San Diego Bioinformatics Lunch Forum: Hackathons

At this week’s Bioinformatics Lunch Forum we discussed the first in the upcoming series of Hackathons designed to help bioinformatics and cheminformatics professionals learn about new technologies in an informal and hands-on environment.

In general, Hackathons are intended to be free, informal gatherings, with an emphasis on practical, hands-on learning. They can also serve as a means of identifying and working on collaborative projects. Bring your laptop and leave with experience, potential collaborators and working code.

It was agreed that the first hackathon will be an introduction to BioJava, with follow-on topics to include:

  • Using PDB REST Services
  • Using BioGPS REST Services
  • Using GeneWiki/Media Wiki APIs
  • BioGroovy
  • Text mining
  • R/Bioconductor
  • Cloud Computing
  • AutoDock

Additional cheminformatics topics would be added as volunteers were identified to coordinate those Hackathons. After our meeting, volunteers stepped forward to coordinate the Cloud Computing and AutoDock Hackathons.

Future topics might also include more generic subjects which would be of benefit to both a scientific and non-scientific audiences:

  • Using Google APIs
  • Developing Web Applications With Grails

These hackathons could start out with a generic discussion of the subject, and then focus on how to apply the technologies involved to solve problems in a scientific computing environment. This would, of course, depend on the audience in attendance at the time.


  • Location: Scripps
  • Hackathons will be held after work 7-9pm.
  • There should be 2 45-min sessions. The first session provides an overview of the technology. The second session, provides hands-on experience solving various common problems.

Each Hackathon coordinator should describe:

  • Where/When the course will held
  • Course Objectives (what people will learn)
  • Installation Information (what do I need to setup before I arrive for the course. Might use VMs to simplify installation)
  • Where to get help before the course starts if I have installation difficulties

Next Steps

  • Andreas: put together information on first session (Google Site to contain details)
  • Ben & Andreas to coordinate logistics
  • Mark: publicize session to SDBioInfo List, Bioinfo Lunch List, SDJUG

Eric Clarke: (Gene Wiki)
Ben Good: (Gene Wiki)
Mark Fortner: (BioGroovy)
Andreas Prlic (PDB & BioJava)
Peter Rose (PDB)


About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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