Research | Writing | Digital Humanities | Biblical Studies

Software for Writing a PhD Thesis

There are four categories of software for thesis writing: (1) project organizing; (2) word-processing; (3) bibliographic organization; and (4) specialty software. Here are some of the best programs, along with those I find essential to my PhD thesis and scholarly writing workflow.

[UPDATED 2 February 2019 – And I have successfully completed the PhD! Hooray!]

Now I’ll be using a macbook pro for the task, but many of the software programs I mentioned can run on mac or pc (though some run better on one or the other).

Project organizing/note taking.

Some might use a word-processing program for this while others might find a specialized program instead. I’ve heard of many people using Evernote, a free program I also have and like okay but use very little. (If you use Evernote, you must consider Brett Kelly’s guide, Evernote Essentials!) There’s also MS OneNote, Simplenote, and Springpad (see a review of these here).

I’ve decided on a more complicated yet powerful program, Scrivener. It’s difficult to describe what this program does in few words. It is similar to a word-processor–it in fact has a streamlined word processor as a main feature. But it is much more. It allows you to compose, organize and edit a complicated project (like a dissertation, book, or screenplay), its various chapters (or documents), notes and relevant documents (pdfs of articles, summary notes or quotes, etc.), among other things. Learning the program takes an initial investment in time (perhaps a Saturday morning), but the tutorial document walks you through the program’s main features quite nicely. I think this might be the single most powerful program I’ve been using in writing my thesis. In fact, I now have dozens of projects in Scrivener, from academic projects to business ventures. I love it.

So why use this and a word processor? For me, Scrivener’s real power is in the research/note-taking, initial composition and organization–especially organization!–phase of thesis work. While using Scrivener will add a step to the process (as opposed to using Word from the start), I Scrivener saves me time in the long run.

Scrivener is very affordable and they offer great customer support. Here are your four options for when you’re ready to purchase (education licenses are discounted):

Scrivener 3 for Mac OS X (Education Licence)
Scrivener 3 for Mac OS X (Regular Licence)
Scrivener for Windows (Education Licence)
Scrivener for Windows (Regular Licence)

For how the program can be used by students writing in the area of Theology/Religion, see the video below.

Though I’ve not used it, the Dummies guide for Scrivener has excellent reviews for those wanting more help.

File Syncing/Backup

While more a ‘service’ than ‘software’, consider a plan for backing up the files you create with all this software! I recommend a physical home back up solution that you perform at least monthly (preferably more often) in addition to a cloud backup of your most important files. For the latter, DropBox is my choice–sign up for free!


One must, after all, be able to compose, format, and publish the thesis. Some use Scrivener for this (see above), and that is an option. Other opt for Microsoft Word (amzn). While Pages for Mac has some nice features, OpenOffice is capable, too, and I’ve heard a few, mostly those working with the Hebrew language extensively, recommend Mellel (amzn) I have years of experience on Word and it is very widely used. Further, the University of Michigan Library has published a pdf online entitled “Using Microsoft Word 2011 (Mac) for Your Dissertation” to help! If you’re using Word for Mac for academic writing, it’s a must-read.


wordpressYes. WordPress. Starting a blog and writing consistently can not only have a positive impact on your thesis, but it can help you develop professionally and even advance your career. I am convinced my blog contributed to a committee’s decision to award one of Edinburgh’s most competitive scholarships, worth around $65,000 over three years. I have a whole article on just this subject called Start an Academic Blog.

Bibliography organization.

Various programs on the market today specialize in organizing bibliographic data and integrating this data easily into word-processing documents. The top two I’ve heard people using are EndNote (amzn), and Zotero (one might add Nota Bene or Sente). I’ve only used Zotero, but its powerful, efficient, easy to learn/use, and costs nothing! I won’t be looking elsewhere. It also powerfully integrates into Word (for Windows or PC). I can also use it with Scrivener, my organizational and initial composition program. For a video on the power of Zotero for a theological library, see Andy Naselli’s helpful blog post here.

ResearchreSearch Engine logo

A lot of research goes into thesis writing. Let me introduce you to a web tool I’ve created to help: reSearch Engine. Just enter a search term, press enter, and presto.

Specialty Software.

Many disciplines have powerful niche programs suitable for research in a particular area. For me, the ability to powerfully search and collate data regarding an ancient language is enhanced and streamlined with the aid of one of the handful of such programs available today. The top three programs in this regard are Accordance, Logos, and BibleWorks, all now running on both Mac and PC.

