From chapmanb at 50mail.com Fri Apr 2 09:05:05 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 2 Apr 2010 09:05:05 -0400 Subject: [Open-bio-l] BOSC and OpenBio solution challenge reminder -- April 15th Message-ID: <20100402130505.GE36623@sobchak.mgh.harvard.edu> Hello all; A friendly reminder that the deadline for the Bioinformatics Open Source Conference (BOSC) is coming up on April 15th: http://www.open-bio.org/wiki/BOSC_2010 This is a great opportunity to discuss code and biology with fellow developers. One session which I'd like to emphasize is the OpenBio Solution Challenge, a section of talks that describes how to solve practical problems in bioinformatics using a variety of approaches: http://www.open-bio.org/wiki/SolutionChallenge Any toolkit developers who are interested in giving a talk are encouraged to submit an abstract for the challenge. We have some initial project ideas on the page and welcome your feedback for other useful workflows that would emphasize the advantages of using open source toolkits to solve biological problems. Please copy messages to the OpenBio mailing list as a central point for discussion and questions: http://lists.open-bio.org/mailman/listinfo/open-bio-l Looking forward to seeing everyone in July, Brad BOSC contact and dates: Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010 Abstract submission via Open Conference System site: http://events.open-bio.org/BOSC2010/openconf.php E-mail: bosc at open-bio.org Bosc-announce list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates April 15: Abstract deadline May 5: Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9: Codefest 2010 July 9-10: BOSC 2010 August 15: Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics From cjfields at illinois.edu Wed Apr 7 10:15:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Apr 2010 09:15:15 -0500 Subject: [Open-bio-l] OBF Proposals Message-ID: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> All mentors, We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf chris From rmb32 at cornell.edu Wed Apr 7 13:09:46 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 07 Apr 2010 10:09:46 -0700 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals In-Reply-To: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> References: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> Message-ID: <4BBCBC5A.1070901@cornell.edu> Based on the discussions on the GSoC-wide mentors list, the difficulty with starting to review proposals before the deadline is that it can introduce bias toward lower scores for proposals submitted at or near the deadline. Also, some of these proposals might still be edited by students. However, I think it would be a good idea for mentors to start taking a look *through* the proposals, just don't really score them yet. Rob Chris Fields wrote: > All mentors, > > We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. > > http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf > > chris > > > _______________________________________________ > Gsoc-mentors mailing list > Gsoc-mentors at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > From cjfields at illinois.edu Wed Apr 7 13:58:04 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 07 Apr 2010 12:58:04 -0500 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals In-Reply-To: <4BBCBC5A.1070901@cornell.edu> References: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> <4BBCBC5A.1070901@cornell.edu> Message-ID: <1270663084.12446.64.camel@pyrimidine.igb.uiuc.edu> Agreed. The critical thing is to not lose students due to lack of evaluation (I saw that one in particular has withdrawn or is ineligible). chris On Wed, 2010-04-07 at 10:09 -0700, Robert Buels wrote: > Based on the discussions on the GSoC-wide mentors list, the difficulty > with starting to review proposals before the deadline is that it can > introduce bias toward lower scores for proposals submitted at or near > the deadline. Also, some of these proposals might still be edited by > students. > > However, I think it would be a good idea for mentors to start taking a > look *through* the proposals, just don't really score them yet. > > Rob > > > Chris Fields wrote: > > All mentors, > > > > We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. > > > > http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf > > > > chris > > > > > > _______________________________________________ > > Gsoc-mentors mailing list > > Gsoc-mentors at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From maj at fortinbras.us Wed Apr 7 20:06:00 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 08 Apr 2010 00:06:00 +0000 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals Message-ID: Rob, Chris -- do we have a protocol in place for scoring/evaluation? >-----Original Message----- >From: Robert Buels [mailto:rmb32 at cornell.edu] >Sent: Wednesday, April 7, 2010 01:09 PM >To: 'GSoC - mentors only' >Cc: open-bio-l at lists.open-bio.org >Subject: Re: [GSoC-mentors] OBF Proposals > >Based on the discussions on the GSoC-wide mentors list, the difficulty >with starting to review proposals before the deadline is that it can >introduce bias toward lower scores for proposals submitted at or near >the deadline. Also, some of these proposals might still be edited by >students. > >However, I think it would be a good idea for mentors to start taking a >look *through* the proposals, just don't really score them yet. > >Rob > > >Chris Fields wrote: >> All mentors, >> >> We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. >> >> http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf >> >> chris >> >> >> _______________________________________________ >> Gsoc-mentors mailing list >> Gsoc-mentors at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/gsoc-mentors >> > >_______________________________________________ >Gsoc-mentors mailing list >Gsoc-mentors at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > From biopython at maubp.freeserve.co.uk Tue Apr 13 06:26:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 13 Apr 2010 11:26:40 +0100 Subject: [Open-bio-l] Common SQLite3 schema for flat file indexing (a new OBDA standard)? Message-ID: Hello all, Last year we had a brief disucssion about the Open Biological Database Access (OBDA) indexing for "flat files" which BioPerl and BioRuby at least still support (despite some confusion over the spec): http://lists.open-bio.org/pipermail/open-bio-l/2009-August/000561.html There may still be life in the current Berkeley DB (DBD) based OBDA index, but with ever larger sequences files needed in next generation sequencing this could be a problem. Is anyone finding problems with the current BDB index scaling to larger files (with tens of millions of entries to index)? >From the Biopython perspective, we have a small external incentive to favour SQLite3 over BDB: The python standard library has historically included a BerkleyDB module (bsddb) but it has been deprecated in Python 3. On the other hand, all recent versions of Python include SQLite3 support. Those of you on the BioPerl or Biopython mailing lists will have heard me mention the idea of using SQLite to hold a flat file index, e.g. http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032713.html http://lists.open-bio.org/pipermail/biopython/2009-December/005997.html >From the BioPerl thread I know they are now looking at using SQLite to hold a lookup table of file offsets. Are any of the other Bio* projects interested in this approach? I'd idealy like us to agree something shared with all the Bio* libraries (a new OBDA standard using SQLite3 instead of BDB). I was thinking something along these lines if we want to support an index for multiple files - just three tables: * meta - table with string key/values (in particular to hold a schema version number, plus perhaps the tool which built the index) * offsets - table with entry accessions, file number (key to next table), file offset * files - table with filenames, file type (e.g. FASTA), datestamp (so we can spot if the index is older than the file and needs to be updated), perhaps other things like if the file is compressed (gzip, bz2, ...). Of course, there are complications. For instance, calculating the offsets when dealing with different file encodings and new lines. Mark Schreiber raised this as a concern with Java (see open-bio-l thread linked to above, email dated 2 Sept 2009). The new line issue could also affect Biopython, but this may not be a real issue in practise unless moving indexes between operating systems. Regards, Peter (@Biopython) From asidhu at biomap.org Mon Apr 26 02:00:59 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 26 Apr 2010 14:00:59 +0800 Subject: [Open-bio-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Message-ID: <24BDA6DE-1758-4AD6-9FDF-8D65EF5096D1@biomap.org> IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From rmb32 at cornell.edu Tue Apr 27 01:52:57 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:52:57 -0700 Subject: [Open-bio-l] Google Summer of Code - accepted students Message-ID: <4BD67BB9.3000804@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Mon Apr 26 18:54:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:54:53 -0000 Subject: [Open-bio-l] Google Summer of Code - accepted students Message-ID: <4BD60D63.1040400@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From suryasaha at gmail.com Tue Apr 27 12:43:22 2010 From: suryasaha at gmail.com (Surya Saha) Date: Tue, 27 Apr 2010 16:43:22 -0000 Subject: [Open-bio-l] ISCB Student Council Symposium 6 travel fellowship and abstract submission deadlines on April 30, 2010 Message-ID: [Apologies for spamming and cross posting] Submit your abstract today and apply for travel fellowship to participate in the 6th ISCB Student Council Symposium on July 9th in Boston! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships are available (see website) and awards will be given to best poster and best presentation. Furthermore, the Wellcome Trust provides 4 travel fellowships for students from developing countries that cover travel and lodging expenses. Submission website: http://symposium.iscbsc.org/content/submissions Travel Fellowship information: http://symposium.iscbsc.org/content/travel-fellowships Room sharing information: http://www.iscbsc.org/forum-topic/student-council/6th-student-council-symposium General information: http://symposium.iscbsc.org/ Important dates: April 30: 6th Student Council Symposium Abstract submission closes April 30: 6th Student Council Symposium Travel Fellowships submission closes May 14: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Thomas Abeel Chair, 6th ISCB Student Council Symposium Magali Michaut Co-Chair, 6th ISCB Student Council Symposium Gold Sponsor of the event: EMBL-EBI From chapmanb at 50mail.com Fri Apr 2 13:05:05 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Fri, 2 Apr 2010 09:05:05 -0400 Subject: [Open-bio-l] BOSC