- Posted by John on December 18, 2013
Using WriteLaTeX in our Evolutionary Game Theory Hackathon and beyond
Jake, David and Artem's recent paper on 'Edge effects in game theoretic dynamics of spatially structured tumours' came about after an impromptu 4-day hackathon. It was also the first time they'd used writeLaTeX for collaboration, and to get their perspective on the experience we asked them some follow up questions. Here's what they said...
Who are you, and what do you do?
My name is Jacob Scott, I am a radiation oncologist and mathematical biology DPhil student. I work in between the Oxford Centre for mathematical biology and the Integrative Mathematical Oncology group at Moffitt Cancer Center in Tampa, Florida.
I'm hoping to be able to help bring the rigor that physics has always enjoyed to the oncologic sciences in order to provide better treatments through deeper understanding.
My name is David Basanta and I am a mathematical oncologists at the Moffitt Cancer Center. I did my PhD in evolutionary computing and since then I am interested in anything and everything evolutionary.
Cancer is, unfortunately, an evolutionary disease driven by Darwinian evolution so having the computational tools to understand how tumours evolve and thus become increasingly more aggressive but also better at being resistant to treatments, is essential.
I'm Artem Kaznatcheev, a theoretical computer scientist (cstheorist) at McGill University. I am finishing my Masters at the School of Computer Science specializing in computational learning theory, and also do some agent-based modeling work as an associate member in the Laboratory of Natural and Simulated Cognition in the Department of Psychology.
I have a strong interest in how applied math -- in particular cstheory -- can be applied to fields like biology. This had led me to start learning evolutionary game theory five years ago when I was in undergrad, and it just happened that Jake and David use EGT to study cancer!
What are the biggest challenges you face in your work?
For me, the biggest challenge is trying to maintain a balance of an open mind and desire for rigor in my research while maintaining a strong grasp on, and trust in, the highly empirical science of evidence based medicine.
I think that, for me, the biggest challenge for my work is striking fruitful collaborations. This is tangentially related to what Jake describes but also adds the challenge of being able to deal with different people, having different interests, motivations, etc. Having the right tools to work helps and I am really hoping that tools like WriteLateX will make using LaTeX so easy and convenient that even my experimental collaborators will start using it!
Keeping the motivation to finish writing up results.
How did you find out about writeLaTeX?
I think I first heard about writeLaTeX on twitter, but who knows!
For me this would be Google+. Most of my contacts at G+ are quite tech savvy and some of them, I distinctively remember Vincent Knight, from Cardiff University, posting about it about a year ago. That certainly caught my interest. Since my work is based on collaborations, being able to work with people like Jake and Artem on a LaTeX document simultaneously seemed like an incredible feature.
When Jake, David, and I sat down to start writing, we were going to use the standard email-back-and-forth approach, but I remembered about WriteLaTeX and recommended it.
My first experience with WriteLaTeX comes from a competitor (I think) -- LaTeXLab. It is an older project that was meant as a LaTeX extension to Google Docs, my colleague Kyler Brown and tried using that for collaboration once but had a hard time getting it to work.
One day I was in the computer labs and I saw some undergrads using a very similar interface, and I asked them: "oh did they fix up LaTeXLab?" and was surprised to learn that "no, this is cooler: WriteLaTeX". After that initial exposure, it was kept fresh in my mind with occasional mentions on Twitter and G+.
How has writeLaTeX helped you?
The first time I used writeLaTeX was for the project that this post is about. I collaborate with quite a few people all around the world, and we have used many different solutions before, and struggled with version control, software compatibility, etc.. This seems, so far, to be the best solution I've come across.
I love LaTeX but the nature of my work makes using it too difficult. I work with different people in different places using different computers. WriteLaTeX makes all this easier.
It really streamlined the process of writing the paper. All my previous collaborations have been via the email-drafts model, so I was happy to find a 21st century solution to this. I am now trying (with good success!) to switch over some of my other ongoing collaborations to WriteLaTeX.
What would you have done if you hadn't used writeLaTeX?
We would have used Dropbox and standard latex files. And, we still have a shared dropbox folder for this project in which we share papers, figures, random thoughts and some backed up versions.
With people that are reluctant to use LaTeX we usually start sketching the document in Google Docs and then move to a Microsoft Word version where we can handle figures and references. At that stage my inbox starts getting flooded by a myriad of versions of the draft.
I had actually assumed that it would resort to the old email-drafts-back-and-forth workflow.
What's next? (and what might you do with writeLaTeX in the future?)
Beyond our next project together, for which we will definitely be using writeLaTeX, I've started using writeLaTeX for some of my supervisions. When I need some help with maths, and my supervisor is in another country (as is usually the case) writeLaTeX has provided a nice way to quickly and accurately do some maths together - like a blackboard of sorts.
As long as I keep working with people like Artem and Jake the use of writeLaTeX seems like the most straightforward version. The challenge now is to get less computer-literate people to use it as well. Certainly comments, tracking changes and an online dictionary would make this easier for me.
I plan to switch most of my collaborations to WriteLaTeX, if possible. The remaining hurdle is that I sometimes work with non-mathematicians that are not familiar with LaTeX! It'd be nice if they could comment on WriteLaTeX drafts without knowing how to use LaTeX at all (like commenting on a pdf on your computer).
On the Friday night of the hackathon, we celebrated by buying a bunch of redbulls and working 'till 2am at my house. I dropped Artem off at his hotel, then picked him up for a late breakfast and we worked, starting our manuscript using this great new on-line app we found called writeLaTeX. This was each of our first experience with this app, and we loved it. We would normally have been forced to use some sort of combination of applications - probably google docs for the body of the text (so we could edit simultaneously), who knows what we would have used for the references, and then someone would have been responsible at the end for putting the whole thing into LaTeX for final typesetting. WriteLaTeX really streamlined this whole process as we could all edit the manuscript itself, including the analytic parts, the figures, and the bibliography, in real time, all the while seeing the results typeset beautifully, in LaTeX.
We have all agreed that we will use writeLaTeX for all collaborations that we can going forward. Some issues remaining, from our perspective are:
1. Still a little annoying for references - there has to be a parent .bib file somewhere (we are using dropbox).
2. I anticipate some struggles getting non-mathematician types to sign up - we work with a lot of biologists and clinicians and we will probably end up asking them for pure text which we upload, though maybe we can convince them otherwise.
3. Some of the errors are hard to divine since they are one extra layer deeper than normal... if one isn't pretty experienced with LaTeX to begin with, this could be difficult.
In any case, we'll certainly be recommending writeLaTeX to our colleagues, and are looking forward to seeing how it develops over the coming months.
Now that there is a Rich Text formatting option, I feel like collaboration just got even easier. I probably won't use the option myself, but sending the link over to my clinical and other non-tex savvy collaborators just went up a notch - pretty much obviating some of Artem and my earlier complaints.
Read more from Jake, David and Artem
Jake posts regularly to his blog and often shares interesting things via twitter and Google+. To find out more about his research head to the Integrated Mathematical Oncology group and the Wolfson Centre for Mathematical Biology (+ blog).
David runs the Cancer Evolutionary dynamics research group at the Moffitt Cancer Center, and you can find him on twitterand Google+.
Artem regularly writes for his Theory, Evolution, and Games Group blog, and you can find out more details about his research and publications, or check out his latest Google+ posts.
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