From y.ghanbari from gmail.com Wed Sep 9 21:06:55 2009 From: y.ghanbari from gmail.com (Yasser) Date: Wed Sep 9 21:36:22 2009 Subject: [Computational-biology] Some Wavelet applications on Speech Enhancement Message-ID: Some Wavelet applications on Speech Enhancement can be found in these publications: http://lyle.smu.edu/~yghanbari/Publications.html From lidiomarx from gmail.com Thu Sep 10 13:08:30 2009 From: lidiomarx from gmail.com (Lidio Meireles) Date: Thu Sep 10 13:25:54 2009 Subject: [Computational-biology] Amphipathic helix prediction Message-ID: Would anyone recommend me a program or web server to predict amphipathic helix from sequence? Thanks. Lidio From Heather.Vincent from manchester.ac.uk Thu Sep 17 04:41:28 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Thu Sep 17 09:58:08 2009 Subject: [Computational-biology] New themes in computational biology Message-ID: <4AB20448.7050308@manchester.ac.uk> At the University of Manchester, UK, we provide advanced, multidisciplinary, training to participants from a range of backgrounds, including Biology, Healthcare, Medicine and Computer Science. We are now extending the range of our distance courses to include new themes in BioHealth Informatics and Computational Systems Biology. The introductory course in the computational biology theme, Bioinformatics for Systems Biology, begins again on 5 October 2009. This will be followed by two new courses within the same theme. They are : # Mathematics for metabolic modelling # Computational simulation and analysis of biochemical networks For information on all our courses, please see : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any queries, please contact Heather.Vincent@manchester.ac.uk From riao2010_review from irit.fr Wed Sep 16 13:33:13 2009 From: riao2010_review from irit.fr (riao2010_review@irit.fr) Date: Thu Sep 17 10:05:11 2009 Subject: [Computational-biology] [RIAO 2010] Call for Papers and Applications Message-ID: <200909161833.n8GIXDhA008275@extra.irit.fr> (apologies for multiple postings) Call for Papers and Applications RIAO 2010 - 9th RIAO Conference Adaptivity, Personalization and Fusion of Heterogeneous Information 28-30 April, 2010 Paris, France (Bibliothèque Nationale de France) http://www.riao2010.org/ Important dates : Paper submission deadline November 30, 2009 Notification to authors February 5, 2010 Camera-Ready copies due March 1, 2010 Conference dates April 28-30, 2010 History This triannual international conference is the 9th RIAO conference. Previous editions were held at Grenoble (1985), MIT (1988), Barcelona (1991), Rockefeller University (1994), Montreal (1997), Paris (2000), Avignon (2004), and Carnegie Mellon University (2007). RIAO conferences have always treated robust and large-scale scientific and industrial solutions to information processing. The conferences are composed of peer-reviewed scientific sessions and demonstrations of innovative industrial applications and advanced research prototypes. Scope of the Conference Submissions are invited which present recent, original and unpublished research on the theme of RIAO 2010: adapting, personalizing and merging heterogeneous information. Submissions may address one or more of the following subjects: Formal Models, Theory Information filtering . Content based filtering . Collaborative filtering . Recommender systems . Spam, protection of minors Personalized IR and User modelling . Adaptive IR . Collaborative IR . Interfaces Information fusion . Mash Ups . Aggregated search . Systems for watch, business decision Web Search and Advertising . Adversial IR . Advertising . Link analysis Machine Learning for IR . Learning to rank . Probabilistic topic models . All kinds of learning techniques applied to IR Information extraction and natural language processing, multilinguality . Summarization . Question answering . Entity/relation extraction . Cross-Language IR, Machine translation for IR Multimedia Information Retrieval . Image IR . Video IR . Speech/audio IR . Music IR, analysis of multimedia content Applications . Cultural heritage . Trademark search . Scientific media . Bio-computing and medical . Database offloading Evaluation, benchmarking Social networks . Folksonomies, tagging . Blogs . Social search . Communities . Opinion and sentiment Paper Submission We welcome submissions from both research and industrial communities addressing the main conference themes. Submitted papers must describe an unpublished origal work, emphasizing completed or advanced research, possibly with releted experiments. A parallel submission to other venues should be clearly indicated to the program committee. All submissions will be reviewed by at least three program committee members. The submissions will be judged on the basis of originality, relevance, technical quality, and presentation. Papers can be submitted in two categories: full papers and short papers, where full papers are appropriate for describing substantial research with related evaluations and short papers will typically describe ongoing research and preliminary results. All accepted papers in both categories will be published in the conference proceedings. At the conference, full papers will be presented as a talk and short papers will be presented as a poster. Long papers must not exceed 12 pages (5000 words), in one column format, starting with an abstract. Short papers must not exceed 6 pages (2500 words), in one column, starting with an abstract. Submissions should be in Microsoft Word format or in PDF. The conference proceedings will be available to conference attendees, and through the CID after the conference. CALL FOR APPLICATIONS The RIAO conferences are meeting places for both scientific and industrial specialists in information retrieval. The facilities allow to present high-level peer-reviewed scientific research conferences and prototypes and of innovative products, selected by a special call for innovative applications. The displayed products are chosen uniquely on the basis of their innovativeness. The general topic of the Call for Applications is: INNOVATIVE TOOLS PROVIDING PERSONNALIZED ACCESS TO MULTIMEDIA AND/OR MULTILINGUAL DATA. Companies whose product fulfills the criteria of novelty and of innovativeness can fill in a submission document designed by the conference organizers that describes their submitted product. In addition to the submission document, product submitters will have to provide access to an online or CD version of the product that demonstrates the claimed innovative functionalities of the product. Every chosen company will be provided with a demonstration space (including table and chair) free of charge. Each company may also be given a special time slot (15 minutes) to give a short presentation about the product. Descriptions of the products demonstrated during RIAO 2010 will be published in the proceedings. The selected companies will also be invited to an event organized with Cap Digital business cluster (http://www.capdigital.com) providing B2B meetings with top members of the cluster followed by a networking event at La Cantine coworking space http://lacantine.org/ Program Chairs Gabriella Pasi (Europe) Tie-Yan Liu (Asia) Prabhakar Raghavan (Americas) Program committee: Agosti Maristella, University of Padova, Italy Amati Giambattista, Fondazione Ugo Bordoni, Italy Amitay Einat, IBM Research, Haifa Lab, Israel Bailey Alex, Google Switzerland GmbH, Switzerland Berendt Bettina, Katholieke Universiteit Leuven, Belgium Boldi Paolo, Consigio Nazionale delle Ricerche, Italy Bordogna Gloria, Università degli Studi di Milano, Italy Boughanem Mohand, Université Paul Sabatier, France Brisaboa Nieves, Universidad de la Coruna, Spain Bruza Peter, Queensland University of Technology, Brisbane, Australia Bruzilovski Peter, University of Pittsburgh, USA Chen Hsin-Hsi, National Taiwan University, Taiwan Clarke Charles L.A., University of Waterloo, Canada Crestani Fabio, University of Lugano, Switzerland Croft Bruce, University of Massachusetts, Amherst, USA Currin Cathal, Dublin University, Ireland de Rijke Maarten, University of Amsterdam, Netherland Dumais Susan, Microsoft research, USA Efthimiadis Efthimis N., University of Washington, USA David A. Evans, JustSystems Evans Research Corporation Fernandez-Luna Juan M., University of Granada, Spain Fluhr Christian, Cadege, France Gallinari Patrick, University of Paris 6, France Gaussier Eric, Universit de Grenoble, France Grefenstette Gregory, Exalead, France Grossman David Adam, ITT, USA Harman Donna, NIST, USA Jarvelin Kalervo, University of Tampere, Finland Joho Hideo, University of Glasgow, United Kingdom Jones Gareth, Dublin City University, United Kingdom Jones Rosie, Yahoo! Inc., USA Jose Joemon M, University of Glasgow, United Kingdom Kando Noriko, National Institute of Informatics, Japan Lam Wai, University of Hong Kong, Hong-Kong Li Yuefeng, Queensland University of Technology, Brisbane, Australia Liddy Liz, Syracuse University, USA Lin Chin-Yew, Microsoft Research, China Maarek Yoelle, Google (Haifa Engineering Center), Israel Marchand-Maillet Stephane, University of Geneva, Switzerland Melucci Massimo, Università di Padova, Italy Mitra Mandar, Indian Statistical Institute, India Moens Marie-Francine, Katholieke Universiteit Leuven, Belgium Moffat Alistair, University of Melbourne, Australia Mothe Josiane, IRIT - CNRS, Toulouse, France Murdock Vanessa, Yahoo! Research, Spain Myaeng Sung Hyon, Information and Communication University, Korea Nie Jian-Yun, University of Montreal, Canada Nrnberger Andreas, Otto-von-Guericke-University Magdeburg, Germany Oard Douglas, University of Maryland, USA Ounis Iadh, University of Glasgow, United Kingdom Pasi Gabriella, Università degli Studi di Milano Bicocca, Italy Peters Carol, Istituto di Elaborazione della Informazione (IEI) -CNR, Italy Piwowarski Benjamin, University of Glasgow, United Kingdom Quénot Georges, IMAG, France Raghavan Prabhakar, Yahoo research, USA Roelleke Thomas, Queen Mary University, United Kingdom Ruthven Ian, University of Strathclyde, United Kingdom Sakai Tetsuya, NewsWatch, Japan Shaoping Ma, Tsinghua University, China Silvestri Fabrizio, Istituto di Scienza e Tecnologie dell'Informazione, Italy Smeaton Alan, Dublin City University, Ireland Soulé-Dupuy Chantal, University of Toulouse 1, France Vigna Sebastiano, Università degli Studi di Milano, Italy Vinciarelli Alessandro, IDIAP, Switzerland Wilkinson Ross, CSIRO ICT Centre, Australia Zaragoza Hugo, Yahoo! Research Barcelona, Spain Zweigenbaum Pierre, Limsi/CNRS, France Application chairs: Philippe Roy, Cap Digital, France (Chair) Josiane Mothe, IRIT, France (co-Chair) Application committee: Irina Blomquist, Digibusiness, Finland Marie Buhot Launay, ARD, France Marie-Odile Charaudeau, Aproged, France David Evans, JustSystems Evans Research, USA Alain Garnier, Jamespot, France Catherine Gouttas, Thalès, France Fabrice Lacroix, Antidot, France Agnès Lainé, CFI, France Marc Michel Pic, Advestigo, France Cyril Rollinde, Freelance, Pondichery, India Bernard Schmid, Vienna IT Enterprises , Austria Jacqueline Thomas, CFI, France ------------------------- From andrea.splendiani from bbsrc.ac.uk Thu Sep 17 10:28:05 2009 From: andrea.splendiani from bbsrc.ac.uk (Andrea Splendiani) Date: Thu Sep 17 10:39:20 2009 Subject: [Computational-biology] SWAT4LS Cfp updates: new deadlines and journal supplement Message-ID: <3A8058EF-45A7-4D36-BB8F-379E66FA63C3@bbsrc.ac.uk> SWAT4LS Semantic Web Applications and Tools for Life Sciences *** apologies for multiple postings *** --- updates --- We are glad to announce that there will be a special issue of the BMC Journal of Biomedical Semantics dedicated to the SWAT4LS workshop. This is a new open access journal published by BMC and we are confident that the supplement will benefit from the additional exposure and promotion associated with its launch (more information on this journal can be found at http://www.jbiomedsem.com/). The call for this special issue will be open to all the contributors to the SWAT4LS workshop (accepted papers, posters and demos). Authors will be invited to submit an extended version of their work, elaborated in the light of the discussion held at the workshop. Workshop proceedings will be published on CEUR. In order to facilitate submissions, we have extended submission deadlines as follows: intention to submit (abstract only): October 5th submission of papers: October 12 submission of posters and demos: October 15 communication of acceptance: October 28 camera ready: November 13 Due to the limited time for reviews, we would ask you to submit an abstract of your paper by October 5th, in order to facilitate assignment of reviews. The lenght of contributions to the workshop as been revised to offer more flexibility: * Submissions for Oral communications should be between 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. Finally, we would like to announce that the special issue BMC Bioinformatics dedicated to SWAT4LS-2008 will be published on October 1st (BMC Bioinformatics, Vol 10, Supp 10) --- call for papers --- ***Location and date Amsterdam, Science Park, November 20th 2009 (http://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 environments. 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 Program The workshop will be interactive and include keynotes, oral presentations, panel discussion and a poster and demo session. The keynote speakers of this edition will be: * Barend Mons (http://www.biosemantics.org/index.php?page=barend-mons ) * Michael Schroeder (http://www.biotec.tu-dresden.de/schroeder) * Alan Ruttenberg (http://sciencecommons.org/about/whoweare/ruttenberg/ ) ***Scientific Committee (committed so far:) * Christopher J. O. Baker, Department of Computer Science and Applied Statistics, University of Brunswick, 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, MD, United States of America * Matt-Mouley Bouamrane, School of Computer Science, University of Machester, manchester, United Kingdom * Werner Ceusters, NY CoE in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, United States of America * Kei Cheung, Center for Medical Informatics, Yale University School of Medicine, New Haven, United States of America * Tim Clark, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States of America * Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France * Olivier Dameron, INSERM U936, University of Rennes 1, France * Michel Dumontier, Carleton University, Ottawa, Ontario, Canada * Huajun Chen, Zhejiang University, China * Duncan Hull, School of Chemistry, University of Manchester, UK * 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, 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, Netherlands * Alan Ruttenberg, Science Commons, Cambridge, MA, 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 ***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 finalizing the agreement to have a dedicated special issue on the 2009 edition of swat4ls in an international scientific journal of the BMC group (open access, pubmed indexed). 