and OpenBio solution challenge reminder -- April 15th Message-ID: <20100402130505.GE36623@sobchak.mgh.harvard.edu> Hello all; A friendly reminder that the deadline for the Bioinformatics Open Source Conference (BOSC) is coming up on April 15th: http://www.open-bio.org/wiki/BOSC_2010 This is a great opportunity to discuss code and biology with fellow developers. One session which I'd like to emphasize is the OpenBio Solution Challenge, a section of talks that describes how to solve practical problems in bioinformatics using a variety of approaches: http://www.open-bio.org/wiki/SolutionChallenge Any toolkit developers who are interested in giving a talk are encouraged to submit an abstract for the challenge. We have some initial project ideas on the page and welcome your feedback for other useful workflows that would emphasize the advantages of using open source toolkits to solve biological problems. Please copy messages to the OpenBio mailing list as a central point for discussion and questions: http://lists.open-bio.org/mailman/listinfo/open-bio-l Looking forward to seeing everyone in July, Brad BOSC contact and dates: Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010 Abstract submission via Open Conference System site: http://events.open-bio.org/BOSC2010/openconf.php E-mail: bosc at open-bio.org Bosc-announce list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates April 15: Abstract deadline May 5: Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9: Codefest 2010 July 9-10: BOSC 2010 August 15: Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics From cjfields at illinois.edu Wed Apr 7 14:15:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Apr 2010 09:15:15 -0500 Subject: [Open-bio-l] OBF Proposals Message-ID: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> All mentors, We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf chris From rmb32 at cornell.edu Wed Apr 7 17:09:46 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 07 Apr 2010 10:09:46 -0700 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals In-Reply-To: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> References: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> Message-ID: <4BBCBC5A.1070901@cornell.edu> Based on the discussions on the GSoC-wide mentors list, the difficulty with starting to review proposals before the deadline is that it can introduce bias toward lower scores for proposals submitted at or near the deadline. Also, some of these proposals might still be edited by students. However, I think it would be a good idea for mentors to start taking a look *through* the proposals, just don't really score them yet. Rob Chris Fields wrote: > All mentors, > > We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. > > http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf > > chris > > > _______________________________________________ > Gsoc-mentors mailing list > Gsoc-mentors at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > From cjfields at illinois.edu Wed Apr 7 17:58:04 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 07 Apr 2010 12:58:04 -0500 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals In-Reply-To: <4BBCBC5A.1070901@cornell.edu> References: <5174B7DA-FDB8-4F4A-B960-1E8BF2A71AE6@illinois.edu> <4BBCBC5A.1070901@cornell.edu> Message-ID: <1270663084.12446.64.camel@pyrimidine.igb.uiuc.edu> Agreed. The critical thing is to not lose students due to lack of evaluation (I saw that one in particular has withdrawn or is ineligible). chris On Wed, 2010-04-07 at 10:09 -0700, Robert Buels wrote: > Based on the discussions on the GSoC-wide mentors list, the difficulty > with starting to review proposals before the deadline is that it can > introduce bias toward lower scores for proposals submitted at or near > the deadline. Also, some of these proposals might still be edited by > students. > > However, I think it would be a good idea for mentors to start taking a > look *through* the proposals, just don't really score them yet. > > Rob > > > Chris Fields wrote: > > All mentors, > > > > We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. > > > > http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf > > > > chris > > > > > > _______________________________________________ > > Gsoc-mentors mailing list > > Gsoc-mentors at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > > > > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l From maj at fortinbras.us Thu Apr 8 00:06:00 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 08 Apr 2010 00:06:00 +0000 Subject: [Open-bio-l] [GSoC-mentors] OBF Proposals Message-ID: Rob, Chris -- do we have a protocol in place for scoring/evaluation? >-----Original Message----- >From: Robert Buels [mailto:rmb32 at cornell.edu] >Sent: Wednesday, April 7, 2010 01:09 PM >To: 'GSoC - mentors only' >Cc: open-bio-l at lists.open-bio.org >Subject: Re: [GSoC-mentors] OBF Proposals > >Based on the discussions on the GSoC-wide mentors list, the difficulty >with starting to review proposals before the deadline is that it can >introduce bias toward lower scores for proposals submitted at or near >the deadline. Also, some of these proposals might still be edited by >students. > >However, I think it would be a good idea for mentors to start taking a >look *through* the proposals, just don't really score them yet. > >Rob > > >Chris Fields wrote: >> All mentors, >> >> We really need to start evaluating the proposals listed on the OBF