org proposal
Bio4j
Bio4j is a high-performance cloud-enabled graph-based bioinformatics data platform, integrating most data available in the most representative open data sources around protein information available today. It models and incorporates most data available in
- UniProtKB (SwissProt + Trembl)
- Gene Ontology (GO)
- UniRef (50, 90, 100)
- RefSeq
- NCBI taxonomy
- Expasy Enzyme
Bio4j is unique in this space as the only truly open effort with code licensed as AGPLv3, integrating only open data, and a 100% public development and release process.
Bio4j was initiated in 2010 and is led by Oh no sequences!, the Era7 bioinformatics R&D group.
graph databases, Titan, Neo4j, Scala, Java, git, github, bioinformatics, biology, data, big data, genomics, cloud computing, aws
https://github.com/bio4j/gsoc14/wiki/ideas
- users: https://groups.google.com/forum/#!forum/bio4j-user
- developers: http://github.com/bio4j/bio4j/issues
Why is your organization applying to participate in Google Summer of Code 2014? What do you hope to gain by participating?
Bio4j is in a unique position to change the way the bioinformatics/biotech community works with structured big data, by democratizing its access at the level of infrastructure and code. For that to happen we are well aware of the need to involve and attract developers outside the current core team, as right now we are reaching the point where it is hard to keep pace with the project needs and user base.
By participating we expect to
- attract developers to the project
- increase the visibility of bio4j, particularly in the non-bioinformatics/biotech space
- make it easier for a more varied spectrum of people to make use of it
How many potential mentors do you have for this year's program? What criteria did you use to select them?
We have selected 4 potential mentors, listing two of them per idea. They are required to satisfy all the following criteria
- deep, daily involvement in bio4j development
- extensive technical knowledge in the areas listed as requirements for the particular idea
- having enough time during the summer to mentor at least one project
Students will be filtered based on the technical knowledge required, but the selection will focus on
- enthusiasm for the idea
- a viable work plan
- a good connection with their mentor/s
Skype interviews will take place between mentors and tentative students. All this together makes unlikely the case of a disappearing student; at any rate this will be detected really fast (hours): all of our work and discussion is done at github and we maintain (and will expect from the students) almost real-time communication. Those students not able/willing to do this will be dropped.
Our proposed mentors are working daily on bio4j, with most of them even being funded to specifically work on bio4j. In the unlikely event of a disappearing mentor, as in the case of students this will be detected in a matter of hours; in that case each idea/project has assigned at least one backup mentor who will be up-to-date on the project state, with the right technical expertise and ready to take that role.
What steps will you take to encourage students to interact with your project's community before and during the program?
Before the program:
We will encourage anyone to submit new ideas and/or provide any sort of feedback to existing ones, in the form of email, comments, issues and/or pull requests (our ideas list is part of a github repository). Each idea clearly displays a list of possible mentors and how to contact them. We will try to give as much visibility as possible to the ideas list, using for that the users' mailing list, the organization and mentors twitter accounts, related technologies mailing lists and groups, etc.
During the program:
We maintain short weekly meetings (hangouts or Skype) between all developers, in which the students will of course participate. Apart from mentors, all other developers will be watching the students' repositories, and will participate as much as possible in code reviews through pull requests. We will also try to get him involved with what is happening with bio4j as a whole, encouraging him to watch and participate in all of the bio4j repositories and projects.
What will you do to encourage your accepted students to stick with the project after Google Summer of Code concludes?
Our top priority will be for the students to create something that will be part of bio4j; thus, if interested, they will act together with their mentors as maintainers of their project.
We will also encourage them and plan as part of their projects submitting the results of their work to scientific and technical conferences.
Is there anything else we should know or you'd like to tell us that doesn't fit anywhere else on the application?
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