A success story for Warburg's Lens

I've been travelling a lot of late, which I'll blog about on its own in a bit (including a 'best of the best' coffee machines post), but I heard a story from a friend, which triggered a memory which I want to share. It took a moment, but I realised that a whole chain of events that I was unaware of, yet intimately involved in) added up to a success story for Warburg's Lens, the theoretical oncology preprint discussion forum that some colleagues and I started to try to speed up the process of scientific discussion.

So the story goes like this:

I was trolling the qBio section of the arXiv, as you do on a Friday night, looking for interesting papers. For the record, I also always scan the +bioRxiv Preprints. On this night, I came across one from one of my favorite authors, +Arne Traulsen, who has an evolutionary theory group at the Max Planck Institute in Plon, Germany. The #preprint, entitled, Cancer initiation with epistatic interactions between driver and passenger mutations, seemed like a very interesting one, so I put it on Warburg's Lens for discussion. It generated some nice discussion on the site which even included the authors, who were able to defend some of the points, but also take on board some very relevant (non-anonymous) feedback.

Fast forward a bit, and I'm minding my own business trying to get a job, and I get a request from a journal to review an article.... lo and behold it is the same one we are talking about. For various reasons, I declined to review it, but I remembered that there were some very constructive criticisms from people on Warburg's Lens (people who have published significant works in this direct area), so I knew who I could suggest as a replacement reviewer, which I did. Readers won't have a problem guessing who any of the anonymous people are, but I will not divulge that here.

Fast forward again, and I'm visiting some colleagues in Boston (again, post to follow, there was wide #heterogeneity in coffee machines) and a friend mentioned that this great paper that he had reviewed just came out...  and on the same day, my colleague and supervisor, +Alex Fletcher sent me an email notifying me of the paper, which is now out, and you can find it online here, but of course, I can't get it at home without dropping $40. I am eager to read the paper and compare it to the #preprint.

Either way, congrats to +Arne Traulsen et al. on the nice paper and thanks to all who contribute to the discussion on Warburg's Lens - and it's inspiration website, Haldane's Sieve. Keep submitting your #preprints to repositories like the arXiv and +bioRxiv Preprints, keep doing good #openscience. This seems like a win for everyone.

Also, lest I forget, cheers to the Journal of Theoretical Biology for being cool with preprints. Let's keep adding to the list.  This is a tangible example of how preprint servers help EVERYONE, even the journals. We got faster, more on target review, because of the preprint. A list of journals and their preprint policies can be found here:

http://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy

The role of mathematics in oncology - a discussion

A few weeks ago, my friend and colleague +Philip Gerlee wrote a post on his blog with about the role of mathematics in oncology in which he generally suggested that our role, to date, as mathematical/theoretical oncologists has been to help see old data in new ways.  In the post he said further that there has yet to be a 'seminal paper' in the field that has changed the way that biologists (or clinicians) think about a problem or disease. In an addition to the post, at the suggestion of another friend and colleague, +Heiko Enderling, Philip added an errata, which suggested that maybe he was wrong, and that maybe an early paper on chronic myelogenous leukemia (which you can find our more about here) represented the 'seminal paper' that we needed.

I commented that, while I thought that paper added valuable insight to the field, that it hadn't really changed the way we think of (or treat) the disease. This comment kick-started a much more cogent, and thorough, blog post from +Artem Kaznatcheev

which was re-blogged and further discussed by +David Basanta on his blog, cancerevo.

I think that this debate is an important one.  As our field, mathematical oncology, is still young, defining our role is extremely important, especially for the new generation, as only by understanding our role can we measure our success and plan for the future. While I'm working as hard as I can to finish my DPhil at the Wolfson Centre for Mathematical Biology, I'm excited to think about trying to build a group centered around meeting these goals. Other fields of mathematical biology have better established roles (take for example, developmental biology in which many important advances have been made by theorists, like our own +Ruth Baker and her mathematical model of the clock and wavefront model, for instance), and I fear we'll lose promising theorists to this field (I'm talking to you +Alex Fletcher) if we don't better define our role.

So, take a look at the discussions and posts I've linked above, have a read and think, and chime in.