site; a vast majority are still listed under new proposals (i.e. not under review). This doesn't need to include assigning some score just yet, though I have noticed a few orgs (TPF, NESCent) are doing so. >> >> http://socghop.appspot.com/gsoc/org/list_proposals/google/gsoc2010/obf >> >> chris >> >> >> _______________________________________________ >> Gsoc-mentors mailing list >> Gsoc-mentors at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/gsoc-mentors >> > >_______________________________________________ >Gsoc-mentors mailing list >Gsoc-mentors at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/gsoc-mentors > From biopython at maubp.freeserve.co.uk Tue Apr 13 10:26:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 13 Apr 2010 11:26:40 +0100 Subject: [Open-bio-l] Common SQLite3 schema for flat file indexing (a new OBDA standard)? Message-ID: Hello all, Last year we had a brief disucssion about the Open Biological Database Access (OBDA) indexing for "flat files" which BioPerl and BioRuby at least still support (despite some confusion over the spec): http://lists.open-bio.org/pipermail/open-bio-l/2009-August/000561.html There may still be life in the current Berkeley DB (DBD) based OBDA index, but with ever larger sequences files needed in next generation sequencing this could be a problem. Is anyone finding problems with the current BDB index scaling to larger files (with tens of millions of entries to index)? >From the Biopython perspective, we have a small external incentive to favour SQLite3 over BDB: The python standard library has historically included a BerkleyDB module (bsddb) but it has been deprecated in Python 3. On the other hand, all recent versions of Python include SQLite3 support. Those of you on the BioPerl or Biopython mailing lists will have heard me mention the idea of using SQLite to hold a flat file index, e.g. http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032713.html http://lists.open-bio.org/pipermail/biopython/2009-December/005997.html >From the BioPerl thread I know they are now looking at using SQLite to hold a lookup table of file offsets. Are any of the other Bio* projects interested in this approach? I'd idealy like us to agree something shared with all the Bio* libraries (a new OBDA standard using SQLite3 instead of BDB). I was thinking something along these lines if we want to support an index for multiple files - just three tables: * meta - table with string key/values (in particular to hold a schema version number, plus perhaps the tool which built the index) * offsets - table with entry accessions, file number (key to next table), file offset * files - table with filenames, file type (e.g. FASTA), datestamp (so we can spot if the index is older than the file and needs to be updated), perhaps other things like if the file is compressed (gzip, bz2, ...). Of course, there are complications. For instance, calculating the offsets when dealing with different file encodings and new lines. Mark Schreiber raised this as a concern with Java (see open-bio-l thread linked to above, email dated 2 Sept 2009). The new line issue could also affect Biopython, but this may not be a real issue in practise unless moving indexes between operating systems. Regards, Peter (@Biopython) From asidhu at biomap.org Mon Apr 26 06:00:59 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 26 Apr 2010 14:00:59 +0800 Subject: [Open-bio-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Message-ID: <24BDA6DE-1758-4AD6-9FDF-8D65EF5096D1@biomap.org> IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From rmb32 at cornell.edu Tue Apr 27 05:52:57 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:52:57 -0700 Subject: [Open-bio-l] Google Summer of Code - accepted students Message-ID: <4BD67BB9.3000804@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Mon Apr 26 22:54:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:54:53 -0000 Subject: [Open-bio-l] Google Summer of Code - accepted students Message-ID: <4BD60D63.1040400@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From suryasaha at gmail.com Tue Apr 27 16:43:22 2010 From: suryasaha at gmail.com (Surya Saha) Date: Tue, 27 Apr 2010 16:43:22 -0000 Subject: [Open-bio-l] ISCB Student Council Symposium 6 travel fellowship and abstract submission deadlines on April 30, 2010 Message-ID: [Apologies for spamming and cross posting] Submit your abstract today and apply for travel fellowship to participate in the 6th ISCB Student Council Symposium on July 9th in Boston! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships are available (see website) and awards will be given to best poster and best presentation. Furthermore, the Wellcome Trust provides 4 travel fellowships for students from developing countries that cover travel and lodging expenses. Submission website: http://symposium.iscbsc.org/content/submissions Travel Fellowship information: http://symposium.iscbsc.org/content/travel-fellowships Room sharing information: http://www.iscbsc.org/forum-topic/student-council/6th-student-council-symposium General information: http://symposium.iscbsc.org/ Important dates: April 30: 6th Student Council Symposium Abstract submission closes April 30: 6th Student Council Symposium Travel Fellowships submission closes May 14: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Thomas Abeel Chair, 6th ISCB Student Council Symposium Magali Michaut Co-Chair, 6th ISCB Student Council Symposium Gold Sponsor of the event: EMBL-EBI