What software do I really need for academic work on Mac?

A reader has just challenged me to re-think the software I use for academic work on Mac. Well, there are over 250 items in my Applications folder, but how many do I need to remain productive? So imagine that I have a completely new Mac with no software (except OS and its standard apps). Also imagine that I am not bound to any historical file or data formats. What would I choose? To answer this, I have made a mission critical list of 25 apps in five categories. These apps do not duplicate each other, on the contrary some of them are mentioned under more than one heading and some are used together (e.g. NValt and Ulysses or Byword and Scrivener). I am pretty sure that I could do my professor work with these 25 apps but if any one was removed without replacement I would be severely handicapped.  

Reflections and explanations are at the end of the list

A. General tools

  1. LaunchBar – a launcher and an automator (€24) /alt: Alfred, check here for comparison
  2. TextExpander* – Mac typing shortcut utility (€35)
  3. 1Password* – password, identities and other sensitive information management (€40)
  4. Dropbox* – file sharing (free) /alt: Box

B. File and e-mail organizing and management

  1. Hazel – file management automator, indispensable for managing reference files (€20)
  2. Papers – managing scientific articles, also used for annotation, citation and bibliographies in writing (see D); check Macademic reviews (€60) /alt: Sente, Bookends
  3. Foxtrot – a professional search engine; “goodbye haystack, hello needle!” ($40 or $130 for the professional version) /alt: Leap, DevonThink, HoudahSpot
  4. MailTags – tagging mail messages in Apple Mail ($30)
  5. Mail Act-On – processing and organizing email with keyboard shortcuts in Apple Mail ($25)

C. Calendar, task and project management

  1. Fantastical* – natural language calendaring, part of the Macademic Ninja Kit (€16)
  2. BusyCal – professional calendar management (€40) /alt: Mac’s native Calendar
  3. OmniOutliner* – outlining for brainstorming and project planning; also used for writing outlines (see D) ($50 or $100 for professional version) /alt: MindNote
  4. Notebook – project management and planning ($50) /alt: Daylite
  5. OmniFocus* – unparalleled task management app extensively reviewed on Macademic; however tempting it is, don’t try to put all your life in there! ($40 or $80 for the professional version /alt: Things, TheHitList, TaskPaper

D. Note-taking, research and writing

  1. NValt – plain text and markdown no-frills note-taking (free) /many alternatives
  2. Evernote* – capturing text notes, documents, contacts, images, photos and screenshots and sharing them including on iOS devices (free with some paid features)
  3. Ulysses – a rapidly evolving software for taking and organizing notes using searches, tags and folders; I use it extensively for teaching (€37) /many alternatives
  4. OmniOutliner* - writing outlines, also used for project management (see C) ($50 or $99 for the professional version) /many alternatives
  5. Byword* – simple and efficient text and markdown editor for Mac (€8) /many alternatives
  6. Scrivener – writing software, especially suitable for theses and other complex texts ($45)
  7. Pages* – Apple native word processor producing beautifully formatted documents, features sharing through iCloud (free with OS X) /alt: Mellel, Nisus
  8. Microsoft Word for Mac - very powerful word processor, a standard for many publishers and in the Windows world, sometimes irreplaceable but should not be over- or misused (various pricing models) /alt: MellelNisus
  9. Papers – citation and bibliography management, article annotation, also used for managing scientific articles (see B) (€59) /alt: Sente, Bookends, EndNote, Mendeley, Zotero

E. Data processing, presentation and graphic design

  1. Microsoft Excel for Mac – an extremely powerful electronic spreadsheet (various pricing models) /alt: Numbers
  2. OmniGraffle – vector graphic software for diagrams and other illustrations ($100 or $200 for the professional version) /alt: Adobe Illustrator, iDraw
  3. Keynote* – the most powerful presentation software with amazing possibilities (free with OS X) /alt: Microsoft Powerpoint, Prezi
  4. PDFPen – editing pdf files ($60, $100 for the professional version) /alt: Adobe Acrobat

Observations and explanations

The cost of this package varies between ca €600 ($800) and ca €850 ($1,150) depending on whether one chooses light or professional versions. This is without discounts but excluding the cost of MS Office.

* indicates that I also use a related and synced app on iOS

Italics indicate software which I am still trying and may decide not to use. This software has not been reviewed on Macademic but it has a critical function in the academic workflow;

  • I did not list the standard components of Apple OS X (most importantly Mail, Contacts, Safari, iPhoto, Spotlight, and Preview);
  • I excluded several web-based services such as Google Drive and SaneBox;
  • I excluded browser extensions (e.g. Pinboard and Getpocket) and a news reader since I use them more for personal rather than professional needs.
  • I excluded communication utilities such as Skype, Google Hangout, Webex, etc.
  • I only listed alternatives which perform more or less similar functions and which I have actually tried;
  • Prices indicate non-discounted prices in Sweden as of July 4, 2014 converted with current exchange rates and rounded to the nearest 10 € or $.

About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He also coordinates MESPOM, a Masters course operated by six Universities.
This entry was posted in Automation, Bibliographies, Email, Files, Graphics, Notes, Presentations, Projects, Tasks, Workflows, Writing and tagged , , . Bookmark the permalink.

73 Responses to What software do I really need for academic work on Mac?

  1. John Pumphrey says:

    Aleh,

    Your response to my query has dramatically exceeded all expectations. Wow! Thank you for your insights and advice.

    I have a few of the programs on your list (Omnigraffle/Scrivener/Papers3/MS-Office Suite for Mac…), but I will take time over the summer to give my workflow a serious think and getting organised before beginning the last two courses associated with my doctoral programme. I know that the real work is on the horizon and am already struggling with organising my information/articles.

    With so much choice on the market, I really appreciate the time and effort that you’ve put into assessing the software tools that exist and sharing your thoughts with us all. I’m going to use your list as THE list to get my own workflow sorted.

    Thanks again, Aleh.

    Like

  2. Dellu says:

    Great list; but, i think i need much less number of app than you do.

    Aflred in place of LaunchBar
    keyboard maestro in place of TextExpander*
    Lastpass in place of 1Password*
    Dropbox* —dropbox
    Fantastical* (for all my calendar needs)
    NValt (manage my tasks in it)
    Scrivener
    BibDesk (Sente)
    Latex (with TexStudio)
    Acrobat instead of PDFpen
    FoxTrot
    DEvonthink

    Like

    • Aleh Cherp says:

      Thanks! There is no “but” – we’re all different and probably doing slightly different things. It’s interesting that you’re using about one-half of the apps I use. I think I could survive with your list too but I would need to add TextExpander, Calendar (Fantastical does not give me enough overview), OmniFocus, OmniOutliner, Pages or Word (I need to write recommendation letters!) and Keynote.

      Like

    • Aleh Cherp says:

      so no TextExpander?

      Like

      • Eric says:

        How come you need Textexpander when you’ve got the snippet feature in Alfred?

        Like

      • Aleh Cherp says:

        I am not using Alfred and not quite sure how the snippet feature works. There are a couple of things I love about TextExpander (which I assume don’t exist in Alfred). First, you don’t need to “launch” anything in order to activate your snippet feature. It just replaces the words as you type. Second, it allows you to use forms as I explain, for example, here.

        Like

      • Eric says:

        I didn’t know about the form-feature in text expander. I’ve hesitated to get Textexpander since Alfred has mostly covered my needs. However, I’ve missed that extra oomph! The snippet feature in Alfred is very basic. It pretty much just adds plain text when you type your designated keyword. I think I’ll have to give Textexpander a second chance since it seems to offer more power than initially meets the eye.

        Thanks for the reply, much appreciated!

        Like

  3. Dellu says:

    oh, Hazel is crucial to me too

    Like

  4. Stan says:

    I warmly reccomend http://www.conceptdraw.com for all diagramming and slides – I’ve just started using them and am impressed by the breadth of their different ‘solutions’ which are templates fo different chemes, drawings etc.

    Like

  5. James says:

    I would not recommend neither Papers or Sente for reference management. Bookends is far, far better. Bookends is much more stable and significantly more usable than Sente/Papers. Papers 3 is just a mess.

    Like

  6. Roland Spickermann says:

    NisusWriter has worked just as well for me as Word ever did, and is much cheaper. I might put in a good word for NoteTaker from AquaMinds, too.

    Like

  7. Mark says:

    For statistics and resultant graphs i find graphpad prism a must-have.

    I have always wondered about project management software. Currently I use evernote to create separate notebooks for each project and keep a log that acts like a lab notebook. I was curious if others have suggestions for other programs and would like to know how these other programs improve workflow and efficiency? Thanks, m

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    • Aleh Cherp says:

      I have been trying Outliner for project management, but the problem is that it must have a separate file for each project. Managing projects in Ulysses is too inefficient. Eventually after long trying I bought Daylite from Marketcircle and it is very promising but I can’t say there was a sudden revolution in my project management. I will probably use Daylite as a CRM in the future. Now I am trying Circusponies notebooks. Good experience but too early to say whether it will be sustainable. Sorry, I know it’s not a clear-cut solution.

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      • Mark says:

        I have been reviewing your suggestions as well as others and have a more focused idea of what i would like: Im looking for a program that makes Gantt charts — visual timeline, that i can use for project management. The only prgram that does so in your list is omnifocus. The program is on the more pricey side but if it is easy to use and no one else has an alternate i may pull the trigger. Any thoughts from you or others about gantt chart programs?
        Thanks
        M

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      • Aleh Cherp says:

        OmniFocus does not make that good Gantt Charts. I have tried Microsoft Project (does not exist for Mac) and then more recently OmniPlan. Both are expensive and require a lot of information input (and update) before they become any useful. But they For simpler needs you may look at Tom’s Planner.

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    • Aleh Cherp says:

      Finding a project management software is a pain. I used to keep project notes in OmniOutliner, and I still largely do. The problem is that then you have to keep a separate file for each project and it complicates capturing and review. I am also using Daylite, it still has not taken up the main project management load despite a lot of work I have put into it. I have started using CircusPonies Notebook, it’s pretty cool for dynamic open-ended ideas but I have no idea whether it will hold for serious projects.

      Like

      • Manuel Kuhs says:

        Have you made any progress on what to use for project management? I’m about to start a postdoc position and am undecided particularly on what to use for project management…

        Like

      • Aleh Cherp says:

        Manuel, project management is still a bit of a pain. I am coming to a conclusion that it depends on a “project”. Some are so simple that they can comfortably live in OmniFocus or even in Mail. Some need a lot of scheduling, but not much thinking and some need a lot of thinking too. Teaching projects are different from writing projects. Yet if you have to have consistency over what software you use for what project. I am now consistently using Daylite for publications. I use Ulysses a lot for teaching (e.g. making notes on students presentations), but it’s also backed by OmniOutliner and Scrivener. Ulysses is also good for supervision. I keep using CP Notebooks but it’s not a rigorous PM software for me.

        Liked by 1 person

  8. Bryan Burwick says:

    I am an avid Mac User and IT Manager in Financial Services, that just started my MBA/MS in Leadership studies. I have spent a lot of dollars in software already, but feel like i am still missing major pieces to help me with taking notes on what i am reading, and making links and managing all the different articles and possibilities. ( It is feeling a bit overwhelming and concerned it will continue to be expensive trying out overlapping tools with the risk of still coming up short.

    I haven’t figured out how to properly annotate yet. I have been cutting and pasting paragraphs from PDFs into OmniOutliner so i can highlight important sections, and have a column for summarizing the idea. But it is getting unwieldy at best.

    I use Alfred, Keyboard Maestro, Textexpander, 1Password, NVAlt, Hazel, Fantastical, OmniOutliner, Omnifocus, EverNote, Scrivener, and MS Word.

    I also have several other tools that i haven’t even touched like Aeon Timeline, and have been trying my hand at Markdown apps as well, but tend to stop at just writing the notes in NVAlt.

    I am trying to figure out my academic workflow. I keep bouncing back and forth between different tools. The SUMMERFEST is going on for 25% off Tinderbox, DevonThink Pro and NisusWriter Pro, Scrivener. So i was about to invest in all three, hoping it would help me make some sense of a useful workflow.

    I am wondering if someone can suggest which tools are worth going after, at this point?. DevonThink? or Papers or Foxtrot or Bookends? Tinderbox? etc., There are so many opinions and I don’t have enough experience in graduate work to know what is useful or not.

    I have spent a lot of money already, and am about tapped out. While Scrivener is working for writing, i need something to manage my PDFs that are sitting in my inbox from my research on Leadership. I’d like to understand how to do annotations that i can refer to when writing my discussion questions and weekly assignments.

    What would you sink your money into at this point? Any suggestions would be helpful.

    Like

  9. Aleh Cherp says:

    Bryan, I understand your frustration. One advice is that you have to find a balance between acquiring and experimenting with new exciting software and actually doing your work, which often requires sticking to software that definitely works for you, however boring. Another advice is to try to analyze and understand your workflows before you jump into a new software. This is important: not to ponder of what you would ideally like to have (because such an ideal thing may not exist in principle), but rather to get insights into how you actually work. Software should work for you, not against you. So study yourself: do you like outlines? do you need a distraction-free environment for writing? how would you like to access your notes (and in what contexts)? Then go with some compromises and do not switch to new software before you clearly understand why the old one does not work.
    More specifically, I think you should get yourself three things: (a) Scrivener. It will make managing all writing projects easier and may also help with note-taking and research. (b) Papers (or another reference manager, e.g. cheaper Bookends) to hold your pdf documents and references together and to cite them in your writings; and (c) a word processor. The tastes on (c) wildly differ, if you’re not sure what to use why don’t you use Pages and make a list of functions that they don’t have. MS Word has almost all functions imaginable, but you may prefer another alternative.
    With respect to note-taking and annotation it is a bit more difficult for me to recommend, because my needs are probably quite different. It depends on how many notes you take, to how many subjects they relate, how many papers you annotate etc. For structured notes I used NValt but now I am more comfortable with Ulysses (which also reads NValt notes). It is important that you have a list of your notes at hand. Scrivener may also do for note-taking. See whether CircusPonies Notebook works for you – it uses another mentality. Finally, why not try Evernote/
    Tinderbox is probably better for project management and brainstorming, I find the learning curve pretty steep and I would not recommend to start with it. DevonThink is a powerful tool but once again you have to be sure it’ll work for you.
    My (very cautious) reflection is that reading and commenting on literature is a “slow” process. It’s effectiveness depends on how well you’re thinking about the paper, not how beautifully and efficiently you link your notes to it. So while I am leaving some annotations in Papers I often create a separate review/comment document for papers I read (e.g. in Ulysses). I rely on my head rather than software to maintain a link between annotations and the paper.
    Finally, I have learned to trust myself and to tolerate some imperfection. It is a natural urge to capture, tag, index, cross-link everything so that it hops back at you at precisely the right moment. But knowledge management reality is more complex than this. You can never anticipate all keywords, groupings and links between your data. On the other hand your mind is amazing: it will often remember things better than you thought. So it is a tango between your brain and a Mac you have to organize in research. Listen to the rhythm first!

