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TranSMART Boston Hackathon : Glued together the dispersed features

March 20, 2014 | By Riza Nugraha

“Hackathon?” the guy behind the immigration desk at Amsterdam Airport immediately raised his left eyebrow when we told him about our purpose of visit to US. Yes, it was the TranSMART Boston Hackathon; the joint collaboration between the open source community, pharmacies, research institutions and bioinformatic solution providers to jump into the TranSMART code from Feb 5th - 7th 2014. Up till now, TranSMART hackathons have been organized three times last year and it is expected to become a regular event in the future. This time it was organized by Recombinant by Deloitte which was located in Boston, the United States.

The main goal of this hackathon was to start the initial implementation of TranSMART v1.2 by incorporating diverse features from different versions and branches among the community members. As one of the main contributors to the open source community, The Hyve participated in this event by sending its three developers (Gustavo, Ruslan and myself) representing three main areas of TranSMART: backend, database/ETL and front-end. Two flights and twelve hours later we finally arrived in Newton; a quiet suburban city in Massachusetts located around 10 km from Boston.

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Snowstorm on our first day of hackathon

It was snowing quite heavily in Newton. We began our first day of hackathon by a welcome greeting from Recombinant by Deloitte as the host of the event. There were approximately 20 participants from different companies and institutions. Dave from Recombinant acted as facilitator and led the discussion. Based on the result from community meeting in Paris, we recollected the user stories and future wishes whereas most of them were actually already implemented in different instances of TranSMART.  Using SCRUM approach we broke down user stories into real tasks. After they were defined, we converted them into task-cards, and then finally we put them all in the “To Do” column on our SCRUM board. Apart from that, we also discussed about best merging strategy that can fit our situation. Finally tasks were grouped into four epic teams:

  1. Application Merge

  2. RModules

  3. Database/ETL

  4. Governance

All participants were free to choose which epics they would like to join based on their interests and skill sets. We immediately started picking up tasks which also means moving them into “In Progress” column, grab our laptops and and hacked the codes away. I was joining the RModules epic team together with Terry from TranSMART Foundation and Mike from Harvard Medical School. Gustavo and Ruslan were joining Application Merge and Database epic team respectively. Kees who was also with us, was in Governance epic team. As soon as we were formed into group, more ideas and problems emerged. The task we picked up didn’t feel so simple anymore and that was the challenge! First day was gone so fast and it was closed by a checkpoint on what’s the last updated status of the tasks we were working on.

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Converted office wall into SCRUM board

Second day of hackathon was started by a short daily standup meeting. Going in circle, we updated each other on what we have achieved on the previous day, what we’re going to do for today and impediments if there’s any. Ami from Pfizer who couldn’t join us on the first day due to the snowstorm was also there to join the Application Merge epic team. The most challenging part in every hackathon is that you’re formed into a group with persons that you barely know to accomplish things in a very limited time. It’s totally different with our daily work whereas most of the times we’ve already been familiar with the working style of our colleagues. It could be difficult, but the advantage we can pick up from such a situation is we can learn from each other on how to approach solutions of problems. More impediments were found on the second day. For example, since we upgraded Grails version to 2.3.5 it apparently has caused some modules refused to run. We needed to figure out the workaround for that. Just like the previous day, our second day was also closed by a checkpoint on our progress. Most of the groups were actually surprisingly productive since we could see that most of the tasks were moved into the “In Progress” column. Some of them were even already in the “Done” column. So great jobs, team! As an award for our productiveness, the organizator brought us to the nearest bar for the happy hour. It was a nice and decent bar close to the venue. As the cocktails flowed, we got a chance to get to know all the participants even better. It was a nice moment to find out great stories behind TranSMART as a bioinformatic platform from the people who were already involved from the earliest stages.

The sun shined brighter than before on the third day of hackathon. Snow started to melt down in Newton, so that the streets were almost clean and dry - and yes, no more wet shoes! It was our last day in Newton and as usual we started the day with a stand up meeting. We were told that the last day of hackathon was going to be shorter since some of the participants had to catch some flights. By the end of the day, we did our last review of what we’ve accomplished so far and which tasks were still to be followed up.

  • Application Merge epic team managed to merge The Hyve/ CTMM TraIT master branch and Recombinant branch and will use this as a base to move forward for v1.2. There were still more to come for this epic. To merge Pfizer and Sanofi branch was still to be followed up.

  • The RModules epic team managed to merge features from The Hyve/CTMM TraiT with Recombinant which will make tranSMART have two additional analyses.  

  • Database/ETL epic team has successfully added studies to the master branch, merged the GWAS features and the Recombinant ETL to the master branch.

  • Governance team managed to have initial proposal to develop a policy to govern architecture, code standards, documentation, etc. as well as to set up the CIM environment.

Other than that we’ve also agreed to use Geb as our standard automated testing framework. Gustavo presented a small demo on how to create test scripts and execute them. After the closing session, some of the participants bade a farewell but the rest, including us, still had a little bit of time. What about a bit of sports after three intensive hacking days? We spotted a ping pong table in the office and started to play against each other. It turned out that some of us were very good at it!

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Group picture with all the participants

Overall, Boston Hackathon might not be the first hackathon for TranSMART community. However, it can be said that it was the first hackathon that was organized quite intensively so that it achieved more results. Big thanks to Recombinant by Deloitte for organizing the event!

The complete technical result summary of Boston Hackhathon can be found here:

https://wiki.transmartfoundation.org/display/TSMTGPL/Hackathon+Boston+Feb+2014