From nlharris at gmail.com Mon Mar 5 13:31:07 2012 From: nlharris at gmail.com (Nomi Harris) Date: Mon, 5 Mar 2012 10:31:07 -0800 Subject: [Open-bio-l] BOSC 2012 Call for Abstracts Message-ID: <3BE64E5D-C120-4302-A159-76A0316811BB@gmail.com> Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012) A Special Interest Group (SIG) of ISMB 2012 Dates: July 13-14, 2012 Location: Long Beach, California Web site: http://www.open-bio.org/wiki/BOSC_2012 Email: bosc at open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 13, 2012: Deadline for submitting abstracts May 7, 2012: Notification of accepted talk abstracts emailed to authors July 11-12, 2012: Codefest 2012 programming session July 13-14, 2012: BOSC 2012 July 15-17, 2012: ISMB 2012 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 one-page abstracts for talks and posters. This year's session topics are: - Cloud and Parallel Computing - Linked Data - Genome-scale Data Management - Data Visualization and Imaging - Translational Bioinformatics - Software Interoperability (possibly a joint session with BSI-SIG, the Bioinformatics Software Interoperability SIG) - Bioinformatics Open Source Project Updates - Interfacing with Industry (panel) Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts BOSC 2012 Organizing Committee: Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice From rbuels at gmail.com Fri Mar 16 15:47:52 2012 From: rbuels at gmail.com (Robert Buels) Date: Fri, 16 Mar 2012 12:47:52 -0700 Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects! Message-ID: <4F6398E8.4010806@gmail.com> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2012 FAQ at http://goo.gl/kNv48 Student applications are due April 6, 2012 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and whom to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2012 Administrator From hlapp at drycafe.net Fri Mar 16 15:52:43 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 16 Mar 2012 15:52:43 -0400 Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects! In-Reply-To: <4F6398E8.4010806@gmail.com> References: <4F6398E8.4010806@gmail.com> Message-ID: <4CD11DFC-33FB-4493-B8EF-5626263AE264@drycafe.net> Congrats everyone!! -hilmar On Mar 16, 2012, at 3:47 PM, Robert Buels wrote: > Hi all, > > Great news: Google announced today that the Open Bioinformatics > Foundation has been accepted as a mentoring organization for this > summer's Google Summer of Code! > > GSoC is a Google-sponsored student internship program for open-source > projects, open to students from around the world (not just US > residents). Students are paid a $5000 USD stipend to work as a > developer on an open-source project for the summer. For more on GSoC, > see GSoC 2012 FAQ at http://goo.gl/kNv48 > > Student applications are due April 6, 2012 at 19:00 UTC. Students who > are interested in participating should look at the OBF's GSoC page at > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project > ideas, and whom to contact about applying. > > For current developers on OBF projects, please consider volunteering to > be a mentor if you have not already, and contribute project ideas. Just > list your name and project ideas on OBF wiki and on the relevant > project's GSoC wiki page. > > Thanks to all who helped make OBF's application to GSoC a success, and > let's have a great, productive summer of code! > > Rob Buels > OBF GSoC 2012 Administrator > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From rbuels at gmail.com Sun Mar 25 16:09:50 2012 From: rbuels at gmail.com (Robert Buels) Date: Sun, 25 Mar 2012 13:09:50 -0700 Subject: [Open-bio-l] Announcing OBF Summer of Code - please forward! Message-ID: <4F6F7B8E.1050903@gmail.com> Hi all, Here's an advertising-ready announcement for OBF's Summer of Code, thanks to Christian Zmasek and Hilmar Lapp for their excellent writing. Student applications are due April 6! Please spread it widely, we need to reach lots of students with it! Rob Buels OBF GSoC 2012 Admin ============================================================ *** Please disseminate widely at your local institutions *** *** including posting to message and job boards, so that *** *** we reach as many students as possible. *** ============================================================ OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011 Applications due 19:00 UTC, April 6, 2012. http://www.open-bio.org/wiki/Google_Summer_of_Code The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from sequence search I/O in BioPython to lightweight sequence objects and lazy parsing in BioPerl, a next-generation BioRuby interface to Ensembl to developing cloud-optimized versions of BioJava modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012. INQUIRIES: We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details. 