These are chat archives for bio4j/bio4j

12th
Feb 2015
Eduardo Pareja Tobes
@eparejatobes
Feb 12 2015 10:15
@laughedelic I just created https://github.com/bio4j/gsoc15
if you could do the scaffolding for something like what we had past year: https://github.com/bio4j/gsoc14/
but without any wiki, jus putting everything inside the repo
I think we should keep for this year (updated of course) the following ideas:
  • bio4j/gsoc14#1
  • bio4j/gsoc14#8
  • bio4j/gsoc14#2
  • bio4j/gsoc14#15
Alexey Alekhin
@laughedelic
Feb 12 2015 13:08
ok! (sorry, just saw the message)
jyosoman
@jyosoman
Feb 12 2015 16:52
@eparejatobes I was planning to apply to GSoC and was interested in the #15 idea, the range based one. Is it possible to have some pointers to some completed work in this direction withing bio4j, or is it a fresh start?
Eduardo Pareja Tobes
@eparejatobes
Feb 12 2015 16:56
hey @jyosoman
well it would certainly depend on exactly what we will be doing
At the infrastructure level if the underlying graph DB engine supports vertex-centric indexes and range queries
like Titan for example
the hard work would be in integrating this into the Bio4j API in a sensible way
Another option could be to work on adding this to our soon to be released Scala API
Or simply integrate datasets where having this is a must
like reference genomes for model organisms
lot of options there depending on background and interests :)
jyosoman
@jyosoman
Feb 12 2015 17:01
These are all quite different directions
Eduardo Pareja Tobes
@eparejatobes
Feb 12 2015 17:01
yup
jyosoman
@jyosoman
Feb 12 2015 17:02
doesn't moving forward sound like a better idea, rather than a patchy model organism based method
scala and titan sound like good progressive ideas. but time wise model based might be more practical.
Eduardo Pareja Tobes
@eparejatobes
Feb 12 2015 17:04
I will publish something like a roadmap for what we are doing independently of gsoc
hopefully this week
that will also help people framing the gsoc ideas etc
related with this, something we are doing either way is integrating "the" human genome data
with some support for retrieving annotations etc within an interval
and this will be finished before gsoc would actually start
So something around this idea will not be starting from scratch
jyosoman
@jyosoman
Feb 12 2015 17:07
so, there will be something to start from. cool
I will be happy to help on this if you want, this will give me some internals of the code etc. and make for a stronger gsoc application. I hope that sounds alright.
Eduardo Pareja Tobes
@eparejatobes
Feb 12 2015 17:10
Yes sure
@evdokim will be working on this mostly