Monday, 25 August 2014

PhD Tools

This is the set up I've used during my undergrad/Masters and that I'm going to carry through onto the PhD.

I'm using a whole bunch of different tools to streamline my work and offload my brain - I have a goldfish memory (the castle around the corner is a surprise every time!*) and tend to worry about everything. All the time. I can't be very efficient without knowing that I can "forget" certain things because they have been recorded somewhere (and that I will get a reminder when the time comes).

The ease of recording things, as well as the ability to access the information is paramount, as I work from several locations and need to be able to get my hands on all that data anytime, anywhere. I need a set up that will not only work between office and home, but also between 4 different countries on 2 different continents. Something that will work cross-platform, as I use both a tower PC and a MacBook, as well as an iPad and an Android phone.

I am currently using:

The Trio of Skim, Scrivener and LaTeX - Skim for reading and marking scientific papers, Scrivener for the bulk of my writing, including notes taken on the papers all the way to, hopefully, the Thesis. LaTeX is my secret weapon of choice when it comes to formatting, it's really second to none in this category.
Mendeley - for keeping track of my references. It produces a bibtex file that can be used with LaTeX to automatically input and format references, both in text and at the end of the document as a bibliography.

For keeping track of most of my life I'm using Calendars (used to do Google, but swapped to iCloud now for no real reason), Evernote and Wunderlist. Each of those plays a slightly different role, Calendars organise my day/week/month, Evernote collects things that might be of use one day (meeting and lecture notes, recipes, manuals, travel arrangements, blog ideas…), while Wunderlist is there, well, to keep track of my multiple to-do lists and my daily agenda.

Mailbox - I have also recently started using Mailbox on my iPad and Android in order to achieve "inbox zero". I wasn't sure I will likely, but I'm totally digging it.

I'm also using Bloglovin' and Pocket to read things that are not scientific papers. Bloglovin' keeps track of all blogs (I read mainly academia/science-related blogs). Pocket is the "I'll read it sometime later" bucket, where I throw stuff that might be interesting, but that I'm not sure I want to keep - if I do want to keep it, it will probably end up in Evernote.

I am still working on my cross-platform links, as an iPad is a fairly new addition to the family - I was lucky enough to win one in a contest and so haven't been building those systems with an iPad in mind. I am also attempting to use IFTTT to automate some processes, but I think I have a long way to go here.

I am going to write a separate blog post on how I'm using each of the above, in case anyone out there is curious, but also so that I can see how my habits evolve over time. Once the posts are written I will link to them in this post (probably make the names of the programs clickable too).

*I'm pretty sure I have heard this somewhere, but for the life of me can't remember where.


  1. Hi there, came across this post via Twitter. Thanks, very useful.
    Would love to hear how you're using Mendeley and Scrivener. I'm using Scrivener to write - but have been told it's better to export to Word when you need to format near the end of the thesis. Am looking for a reference manager that can integrate with Scrivener. My uni gives us free premium Mendeley, so am keen to use that, but from what I can tell online, it won't really integrate with Scrivener. I was thinking I'm going to have to write in references manually as footnotes into Scrivener and then, once exported to Word, will have to manually go through each footnote and convert to Harvard format citation from Mendeley. This is obviously not ideal at all!
    I've not used Latex before - could it help this workflow somehow? Would love to hear how you use it!

    1. Hello Candice, thank you for your comment. As I said on Twitter I will definitely write a blog post outlining the workflow in a bit more detail, but basically I don't think there is a reference manager out there that integrates with Scrivener seamlessly - as far as I know all of the require some sort of a workaround. Which workaround is best for you might depend on the way you work/what you want to achieve (I definitely have heard of people using footnotes in a similar way to what you describe).

      To be perfectly honest with you Scrivener is a fairly new addition to my workflow - I used to simply do plain text editors + LaTeX, but figured for bigger project (like the PhD thesis!) Scrivener will help.

      The way I worked with references so far was to input them into Mendeley and assign a unique cite-key to each reference. Then export the library (this can be automated) to a bibtex file that can be used by LaTeX. I then input the cite-keys for references as I go (so I will do that in Scrivener now) and leave formatting and bibliography compiling and outsetting to LaTeX (which reads the bibtex file and does all the heavy lifting). People say LaTeX has a steep learning curve - but I didn't find it too complicated for what I needed it to do, the help forums are excellent and most of the problems can be easily fixed. It can basically sort all your formatting for you, from placement and numbering of figures/tables, through titles/subsections, references and so on. You can focus on the content and stop fidling with font. It's also a lot more stable than Word when it comes to big projects. It's worth checking out, but it might not feel super-intuitive to start with.

      So I'm thinking about using LaTeX code in Scrivener as I write (just like I'd use it when I write in LaTeX directly) and then exporting to LaTeX for final compiling/formatting/reference sorting, however I have to also look into the Multimarkdown to see whether that's not a better option - it keeps getting mentioned when people talk about Scrivener/LaTeX.