love Circusponies Notebook back in 2008, then in 2009, and also still in 2010. Then not any longer, as their iPad app is a huge disappointment (the last time I looked). I moved on to Evernote, which is far superior because it works across all devices I have.

    I write all my notes and ideas and even idea sketches / outlines in Evernote. I also use it to collect field notes and interview memos.

    When I actually start writing, I migrate over to Ulysses. It is similar to Scrivener, but I like it more since it is easier to learn. The markup language allows me to also use different writing apps when I am stuck (OmmWriter and Grandview are two apps that I use to overcome writing blocks), since I can just write in markup in let's say OmmWriter and then copy and paste it over to Ulysses and it still looks good. Ulysses also has a good export function now that lets you create your own CSS styles (though a little bumpy still. I had to try twice before I got a CSS file to work), though they don't have a direct *.doc or *docx export yet (*.rtf or *pdf is fine). Ulysses also works ok with Daedalus, their iPad app.

    Ulysses' own export is good enough to quickly send drafts to co-authors who work in the backwaters of Microsoft work. In the final stage, I still have to go over word or pages to get the formatting right and to build the bibliography.

    Sente is my core app for collecting, organizing, reading, annotating and citing journal articles. I write in many different writing apps, and using the markup language in Sente is just more robust than Papers Magic Manuscript. I just through in [%CS13@551], and Sente knows what I mean. I define my core papers with my short cuts (CS13 is short for Canniford and Shankar 2013), but a not so often cited paper would also be found without defining it by simply putting the first author and year.

    One thing that is missing from your list is Textexpander. Great app!

    So overall, my personal preferences would be to ditch Notebook for Evernote, and to check out Ulysses for a potential replacement for Scrivener if you find it too complicated and to check out how much you can just rely on Sente.
     
  7. exegete77 macrumors 6502a

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    #7
    Just a note that Scrivener also can use Markdown.
     
  8. skaertus thread starter macrumors 68030

    skaertus

    Joined:
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    #8
    Thanks for the post.

    Actually I do not get along well with mindmapping. I have tried it, and, for me, it is just a time waster.

    Evernote looks fine as well. I still prefer the cleaner interface and outline mode of Notebook, but Evernote is very fine. The thing is, I do not use my iPad for much. And I think writing on the iPad is really awful (even with a keyboard; I cannot have side-to-side apps and the trackpad is not half as precise as a mouse pointer).

    I do have a Ulysses III license and I think it is a really neat app. I like its interface. However, I do not like the way Ulysses handles footnotes. I like to see all footnotes at once, because I use a lot of them. My PhD thesis had over 1,000 footnotes, so you have an idea. I could not do that with Ulysses, but Scrivener allows it. In Word, I tend to use draft mode because it allows me to better work with footnotes. Scriver seems to do a similar job. I did not find any other word processor (in both Mac and Windows) that does a similar job of handling footnotes.

    Microsoft Word is, of course, necessary. Everybody uses it and so must I. If I were alone in the world, then I might not use it at all. However, I must send files in Word format to publishers, otherwise they will not even consider it. And then Word comes into play.

    How exactly do you do that?

    I do have TextExpander, but how is it better than the current text expansion functionality that Apple incorporated into OS X Mavericks?

    Thanks. I will take a look at these. By the way, do you use Sente for citations?
     
  9. The Mercurian macrumors 65816

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    Mar 17, 2012
    #9
    Wow you have alot of software there - I get by with Word for writing, Adobe Acrobat for OCR, and Mendeley. I'd find your setup too much to be honest - too much software to manage, update, use, move files between etc.

    I think maybe you dismiss Mendeley too easily - I've found it to be the best reference manager - it organises your pdf files, allows you to search titles, keyboards and even search within files. It also allows annotations and has a reasonably good Word plugin. It lets yous search document detials by id on academic websites and probably other stuff I don't use
     
  10. skaertus thread starter macrumors 68030

    skaertus

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    #10
    Perhaps I can give Mendeley another go. I found Sente to be very good and to have a great interface. Would Mendeley be better?
     
  11. saberahul macrumors 68040

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    #11
    I like Mendeley more. It also offers a web browser add-on for easy importing.
     
  12. skaertus thread starter macrumors 68030

    skaertus

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    #12
    Zotero offers that as well. Does Mendeley add-on works with Safari? Does Mendeley works with Word only or does it work with other word processors as well?
     
  13. saberahul macrumors 68040

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    #13
    The add-on works with Safari. As per your second question, I do not use direct integration so I don't know if it even offers it. I just make folders and for all citations I need, I manually copy and paste them. I go about scientific papers in a different way: most are done with LaTex and if I need to use a Doc processor, Pages is my preference.
     
  14. mvmanolov macrumors 6502a

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    Aug 27, 2013
    #14
    I am currently a PhD Student and i like MS Word for writing, but i really like Mendeley, the MS plugin simplifies things quite a bit, and it makes citations infinitely easier. The other thing i really like about it is you can share library across devices simultaneously (my partner is also a PhD student and we often work at the same time).

    Anyways, give is another go, i'd say.

