From clements at nescent.org Thu Aug 5 19:24:22 2010 From: clements at nescent.org (Dave Clements) Date: Thu, 5 Aug 2010 11:24:22 -0700 Subject: [Sbforum-general] GMOD Europe 2010, 13-16 Sept, Cambridge, UK In-Reply-To: References: Message-ID: GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a ?50 registration fee for the GMOD Meeting to cover catered lunches and other expenses. Registration for all other events is free, but required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. See http://gmod.org/wiki/January_2010_GMOD_Meeting for an idea of what goes on at GMOD meetings, GMOD is a collection of interoperable open source software components for managing, visualizing and annotating biological data. GMOD incorporates many widely used tools, including GBrowse and JBrowse for genome browsing, InterMine and BioMart for data mining, Galaxy and Ergatis for workflow, Chado for data management, GBrowse_syn and CMap for comparative genomics, plus many other tools (Apollo, MAKER, Pathway Tools, Textpresso, ...). GMOD is also an active community of researchers and developers addressing common challenges in exploiting their data. If you are struggling to fully exploit your data then please consider attending GMOD Europe 2010. Please let us know if you have any questions, and we hope to see you in Cambridge. Thanks, Scott Cain and Dave Clements -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback -------------- next part -------------- An HTML attachment was scrubbed... URL: From sandra.borthwick at sbforum.org Thu Aug 12 11:40:52 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Thu, 12 Aug 2010 11:40:52 +0100 Subject: [Sbforum-general] Biomedical and Life Science Data Management Challenges In-Reply-To: References: Message-ID: We would like to draw your attention to ?the upcoming workshop: ?Storing, Accessing and Sharing Data: Addressing the Challenges and Solutions,? on the 9th September, at the Royal Society of Edinburgh. We have organised this workshop, on handling large data in life science and biomedical research, in response to requests from the community, to assist in finding solutions to problems arising from requirements for storing, sharing and accessing high volumes of data. We have managed to get Phil Butcher, Head of IT at the Sanger Institute, Jeremy Olsen, Head of IT, Cancer Research UK, and other expert speakers from industry and academia to come and share their expertise and experience. ?Please see the program at http://www.sbforum.org/events.php?e_id=95 for details. ?Further, we have managed to get 9 leading technology providers to come and exhibit. The aim of the workshop is to learn from experts in the field, as well as provide a forum for sharing of experiences/ needs/ solutions pan-Scotland. ?We expect that this workshop will lead to discussions on solutions to data problems across research groups throughout Scotland. We hope you will manage to attend the event; please register at the bottom of the page: http://www.sbforum.org/events.php?e_id=95 Kind regards, Sandra -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel:? +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk? www.sbforum.org From jprocter at compbio.dundee.ac.uk Mon Aug 2 12:01:28 2010 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 02 Aug 2010 12:01:28 +0100 Subject: [Sbforum-general] Fwd: CFP: Semantic Web Applications and Tools Workshop (SWAT4LS 2010) Message-ID: <4C56A588.8090405@compbio.dundee.ac.uk> -------- Original Message -------- Subject: CFP: Semantic Web Applications and Tools Workshop (SWAT4LS 2010) Date: Sat, 24 Jul 2010 18:24:52 +0200 From: Adrian Paschke 3^rd Int. Semantic Web Applications and Tools for Life Sciences */Berlin, 10/*/th //December 2010/ */http://www.swat4ls.org/2010//*// *Overview* SWAT4LS is a workshop that provides a venue to present and discuss benefits and limits of the adoption of Web based information systems and semantic technologies in life sciences, biomedical informatics and computational biology. ------------------------------------------------------------------------ *Rationale* The web is a key medium for information publishing, and web based information systems play a key role in biomedical information exchange and integration. At the same time, the variety and complexity of biomedical information call for the adoption of semantic-based solutions. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the web-based semantic-enabled technologies in the Life Sciences has potential impact on the future of publishing, biological research and medicine. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. ------------------------------------------------------------------------ *Topics* Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards and new proposals (RDF, OWL, SKOS, Linked Data, ? ) o Biomedical Ontologies and related tools o Alternative approaches to integrate semantic representations and web based solutions o Formal approaches to large biomedical knowledge bases * Systems for a Semantic Web for Bioinformatics o RDF stores, Reasoners, query and visualization systems for life sciences o Semantic biomedical Web Services o Semantics aware Biological Data Integration Systems * Existing and prospective applications of the Semantic Web for Bioinformatics o Semantics aware application tools o Semantic Wikis o Semantic collaborative research environments o Case studies, use cases, and scenarios ------------------------------------------------------------------------ *Type of contributions* The following possible contributions are sought: * Research papers * Position papers * Posters * Software demos We are also accepting proposals for tutorials, hackathons or other related events to be held on Dec 8th (hackathons) and Dec 9th (tutorials). If interested, please contact info at swat4ls.org ------------------------------------------------------------------------ *Proceedings* All accepted communications will be published in the proceedings. Proceedings for the last editions of the workshop have been pubslished via the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Best papers will be invited to a journal special issue (probably BMC Bioinformatics). ------------------------------------------------------------------------ *Special issue* Authors of accepted contributions to the last editions of SWAT4LS have been invited to submit extended and revised contributions for a special issue