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    • Joyce says:

      Re: notetaking–I found that I’m struggling with too much of a good thing. I learned with real index cards and a pen, and of course in those days we were much more selective about what we took down verbatim. I have been trying recently to only copy and paste if there’s a high probability that I would want to quote from the material directly in an article or lecture. Otherwise, a quick note (“good history of X on pp. 31-35) is sufficient. I remind myself that I access the original almost as quickly as I can access my notes. I’m still getting tripped up with whether to organize by subject and tag with author, organize with author and tag with subject, or keep double (or more) copies of notes so I can find them easily without too many tags. I completely agree that it takes self-restraint to remember that all the tagging and cross-linking is a means to an end, not an end in itself.

      Like

      • Aleh Cherp says:

        These are some brilliant thoughts, Joyce. Especially “I access the original almost as quickly as I can access my notes”. Regarding your wondering about Author vs. Tagging, here is how I distinguish their functions. If I want a specific paper I very often remember the author (or the title) and have no problem finding it. However, if I want all papers about a specific subject (there is often more than a dozen about a narrowly defined subject of study) I often use search by tags to find all of them. I often perform it when I want to share papers on a particular subject with a student or a colleague or do a literature review and not miss anything.

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    • Bryan Burwick says:

      Aleh, Thank you for taking the time to write such an insightful response to my questions and frustrations. I greatly appreciate your advice am amazed at how clearly your words described my approach to the myriad of tools and potential workflows. I will be taking time, after my next assignment, to slow down and reflect on my process and begin to rely on my abilities more than those of the tools upon which i am trying to lean. I look forward to continuing to follow your blog and hear how your workflows evolve.

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  10. Joyce says:

    Thanks for this post. I thought I was so cutting edge using Scrivener but I see I haven’t scratched the surface of what I can do with the Mac. I have no intention of trying out 20 new apps… would love any suggestions for the best addition to my current setup, the biggest “must have” that’s not on my list. Here’s what I’m using:

    A. General Tools: DROPBOX
    B. File and e-mail organizing and management – GMAIL online, was using APPLE MAIL but it’s not doing well after downloading Mavericks
    C. Calendar, task and project management – GOOGLE CALENDAR online, CALENGOO iPhone app (love it)
    D. Note-taking, research and writing – SCRIVENER (note-taking, writing, lecture notes), KINDLE (device and Mac app for highlighting books and importing to Scrivener), ZOTERO standalone (for keeping track of references), SIMPLENOTE iPhone app (for recording ideas on iPhone to be imported to Scrivener and then deleted), TOODLEDO online and iPhone app (for information that I need to access anywhere), WORD
    E. Data processing, presentation and graphic design – EXCEL, POWERPOINT

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    • Peter Ryan says:

      ~> File and e-mail organizing and management – GMAIL online, was using APPLE MAIL but it’s not doing well after downloading Mavericks

      I’m testing Yosemite which has taken my Maverick degraded Apple Mail and totally trashed it. Unusable now.

      Like

  11. Aleh Cherp says:

    → File and e-mail organizing and management – GMAIL online, was using APPLE MAIL but it’s not doing well after downloading Mavericks
    I assume that was because Apple Mail on Mavericks did not work well with Gmail? It was the same for me, but after several upgrades it started to work pretty smoothly.

    Like

  12. C.K. says:

    Aleh,

    I was wondering if you have ever considered QDA apps like NVivo, ATLAS.ti, MAXqda, etc, which would potentially level up, if not revolutionise, your academic workflow beyond note-taking. As they can tag or code/highlight/comment individual parts of PDFs, audio and video files, they seem to be able to replace the note-taking functions of Papers2 or Sente (and without the need to export them). They can also visualise the notes in forms of mind maps, chart, etc. So would they potentially become THE kind of apps for note-taking, literature review, and data analysis? I’m trying NVivo and MAXqda right now, and thinking of replacing DTP as my main academic repository in the future.

    P.S.: all the three apps above just have released, or will very soon, their Mac versions and two of which, MAXqda and ATLAS.ti have IOS apps as well, albeit with fairly limited functionality. Although their prices are absurdly high for commercial uses, I, as a student, could buy them at about $100, which is significantly less expensive than other popular apps on Mac like Tinderbox, whose steep learning curve has kept me far away from it…

    Like

    • Aleh Cherp says:

      Dear C.K. I have actually not heard of NVivo. I will see if I can try it, but very often the texts are analyzed are not very ‘deep’ (they are merely scientific articles with a lot of meaningless babble).

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  13. Pingback: 9 essential writing software for academic work on Mac | Writing Software

  14. Samuel says:

    Thanks for an interesting article. However, I am surprised of the vast number of apps in your workflow. Personally, being a student majoring in philosophy, i take great pleasure in using a mac computer, but have a much thinner list of apps to show for. Of course, I don’t do presentations or graphic design, so that limits the list some. Anyway, what I value important in terms of applications, besides its functions and usability, is flexibility and also the company that make the app. If I take a look at the apps in App Store I will see a great many of them at version 1.0 and last updated years ago. Technology is rapidly changing and evolving, therefore its important to find apps made by companies that will last. Anyway, I just wanted to throw my own list out there and perhaps some of them might serve someone great use.

    Note-taking, research and writing:
    Microsoft Onenote. This has been a reason, perhaps the only one, to stick with a pc until just recently. Microsoft finally made it a native mac app early this year, and it is in my opinion, great. It’s a mac app, iOS app and also web-app, which makes it flexible and as Microsoft is creator, it will last for a while. It’s intuitive, easy to maintain and to get your stuff both in and out of. Another cool thing is that you can share your notebook with people, so others can edit and contribute.

    Microsoft word for mac. Being a student i have to follow university rules and formats and docx is what counts. Besides, this is what most of the other non-academic-ninjas use. Exchanging documents and commenting each other etc. works better when you use the same application and format. Besides, I think when Office 2014 for mac arrives, the integration between the Office Suite and Onenote will be richer, as it is on the pc today.

    Omnioutliner. For outlining academic work such as assignments and papers. Also great for taking notes in lectures and brainstorming.

    Scrivener: For dynamic works of complexity that involves research, notes, drafts and revisions.

    Adobe Acrobat Pro: Lots of the articles and pdf’s i get are copied material from books, making them impossible to mark and annotate. The OCR module in acrobat pro is superb and makes the pdf’s workable. The edu prices on this piece of software is pretty affordable.

    Organizing and management

    Endnote: For references and pdf management. Industry standard, robust company, flexible, often updated and syncs to the cloud. I want to be particularly sure on this piece of software because this is where i store the material i find for my studies that eventually turns into exams and grades.

    Todoist: Great to-do manager, available on all platforms. Nice design, great sync and a cool set of features. Really cheap too, considering to the functionality you get.

    Thats it really, for the rest i use the basic stuff already loaded on the mac..besides of course dropbox for storing the files.

    My workflow is like this:
    I add tasks in Todoist. Notes and research starts in Onenote. I outline it in Omnioutliner and reference it in Endnote. Then i write and deliver it in Word.

    I guess i’m a lightweight ninja, but perhaps ninjas shouldn’t carry that much stuff around:)

    Best regards
    Samuel

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  15. Jaroslaw says:

    1. General Tools: LaunchBar, PathFinder, Things, TaskPaper, Dropbox, 1Password, TextExpander, Keynote, Unclutter, PopClip, etc.

    2. Bucket apps (sort, organize, categorize, tag, naming, searching, linking): Sente, DEVONthink Pro Office, MacJournal, Clearview.

    3. Note taking (read, extract, paraphrase, summarize): DEVONthink, MacJournal, Sente, Skim, SimpleNote, WriteRoom, OmniOutliner (research notes from others applications are imported to DEVONthink „Zettelkasten” database).

    4. Deeper sense-making (outline, mind-mapping, visualize, hypothesize, structure): OmniOutliner, Scapple, Tinderbox, iThoughtsX, NovaMind.

    5. Writing: Scrivener, Nisus Writer Pro, Pages.

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  16. Arno Wouters says:

    To those who want to save money try NeO instead of OmniOutliner. It is more powerfull and much cheaper!

    Like

  17. Frank says:

    Brainstorming and organizing ideas: MindNode or iThoughtsX.

    Search: DevonAgent Pro to do deep Web searches (it takes a while to do a deep search). Highly recommended, especially if used in combination with Devonthink. HoudahSpot for local search.

    Gather: Devonthink Pro Office for gathering information directly from DevonAgent; and CP Notebook for note taking and organizing notes. Bookends for gathering references from Pubmed, Scopus, and other DBs.

    Composing and referencing: After I have my map completed, I save the map as an OPML file and open in Omnioutliner, if I’m working on a paper; or in Scrivener if I’m working on a book. I insert most references at this point (Cmd-Y in Bookends to either OO or Scrivener). Save the file as rtf to open in a word processor.

    Formatting: NisusWriter Pro or Pages for final referencing and final format. If I have to work with colleagues, I import them into MSW as rtf files before sending.

    My workflow changes depending on whether I’m first author or not. When I’m not first author I just receive the document in Word and use that. If I’m first author I follow my workflow and at the end take other authors’ inputs into my workflow (I request my colleagues to use rtf or txt as a file format).

    Output: MSWord or PDF

    Other writing/formatting program I use for personal documents, such as a course syllabus or my CVs, is Lyx, which I use also when I have to submit the paper formatted as a LaTeX document, with Output in PDF. The useful thing about using a LaTeX app is that you don’t have to worry about formatting, and that it produces beautiful outputs.

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  18. GediWorrier says:

    I use many of the apps that you have. One question for you…how do you deal with Ulysses’ lack of support for tables? Drives me crazy!

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    • Aleh Cherp says:

      I don’t make tables in Ulysses. I use Ulysses only for simply straightforward texts such as meeting notes, memos, records of student presentations, recommendation letters. Anything that requires creative thinking is in Scrivener and other more advanced software. This having said, if I ever needed to use a table in Ulysses I’d make it in Pages and attached it to an Ulysses sheet.

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  19. Aziz says:

    nvALT is awesome. thanks for the list. I would also suggest Docear http://www.docear.org/ to be on the list. Docear is great tool for literature management.

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  20. Randy says:

    Thanks, Aleh, for more terrific advice. I trust your judgement and value your opinions.

    Quick question: they just released Papers 3.2, and I was wondering if you’ve had a chance to try it out? Does it address any of your previously noted deficiencies? I am hesitant to upgrade based upon your June entry.

    Like

    • Aleh Cherp says:

      Thanks, Randy! Have not tried it yet, but read my most recent assessment here and comments – some of the issues would have been fixed in this first official release. The most important issue is accessibility of pdf files stored in Papers library to other software and specifically to search engines. If this is not critical for you – upgrade. If it is, keep a good backup of your pdfs and still upgrade and test.

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  21. Adam says:

    Wow. So many apps. I have to say, I think it sounds like a system like that works you, and not -for- you.

    I think that file-management, research, note taking, and writing are all part of the same thing. As a hobbiest software developer, I realize that it is much easier to focus on narrow problems and solutions. But I am exceptionally frustrated that there are so many apps that do one -tiny- piece of the puzzle well, and fail at, or don’t consider, the other tasks.

    I feel like Charlie Gordon: can’t you software developers see the connections!!! Why is there a distinction between annotating academic PDFs and storing notes about them, and the eventual text used for a paper or thesis? Why does DevonThink do a great job of storing files and even finding similarities, but doesn’t let me add connections, or prune improper ones? Why does Evernote hoover everything up so well… into a giant blackhole, from which everything seems to get lost? Why should I have a tool just to manage citations? Seriously!

    I’d like to see the baby of DevonThink, Scrivener, OneNote, Papers, GoodReader, and OmniOutliner. One tool to rule all the researching, thought-development, notes, writing, and file management.

    On a related note, I have a similar beef with OmniFocus. It’s great for tracking tasks for large projects (although the iPhone version is missing the most powerful features). But if you use it for personal tasks, especially daily habits or reminders (which I consider just as important), their very strange database just blows up; it can’t handle you completing dozens of repeating tasks every day. And the priority and tagging mechanism is exceptionally limited.

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  22. atibbs says:

    I was just wondering what you use for managing contacts and/or keeping track of funding applications?

    I’m about to apply for a large number of grants and am looking desperately for something which will let me record contact with each potential funder, preferably something a bit more intelligent than an excel spreadsheet. At the same time, I’m also about to embark on some fieldwork, so it would be good to record contact details and log correspondence with various people. I’m guessing my last resort would be Devonthink and storing spreadsheets and notes, but I was hoping for a more database like software – perhaps such a thing doesn’t exist?

    Like

  23. Hi Aleh,

    One app I can’t live without right now is TapForms. It is a personal database manager, it syncs with iPhone and its very versatile nature allows me to add almost any kind of information in it. I use it for both personal and professional matters. For instance I have a “database” (called “form”) specifically designed to handle part of theories, linked with another database related to papers. That way I can track what I’ve read very precisely, with almost no impact on my reading speed.

    And I’m sure I don’t have discovered yet all its usages.

    Like

  24. Jonathan Alix says:

    Any comments about Zotero? Especially in comparison with Bookends or Papers?

    Like

  25. Fred Callaway says:

    Wow that looks like an expensive list! Here’s my broke student alternative recommendations:

    application launching, file searching, automation – alfredapp ($28 for pro)
    text expander – atext ($4)
    reference/pdf management – bibdesk
    calendar – iCal + quick cal ($3)
    notes+task management – workflowy
    writing – LyX or Sublime Text
    PDF reading – skim
    data processing – Rstudio
    vector graphics – Dia

    In many cases, the free/inexpensive version is equal or superior to the expensive alternatives. The expensive ones only exist because people don’t bother to look around, and large businesses like to have fancy brand names. For example, atext has more functionality than text expander. Bib desk and Skim are highly scriptable and thus can be extended far beyond their paid counterparts (you don’t have to do this work because someone else already has). Workflowy blows omni-outliner/focus out of the water in my opinion.

    Alfred app is the only app over $5 I recommended because it changed my computer use in a huge way. It is highly extendable and thus has been integrated with most scriptable applications out there. For example, if I want to check out a paper, I hit ⌘-space, type “ref tamasello item based nature 2000″, hit enter, and bib desk opens up with a formatted and bibtel-form citation, along with a pdf of the paper. (Reference Importer Workflow).

    You don’t need to spend a whole bunch of money to have a great workflow.