2012 OBF Summer of Code: http://www.open-bio.org/wiki/Google_Summer_of_Code Google Summer of Code FAQ: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs From nlharris at gmail.com Mon Mar 5 18:31:07 2012 From: nlharris at gmail.com (Nomi Harris) Date: Mon, 5 Mar 2012 10:31:07 -0800 Subject: [Open-bio-l] BOSC 2012 Call for Abstracts Message-ID: <3BE64E5D-C120-4302-A159-76A0316811BB@gmail.com> Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012) A Special Interest Group (SIG) of ISMB 2012 Dates: July 13-14, 2012 Location: Long Beach, California Web site: http://www.open-bio.org/wiki/BOSC_2012 Email: bosc at open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 13, 2012: Deadline for submitting abstracts May 7, 2012: Notification of accepted talk abstracts emailed to authors July 11-12, 2012: Codefest 2012 programming session July 13-14, 2012: BOSC 2012 July 15-17, 2012: ISMB 2012 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 one-page abstracts for talks and posters. This year's session topics are: - Cloud and Parallel Computing - Linked Data - Genome-scale Data Management - Data Visualization and Imaging - Translational Bioinformatics - Software Interoperability (possibly a joint session with BSI-SIG, the Bioinformatics Software Interoperability SIG) - Bioinformatics Open Source Project Updates - Interfacing with Industry (panel) Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts BOSC 2012 Organizing Committee: Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice From rbuels at gmail.com Fri Mar 16 19:47:52 2012 From: rbuels at gmail.com (Robert Buels) Date: Fri, 16 Mar 2012 12:47:52 -0700 Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects! Message-ID: <4F6398E8.4010806@gmail.com> Hi all, Great news: Google announced today that the Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code! GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2012 FAQ at http://goo.gl/kNv48 Student applications are due April 6, 2012 at 19:00 UTC. Students who are interested in participating should look at the OBF's GSoC page at http://open-bio.org/wiki/Google_Summer_of_Code, which lists project ideas, and whom to contact about applying. For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page. Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code! Rob Buels OBF GSoC 2012 Administrator From hlapp at drycafe.net Fri Mar 16 19:52:43 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Fri, 16 Mar 2012 15:52:43 -0400 Subject: [Open-bio-l] Google Summer of Code is *ON* for OBF projects! In-Reply-To: <4F6398E8.4010806@gmail.com> References: <4F6398E8.4010806@gmail.com> Message-ID: <4CD11DFC-33FB-4493-B8EF-5626263AE264@drycafe.net> Congrats everyone!! -hilmar On Mar 16, 2012, at 3:47 PM, Robert Buels wrote: > Hi all, > > Great news: Google announced today that the Open Bioinformatics > Foundation has been accepted as a mentoring organization for this > summer's Google Summer of Code! > > GSoC is a Google-sponsored student internship program for open-source > projects, open to students from around the world (not just US > residents). Students are paid a $5000 USD stipend to work as a > developer on an open-source project for the summer. For more on GSoC, > see GSoC 2012 FAQ at http://goo.gl/kNv48 > > Student applications are due April 6, 2012 at 19:00 UTC. Students who > are interested in participating should look at the OBF's GSoC page at > http://open-bio.org/wiki/Google_Summer_of_Code, which lists project > ideas, and whom to contact about applying. > > For current developers on OBF projects, please consider volunteering to > be a mentor if you have not already, and contribute project ideas. Just > list your name and project ideas on OBF wiki and on the relevant > project's GSoC wiki page. > > Thanks to all who helped make OBF's application to GSoC a success, and > let's have a great, productive summer of code! > > Rob Buels > OBF GSoC 2012 Administrator > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From rbuels at gmail.com Sun Mar 25 20:09:50 2012 From: rbuels at gmail.com (Robert Buels) Date: Sun, 25 Mar 2012 13:09:50 -0700 Subject: [Open-bio-l] Announcing OBF Summer of Code - please forward! Message-ID: <4F6F7B8E.1050903@gmail.com> Hi all, Here's an advertising-ready announcement for OBF's Summer of Code, thanks to Christian Zmasek and Hilmar Lapp for their excellent writing. Student applications are due April 6! Please spread it widely, we need to reach lots of students with it! Rob Buels OBF GSoC 2012 Admin ============================================================ *** Please disseminate widely at your local institutions *** *** including posting to message and job boards, so that *** *** we reach as many students as possible. *** ============================================================ OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011 Applications due 19:00 UTC, April 6, 2012. http://www.open-bio.org/wiki/Google_Summer_of_Code The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from sequence search I/O in BioPython to lightweight sequence objects and lazy parsing in BioPerl, a next-generation BioRuby interface to Ensembl to developing cloud-optimized versions of BioJava modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012. INQUIRIES: We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details. 2012 OBF Summer of Code: http://www.open-bio.org/wiki/Google_Summer_of_Code Google Summer of Code FAQ: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs