The First SSI / 2020 Science Paper Hackathon

10-12 September 2014 at The Real Retreat, Flore, Northants

by Derek Groen, SSI Fellow and Research Associate at the Centre for Computational Science, Department of Chemistry, University College London

Highlights:

  • We pursued 5 research projects over the course of 2.5 days, and had a total of 21 (mostly early career) participants. These projects resulted in 5 paper drafts and 2 software packages and a cloud-based toolkit.
  • The Paper Hackathon was the very first of its kind, and it was a great success. The feedback from the participants has been highly positive (we did a few surveys asking for feedback as part of the event), we have managed to create 5 focused collaborative efforts, with each of these projects consisting of members combined from different institutions.
  • As a result of the event, we believe that Paper Hackathons are a highly viable format for concentrating collaborative effort and establishing new, and in-depth, collaborations.
  • In terms of follow-up actions, I think that most of these are on my table. I am currently preparing two blog posts, one summarising the PaperHack and one describing the experience of organising one, and providing tips for other people. The SSI could definitely assist me by placing the two blog posts on the SSI blog, and possibly a third one in a few months time, which reports on further progress after the PaperHack.
  • I have received requests to organise a short one-day follow-up meeting, to extend the progress made during the PaperHack. I'll discuss that separately from this report.
  • An impression of the Paper Hackathon can be found on Twitter, by looking for the #paperhack hash tag.
  • Finally, I co-organised the event with my colleague Joanna Lewis at 2020 Science, who has done a great job at arranging all sorts of aspects of the Paper Hackathon.

Event report

In the end, we ended up with 21 participants in total. This included:

  • Joanna and myself, who ended up organising it together.
  • 1 other SSI Fellow (Jane Charlesworth).
  • 8 other 2020 Science Fellows, including several who proposed the projects.
  • Mayeul d'Avezac, who replaced James Hetherington in leading the LB for Julia project.
  • 9 external participants, which were obtained from 11 proposals. Of these 11 proposed candidates, one participant had to withdraw due to family circumstances, and we ended up rejecting one proposal.

The external participants included one candidate from Leeds, one from Daresbury, two from Manchester, one from Oxford, one from University of Rostock in Germany, and three candidates from London-based universities. Five women participated in the event, two of whom lead events in the project. In addition, we had candidates ranging from early PhD students to post-docs (most of the participants were post-docs) and participants working for research-supporting organisations (e.g., Xiaohu Guo from STFC and Samantha Ahern from ISD, UCL).

We informed everyone about the SSI, and over the course of the event it became apparent that several candidates were keen to apply for a Fellowship themselves.

The PaperHack touched heavily on Life Sciences and Computer/Computational Science, and we have produced 5 draft papers (the longest of which was 24 pages!), 2 software tools and one cloud-based toolkit.

I strongly encouraged participants to share their experiences on Twitter, and we ended up with a colourful range of content being launched into the Twittersphere under the #paperhack hash tag.

The final impact of this event is not fully apparent at this stage, but I plan to do further enquiries in a few month's time, and I am considering to organise a one-day follow-up meeting.

Finally, for reference, here is a summary of the 5 accepted projects

  1. A software reproducibility investigation where we aim to go far beyond just replicating existing studies, to be able to reproduce the key features/results of experiments, and extend them to look at related scenarios or new questions. We ask each participant to bring a case study, along with some thoughts on what it would take (or has already taken) to make it usefully reproducible. What could lead to errors in your papers, how costly could each be, how do they influence each other, how could you guard against each, and what are the costs of doing so?
  2. A comparison of code development approaches and techniques, with the aim of assessing the benefits of formal development techniques, and how they should be modified to better suit academia. We are looking for participants who are involved in collaborative code development and are willing to share their experiences, or with knowledge about software engineering.
  3. A complete study of animal/cell dispersal, where we will aim to put together the different stages involved in studying a specific system of interacting agents (from getting the individual paths from a experimental data set, inferring the individual-based model and deriving a continuum model for the population density). Crucially, we will try to close the loop and see if the resulting model can be used to predict the experimental data, which is something lacking in most existing studies. We will be looking at people with expertise in any of these study stages (tracking data acquisition, stochastic modelling, model inference) and/or with an experimental data set to test.
  4. A protocol paper on Bayesian inference of animal receptor models, which will allow researchers to estimate an important new parameter (namely the refractory period distribution) in a robust and reproducible manner. We are looking for participants with expertise in webpage based cloud computing interfaces, general user interfaces and software automation, Markov-chain Monte Carlo techniques and data visualisation.
  5. A paper describing the development experience of writing a Lattice-Boltzmann code for the first time in a new programming language (Julia). We are looking for participants with some knowledge of Lattice-Boltzmann, or who are keen to develop using the Julia programming language.