    Like

  26. Joel says:

    Do you have a preferred Mac setup for your academic workflow?
    I’m asking about hardware here so what type of mac, ipad, iphone, etc.

    Like

    • Aleh Cherp says:

      I have a 15” retina MacBook Pro which I use at home, different offices and also carry with me to classrooms and conferences. In my office I have an extra screen which I connect to it. I have an iPhone which I virtually don’t use for my professional work. Finally, about 2 months ago I started using iPad air, mostly for reading and marking pdfs when traveling.

      Like

      • Joel says:

        Thanks for the reply. Are you finding the iPad to be integral at this point? Or a luxury…
        I have a macbook pro 13″ non-retina that I also use at home and different offices. I also have an iphone 6+, and am considering either upgrading the macbook to the 15″ w retina or getting an ipad air for reading pdf journal articles mostly, but also for marking papers.
        Any thoughts on which you’d think would make a bigger difference? the macbook 15″ or the ipad?

        Like

      • OSC says:

        Isn’t the 15″ too big to carry all the time? I have a 2009 13″ MBP and I’m thinking about upgrading it. I’m thinking to go to a 13″ Retina MBP, but 15″ is obviously a more comfortable size. But also bigger… How did you solve this tradeoff? With your iPad Air?

        Like

      • Aleh Cherp says:

        OK, so here were my computers:
        * 2009 MBP 15” + iPad 1 – very unwieldy and sync with iPad was very painful at that time;
        * 2011 – 13” MBAir, no iPad; was a huge relief in the beginning, then I got gradually frustrated with the screen and 4GB RAM was no longer enough;
        * 2013 – 15” MBP Retina – it was actually much lighter than the first MBP and even lighter than older MBP 13”; yes, it’s a bit too heavy, but i LOVE the screen and speed;
        * 2014 – added iPad Air so I no longer need to get MBP out of my bag on the airplanes and in meetings; significant improvement.

        Like

  27. Aleh Cherp says:

    No doubt MacBook Pro 15” Retina. I think iPad is indeed a luxury in my profession. I use it almost exclusively in airplanes where it is clumsy (but still possible) to get my MacBook out. I travel a lot, but it still does not make a fundamental difference. A lot has been written how it is good to come with an iPad to meetings (it is … but then a paper notebook also works) and sit on a sofa doing OmniFocus reviews … But that’s a definition of luxury. On the other hand MacBook Pro 15” retina would be a huge change in your daily work experience.

    Like

  28. Pingback: 221: Academic Workflows with Aleh Cherp | Mac Power Users

  29. Ken Case says:

    Thank you for including OmniFocus, OmniGraffle, and OmniOutliner on this list!

    I thought your academic readers might like to know that educational discounts are available for all of our apps when you buy direct from our online store (store.omnigroup.com/edu). For example, while you noted above that OmniGraffle has a list price $100 (or $200 for Pro), with the educational discount you can save 40%—so our academic customers only end up paying $60 (or $120 for Pro).

    Hope this is helpful!

    Liked by 1 person

  30. Hi Aleh, have you used Omni Plan at all for project timelines or gantt charts? Thanks :)

    Like

  31. Aleh Cherp says:

    No I am still hesitating to buy it. It’s on the expensive side. But I am getting closer to do it. Have you used it? What’s your experience?

    Like

  32. Eliana says:

    Hi Aleh!
    Thanks for all your Mac software articles, they’ve been quite helpful. I’ve been particularly following everything you have to say on Papers3 as I’m beginning to compile a library of papers for my PhD work (in Papers2) and don’t want to be stuck using a buggy program – I’d like to migrate to a different platform earlier rather than later if need be.

    Given your familiarity with so many productivity apps, do you know of any good way to snag pictures of figures from the articles I’m reading so I can tag them/comment on them to search for later?
    Thanks!
    Eliana

    Like

  33. Thanks for the great post and comments. I had been using the Scapple software to do quick conceptual maps/models. I find very simple to master. However, not having an iPad version is a deal breaker for me. Are you aware of a similar products? I looked into iThoughtsHD, but didn’t seem to fit the bill.

    BTW, I used to be a heavy OneNote user back in the Windows days, and since the release of the Mac version, I am in love with it again. I have moved most of my notes from Evernote. Their iOS app is a great companion.

    Like

  34. ybin says:

    Hi Aleh,

    I wonder whether you or anyone else can give me some advice on file backup and file synchronization solutions. I am currently using a cloud-based synchronization software to sync files between my office and home computers. Because of some serious issues encountered, I am thinking of either 1) abandoning this software in search of a better one for file synchronization, or 2) abandoning the idea of cloud-based synchronization entirely and stick to only file backup solutions (cloud based or not). Under this scenario, I would use one dedicated computer for all my academic work.

    Below is more details:

    I see that you listed ‘DropBox’ under General Tools. However, a serious disadvantage with DropBox is that you have to drag things into the DropBox drive/folder, which can destroy your file/folder structure/path.