    Cheers,
     
  15. skaertus thread starter macrumors 68030

    skaertus

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    #15
    I will give it another go. However, I do not need any of its "social network" capabilities. Is it any better than Zotero as far as citations alone are concerned?
     
  16. mvmanolov macrumors 6502a

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    #16
    i do not use any of the social networking stuff either...

    I found it really quite easy to use. it installs a toolbar for MS word (i think called a plugin) so inserting a citation/bibliography is only a click away.

    It closely resembles the MS word citation manager in ease of use and functionality, but you never loose your list.

    By the way, what was your PhD in?
     
  17. skaertus thread starter macrumors 68030

    skaertus

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    #17
    My PhD was in law.
     
  18. ssmed macrumors 6502

    ssmed

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    #18
    In biological science at least, Word (2011) and Endnote (7.1) are currently working well together and a well developed Endnote library is a great resource that can be used in all kind of ways. For quick jobs (such as presentations for teaching) the copy formatted citation (cmd-k) is really useful and on a big screen the groups, list, detail, PDF layout suits me. Keeping several libraries helps avoid massive libraries and allows then to have various levels of care, with my main library being carefully annotated and grouped, but others being more random.

    I have tried a few of the other bibliography programmes, but have not got on with them, but have been using Endnote since 2.1 (1992) so may be a familiarity thing.

    In the end you will just have to find what is useful. Trying to get residents and interns to follow your ways, just shows how individual people can be and how poor your own systems can seem to other people.
     
  19. Cassady, Apr 27, 2014
    Last edited: Apr 27, 2014

    Cassady macrumors 6502a

    Cassady

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    #19
    Academic Workflow

    Great thread.

    I use DTPO, Bookends and Scrivener. Consider them to be my holy-trifecta. Everything I need, is managed by them.

    Word is a given, but only in my having to convert it for my supervisor, and then for the final publication.

    BE does not have the friendliest manual etc., but it constantly amazes me at what it can do - will NEVER touch Endnote again. Oh - and BE's support is second to none.

    Hazel is not really academic specific, but can certainly help in keeping things tidy.

    Have been doing the majority of my PDF annotating on my iPad -- DevonthinkToGo Goodreader - have quite the workaround setup to ensure that annotation notes made in Goodreader, are searchable in DTPO. It's clunky, but it works.

    Recently took delivery of a Wacom Bamboo pad, to see if annotating on the Mac can be made more bearable, and user-friendly. Early days still - but might just have managed it.
     
  20. The Mercurian macrumors 65816

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    #20
    Zotero's word plugin is a little bit better than Mendeley in terms of speed - the Mendeley one slows down a bit if you get alot of citations in one document.

    Mendeley is far better than Zotero as a document manager in my estimation. It is good for organising files on your hard drive as it gives you alot of options for customising filenames aetc (it will rename files as you preset it to in given folders). And I also find it better for searching and reviewing files - Mendeley has its own built in pdf viewing ability that I find good. Zotero simply opens whatever your default pdf viewer is.
     
  21. Cubytus macrumors 65816

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    #21
    PhD aspirant here chiming in. While writing my thesis, I always lived by the motto "never, ever trust your hardware", exacerbated by the fact true deadline was usually yesterday :D It probably had an influence on my software choices. I wanted the ability, in case of a hardware failure, to be able to recover in less than an hour, on any machine I happened to lay my hands upon.

    I took a crash course once on Endnote, and found it really complicated. I was new to reference manager software back then, and learnt that, while I had a license for it as part of my tuition fees, it wasn't tri-platform, and didn't integrate with OpenOffice. Still, Zotero's support persons in their forum express much contempt, but I seldom had to cope with their lack of respect since Zotero worked reliably from the start. I wasted an insane amount of time trying out various reference managers (including online ones as they promised automated linking to relevant articles I first considered an incredible time-saver, since finding a relevant article usually takes much more time than reading it) on my own since advisors were old-schooly using Word's integrated reference manager, before settling with Zotero because it had the least constraint on import and exportable library formats. Plus, it had online synchronization both with Zotero's servers and my own WebDAV space. Plus, I loved how it handles citation styles as mine required minor modifications to be valid in my mother tongue. Citing was a bliss.

    If I had to choose again I would use Mendeley. Although proprietary, it's tri-platform, and support people is nice.

    So I decided to play it safe with Zotero + OpenOffice.

    I used a combination of Skim and Preview for annotating PDFs.

    However I never had a strong need to organize PDF search results as I always had to read them first, then attach tags to them, before filing them in library folders inside Zotero.

    Although not tri-platform, I used Evernote, for lack of a better option for outlines, links, and overall "scrapbook".

    I ditched MS Word very early when I had to quickly come up with a working workflow. Despite using it for many years, I still found it very convoluted, with a highly illogical organization, annoying features/bugs that hindered productivity. Plus, obviously, it isn't cross-plarform.

    I already used OpenOffice to build my data spreadsheet (though this turned to be unwise), as it needed to be Gnumeric-accessible for statistical purposes. Excel offered no compatibility with Gnumeric thanks to its proprietary format, and screwed up ODS format as well, often invisibly until it was too late. However OOo Calc often stalled under the heavy load of this giant spreadsheet. If I had to do it again, I would use a more cumbersome but maybe more efficient overall Excel-CSV export.

    So I just used OOo Writer. Perfect integration with Zotero, rather logical menu hierarchy. Never felt cheap, and one IT support guy routinely recommends it as doing 80% of what Word does, the remaining 20% being advanced functions very few people actually use. Plus, there's a ton of free help and tutorials available for Writer. Not so much for Word.

    Exchanging with advisors was bumpy, though, as for a while they required conversion to DOC format until they upgraded their Word version. I said I wouldn't be responsible for any error in conversion, and used these versions only for proofreading. But since no publication was involved back then, I never had the "submit-to-publishers" dilemma. The required PDF final version came out very clean.

    I would have surely seen the requirement to use Word as crippling to my workflow, especially with advanced formatting, but eventually will have to find a way to make it follow the standards to be used with the LibreOffice suite.

    Admittedly, Zotero's interface leaves a lot to be desired. However, it has very strong integration with Firefox, and since this browser was my primary mean to access articles, I could save them in one click and get the PDF automatically.

    Firefox as a browser because of its unparalleled flexibility (I wrote a short post about this academic-centric setup of Firefox on my blog). One-click activation of proxy, not system-wide: necessary since proxy slows down browsing overall. Adblock, Flashblock, TabMix as I usually open an insane amount of tabs in academic research, LibX extension (though I dislike the new, 2.0-based one) to get one-clic access to documents referenced by the university's library.

    Plus various software for plotting data (Calc never cut it with settings as arcane as Excel's): SciDavis, beautiful results but very buggy and unstable, and some other ones I can't remember. Maybe Qtiplis.

    True, I would also have the iPad-compatibility requirement now I have one, and considering I don't like reading long articles on a laptop. I usually printed them (sorry for all the dead trees) to read them on the go.
    How do that works, exactly? As many grad students know, writing blocks are very common, and I dealt with them by adding more caffeine in my diet, and re-reading articles, surely a time-waster.

    Same with Zotero.

    Same question. I'd love to know if LibreOffice compatibility is a reality.

    A given workflow is highly dependent upon personal preferences and requirements. I put a strong emphasis on recoverability since I was doing all this work on an inexistent budget for replacing the machine should it fail, and deadlines that left no possible downtime. For that reason I had a very strict compatibility regimen, with most of my critical software being available on all three platforms, and backup habits. At any given time, I had 5 copies of the most critical files: thesis, treated data, graph data on 1- Internal laptop HDD 2- Time Machine 3- USB key 4- external HDD, also used for the necessary Ubuntu virtual machine (Gnumeric didn't work reliably on OS X) 5- DVD burned wekly, stored at a friend's house.
     
  22. skaertus thread starter macrumors 68030

    skaertus

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    #22
    Thanks.

    How does Bookends work with Scrivener? Does it work well? I do have a Bookends license, but its interface does not look and feel so good as the one in Sente or Papers. Is it as solid as people say? How does it work for inserting citations? I always found its system a little clunky.

    ----------

    Thanks.

    For organizing PDFs, I use DevonThink Pro Office, which is really powerful. And I guess way powerful than anything else for this purpose, never found anything like it...

    ----------

    Wow, your post is just huge. It appears that you are seriously worried about cross-compatibility. When you talk tri-platform, what do you mean? Mac, Windows and Linux?

    I tried to go that way once, but I found it to be too complicated. In fact, I figured out that I don't need cross-compatibility. I don't use Linux and I plan to never use it. It may be free and open source, but it is not half as popular as it should be and it is used by 1% or 2% of the computers in the world, according to data tracking websites. So, I can live without it.

    Ditto for OpenOffice and LibreOffice. It is cross-platform, works in Windows, Linux and Mac. But there is not a version for the iPad available, nor for Android tablets, nor a cloud version that I am aware of. Yes, it may be open source, but that alone is not guarantee of anything. The ODT files are not a de facto standard as DOC and DOCX files came to be. Word is what everybody else uses, and if you save your files in DOCX you will never run the risk of losing the content. If you are really worried about cross-platform compatibility, have you tried to use a cloud solution such as Google Docs and Spreadsheets? Or even Microsoft Office, which has an online version that you can use from anywhere?

    As I do have a Mac, I want to take advantage of it. I want to use Mac-only software if such software is superior to the cross-platform alternatives.
     
  23. mvmanolov macrumors 6502a

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    #23
    Ha, mine is in Legal Studies :)

    What an interesting coincidence...

    What was you dissertation on?
     
  24. The Mercurian macrumors 65816

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    #24
    Never even heard of DevonThink Pro before this thread. But won't be trying it either as it costs money - Mendeley is free and does all I need!
     
  25. skaertus thread starter macrumors 68030

    skaertus

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    #25
    Yes, it costs money, but it is way better than anything else due to its search capabilities. You get what you pay for. Said that, it is not really expensive. DEVONThink Personal costs US$ 50 and the Pro version costs US$ 80. They also have academic discounts.
     

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