I have and use all three and each has its pros and cons. I will likely use Accordance for my “quick and dirty” searching and copy-pasting of ancient languages. Of course, its a powerful program that can do intense searches, and I will likely use it for this when such searches are needed. Logos is my go to program for secondary resources, especially exegetical commentaries and quick referencing church fathers or other ancient sources. Logos has not just saved me money on print books, it has saved me from needing multiple book shelves!

I find myself using BibleWorks less and less, but this is primarily because using it requires me to boot up Windows with my LogosLogoVTrans200x286virtualization software (Parallels for Mac is great, by the way)–though this is changing–and Accordance can do virtually everything BibleWorks can. I am a bit more comfortable doing complicated searches in BibleWorks vs. Accordance, but that may reflect my own inexperience with Accordance. Logos is also capable of original language searching, but I have not used it for this. I suppose I ought to invest some time in each of these programs and check back in with what I find.

I’d be happy to hear what others are using and find helpful.

106 Responses to Software for Writing a PhD Thesis

  1. What I can’t seem to figure out is how to load ZOTERO on my MAC. I did it once a while back, but have a new computer now. I spent a couple hours once trying to download it and make it work… no joy 🙁 a post on where/how to install would help me… I may be hopeless, I still like binders and paper copies to organize research by chapter…

    • John Mark, good to hear from you! Do you remember when this was you tried to load it and whether it was the version that runs in the Firefox web browser or the stand-alone version? I’m now using the stand-alone version for mac which functions like a normal app. The other version I used (which is still available) was actually an extension in Firefox and, as I recall, was loaded differently. Here’s the Zotero download page–you’ll see the stand-alone versions down the page a bit. If you happen to have used one version or there other (or both), your library is sync-able, one to the other. I hope that helps a little.

  2. > OpenOffice is capable, too

    The development of OpenOffice has been stalled for a while, since its sponsoring company (Oracle) dropped it and its new home (Apache) is still trying to get organized. LibreOffice is its main successor, with an active development community and several new releases. I enjoy LibreOffice and have been using it for a study I’ve been writing over the last year (currently 60+ pages).

    • David, thanks for commenting–it’s been a while since we’ve talked! I wasn’t aware of the circumstances of development you’ve mentioned. I’ve used OpenOffice just a bit on Ubuntu, but since I already had Word, I wasn’t motivated enough to invest time into it (nor Ubuntu for the matter). Sounds like LibreOffice is serving your needs quite well. I’ll have to give it a look.

    • This looks interesting, but perhaps you can tell me how it is superior to Scrivener or other alternatives? It looks like the special pricing for your product is still twice the cost of Scrivener, and, correct me if I’m wrong, yours requires the user to also use MS Word?

    • I don’t know much about ActiveScholar, but from fiddling with it for about 5 minutes, I would instead recommend the free, more robust Citavi. Citavi is WONDERFUL and easily surpasses ActiveScholar, from what I can see. One can watch Citavi videos at Note: Citavi is for Windows computers, and if you want to run it on a Mac, you’d have to run Windows on your Mac.

    • +1 to Mendeley.

      I have tried all of them–Zotero, Endnote, etc., etc. Mendeley wins HANDS DOWN! The one and only, ONLY thing Zotero may do better than Mendeley is handle web snippets better than does Mendeley. Maybe. I haven’t tried to hard to deal with web snippets in Mendeley. I have gotten around this by using the snippet program provided on my laptop, saving my snippet in PDF format, and storing it in Mendeley. Also, snippets can also easily be stored in Citavi (another program worth a serious gander for Windows users or those willing to run Windows on their Mac). I tweak my academic workflow periodically, and at the moment Mendeley and Citavi are essential to my workflow. Citavi allows you to manage your note-taking and bibliography generation near flawlessly. I do not use Mendeley for bibliography generation, just FYI.

      Some of what it is about Mendeley: the deep searching capability; the ability to annotate and note take and tag and key . . . all while leaving the PDF clean; the collaborative capabilities; the backup; the simplicity of syncing between its desktop and web versions . . . I could go on.

      Once reason I can’t leave Mendeley: Say I vaguely remember an article I collected, but not too well. Perhaps I remember that it was about Peirce and Radford and algebra. Mendeley will allow me to quickly, quickly see which of the 1000+ PDF articles or book excerpts in the collection contain these three words. Then I can open and search the PDFs side-by-side, and deeply.

      Mendeley and Zotero do “speak with one another,” from what I’ve read. However, I only deal with Mendeley and Citavi for source management. I blog a bit about this. 🙂 It’s a great topic.

      • Thanks for sharing your experience. Using Scrivener and Zotero, it seems I can get similar results as you describe here, though since I have not tried it with Mendeley and Citavi, I can’t offer a comparison. One difference appears to be Mendeley’s ability to handle pdfs, especially in annotating, etc. I can’t imagine the “time saving factor” is too different, but of course it all depends on what exactly you’re doing.

    • So far as I know, Scrivener is able to use all (or at least most) the fonts you have installed on your system, including Greek and Hebrew. I copy and paste a lot of my Greek and Hebrew in unicode, and I’ve had no issues with them in Scrivener.

  3. I’m just diving in to the writing of my dissertation (DBA) and I’m curious as to what “original language research” is. Is this specific to your topic? or do all research projects entail some form of original language research to some degree?

    Excellent post by thew way, I definitely think that Scrivner looks promising.

  4. i study theater literature in masters degree in iran.i wanna know which software is best for me to use. i should be compatible with office word and i can use persian font in it…what kind of software do you suggest??
    is zotero good?can i use persian font in it?…my operating system is windows 7.

    • I have Evernote, but just haven’t found it as useful as many say it is. If your primary purpose is note taking, data organization, etc., then Evernote is probably great. Scrivener offers a lot of other organization and word-processing features. I’m sure the two could be incorporated together fairly effectively, too.

    • Indeed, Evernote is great to take note and organize your digital information (the notes, pdfs or any type of digital information).
      However, it is a poor word processor and I would never recommend its use for that purpose!

  5. […] By the way, I’ve begun gathering information and advice to incorporate in an ebook for anyone interested in better writing (e.g., theses, essays, etc.). The goal is to be thorough yet concise. Topics include research, organization, writing style, process of writing, and technological aids (software, web, etc.). If you want to hear when its finished, sign up below. If not, no worries!  See also: writing software recommendations. […]

  6. […] By the way, I’ve begun gathering information and advice to incorporate in an ebook for anyone interested in better writing (e.g., theses, essays, etc.). The goal is to be thorough yet concise. Topics include research, organization, writing style, process of writing, and technological aids (software, web, etc.). If you want to hear when its finished, sign up below. If not, no worries!  See also: writing software recommendations. […]

  7. I have developed a thesis writing software in the true meaning. Have a look at my site. My software helps you to create the thesis title, thesis statement, research questions, hypothesis tests and conclusion. See my audio and video descriptions.

    • @ Joshua L. Mann
      i am a ph.d researcher and i want to know is there any good free version software that can do all my thesis writing work like bibilography organisation, chapter preparations etc.

      • Vinay, for bibliography management, I use a free program called Zotero (see links above). For writing, one of the better free word processors is part of the Open Office software (google it). I assume at this point in your education you have written a fair bit, so I would consider sticking with the word processor you feel most comfortable with, so long as it can handle your subject, field, etc. If it is a matter of money, talk to the IT dept. at your institution about your problem. Perhaps they will work with you on obtaining the software you need.

  8. Thank you for these very helpful posts! I currently use a Mac, but am planning to go back to a PC, and I want academic humanities outlining and note organization software that has longevity, so I don’t have to learn a new program in a year or two. I’m almost ready to try Scrivener, on the basis of your review. But I’m not clear from your posts whether it does the two things I most need: a) allow one to expand and collapse outlines, so that one can view a short version, longer version, and longest version; and b) allow one to attach one’s notes to an outline section and then, as one writes, delete them from that section (so one can “crunch” the notes into text, till they’re no longer notes!)
    For instance:
    1. TOPIC 1
    A. subtopic A
    i. sub-subtopic i.
    ii. sub-subtopic ii.
    B. subtopic B
    2. TOPIC 2
    Sometimes I want to look at only the TOPICS (i.e. Arabic numerals), to see the broad shape of the project. Sometimes I want to look only at the TOPICS and subtopics, but not the sub-subtopics, to see a slightly more detailed version without all the detail. And sometimes I want the whole thing (when I’m writing, for instance). My current technique is to have three outlines in three separate documents–short, medium, and long–and I’m constantly editing them all, trying to keep them in alignment, and failing!
    Re turning notes into text: currently I write my notes in paragraphs with headings (each paragraph is like a notecard). I then copy them into Word endnotes attached to each relevant outline section, and then take them out of the endnote when I’m writing that section and organize them, deleting each one as I incorporate it into text. This doesn’t allow me to see them the way I would if they were notecards on my desk. And it’s very cumbersome (and I’ve occasionally accidentally deleted a whole endnote full of notes). This system also doesn’t keep them connected to their source texts, so I have to type out bibliographic info for each of them.
    My question: can Scrivener a) collapse and expand my outline; b) allow me to attach my notes to outline sections, and delete as I go (ideally keeping notes linked to bibliographic entries).
    Grateful for your help!

    • JP,
      Scrivener should be able to do all that you’re asking. If you have some doubts, I recommend that you download a trial version and give it a test drive. It should come with an instruction file which leads you through the functions of the program. I went through it in a weekend (about 2 afternoons). As far as longevity, Scrivener seems stable to me.

      I’m glad you found this helpful. If you decide to purchase, you can go through my link in the post which helps me (at no extra cost to you), but no worries if you decide not to. Up to you. Drop me a line if you have further questions.

  9. hi! i’m a phd student. i find scrivener very useful for organising n writing my thesis as it compiles everything in one place. however, i’ve got some questions to ask before considering to purchase:

    1. does it crashes on a windows pc/laptop? my laptop specs are toshiba win 7 core i5 vpro running on a 2.5ghz processor 4GB ram 64 bit os.
    2. i’m using mendeley for organising my references. does scrivener allows integration with mendeley? if yes, that is a bonus!!!

    • Hanna, (1) I’m not aware of any issues in the windows version that would make it crash, but since I do not use it on windows, I would do a little research. It looks to me like your hardware will handle it just fine. (2) I’m not sure where Mendeley is at it terms of Scrivener support. There is demand for it (see here)!

  10. scrivener is UH-GLEE!!! very windows 98 at least on pc. it didn’t work for me. perhaps i needed a financial incentive. LMFAO 🙂

    • I think the appearance reflects the intentionally minimalistic design. I never thought of it as ugly, but I suppose I am not surprised that others might. (I’m not sure what you mean by “financial incentive,” but if you mean to imply that my recommendation of Scrivener is based on a financial incentive, you are wrong.)

      • I started using Scrivener for Mac a week or two on Joshua’s recommendation (thank you Joshua!) I’m happy with many aspects of it. However, I’ve found that I can’t load the many articles that are the sources for my project: trying to do so crashes the system. I plan to create reference links to these articles, but… this is a downside. Second, I’m having trouble managing the formatting, both of documents I’ve transferred in and documents I’ve created. For instance, I use hanging indents for my bibliographies. But I can’t seem to create new hanging indents (only increase or decrease existing ones). Finally, there are times when folders seem to disappear from my binder (only some folders and only sometimes). When I open the binder category (with the small arrow at the left), they don’t appear (causing panic that I’ve lost my work!) But if I close the system and reopen it, they then appear again. Any help appreciated!

        • Thanks for the info. I’m not sure I have answers for you since I have not had those specific issues, but I would certainly let the folks at Scrivener know. I assume your Scrivener and Mac OSX software is up to date?

  11. Joshua, have you tried BookEnds for Bibliography?

    I have just started on my dissertation and am looking at software to use. I intend to use Apple Pages instead of MS Word, since I already have it. The University also provides EndNote license to use, but I had some issues with it on a Mac and especially with Pages. I have used BookEnds for other papers, and if it is setup the way you intend to use it, it is very good.

    I will try Scrivener and see if it will be helpful for my dissertation.
    Thank you for the information.

    • I have not used BookEnds, but from what I’ve heard, it is comparable to its competitors. I can’t speak to how well Pages will work with it or any other program. I have Pages but never use it. I would hesitate to use Pages, mostly because Word is so dominant in my field (including with publishers). Also, your software developers are going to be absolutely sure their program plays nicely with Word since a majority of their users are going to be also using Word. Something to consider. Thanks for stopping by!

  12. Mendeley is a nice software but I will not recommend it at all for a writing a phd thesis. Works fine for small papers, but It’s incredibly slow if you have more than 100 references. If you google “mendeley slow” you’ll see what I mean

  13. Hey Josh, thank you for the article. Have a question on Hebrew font within the Scrivener document. Did you notice any “space” issues between the lines when you copy and past Hebrew Text or type Hebrew words? It happens in the MS Word for me, and in Scrivener. So, I am wondering if you know of any solution for that. I use SBL Hebrew or Ezra SIL, no matter what font I use, the second I resize them, I will see so much space in between two lines. I am in the process of writing dissertation – OT Concentration (well, just getting started, actually). Hopefully I will be able to use Scrivener and others you suggested.

    • Joel, I have noticed issues with Hebrew fonts. Few Word processors offer really great right to left Hebrew font support. Mellel is an exception ( However, I think you might be able to fix your line spacing problem in Word by going to the “Format” menu, selecting “paragraph,” and changing the line spacing to “Exactly” and then entering the desired size of line spacing (e.g., 12 point, 24 point, or whatever). This ought to make the line spacing consistent no matter the font used. Scrivener should be able to do similar formatting.

  14. Hi Josh,
    Thanks for the reply. I do have Mellel, but I am not sure how to use it well. I just do not want to run into compiling/exporting after working in Mellel or Scrivener, since my professors like “Word” 🙂 So they can edit and send comments/remarks etc. Do you work with Mellel as well? My paper will be mostly with Hebrew Text. Also, I have noticed “numbering” format in your video. How did you do that in Scrivener?

    Thanks for your help!

    • I don’t use Mellel, but I know some others who do and like it.

      As for the numbering question, I am not entirely sure what you mean. Could you explain? (Also, I should also note that the video was done by someone else.)

  15. Ok. The numbering format I was talking about was the numbers I have noticed in the video, right before the blue folders: 2.1, 2.2, 2.3 and so on…

  16. Hi Joshua,
    I wondered if you knew about any software available for doing a PhD thesis in APA format? Or can you tell me at least how to hunt one down,
    thanks, Angelique

    • Angelique, any of the major bibliography programs will handle APA, so which one you go with is a matter of (1) how much you like the program and (2) if it’s compatible with your word processor. For example, the bibliography manager I use is free (Zotero), and I can use it with the two word processors I use, Word and Scrivener. Hope that helps!

  17. Hi, i have used Scrivener for a few years on both Mac and now on PC. It is a very versatile and powerful tool. However …
    I understand that Scrivener is meant for writing and not formatting but as I construct my text I find that even maintaining consistent fonts, indents, bullets and line spaces to be a constant drama. Even basic bulleted lists are problematic. The whole visual issue with Scrivener I find distracting.
    Thanks for your article

  18. Joshua,

    Thanks for this helpful post. I’m in crisis trying to decide a word processor and bibliographic manager as I begin my dissertation. I’ve been using Nota Bene for academic work for several years but need to move into the MS Word and unicode world. I have a MacBook but am glad to use a PC. My dissertation will include biblical Greek and Hebrew. Here are the combinations I am considering:

    – Mellel with Bookends (I’m not attracted to the Mellel learning curve.)

    – Word with Bookends

    – Word with Zotero
    Will Zotero allow me to customize the Turabian format if my university has it’s own unique tweaks to this academic style?

    • I’m using QIQQA for bibliographic management, PDF annotation and citations directly into Word, it has automatic keywords and theme generation. It imports Bibtex directly from Google Scholar. It has brainstorming tools and online library syncing.
      The problem I have with it is that the citation fields are only designed for Word, so for Scrivener I have to cite as a comment inline with my text and then insert citations once I have exported to Word. This works but isn’t as streamlined as I would like.
      An alternative for use with Scrivener is Mekentosj’s ‘Papers’ which uses plain text code for its citation tool. I was using Papers a lot (Windows and Mac) but as I started to use more of the features I discovers more and more features had bugs. Papers is however a potentially great solution on either platform.
      I used Endnote for years but always found it had a very old style interface and wasn’t very helpful for the note and PDF annotation process.

    • Yes, you can customize with Zotero, so Turabian should not be a problem. I have not used Mellel to any major extent, but I have two friends who are using it and like it (one is doing an OT in the NT sort of thesis, so he needs a Hebrew-friendly processor). Word for mac does not support right to left unicode which is silly but true, so you may have to use Word on Windows. Hope that helps!

  19. “For this category, Microsoft Word for Mac (2011) was the clear winner. ”

    I wrote my Thesis in Latex and the results certainly look better than Theses produced in Word. Assembling a large document with many figures and citations was a lot easier in Latex than it would have been in Word (based on what I’ve seen others have to go through).

    • Rob, I would honestly love to give Latex a good try, but I’m afraid I’m intimidated by the learning curve (I think is) required for it. In any case, when I say “winner,” I also take into account pragmatic concerns that are specific to me. But thanks for sharing your experience!

  20. Hi,

    Scrivener looks good, just downloaded it. Still trying to figure out how to do referencing in it. Might not use it due the same reason as with dissertation writing the reference management is a must. Also, In terms of attaching the documents to the chapter of concept looks weak.Perhaps, it is meant for book writing primarily. I guess there is no one answer to managing whole writing dissertation bit, where one software can help manage your writing, your pdf files and references.
    Please suggest, Thanks

    • I continue to use Scrivener (more than one year now) for organizing notes. Word continues to be my main word-processing program, however. One can use shortcode references in Scrivener and then run the (.rtf) file through a bibliography management program which will convert shortcode to full citations. Since Word files are so standard in my field, I just can’t escape it as a word processor.

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  22. Thank you Mr Joshua for your thoughts. Iam regular user in Mendeley only and into Material Sciences. Shortly in a few weeks i’l be commencing my Research project and currently collecting relevant papers to my topic. If you have knowledge of any Science oriented softwares please do list them out.

    • Much of the software in the post should be applicable, though you may find some kind of database software useful for tracking results, statistics, etc. I suggest you talk to some experienced scholars in your field and see if they have any software specific to your work.

  23. Hi,

    I would like to be able to highlight multiple documents/PDFs/Articles and then be able to easily scan/search and be able to see a list of information highlighted or noted from multiple articles. Which program does this best? I realize none seem to do this from simple highlighting. But can I cut and paste in a note or annotate somehow and d this? Or must is simply be done manually in a large word doc?



    • Mike,
      Some pdf viewers (like Mac Preview) will display a list of highlighted material per pdf, but I’m not sure of a solution that can collect the material as you’ve described–That doesn’t mean there isn’t something out there.

      Two thoughts: (1) Evernote can auto OCR all documents (included PDFs and images) and these become easily searchable as a whole; (2) One way to speed up the manual highlighting is to select the line(s) you wish once, press ‘ctrl-C’ (or cmd-C) to copy, then toggle the highlighting (your PDF viewer likely has a shortcut, perhaps cmd-H). With the line also copied to the clipboard, you can quickly paste it into your preferred word processor. So you essential select text, press cmd-C then cmd-H, then cmd-V to paste in document.

    • I only know of one application on a Mac that will present a list of all highlighted and annotated sections of a PDF: Sente. ( It is free for a small library, so you can find out if will work for you without having to pay anything.

      It has a very nice interface for highlighting, taking notes, and writing comments on quotations. There are also scripts for exporting your highlights and notes into an external file.

    • I just read Joshua’s comment, and indeed Preview will give you a list of highlights. I didn’t know it would do that! However, Sente may work well for you with multiple PDFs because you can export those annotations into an extra file, and then combine them. That will avoid having to copy/paste everything.

  24. Hi Joshua

    thank you so much for this incredible post.

    I’m hoping you can point me in the right direction
    i am a graduate student writing my Master’s Thesis in Special Ed and could use a few pointers

    after 30 years, i have returned to college.
    don’t laugh but i never had to write a research paper before.

    i have a collection of articles that i am reading and need to take notes
    my kids use index cards and then sort them as they begin to compile and organize their thoughts

    i’ve watched a number of tutorials and i’m not sure what is the best way for me to implement a form of note taking that would enable me to best leverage the feature set of scrivener

    all my research (so far) is in PDF. i know that i can import the files –
    Can i highlight in Scrivener?
    is it possible to create a separate note card for individual notes that i take while reading each article?
    or is there a better way?
    i.e. – would it be better to create color coded tags for each article and then color code the notes – not sure how that would work as far as sorting and organizing

    thank you all so much for your help.

    with warm wishes

    • Ethan, Glad to hear you’re back at it. Best of luck in your essay writing. I’ll answer your specific questions first:

      Can i highlight in Scrivener?

      You can highlight entered text, but not within pdf files (to my knowledge). Evernote premium would have an advantage here, as it can OCR pdfs and, I believe, offer highlighting functions.

      is it possible to create a separate note card for individual notes that i take while reading each article?
      or is there a better way?

      Yes, you can create a new “document” for each article, each article section, or more narrow if you wish. You can also nest them inside of each other, color code them, and add tags. I’m not sure there is a ‘best way’. I think you’ll have to experiment a bit to find what works best for you.

      Generally, I will create a rough outline of my paper (project, etc.) as early as possible, and begin filing notes under the headings of the rough outline. Now, this outline may change over time, and if/when it does, I will reshuffle my notes. That seems to be the pattern I’ve settled into at the moment. Hope that helps!

  25. Dear sir, i am doing my Ph.D in India and i am looking for good grammar checking software for my thesis, so please suggest the software that fulfill my needs. thanking you advance for your kind courtesy.

    • Given the complexity of language (its grammar and syntax, etc.), computer programs do a poor job at consistently ‘checking’ or ‘correcting’ it. Rather than look to software, I suggest you seek some help from you institution. Sitting down with someone who can read your writing and offer feedback will help you in the short AND long run. If you cannot find anyone to work with you, I may be able to help if you’re writing in the English language. Do check the resources on offer at your institution, first, though–they will usually be freely offered.

    • Thanks for letting me know you had problems on your phone. Because the slide in message is not functioning correctly on certain phones, I have now prevented it from appearing on mobile devices. Sorry for the inconvenience. It is a temporary announcement that will remain for the duration of the KickStarter project.

  26. Hi, I’m going to be writing a thesis; I’m a windows user thinking of switching to mac. However I’ve heard that ms word for mac struggles with large text documents and the track changes function. I’ll be sending such files to pc users; also I’ll be using footnotes for references, obv if word for mac does struggle with large docs then I wouldn’t make the switch.

    Any advice please.


    • Sean, I have not had any issues with Word for Mac as you describe, but I tend to make my documents chapter length rather than writing chapters within one document. I also use footnotes and have no issues. (If by chance you need right-to-left unicode, as with Semitic languages, avoid Word for Mac).

  27. Man, there is so much stuff to digest here as a first year graduate student that hopes to be Biblical scholar one day, what seems to be the best way to organize notes/research with a word processor that makes your bibliographic information a breeze?

    I am willing to spend money.

    I use Logos and Accordance to study/research.

    Seems like finding one program that can do it all would be more user friendly? thoughts on using two different programs? (Ex. one for notes/research and another for Bib. work?)

    D.A. Carson and N.T. Wright have suggested using Nota Bene, so that makes that tempting just based on what those men have written, but in this post and comments, it seems the best options are MS with Zotera or Mendeley?

    I am so confused, and I don’t want to make the wrong choice. Please help!

  28. Hi i am a Ph.D. researcher and i kindly request you to provide me the details of getting full versions of scriviner, plagiarism detector, zotero and other thesis writing softwares as i am feeling difficulty in writing my Ph.D. thesis.

  29. Joshua Mann
    thank you very much for your patients explaining this initial step of thesis.
    I am a master in Rheumatology, I would ask if there is any software for processing clinical trials data and integrated it’s reports in microsoft word?

  30. I am a doctoral student. My university suggests getting the dissertation professionally edited. I cannot afford this service. Can you recommend an APA editing software to replace the professional editor?

    • Ken, I personally do not know of any software I would depend upon for editing. You could swap services with a fellow student who you trust. I’ve also known of peers gifted in editing skills who will do it for a reasonable price.

  31. Hi,

    I am interested in using Scrivener for my dissertation but I use a Chromebook. Can you recommend any comparable programs that are compatible with the OS operating system.

  32. Joshua: Congratulations on being awarded your PhD! Thank you for your research and work on “Software for Writing a PhD Thesis”. I am also working on a PhD in Interdisciplinary Studies (Biblical Studies, Ministry, & Leadership). Question: Does Scrivener allow me to deposit multiple PDF references in one folder and Scrivener search a term, subject, phrase, or date within all those PDFs, like Logos Bible software? Thanks and In His Service!

  33. Hi Josh, I’ve been considering a field in academic theology and digital humanities and this blog seems to do just that! Would you mind answering some questions on this career path?

    • Hi Russell. I’d be happy to answer your questions. I’ll send you an email and you can follow up there.

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