Handling collaborative projects in the age of the cloud - how to manage without spending any money!

As a clinician cum scientist, I am almost always involved in collaborations with multi-disciplinary groups.  And, as an american who has done some training in the UK, many of those groups are NOWHERE REMOTELY NEAR one another.  To keep myself, and my collaborators sane, I've been constantly experimenting with different combinations of cloud based repositories so that we can all work on things together.

So, I started out with +Dropbox by itself, but quickly found that, without spending money, I quickly filled up my allotted space.  Even after totally maxing out the freebie upgrades (I think I have like 35Gb or something thanks to some promo at Oxford, referring everyone I know and being a shameless social media promoter - every Mb counts!), I still am limited.  So I added +SugarSync for my personal files, to clear off dropbox and leave it for just collaboration.  Well, that filled up pretty quick too, and as I haven't found sugarsync to be as easy to navigate as dropbox, I haven't worked as hard to maximize my space there.  I muddled along with these two but still struggled with things like version control and the desire for contemporaneous editing.  Which led to...

Google drive and google docs.  So, with google drive, you get 25Gb or something, but I started to get confused as to where things were.  When I wanted to collaborate real time though, I was stuck, as google docs was really the best thing going (and still is, for many things).  However, in the last few months, I discovered +writeLaTeX, which has really changed the way I do business.  This is a (mostly) free service (I haven't hit the wall yet, and it is pretty big considering that you don't store data there really) in which you can create, manage and edit LaTeX documents with as many people as you like. For me, as a mathematical biologist, this was great - so long as my collaborators were also theorists who were tex-savvy.  I first used it doing a little hack-a-thon with some friends that I blogged about before. Recently though, as in, in the last few days, they have added a Rich Text formatting layer which, I think, will change everything again.  No longer will I have to give the link to a document to my biological/clinical collaborator with the caveat 'just ignore everything that isn't text - squint a bit if you have to'.  Now, they can just go ahead and edit away just like they are in word or whatever, but I can come in behind and have the full functionality of LaTeX.  So that aspect seems solved.

**note - I LOVE writelatex, and you should check it out... and if you do, use this code and I get 50MB more space.  https://www.writelatex.com/signup?ref=5ed6049a8e70 **

The only issue left for me is, now that I'm cranking TONS of simulations in (what I hope is) the final push toward this whole PhD thing, how to work on a DATA-HOG of a project on two computers (I can't stay at work late because I want to go home to my super sweet little kids, but then I DO want to work after they go to bed without driving back to work) or to share this with someone else.  I thought, at first, that I'd just clear out my dropbox a bit, and try to be parsimonious with what I saved...  but, as the output for my simulations is \mathcal{O} 30Gb/simulation, this quickly became unfeasible.  Enter bittorrentsync - my saviour.  This little gem (free) lets you have a synced drive on as many computers as you like.  The freeing move here is that there is no cloud interaction, so there is NO SPACE LIMITATION.  (There is also no auto-backup for the same reason... but this is obviated if you use Time Machine or something similar).  All you do is download the software (a couple Mb's) and then, to set up a shared directory, it generates a 'secret' which you share with whomever you want to share.  The secret is a massive string of letters/numbers that is autogenerated - and I bet even the guy at xkcd.com would approve.

So, now I'm set and I don't have to think too hard.  I also don't forsee ever having to spend any money (until maybe I have a lab or my own and lots of people, but by then - if that time ever comes - I will have grant money to spend on such things...  ?).

Summary: I use dropbox for shared/travelling talks, figures, syncing my papers library, shared simple code (matlab, etc).  I use sugarsync for my personal documents (though I might phase this out...). I use writelatex for (now and going forward) ALL papers I write and bittorrent sync for shared working directories (also home/office syncing of working directories).

As an aside, dropbox has a cool feature - since everyone can modify things at will, they have a nice cloud backup system, which includes who the last person to interact with a document was, so in case your supervisor starts randomly deleting hunks of your thesis, you can call them on it - not naming any names...  +Alexander Anderson :)

To be fair, I don't think Sandy actually deleted this stuff... and I was able to recover it, but it was pretty funny :)