OK, so Joao, I would recommend building OSCAR packages for the
appropriate bioinformatics codes.
In addition to mpiBLAST don't forget plain ol' NCBI BLAST and it's
various incarnations. IMHO, you should also consider consider a package
with the *binaries* direct from NCBI.
Well, in my application I mentoined( I just submitted today):
NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE,
FASTA, and EMBOSS etc
EMBOSS itself it is a little big.
My question to you: Are there guidelines on what is appropriate
(sufficient) for the stipend?
From Google's point of view it I think it is up to the mentors choose
which project would be most useful and attainable within 3 months, based
on the applicants descripiton of the project. Or I didn't understand
your question well?
Based on sugestions by Bernard et al :) I decided to focus on
bioinformatics tools and I put a lot of enphasis on SGE itself.
I think we could start wich SGE and I'll choose a good subset(there is
a certain redundancy on the softwares) of bioinformatics tools along the
way..
I'm copying my submnission after the === (BTW, this list support
attachents?)
=======================================================================
Project Title
OSCAR Grid engine support and bioinformatics packages
Synopsis
Quoting the project's web page, "OSCAR (Open Source Cluster
Application Resources) is a snapshot of the best known methods for
building, programming, and using clusters. It consists of a fully
integrated and easy to install software bundle designed for high
performance cluster computing".
My project aim to contribute to project OSCAR in two ways: First,
this project will integrate Sun Grid Engine, a powerful,
state-of-the-art workload and job scheduler for clusters and large grids.
Secondly, this project will integrate into OSCAR important software
for research environments in the Biosciences field that run on clusters.
Deliverables
- Create the Sun Grid Engine package.
- Create OSCAR packages for all relevant bioinformatics tools that
run on clusters (NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW,
GROMACS, PHYLIP, WISE, FASTA, and EMBOSS etc).
Project Details
The Sun Grid Engine is a powerful workload balancing and job
scheduler ranging from small clusters through large heterogeneous
distributed computer grids. It is a very valuable tool for the OSCAR
project, and it involves coding on OSCAR's core components.
BioInformatics, a somewhat new and ever growing field, has many
complex algorithms that can only be handled by powerful clusters. My
second task will be to select several applications of interest and
integrate properly with
OSCAR. This would be of great value to the scientific community.
Scope
The above two tasks can be completed under Google's schedule.
I hope I can continue to improve OSCAR beyond this period.
Bio
I'm a 24 years old undergraduate in Electrical Engineering from
University of Sao Paulo, Brazil.
My email at the university is [EMAIL PROTECTED]
I have a background in Assembly(i386), ObjectPascal, C, C++, Perl and
JAVA, acquired by working as a free lancer to small to medium projects
for Brazilian enterprises.
I am currently involved in program called Viral Genetic Diversity
Network (VGDN) (http://www.lemb.icb.usp.br/lemb/vgdn/www/)
which aims to sequence HIV-1, HCV and RSV variants collected across 23
labs in Brazil. This project is supported by the Major Research support
agency in Brazil.
I think that it the perfect opportunity for me to learn, help the
university main lab in this program, contribute to OSCAR project and get
involved on the open source community in a active way.
==========================================================================
--
========================================================
Joao Paulo P. L. Samara, Research Associate
========================================================
University of Sao Paulo - USP
Biomedical Sciences Institute - ICB II
Department of Microbiology
Av. Prof. Lineu Prestes, 1734
Sao Paulo - SP - Brazil - 05508-000
Phone: +55 11 3091-7290
FAX: +55 11 3091-7354
Mobile: +55 11 8121-4293
http://www.lemb.icb.usp.br
========================================================
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