Tuesday, 23 December 2014

Google Genomics: next step?

Recently Google came up with Google Genomics to store genomes and work with them. The easiest way to explore it is through their genome browser (GA browser). 

Position 132564975 of chromosome 7 of genome HG01440 from the Google repository of the 1000 Genomes Project.

Which are the next steps?

For developers it has come up with a new API. The system is currently in open beta, so the income of comments and early adopters is going on. This is part of the feed back I want o give as well as some thoughts about it.

  • Improve help pages
In my experience a better documentation is better than a better version. What do I mean? I try to do more with less time, when I look for help I want a quick and easy (to follow) answer (if possible). Thats why Stack Overflow has so many questions, or why the mailing list are open, to help more people with less effort. In fact the help is now divided between Stack Overflow' tag google-genomics and google-genomics-api and a Google Group.
StackOverflow information tag for Google Genomics

I commit myself to write a Python getting started guide for Google genomics. As always the community is strong and with great feedback and it will 

  • Improve interoperability
There are other open software available to manage with biological data: Biopython, BioPerl, BioJava, BioHaskellbioconductor, as well as specific programs. The easier it will become to work with them, the more users will use Google Genomics. Most of the work is done with standalone programs which make interoperability difficult. In bioinformatics a movement against reinventing the wheel is growing, at the same time, making it easier to work with differents programs.
O|B|F promotes Open Source software development and Open Science within the biological research community

  • Adding new functions
The API will grow and I am sure the github project repository too. I don't know how will it change or what kind of functions, examples, problems will be added, but you know, you can contribute, and each one need different thinks.



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