From sborthwick at royalsoced.org.uk Wed Aug 5 11:37:30 2009 From: sborthwick at royalsoced.org.uk (Sandra Borthwick) Date: Wed, 5 Aug 2009 11:37:30 +0100 Subject: [Sbforum-general] EXTENSION FOR SUBMISSIONS OF ABSTRACTS Comparative Genomics one-day International Conference 18th Aug 2009 ** Message-ID: <818406367E54EC499E989D011C0025CF4A09FE@rsoe_server4.society.local> ____________________________________________________________ *** EXTENTION FOR SUBMISSIONS OF ABSTRACTS FOR POSTERS *** ____________________________________________________________ Comparative Genomics One-day International Conference Date: 18th August 2009, 9:30 am Location: Bute Building, University of St Andrews * * * * * * * * * * * * * * * *** We are inviting submissions of abstracts for posters. Maximum abstract length 200 words. Submission deadline: 13 August. Please send your abstract to cjanssen (at) sbforum.org *** Comparative genomics is a new field of increasing power. Thousands of genome sequences are now available, and the amount of data on genomes continues to increase. This presents enormous opportunities to make discoveries of biological and medical interest, but also requires newapproaches. The bottleneck has shifted from the effort required to obtain genomic data, to the effort required to analyse them. However, exciting and novel results are already emerging, in a vast range of areas within biology and medicine. Internationally renowned invited speakers and a poster session will present new developments in this cutting-edge field. Confirmed speakers: - Prof MARK BLAXTER, University of Edinburgh. "Comparative Nematode Genomics". - Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs". - Prof DANNIE DURAND, Carnegie Mellon University. "The Evolution of Multidomain Families". - Prof NEIL HALL, University of Liverpool. "Fast forward Genetics using second generation sequencing". - Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the consequences of hybridisation and polyploidy in Senecio". - Prof IAN KORF, University of California Davis Genome Center. "Intron mediated enhancement". - Prof ALAN ARCHIBALD FRSE, Roslin Institute. "Title" tbc. - Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome assemblies and variation detection between normal and tumor human cells". - Prof ZIHENG YANG FRS, University College London. "Population genomics and human-chimpanzee speciation". - Prof ANDY WATERS, University of Glasgow, "Translation of Translation: Comparative genomics yields practical insights into sexual development in malaria parasites" More information can be found at http://www.sbforum.org/events.php?e_id=70 Registration details: Early registration is encouraged. Registration fees are ?40; students can register for a reduced fee of ?20. ** Please register on-line at: www.sbforum.org/events.php The event is followed by a networking buffet dinner. Please book early to help us gauge numbers for the catering http://www.sbforum.org/eregister.php?e_id=70 * * * * * * * * * * * * * * * We look forward to seeing you on Tuesday 18th August. 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 is 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 The Royal Society of Edinburgh, Scotland's National Academy, is Scottish Charity No. SC000470 The RSE Scotland Foundation, a charitable body connected to the Society, is 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 RSE/RSE Scotland Foundation, unless specifically stated Tel: 0131 240 5000. Fax: 0131 240 5024 http://www.royalsoced.org.uk ____________________________________________________________________________ All RSE staff now have direct dial telephone lines. See http://www.royalsoced.org.uk/organisation/staff.htm SAVE PAPER. DO YOU NEED TO PRINT THIS EMAIL? From ab at macs.hw.ac.uk Thu Aug 6 10:55:08 2009 From: ab at macs.hw.ac.uk (ab at macs.hw.ac.uk) Date: Thu, 6 Aug 2009 10:55:08 +0100 (BST) Subject: [Sbforum-general] First CFP: SWAT4LS Semantic Web Applications and Tools for Life Sciences 2009 Message-ID: <51858.94.193.240.4.1249552508.squirrel@www.macs.hw.ac.uk> Apologies for possible multiple posts ----------------------------------------------------- First CFP: SWAT4LS Semantic Web Applications and Tools for Life Sciences 2009 ***Location and date Amsterdam, Science Park, November 20th 2009 (http://www.swat4ls.org/2009/) ***Rationale The adoption of semantic-enabled applications and collaborative social environments is ever more common in the Life Sciences. 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 environemnts. Altogether the adoption of the Semantic Web in the Life Sciences has potential impact on the future of publishing, biological research and medecine. 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,... ) o Biomedical Ontologies and related tools 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 collaborative research environments o Case studies, use cases, and scenarios ***Scientific Committee (committed so far) * Christopher J. O. Baker, Department of Computer Science and Applied Statistics, University of New Brunswick, Saint John, Canada * Pedro Barahona, Department of Informatics, New University of Lisboa, Lisboa, Portugal * Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany * Olivier Bodenreider, National Library of Medicine, Bethesda, United States of America * Matt-Mouley Bouamrane, School of Computer Science, University of Manchester, Manchester, United Kingdom * Werner Ceusters, NY CoE in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, United States of America * Kei Cheung, Center for Medical Informatics, Yale University School of Medicine, New Haven, United States of America * Tim Clark, Center for Innovative Computing, Harvard University, United States of America * Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France * Olivier Dameron, INSERM U936, University of Rennes 1, Rennes, France * Michel Dumontier, Carleton University, Ottawa, Ontario, Canada * Huajun Chen, Zhejiang University, Hangzhou, China * Duncan Hull, School of Chemistry, University of Manchester, Manchester, United Kingdom * C. Maria Keet, Faculty of Computer Science, Free University of Bozen-Bolzano, Bolzano, Italy * Graham Kemp, Chalmers University of Technology, Sweden * Jacob Tilman Koehler, Department of Molecular Biotechnology, Institute of Medical Biology, University of Troms?, Troms?, Norway * Michael Krauthammer, Department of Pathology, Yale University School of Medicine, United States of America * Martin Kuiper, Department of Pathology, Systems Biology group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway * Patrick Lambrix, Department of Computer and Information Science, Link?ping University, Link?ping, Sweden * Phillip Lord, School of