---
layout: post
status: publish
published: true
title: Doing a Ph.D using only free, open source software

wordpress_id: 1900
wordpress_url: https://www.martineve.com/2012/02/06/doing-a-ph-d-using-only-free-open-source-software/
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categories:
- Technology
- Open Access
- Academia
- Linux
tags:
- PhD
- PhDchat
- FOSS
comments:
- id: 6624
  author: Steve Cooke
  author_email: stephen.cooke@manchester.ac.uk
  author_url: http://twitter.com/SteveCooke
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  content: I did my thesis in LibreOffice, using Zotero in Firefox for reference management
    and citation- all running on Ubuntu, with Ubuntu One as my backup solution. More
    recently I've started using Mendeley for PDF management & annotation, which
    isn't open source, but is free. Having to convert to Word format to send documents
    to supervisors caused problems when I got commented work back - as the conversion
    killed field codes for Zotero, but other than that the set-up was brilliant. There's
    a useful add-on for Libreoffice that lets you apply a template to a document after
    it's been created, which I found incredibly helpful. The Android app for Zotero
    that lets you scan a book's barcode to generate a reference in the Zotero database
    was also brilliant (though that cost a couple of pounds). Also useful are Labyrinth
    Mind Mapping for Gnome and  NixNote.
- id: 6625
  author: Ross Mounce
  author_email: ross.mounce@gmail.com
  author_url: http://bath.academia.edu/RossMounce
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  content: ! 'Bibliographic manager: Mozilla Thunderbird ???


    Interesting. I''d recommend Mendeley, Citeulike or Zotero though. They surely
    must be easier options?!?!'
- id: 6626
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: https://www.martineve.com
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  content:  The peril of neglecting to close a single " in an href attribute is that
    it overwrites the rest of the line. Thanks for pointing out, though!
- id: 6627
  author: Andrew Farke
  author_email: andrew.farke@gmail.com
  author_url: ''
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  content: I <a href="http://openpaleo.blogspot.com/2008/05/open-source-dissertation.html"
    rel="nofollow">came pretty close</a> with my own dissertation. There were one
    or two little pieces of data collection software where I had to use commercial
    versions, but that was it.
- id: 6628
  author: William Roe
  author_email: disqus@wjlr.org.uk
  author_url: ''
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  content: Well I did Computer Science and AI at Sussex some time ago - it's a pretty
    easy task to do such work using only FOSS so I don't think I get any geek points
    for that :)
- id: 6629
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: https://www.martineve.com
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  content: Perhaps so! I suspect it's a rather slimmer percentage in the humanities
    (or, in fact, in the sciences more broadly) though. I wanted to put this out primarily
    for people who might never have considered this aspect and show that it can be
    done.
- id: 6630
  author: William Roe
  author_email: disqus@wjlr.org.uk
  author_url: ''
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  content: Oh indeed - it's a very worthwhile exercise. There are still areas where
    its very difficult to break free of proprietary technology - Matlab for example
    is still the de facto for many students. 
- id: 6631
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: https://www.martineve.com
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  content: It always amazes me, actually, how dependent many of the sciences are on
    this proprietary tech; could do wonders for university budgets if we were liberated.
    it also took me quite a while to realise that it's false to assume technical literacy
    across the scientific disciplines. "Oh you do science, you must be good with computers"
    is such a common presupposition!
- id: 6632
  author: ailsa haxell
  author_email: ahaxell@gmail.com
  author_url: ''
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  content: I admire this. I only used commercial software. Endnote and Word. And they
    would screw each other up. Anytime i updated software one or other would decide
    to sulk. And in receiving Word doc with comments back from supervisor this would
    screw around Endnote citations, reshuffling where they were placed.  I would spend
    weekends crying over this trying to get the two programmes talking to one another
    again. Soon as Im done, Im checking out Mendeley and Zotero.
- id: 6633
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: https://www.martineve.com
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  content: I can't pretend that my tech has always been plain sailing, but it's certainly
    been better than your experience here! Zotero has evolved beyond recognition in
    terms of stability over the course of my use, although I can't profess to have
    ever got on with Mendeley; it simply doesn't seem to *work* for me; a somewhat
    crucial feature. Would be interested to hear how you get on with Zotero, though,
    and give me a shout if you need any help getting started.
- id: 6665
  author: Tim Taylor
  author_email: tijtaylor@cardiffmet.ac.uk
  author_url: ''
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  content: ! "Hi Martin,\r\nI’d be interested to know if you are working with a master
    document in Libre Office to write your thesis? I’m at the stage in my PhD where
    I’m considering the best software to use for writing up, and am currently planning
    to switch from proprietary software (i.e. Microsoft Office) to Libre Office. I
    also use Zotero for managing my bibliography. The Zotero website states that ‘Zotero's
    word processor plugins do not support the use of master documents’ and this was
    something of a concern to me... The two alternatives I’m currently considering
    are:\r\n- Writing the thesis as a single document (my field work generates lots
    of images and so the file size of this document might become very large); or\r\n-
    Writing individual chapters in separate documents and then copying and pasting
    the combined content into one document at the end (which I anticipate may create
    some formatting headaches).\r\nWould be very interested to hear more about your
    experience with this!\r\nI’ve also considered using Latex, but this may create
    problems for receiving feedback from my supervisory team and disseminating work
    to my industry sponsor (both organisations use Microsoft Office).\r\nThanks!\r\nTim"
- id: 6667
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: ''
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  content: ! 'Hi Tim,


    I worked on individual chapters, in separate files, and then pasted them together
    at the end. A trifle clumsy, and there were some formatting irregularities to
    sort out, but in a document this size it would be utopian to expect a solution
    that pieces it all together. This approach worked really well for me.


    Best,


    M'
- id: 6670
  author: Tim Taylor
  author_email: tijtaylor@cardiffmet.ac.uk
  author_url: ''
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  content: Great, thanks for your reply Martin. I think I'll probably follow the same
    approach...
- id: 6672
  author: Martin Paul Eve
  author_email: martin@martineve.com
  author_url: ''
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  content: No worries; I agree -- it's a real shame that there isn't a neater solution,
    but the breakdown into chapters also has its advantages for personal motivation
    -- seems more achievable!
---
<p>Feeling confident of <a href="https://www.martineve.com/2012/01/27/first-draft-of-my-ph-d-is-done/">my current level of progress</a>, I think it's worth pointing out that the entirety of my doctoral thesis work has been done using free, open source software. I wanted to write a quick overview of my system, explain where it falls down and give an honest appraisal of how it went.</p>
<p><b>Operating system:</b> <a href="http://www.ubuntu.com">Ubuntu GNU/Linux</a><br />
<b>Word processor:</b> <a href="http://www.libreoffice.org">LibreOffice [previously OpenOffice] Writer</a><br />
<b>Spreadsheet:</b> <a href="http://www.libreoffice.org">LibreOffice [previously OpenOffice] Calc</a><br />
<b>Bibliographic manager:</b> <a href="http://www.zotero.org">Zotero</a><br />
<b>Email client:</b> <a href="http://www.mozilla.org/en-GB/thunderbird/">Mozilla Thunderbird</a><br />
<b>Web Browser:</b> <a href="http://www.mozilla.org/en-US/firefox/">Mozilla Firefox</a><br />
<b>Backup solution:</b> <a href="http://www.cis.upenn.edu/~bcpierce/unison/">Unison</a></p>
<p>This worked for me for the whole of my thesis work. I have to confess that I have started my (legally licensed) copy of Microsoft Word inside a Windows VM when I needed to submit a file (for a job application) in MS Word format and I wanted to be 100% sure that LibreOffice had converted it successfully. Most of the time, though, the convert to PDF option in LibreOffice is more than enough to ensure cross-platform format.</p>
<p>This could also be discipline specific. I don't know, for instance, whether specific lab software is available in free, open source versions. I somewhat doubt it.</p>
<p>Furthermore, it has not been a smooth ride. I class myself as very technically able and I have had occasions where an upgrade has totally broken my install. That said, I enjoy the challenge of knowing that I am wholly responsible for my computing and take pride in the setup and operation of systems over which I have full control. Has anybody else worked along these lines?</p>
<p><i>Featured image by <a href="http://www.flickr.com/photos/okubax/">okubax</a> under a CC-BY license.</i></p>