    What I have been using is SugarSync which overcomes the Dropbox problem described above. You can select whatever files or folders to sync without having to move anything. I set up synchronization between my Work and Home computers. This way, when I finish work in the office, I go straight home and, after SygarSync finishes updating the files in my home computer, I can continue working on my home laptop. And vice versa. And I thought it was a true liberation (from having to lug around a laptop).

    However, recently, I discovered a serious problem with the software. To put it simply, while it works fine most of the time, sometimes it fails to sync files without any warning, with very grave consequences.

    For example, say a certain file is of Version N and is synced between my two computers (through their server). I do some work on the file on my office computer and the file’s version become N +1 (as an example). When I get home, and my home computer finishes synchronization (via the cloud), I would expect the file to have been updated to N +1. Except that in some cases, the file fails to be updated, remaining version N, unbeknownst to me because there is absolutely no warning about failure. So I open the file and begin to work on it. If I am not very careful, or if the time lapse between N and N+1 is big, there is a good chance that I will not even notice the file’s version is still N. So, I work on the file (could be important things like manuscripts, reading notes, etc), and save it and let’s call this file version N+2.

    SugarSync will consider this version to be the latest one because of the timestamp. It then sends it to the cloud, and, when the other computer (office computer) boots and finishes synchronization, will replace the N+1 file in the office computer with the N +2 file sent from home.

    You now see the sinister nature of this problem. It means the work I did between N and N+1 in my office computer is lost, and I may not even know it.

    Needless to say, when I found out about it, I was in great shock, and I was furious.

    Right now, I am thinking of two solutions:

    1. Keep a cloud-based file/folder synchronization arrangement (between office and home computers) because it is liberating (you can work on the same thing on two computers, and don’t have to lug around a laptop), but search for a better software that does not have the issues I have encountered. If I go for this solution, then what would that problem-free software be? Any suggestions?

    2. Abandon the idea of cloud-based synchronization entirely and recognize the fact that for something as important as academic work, one simply cannot trust a cloud-based software to update and delete files across computers. Instead, do all academic work on one dedicated computer only. Cloud-based backup software can still be used to continuously back up files to the server (backing up files instead of synchronizing them between computers does not come with the problem described above, because the server does not automatically replace files in your computers). At the same time, also use an external hard drive to regularly back up the entire hard drive.

    Any suggestions from you, your colleagues, or fellow readers?

    Thank you!

    Like

  35. Jo says:

    Have you considered building your own cloud service using a network-attached storage (NAS)?
    At the moment I use a Synology NAS to keep my working files syncronized between a Macbook and iMac, which works quite well with “Cloud Station”.
    In our institute it is not permitted to use internet based cloud services because of security issues anyway – and my personal opinion about this is quite the same… I do not feel comfortable keeping my files where I do not have direct control about them, so I do not use Dropbox or similar services for work.
    Synchronizing over NAS is done as soon, as my laptop connects to my network at home, but the NAS can also be configured to have VPN ports, which can be accessed from the internet. Maybe I would do that, if I also had a stationary mac at work, but this is not the case at the moment.

    The NAS is also used for my regular Time Machine backups btw.

    Liked by 1 person

    • Jo says:

      oh, this was meant as a reply @ybin

      Like

    • Bryan says:

      I second this approach. I love, love, love my Synology Diskstation (1513+). It works fantastic as a Time Machine Backup, and I use the Cloud Station capability. I place all my Scrivener docs, OmniOutlines, NValt notes, Mindnode maps and Word docs into my Cloud station folders on each of my Apple devices (supports MacOS, IOS, Windows and Android.) I also scan everything using a Scansnap ix500 connected to my mac-mini. Scans get OCR’d and dropped into an actions folder, which Hazel watches, tags and moves to different folders, all managed by CloudStation. Like Dropbox, it synchs all my folders/docs (or the ones I select per device) to my Diskstation, macbook, mac-mini, iPad and iPhone.
      This Christmas break i plan to test out the Notes app, which is an Evernote substitute for making everything private. I will also test out a few DevonThink databases . I also use it as a video server for my home theater system using Plex. I also have the DiskStation synching a number of critical files (taxes, receipts, research, etc.) with an old Drobo, which is offsite, just for good measure and backup strategy.
      I get the benefit of having a dual-disk redundancy RAID array, with multiple backups of critical files, while maintaining all my data in a privately and with drive encryption.

      Like

      • Jo says:

        @Bryan: I already use the NAS for my “work” DevonThink database. Syncing works great – the only thing to remember is: Aliases within the database need to point to files within the Cloudstation root folder – but this should not be much of a hassle.

        A couple of weeks ago I tried out some task management software and was quite impressed by OmniFocus – one reason is, that it supports private WebDav servers to sync its database, which I feel much more comfortable with compared to the services storing data in the cloud. It was not the easiest task to set up the Synology WebDav server, but after some attempts I have it running now together with OmniFocus.

        Like

    • ybin says:

      Thank you Jo for your reply. I had no idea what NAS is and having just googled it, I still find it a bit too technical for me. But I will try to find out more about it …

      Like

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