in BMC Bioinformatics (dedicated to the SWAT4LS 2008 edition), and for a special issue of the BMC Journal of Biomedical Semantics (dedicated to the SWAT4LS 2009 edition, in preparation). We will continue with this approach and we will announce more detailed infomation as soon as we have reached an agreement with publishers. ------------------------------------------------------------------------ *Deadlines* * Submission openinig: *7 September 2010* * Papers submission deadline: *12 October 2010* * Posters and demo submission deadline: *1 November 2010* * Communication of acceptance: *8 November 2010* * Camera ready: *21 November 2010* ------------------------------------------------------------------------ *Instructions* All papers and posters must be in English, formatted according to LNCS format (http://www.springer.de/comp/lncs/authors.html) and submitted in pdf format. * Submissions for *papers* should report original research, and should be between 8 and 15 pages. * Submissions for *position papers* should report qualified opinions, recommendations or conclusions, and should be between 3 and 6 pages. * Submissions for *posters* should be between 2 and 4 pages. * Submissions for *software demo proposals* should also be between 2 and 4 pages. ------------------------------------------------------------------------ *Submission* All submissions will be handled via the EasyChair submission system. A link will be provided when registrations open. To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Program Committee. * ------------------------------------------------------------------------ * *Workshop Chairs* * *Adrian Paschke *, Corporate Semantic Web , Freie Universitaet Berlin, Germany * *Albert Burger *, School of Mathematical and Computer Sciences , Heriot-Watt University, and Human Genetics Unit , Medical Research Council, Edinburgh, Scotland, United Kingdom * *Paolo Romano *, Bioinformatics , National Cancer Research Institute, Genova, Italy * *M. Scott Marshall *, Adaptive Information Disclosure Group , University of Amsterdam, The Netherlands * *Andrea Splendiani *, Biomathematics and Bioinformatics dept. , Rothamsted Research, UK *Program Committee* See website http://www.swat4ls.org/2010/ -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) 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 sandra.borthwick at sbforum.org Tue Aug 17 11:38:10 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Tue, 17 Aug 2010 11:38:10 +0100 Subject: [Sbforum-general] NextgenBUG meeting - 7th Sept in Glasgow Message-ID: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NextGen Sequencing Bioinformatics User Group Meeting at Glasgow University Tuesday 7th September at 12:30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The 15th NextGen Sequencing Bioinformatics User Group Meeting will be held at Glasgow University on Tuesday 7th September from 12:30. For further details please see the link: http://genepool.bio.ed.ac.uk/nextgenbug/meeting/20100907 Kind regards Sandra -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel:? +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk? www.sbforum.org From urmi.trivedi at ed.ac.uk Tue Aug 17 12:10:23 2010 From: urmi.trivedi at ed.ac.uk (Urmi Trivedi) Date: Tue, 17 Aug 2010 12:10:23 +0100 Subject: [Sbforum-general] NextgenBUG meeting - September 7 at University of Glasgow Message-ID: Dear all, The next NextGenBUG (next generation sequencing Bioinformatics User Group) will be on 2010, September 7, Tuesday from 13:30-16:30 at University of Glasgow (Venue details to be confirmed) A buffet lunch will be provided between 12:30 and 1:30. Agenda: TBC Meeting logistics (parking, etc) and details of other short talks available at http://genepool.bio.ed.ac.uk/nextgenbug/meeting/20100907 Please add your name to the list at http://genepool.bio.ed.ac.uk/nextgenbug/meeting/20100907 Please volunteer to give the usual 15 - 20 minute presentations. See you there. Best regards, Urmi -- Urmi Trivedi Highthroughput sequencing bioinformatician The GenePool Room 3.54, Ashworth Laboratories Kings building's campus University of Edinburgh EH9 3JT, Edinburgh, UK. Phone: +44 131 650 7403 Email: urmi.trivedi at ed.ac.uk NextGenBUG website: http://genepool.bio.ed.ac.uk/nextgenbug/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From sandra.borthwick at sbforum.org Wed Aug 25 17:30:20 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Wed, 25 Aug 2010 17:30:20 +0100 Subject: [Sbforum-general] SBF/S3 - Storing, Accessing and Sharing Data ** Updated Programme available** In-Reply-To: References: Message-ID: *** Updated Programme NOW AVAILABLE *** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Storing, Accessing and Sharing Data: Addressing the Challenges and Solutions Date: 9th September 2010 Location: Royal Society of Edinburgh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The event will showcase how technology can underpin the requirements for biomedical and life science research data management and sharing in Universities and other research organisations. Addressed will be the feasibility of achieving data storage, access, and sharing from a technological perspective. ?The areas that will be addressed/considered are: o ? Cost effectively storing Data o ? Data Mobility/ Accessibility/ Transfer of data o ? Meta Data ? best ways to store the data and also how to make sure the right people can access the material and the wrong people can?t! o ? Effectively managing different data types e.g from millions of small files to lots of large image files o ? Indexing the data and being able to recover the right information o ? Data sustainability and Durability (is it appropriate to move data to tape and if so when and how do you futureproof this?) o ? Tiering of Data to help reduce cost (and the automation of this) o ? Scalability o ? Building a resilient infrastructure *** Updated Programme *** http://www.sbforum.org/cmsimages/event_progs_10/090910_Data_storage_prog_v7.pdf For more information and registration details please see: http://www.sbforum.org/events.php?e_id=95 Thank you for your time, we look forward to seeing you on 9th September. -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel:? +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk? www.sbforum.org -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel:? +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk? www.sbforum.org