[BioRuby] We have 2 and 1/2 days of spare time. Can we help?

Tue Aug 31 10:59:55 UTC 2010

I Anthony,

I wrote a Ruby wrapper for SAMtools. See

  http://thebird.nl/biolib/Adding_BioLib_BAM_SAM_Support.html

If you want to test and use it, we can move it forward.

Pj.

On Tue, Aug 31, 2010 at 11:42:12AM +0100, Anthony Underwood wrote:
> Hi
> 
> Please could I put in my plea for a +1 on (Next Generation sequence) NGS parsing. This field is becoming huge within bioinformatics and bioruby is lagging when it comes to tools to parse the date, specifically wrappers around the C functions found in samtools. I would have a go myself but have no experience in C so am sure others would do a better job.
> 
> Thanks  Anthony
> On 17 Aug 2010, at 12:39, George Githinji wrote:
> 
> > Thank you very much Toshiaki. We really appreciated the call and the
> > much advice and helpful conversation that we held.
> > We are distilling on the various ideas and we will update you and the
> > list on what will be most appropriate and achievable for us.
> > 
> > 
> > On Mon, Aug 16, 2010 at 4:40 PM, Toshiaki Katayama <ktym at hgc.jp> wrote:
> >> Hi George,
> >> 
> >> Oops, I just realized that I missed to read this thread. Sorry. ;)
> >> 
> >> I'm very surprised and excited to know that you guys will organize
> >> a BioHackathon-like event in Kenya.
> >> 
> >> Few hours ago, I finished a Skype meeting with the organizers
> >> and learnt about the plan described at
> >> 
> >> http://rsg-ea-bio-sprint-2010.wikispaces.com/
> >> (design of the poster is awesome, good job! :)
> >> 
> >> Please use this mailing list to distill pre-hackathon preparations.
> >> 
> >> We often asked "what can I contribute to the BioRuby project?" but
> >> it is usually difficult to assign a target and mentoring on it
> >> as the project itself has been self-organized.
> >> (The Google Summer of Code will be an exception. Mentors are working
> >> really hard and I really appreciate about that.)
> >> 
> >> However, I take this opportunity to suggest several potential targets:
> >> (in addition to 1. finishing the newly introduced BioRuby plugin system
> >> and 2. supporting Semantic Web technologies on which we have been
> >> working on since the 3rd DBCLS BioHackathon http://hackathon3.dbcls.jp/
> >> and Codefest 2010 http://www.open-bio.org/wiki/Codefest_2010)
> >> 
> >> === interfaces to external resources:
> >> 
> >> * API for Ensemble (suggested by Jan Aerts)
> >> * API for UCSC (also suggested by Jan)
> >> * API for BioMart, InterMine etc.
> >> * API for Semantic Web resources (BioGateway, Bio2RDF etc.) -- this is what we tried during the last BioHackathon
> >> 
> >> === modern bioinformatics:
> >> 
> >> * handling NGS data - wrappers and parsers for tools and libraries
> >> * Proteomics
> >> * Immunoinformatics - immunology prediction servers (described by someone during the Skype meeting)
> >> 
> >> === classical bioinformatics:
> >> 
> >> * Do benchmark for existing BioRuby modules to find bottlenecks for improving performance (good example was posted by Martin Hansen http://lists.open-bio.org/pipermail/bioruby/2010-August/001426.html and I think this kind of improvements should be welcomed)
> >> 
> >> * Setting up NCBI's BLAST WWW like interface (with SGE or Cloud backends) is still demanded. People who are working with not-yet-public genome often need to setup this kind of server. How about to create a general Rails plugin using BioRuby which can be easily setup and can perform various sequence similarity search (by BLAST, BLAT, EXONERATE, Bowtie, whatever...) with simple configuration (use DSL to setup target DBs and the computational farm). This project should also target on the downstream processes -- phylogenetic annotations, mapping RNA-Seq data, summarizing statistics, visualization, integration with genome browsers etc. -- and cool UI design, to be chosen as a yet another BLAST+alpha interface.
> >> 
> >> === visualization modules:
> >> 
> >> * BioGraphics (already started by Jan) - genome mapping / comparative genomics?
> >> 
> >> * Interface for Cytoscape - so that we can easily generate beautiful graph visualization within BioRuby (e.g. from Semantic Web data) Note: some samples are already provided by Cytoscape group at http://cytoscape.wodaklab.org/wiki/ScriptingPlugins#Ruby
> >> 
> >> === improving docs:
> >> 
> >> * Writing some tutorials on how you used the BioRuby - this should be done by newbie who will have difficulty with finding solutions on the Internet. They can ask mentors how to solve their problems and summarize the result in HOWTO-like tutorials. Some blogs and Wiki pages are the only existing resources as far as I know (and also clearly pointed by Yannick Wurm http://lists.open-bio.org/pipermail/bioruby/2010-July/001373.html)
> >> 
> >> * We should also need to have a document on "how to use GitHub for forking BioRuby", "how to create your own BioRuby plugins" etc.
> >> 
> >> Regards
> >> Toshiaki Katayama
> >> 
> >> 
> >> On 2010/08/10, at 16:37, George Githinji wrote:
> >> 
> >>> Hi all,
> >>> The Regional Students Group for Eastern Africa (RSG-EA) is one of the
> >>> grass-root level bodies of the International Society for Computational
> >>> Biology Student Council (ISCB-SC). The group has membership from ten
> >>> countries namely Burundi, Democratic Republic of Congo, Djibouti,
> >>> Eritrea, Ethiopia, Kenya, Rwanda, Somalia, Tanzania and Uganda.
> >>> Recently we proposed to organize a biohakathon three day event to:
> >>> 
> >>>  1) Learn how to collaborate on bioinformatics programming projects
> >>> using open source tools.
> >>>  2) Forge an East African bioinformatics programming community.
> >>>  3) Contribute a module/code to Bioruby library.
> >>> 
> >>> The event has been sponsored by a grant from ISCB and ILRI/Beca
> >>> bioinformatics platform in Nairobi, Kenya.
> >>> 
> >>> We would like to seek for  a suitable project work from one of the
> >>> developer(s) and the community. The project should ideally be of
> >>> beginner to intermediate level difficulty. A third of the participants
> >>> will be of intermediate level programming skills with experience from
> >>> Java,Python and Perl. while the rest will have beginner level skills.
> >>> 
> >>> We were also wondering whether it would be possible to get one of the
> >>> lead contributors to bioruby project to give a short 15-20 minutes
> >>> introductory talk to the participants. We have excellent video
> >>> conferencing  facilities at the ILRI/Beca hub. The event is slated to
> >>> take place in late September.
> >>> 
> >>> Thank you
> >>> 
> >>> --
> >>> ---------------
> >>> Sincerely
> >>> George
> >>> KEMRI/Wellcome-Trust Research Program
> >>> Skype: george_g2
> >>> Blog: http://biorelated.wordpress.com/
> >>> _______________________________________________
> >>> BioRuby Project - http://www.bioruby.org/
> >>> BioRuby mailing list
> >>> BioRuby at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioruby
> >> 
> >> 
> > 
> > 
> > 
> > -- 
> > ---------------
> > Sincerely
> > George
> > KEMRI/Wellcome-Trust Research Program
> > Skype: george_g2
> > Blog: http://biorelated.wordpress.com/
> > 
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
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