Computing Science, Newcastle University, Newcastle-upon-Tyne, United Kingdom * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, Amsterdam, The Netherlands * Chris Mungall, Lawrence Berkeley National Laboratories, United States of America * Stephan Philippi, Institute for Software Technology, University of Koblenz-Landau, Koblenz, Germany * Marco Roos, Instituut voor Informatica, University of Amsterdam, Amsterdam, The Netherlands * Alan Ruttenberg, Science Commons, Cambridge, United States of America * Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria * Nigam Shah, Center for Biomedical Informatics Research, Stanford, United States of America * Michael Schr?der, Biotechnology Centre, TU Dresden, Dresden, Germany * Robert Stevens, School of Computer Science, University of Manchester, Manchester, United Kingdom * Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan * Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital, Vancouver, Canada and the organizers ***Type of contributions The following possible contributions are sought: * Oral communications (regular papers) * Posters * Software demos All accepted oral communications and posters will be published with CEUR-WS. ***Deadlines * Submission openinig: 1 September 2009 * Submission of oral communications: 28 September 2009 * Submission for posters and demos: 15 October 2009 * Communication of acceptance: 23 October 2009 * Camera ready: 6 November 2009 ***Instructions All papers and posters must be in English and must be submitted through the EasyChair review system at http://www.easychair.org/conferences/?conf=swat4ls-09 . Please upload all submissions as PDF files in LNCS format (see http://www.springer.de/comp/lncs/authors.html). To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Committee. * Submissions for Oral communications should be between 10 and 15 pages. * Posters submissions should be between 4 and 8 pages. * Software demo proposals should also be between 4 and 8 pages. ***Proceedings All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). We are in the process of negotiating the possibility to have a special issue of a major bioinformatics journal related to the 2009 edition of swat4ls. To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. ***Organization * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, The Netherlands * Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom * Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany * Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy * Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted Research, UK ----------- For any further information or clarification, please visit the website at http://www.swat4ls.org/2009 or contact the organization by email at info @ swat4ls.org -- Heriot-Watt University is a Scottish charity registered under charity number SC000278. From sandra.borthwick at sbforum.org Thu Aug 27 17:17:12 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Thu, 27 Aug 2009 17:17:12 +0100 Subject: [Sbforum-general] REMINDER : SBF Event - Microarray Data Analysis - training event - 16-18th September 2009 Message-ID: <130E890E14CF46DC8D33D6DB191412D3@society.local> ** REMINDER ** 3 Day course: 16.09 ? 18.09 2009 ______________________________________________________________ The Scottish Bioinformatics Forum will be hosting a three day workshop "Microarray Data Analysis" With: Joaquin Dopazo, Javier Santoyo and Ana Conesa (Department of Bioinformatics and Functional Genomics Node (INB) Centro de Investigacion Principe Felipe (CIPF) 46013, Valencia, Spain) Date: 16-18th September 2009 Location: NeSC, 246b Kelvin Building, University of Glasgow, G12 8QQ * * * * * * * * * * * * * * Back for the second time, this three day training event on microarray analysis introducing new concepts of transcriptomics with next generation sequencing. More information can be found at http://www.sbforum.org/events.php?e_id=61 Registration details: Early registration is encouraged as numbers are limited. Registration fees are ?60; students can register for a reduced fee of ?40 ** Please register on-line at: www.sbforum.org/events.php * * * * * * * * * * * * * * * We look forward to seeing you on 16th September. 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 The RSE Scotland Foundation is 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 jbom at st-andrews.ac.uk Thu Aug 27 17:51:38 2009 From: jbom at st-andrews.ac.uk (Dr John Mitchell) Date: Thu, 27 Aug 2009 17:51:38 +0100 Subject: [Sbforum-general] PhD studentships at St Andrews Message-ID: <1251391898.4a96b99a67801@webmail.st-andrews.ac.uk> PhD project: Modelling the Evolution of Enzyme Catalysis supervisor: Dr John Mitchell, Biomolecular Sciences, University of St Andrews funding details: Competition Funded Project - UK/EU Students only closing date: 30 Sept 2009 Contact: jbom at st-andrews.ac.uk 01334 467259 In this project, we will develop a computational model for how enzyme mechanisms evolve. Our group's previous work has developed reaction step fingerprints containing information about how the bond order, charge, and chemical connectivity change in each reaction step in our MACiE database of enzyme-catalysed reactions. The fingerprints provide a fine-tuneable means of quantifying mechanism-based similarities between enzyme-catalysed chemical reactions, which can also be used for clustering. First, the pairwise similarities between the steps in two reactions are computed. A global alignment between the two series of steps is then performed using the Needleman-Wunsch algorithm, just as for sequence alignment in bioinformatics. Existing evolutionary models are designed for comparing DNA or protein sequences, and consider insertions, deletions and mutations as the units of evolutionary change. However, an evolutionary model for reaction mechanisms must be adapted in order to compare chemical reactions. We will create a simulation using a population of model enzyme-catalysed reactions, mimicking a state early in evolutionary history, and allow them to evolve in EC space. The reactions will consist of steps and be represented, in a manner familiar from genetic algorithms, by "chromosomes" describing the chemical properties of each step. Parameters will control the likelihood of different kinds of evolutionary event, such as a change of substrate with the same underlying chemical mechanism, taking place. The simulations will be calibrated, and then compared with the results from a study of real-world convergent and divergent evolution. -- Dr John Mitchell Biomolecular Sciences University of St Andrews North Haugh St Andrews Scotland KY16 9ST United Kingdom +44-(0)1334-467259 ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk