--- 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/ date: !binary |- MjAxMi0wMi0wNiAxMDowMDoxMiArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxMDowMDoxMiArMDEwMA== categories: - Technology - Open Access - Academia - Linux tags: - PhD - PhDchat - FOSS comments: - id: 6624 author: Steve Cooke author_email: firstname.lastname@example.org author_url: http://twitter.com/SteveCooke date: !binary |- MjAxMi0wMi0wNiAxMjowNTowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxMjowNTowMCArMDEwMA== 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: email@example.com author_url: http://bath.academia.edu/RossMounce date: !binary |- MjAxMi0wMi0wNiAxMzo1MDowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxMzo1MDowMCArMDEwMA== 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: firstname.lastname@example.org author_url: https://www.martineve.com date: !binary |- MjAxMi0wMi0wNiAxMzo1MzowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxMzo1MzowMCArMDEwMA== 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: email@example.com author_url: '' date: !binary |- MjAxMi0wMi0wNiAxNDoxNjowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxNDoxNjowMCArMDEwMA== content: I came pretty close 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: firstname.lastname@example.org author_url: '' date: !binary |- MjAxMi0wMi0wNiAxNjoxODowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxNjoxODowMCArMDEwMA== 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: email@example.com author_url: https://www.martineve.com date: !binary |- MjAxMi0wMi0wNiAxNjoyNDowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxNjoyNDowMCArMDEwMA== 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: firstname.lastname@example.org author_url: '' date: !binary |- MjAxMi0wMi0wNiAxNjozNzowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxNjozNzowMCArMDEwMA== 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: email@example.com author_url: https://www.martineve.com date: !binary |- MjAxMi0wMi0wNiAxNjo0MDowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxNjo0MDowMCArMDEwMA== 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: firstname.lastname@example.org author_url: '' date: !binary |- MjAxMi0wMi0wNiAxOToxMzowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAxOToxMzowMCArMDEwMA== 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: email@example.com author_url: https://www.martineve.com date: !binary |- MjAxMi0wMi0wNiAyMDowNTowMCArMDEwMA== date_gmt: !binary |- MjAxMi0wMi0wNiAyMDowNTowMCArMDEwMA== 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: firstname.lastname@example.org author_url: '' date: !binary |- MjAxMi0wNC0wMiAxNjoxNzo0OSArMDIwMA== date_gmt: !binary |- MjAxMi0wNC0wMiAxNjoxNzo0OSArMDIwMA== 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: email@example.com author_url: '' date: !binary |- MjAxMi0wNC0wMiAyMDoxMTowNiArMDIwMA== date_gmt: !binary |- MjAxMi0wNC0wMiAyMDoxMTowNiArMDIwMA== 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: firstname.lastname@example.org author_url: '' date: !binary |- MjAxMi0wNC0wMyAxMDoyNToyNCArMDIwMA== date_gmt: !binary |- MjAxMi0wNC0wMyAxMDoyNToyNCArMDIwMA== content: Great, thanks for your reply Martin. I think I'll probably follow the same approach... - id: 6672 author: Martin Paul Eve author_email: email@example.com author_url: '' date: !binary |- MjAxMi0wNC0wMyAxMDoyNzowNCArMDIwMA== date_gmt: !binary |- MjAxMi0wNC0wMyAxMDoyNzowNCArMDIwMA== 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! ---
Feeling confident of my current level of progress, 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.
Operating system: Ubuntu GNU/Linux
Word processor: LibreOffice [previously OpenOffice] Writer
Spreadsheet: LibreOffice [previously OpenOffice] Calc
Bibliographic manager: Zotero
Email client: Mozilla Thunderbird
Web Browser: Mozilla Firefox
Backup solution: Unison
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.
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.
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?
Featured image by okubax under a CC-BY license.