From jprocter at compbio.dundee.ac.uk Fri Oct 15 11:27:08 2010 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 15 Oct 2010 16:27:08 +0100 Subject: [Open-bio-l] Jalview Residential Course - Nov 18th-19th 2010 Message-ID: <4CB872CC.8060501@compbio.dundee.ac.uk> Dear Open Bio members. Please pass the following advert on to any relevant mailing lists or interested colleagues. Apologies in advance for any cross-posting! * Multiple Sequence Alignment and Analysis with Jalview * * An EBI Affiliated Residential Course * The first Jalview residential course will take place from the 18th to 19th November in the EMBL-EBI training facility at the Wellcome Trust Genome Campus, Hinxton, near Cambridge, UK. This course will cover the basic, intermediate and advanced functions of the widely used Jalview sequence alignment, visualisation, annotation, and analysis system. The course begins with a mixer and evening dinner on the 18th November, and continues on the following day with a lecture and series of hands on tutorials covering all aspects of Jalview. There will also be the opportunity for participants to work with their own data, and discuss their analysis problems with the Jalview team. The fee for this course is 25 pounds, and includes food and accommodation for one night. Places are limited, so please register at http://www.ebi.ac.uk/training/onsite/101119-Jalview.html as soon as possible. Best Regards, Jim Procter Jalview Coordinator. -- ------------------------------------------------------------------- Jim Procter (Jalview Coordinator) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From pjotr.public14 at thebird.nl Mon Oct 4 09:40:49 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 04 Oct 2010 13:40:49 -0000 Subject: [Open-bio-l] BOSC and Codefest 2011 plans In-Reply-To: <20100917124740.GH8531@sobchak.mgh.harvard.edu> References: <20100917124740.GH8531@sobchak.mgh.harvard.edu> Message-ID: <20101004133129.GA1220@thebird.nl> Hi Brad, The idea of a code-fest is great - I am game. With regard to the two BOSC days, I would like to propose a change to the format. Rather than listen to all the project updates, and what not, we could opt to have morning talks and spin-off working groups in the afternoon. I like the format of the hackathons, though BOSC could be even more free-flowing as hackathons have a preset purpose. The code-fest is relevant for every project. In contrast BOSC itself could be for working on cross-Bio* project needs. We could have the morning session for every project where, rather than state achievements, we could state needs. Each talk could consist of two slides on achievements and two slides on needs (max 4 slides). If someone cares to give a demo, or show code, that is cool too. Talk is 10 minutes, including questions. Between Bio* projects we can find common ground and work on those needs. It would quickly be mapped out. It is such a small community, and the same faces, why not make good use of our time? I realise BOSC is *also* to promote Open Source to new comers. So it may be a question whether it is better to push talks, or to invite them to participate in OSS project needs. I think that may work well. I would care for a need oriented format. Pj. From denguehost at gmail.com Tue Oct 12 21:23:16 2010 From: denguehost at gmail.com (Chris Baker) Date: Wed, 13 Oct 2010 01:23:16 -0000 Subject: [Open-bio-l] CANARIE C_BRASS Project - 2 Positions at UNB, Saint John, New Brunswick, CA In-Reply-To: References: Message-ID: 2 Open Positions with the CANARIE funded C-BRASS Project ============================================= http://www.unb.ca/postings/eup/eup1286285219_4797.html http://www.unb.ca/postings/eup/eup1286285187_4678.html *C-BRASS: Canadian Bioinformatics Resources as Semantic Services* ------------------------------------------------------------------------------------------------------ C-BRASS will apply Semantic Web technologies to bioinformatics resources across Canada. This will improve research efficiency by encoding 'biological knowledge' into the web itself, reducing researchers? costs and time-to-discovery. C-BRASS will serve as a prototype for Semantic Web services in other domains SADI is an open-source Semantic Web Service framework that aims to maximize interoperability between Web Services by utilizing Semantic Web technologies at all levels of the Web Service "stack". See Also http://twitter.com/sadiframework http://www.facebook.com/sadiframework -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker From denguehost at gmail.com Tue Oct 12 21:36:37 2010 From: denguehost at gmail.com (Chris Baker) Date: Wed, 13 Oct 2010 01:36:37 -0000 Subject: [Open-bio-l] CFP: BMC Bioinformatics Special Issue - ECCB 2010 Workshop AIMM Message-ID: Apologies for cross postings OPEN CALL FOR PAPERS - BMC Bioinformatics Special Issue ================================================= Following the Event: ================ ECCB Workshop: http://www.eccb2010.org/index.php/workshops/workshop2 AIMM2010 Annotation, Interpretation and Management of Mutations http://www.unbsj.ca/sase/csas/data/aimm2010/ A call for papers is now open to all workshop participants and newcomers who could not attend the AIMM 2010 event. See the link below for details of the Special Issue on the AIMM Theme. AIMM Themes =========== Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy. Extraction of mutations and annotations from literature. Impacts of Mutations: Prediction and Bootstrapping. Mutation Data Integration, Phenotype Ontologies, Semantic Support and Reuse. Other related topics will be considered http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html Dates ===== Submissions open October 10th (2010) Abstracts Due November 30th (2010) Submissions due* December 18th (2010) Revised manuscript submitted February 28th (2011) CFP BMC Bioinformatics Page http://www.unbsj.ca/sase/csas/data/aimm2010/bmc.html Any further questions can be sent to bakerc at unb.ca Best regards, Christopher Baker Rene Witte Dietrich Rebholz-Schuhmann -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker From jprocter at compbio.dundee.ac.uk Fri Oct 15 15:27:08 2010 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 15 Oct 2010 16:27:08 +0100 Subject: [Open-bio-l] Jalview Residential Course - Nov 18th-19th 2010 Message-ID: <4CB872CC.8060501@compbio.dundee.ac.uk> Dear Open Bio members. Please pass the following advert on to any relevant mailing lists or interested colleagues. Apologies in advance for any cross-posting! * Multiple Sequence Alignment and Analysis with Jalview * * An EBI Affiliated Residential Course * The first Jalview residential course will take place from the 18th to 19th November in the EMBL-EBI training facility at the Wellcome Trust Genome Campus, Hinxton, near Cambridge, UK. This course will cover the basic, intermediate and advanced functions of the widely used Jalview sequence alignment, visualisation, annotation, and analysis system. The course begins with a mixer and evening dinner on the 18th November, and continues on the following day with a lecture and series of hands on tutorials covering all aspects of Jalview. There will also be the opportunity for participants to work with their own data, and discuss their analysis problems with the Jalview team. The fee for this course is 25 pounds, and includes food and accommodation for one night. Places are limited, so please register at http://www.ebi.ac.uk/training/onsite/101119-Jalview.html as soon as possible. Best Regards, Jim Procter Jalview Coordinator. -- ------------------------------------------------------------------- Jim Procter (Jalview Coordinator) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From pjotr.public14 at thebird.nl Mon Oct 4 13:40:49 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 04 Oct 2010 13:40:49 -0000 Subject: [Open-bio-l] BOSC and Codefest 2011 plans In-Reply-To: <20100917124740.GH8531@sobchak.mgh.harvard.edu> References: <20100917124740.GH8531@sobchak.mgh.harvard.edu> Message-ID: <20101004133129.GA1220@thebird.nl> Hi Brad, The idea of a code-fest is great - I am game. With regard to the two BOSC days, I would like to propose a change to the format. Rather than listen to all the project updates, and what not, we could opt to have morning talks and spin-off working groups in the afternoon. I like the format of the hackathons, though BOSC could be even more free-flowing as hackathons have a preset purpose. The code-fest is relevant for every project. In contrast BOSC itself could be for working on cross-Bio* project needs. We could have the morning session for every project where, rather than state achievements, we could state needs. Each talk could consist of two slides on achievements and two slides on needs (max 4 slides). If someone cares to give a demo, or show code, that is cool too. Talk is 10 minutes, including questions. Between Bio* projects we can find common ground and work on those needs. It would quickly be mapped out. It is such a small community, and the same faces, why not make good use of our time? I realise BOSC is *also* to promote Open Source to new comers. So it may be a question whether it is better to push talks, or to invite them to participate in OSS project needs. I think that may work well. I would care for a need oriented format. Pj. From denguehost at gmail.com Wed Oct 13 01:23:16 2010 From: denguehost at gmail.com (Chris Baker) Date: Wed, 13 Oct 2010 01:23:16 -0000 Subject: [Open-bio-l] CANARIE C_BRASS Project - 2 Positions at UNB, Saint John, New Brunswick, CA In-Reply-To: References: Message-ID: 2 Open Positions with the CANARIE funded C-BRASS Project ============================================= http://www.unb.ca/postings/eup/eup1286285219_4797.html http://www.unb.ca/postings/eup/eup1286285187_4678.html *C-BRASS: Canadian Bioinformatics Resources as Semantic Services* ------------------------------------------------------------------------------------------------------ C-BRASS will apply Semantic Web technologies to bioinformatics resources across Canada. This will improve research efficiency by encoding 'biological knowledge' into the web itself, reducing researchers? costs and time-to-discovery. C-BRASS will serve as a prototype for Semantic Web services in other domains SADI is an open-source Semantic Web Service framework that aims to maximize interoperability between Web Services by utilizing Semantic Web technologies at all levels of the Web Service "stack". See Also http://twitter.com/sadiframework http://www.facebook.com/sadiframework -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker From denguehost at gmail.com Wed Oct 13 01:36:37 2010 From: denguehost at gmail.com (Chris Baker) Date: Wed, 13 Oct 2010 01:36:37 -0000 Subject: [Open-bio-l] CFP: BMC Bioinformatics Special Issue - ECCB 2010 Workshop AIMM Message-ID: Apologies for cross postings OPEN CALL FOR PAPERS - BMC Bioinformatics Special Issue ================================================= Following the Event: ================ ECCB Workshop: http://www.eccb2010.org/index.php/workshops/workshop2 AIMM2010 Annotation, Interpretation and Management of Mutations http://www.unbsj.ca/sase/csas/data/aimm2010/ A call for papers is now open to all workshop participants and newcomers who could not attend the AIMM 2010 event. See the link below for details of the Special Issue on the AIMM Theme. AIMM Themes =========== Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy. Extraction of mutations and annotations from literature. Impacts of Mutations: Prediction and Bootstrapping. Mutation Data Integration, Phenotype Ontologies, Semantic Support and Reuse. Other related topics will be considered http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html Dates ===== Submissions open October 10th (2010) Abstracts Due November 30th (2010) Submissions due* December 18th (2010) Revised manuscript submitted February 28th (2011) CFP BMC Bioinformatics Page http://www.unbsj.ca/sase/csas/data/aimm2010/bmc.html Any further questions can be sent to bakerc at unb.ca Best regards, Christopher Baker Rene Witte Dietrich Rebholz-Schuhmann -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker