From chapmanb at 50mail.com Tue Apr 12 08:37:48 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Tue, 12 Apr 2011 08:37:48 -0400 Subject: [BioSQL-l] Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th! Message-ID: <20110412123748.GI2105@kunkel> Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (Lawrence Hunter and Matt Wood) and session topics that include parallel and cloud-based approaches to bioinformatics, genome content management, and tools for next-generation sequencing. We'd love to hear about your Open Source bioinformatics project! The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) July 15-16, 2011, in Vienna, Austria http://www.open-bio.org/wiki/BOSC_2011 Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. All students whose abstracts are accepted for talks will be considered for this award. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor From rmb32 at cornell.edu Wed Apr 13 11:30:59 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 13 Apr 2011 08:30:59 -0700 Subject: [BioSQL-l] last call for Google Summer of Code mentors Message-ID: <4DA5C1B3.4010504@cornell.edu> Hi all, This is the last call for mentors for Google Summer of Code. We have a good crop of student proposals this year for doing work on OBF projects, and money from Google to fund them, but we need experienced Bio* developers to mentor them. If you'd like to see the student proposals, participate in their scoring, and possibly volunteer to mentor them (remotely of course) over the summer, do two things: 1.) Create an account on http://google-melange.com and send a request to be an admin from the OBF page on there, http://www.google-melange.com/gsoc/org/google/gsoc2011/obf 2.) Join the OBF GSoC mentors mailing list at http://lists.open-bio.org/mailman/listinfo/gsoc-mentors Even if you just want to see the student applications and help with scoring, but don't necessarily have time to mentor a student, your input in the scoring process is appreciated. :-) Rob ---- Robert Buels OBF GSoC 2011 Administrator From rmb32 at cornell.edu Mon Apr 25 17:42:48 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 25 Apr 2011 14:42:48 -0700 Subject: [BioSQL-l] Announcing OBF Google Summer of Code Accepted Students Message-ID: <4DB5EAD8.1020905@cornell.edu> Hello all, I'm very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program. The accepted students, their projects, and their mentors (in alphabetical order): Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich Chuan Hock Koh BioJava - Amino acids physico-chemical properties calculation mentored by Peter Troshin, Andreas Prlic, and Jay Vyas Micha? Koziarski Representing bio-objects and related information with images (BioRuby) mentored by Raoul J.P. Bonnal and Francesco Strozzi Sheena Scroggins Major BioPerl Reorganization mentored by Robert Buels and Chris Fields Mikael Eric Trellet Interface analysis module for BioPython mentored by Jo?o Rodrigues and Eric Talevich Once again this year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF's open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received. For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it's time to "put your money where your mouth is", as the saying goes. Let's get out there and write some great code this summer! Best regards, Rob ---- Robert Buels OBF GSoC 2011 Administrator From chapmanb at 50mail.com Tue Apr 12 12:37:48 2011 From: chapmanb at 50mail.com (Brad Chapman) Date: Tue, 12 Apr 2011 08:37:48 -0400 Subject: [BioSQL-l] Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th! Message-ID: <20110412123748.GI2105@kunkel> Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (Lawrence Hunter and Matt Wood) and session topics that include parallel and cloud-based approaches to bioinformatics, genome content management, and tools for next-generation sequencing. We'd love to hear about your Open Source bioinformatics project! The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) July 15-16, 2011, in Vienna, Austria http://www.open-bio.org/wiki/BOSC_2011 Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. All students whose abstracts are accepted for talks will be considered for this award. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor From rmb32 at cornell.edu Wed Apr 13 15:30:59 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 13 Apr 2011 08:30:59 -0700 Subject: [BioSQL-l] last call for Google Summer of Code mentors Message-ID: <4DA5C1B3.4010504@cornell.edu> Hi all, This is the last call for mentors for Google Summer of Code. We have a good crop of student proposals this year for doing work on OBF projects, and money from Google to fund them, but we need experienced Bio* developers to mentor them. If you'd like to see the student proposals, participate in their scoring, and possibly volunteer to mentor them (remotely of course) over the summer, do two things: 1.) Create an account on http://google-melange.com and send a request to be an admin from the OBF page on there, http://www.google-melange.com/gsoc/org/google/gsoc2011/obf 2.) Join the OBF GSoC mentors mailing list at http://lists.open-bio.org/mailman/listinfo/gsoc-mentors Even if you just want to see the student applications and help with scoring, but don't necessarily have time to mentor a student, your input in the scoring process is appreciated. :-) Rob ---- Robert Buels OBF GSoC 2011 Administrator From rmb32 at cornell.edu Mon Apr 25 21:42:48 2011 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 25 Apr 2011 14:42:48 -0700 Subject: [BioSQL-l] Announcing OBF Google Summer of Code Accepted Students Message-ID: <4DB5EAD8.1020905@cornell.edu> Hello all, I'm very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program. The accepted students, their projects, and their mentors (in alphabetical order): Justinas Vygintas Daugmaudis Michele dos Santos da Silva (2 students!) Mocapy++Biopython: from data to probabilistic models of biomolecules mentored by Thomas Hamelryck and Eric Talevich Chuan Hock Koh BioJava - Amino acids physico-chemical properties calculation mentored by Peter Troshin, Andreas Prlic, and Jay Vyas Micha? Koziarski Representing bio-objects and related information with images (BioRuby) mentored by Raoul J.P. Bonnal and Francesco Strozzi Sheena Scroggins Major BioPerl Reorganization mentored by Robert Buels and Chris Fields Mikael Eric Trellet Interface analysis module for BioPython mentored by Jo?o Rodrigues and Eric Talevich Once again this year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF's open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received. For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it's time to "put your money where your mouth is", as the saying goes. Let's get out there and write some great code this summer! Best regards, Rob ---- Robert Buels OBF GSoC 2011 Administrator