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. ***New Deadlines * Intention to submit (abstract only): October 5th * Submission of papers: October 12 * Submission of posters and demos: October 15 * Communication of acceptance: October 28 * Camera ready: November 13 ***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 (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 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. ***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 ***More information * http://www.swat4ls.org/2009/ * http://swat4ls.blogspot.com * info@swat4ls.org --- Andrea Splendiani Senior Bioinformatics Scientist Rothamsted Research, Harpenden, UK andrea.splendiani@bbsrc.ac.uk +44(0)1582 763133 ext 2004 From Rob.Reedijk from douglasconnect.com Wed Sep 23 07:51:25 2009 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Sep 23 10:00:27 2009 Subject: [Computational-biology] CFP - Latest Advances in Drug Discovery Informatics: eCheminfo 2009 InterAction Meeting; Philadelphia Oct 09. Program Available Message-ID: <6be8853c-6cf9-4747-8b09-2ac868b61424@r36g2000vbn.googlegroups.com> The eCheminfo 2009 community of practice meeting program with abstracts is now complete and available at http://echeminfo.com/comty_conferences This annual community of practice meeting is taking place for the fifth time and brings together a unique combination of pharmaceutical and healthcare industry experts, principal investigators and researchers from the academic and government sectors, and leaders from innovative enterprises. The smaller and more intimate meeting format pursued has fostered the type of collaboration not always found at large conferences. Registration fees include food (lunch, dinner, breaks and evening refreshments) for the days attended. Furthermore, arrangements have been made for some affordable accommodations (preferred rates), making the meeting economical to attend. We now have a great deal of information on preferred rates and travel directions available at http://echeminfo.com/comty_conferencelocation Latest Advances in Drug Discovery Informatics eCheminfo 2009 InterAction Meeting October 13-16, 2009 Bryn Mawr College, Bryn Mawr, Philadelphia, USA The topics addressed this year will include Structure-based Drug Design Applications and Methods, Macromolecular Interactions and Networks, Data Analysis and Visualisation, PDB Ligands, and Predictive Toxicology. More detailed program below. Format: Seminars, Roundtables, Presentations, Panel Q&As, Discussions, Break-out Workshops, Web-supported. Evening Poster sessions, networking, social activities. This meeting will take place concurrently with the InnovationWell 2009 meeting addressing the topics of Collaboration in Discovery and Development, Translational Bioinformatics, Systems Biology and Biomarkers, Blood Brain Barrier modeling and Predictive Toxicology. Call for Abstracts: If you wish to submit a poster abstract for the meeting which will be placed on the program, please send to Barry Hardy (barry.hardy –(at)- douglasconnect.com) for review. Attractive poster prizes will be awarded for best posters at the meeting (subject to peer review). A special peer-reviewed issue of Future Medicinal Chemistry with a focus on collaboration in discovery and development is being published from the meeting. Accepted poster and presentation abstracts are eligible for consideration. Please contact Barry Hardy if interested in submitting a paper for review. A pre-conference best practices workshop will take place October 12, 2009. To register for the meeting right now, please visit: http://echeminfo-bm910.eventsbot.com/ To download a pdf of the program including the registration form: http://barryhardy.blogs.com/files/echeminfoprogrambrynmawr09.pdf eCheminfo 2009 Program Summary MONDAY, OCTOBER 12 Drug Binding Affinities Workshop, Co-chaired by Scott Brown (Abbott Laboratories), Zheng Yang (GlaxoSmithKline Pharmaceuticals), Ruhong Zhou (IBM) and Judith Lalonde (Bryn Mawr College) Dong Xu (University of California, San Diego), Natasja Brooijmans (Wyeth Research) TUESDAY, OCTOBER 13 Structure-based Drug Design, Chaired by Alan Cheng (Amgen) Robert Abel (Schrodinger), Maxwell D. Cummings (Tibotec), Ernesto Friere (Johns Hopkins University), Zhuyan Guo (Schering-Plough), Pu Liu (Johnson & Johnson PR&D), Gergely Toth, Arnout Voet (KU Leuven). Macromolecular Interactions and Networks, Chaired by Emil Alexov (Clemson University) Amos Fatokun (John Hopkins), Marcia Fenley (Florida State University), Eric Hajjar (Universita degli Studi di Cagliari and Sardinian Laboratory for Computational Materials Science), Rameshwar Kadam (University of Berne), Alex Morozov (Rutgers University), Anna Panchenko (National Center for Biotechnology Information). WEDNESDAY, OCTOBER 14 Structure-Based Drug Design, Chaired by Natasja Brooijmans (Wyeth) Jorg Bentzien (Boehringer Ingelheim), Ian Craig (Novartis), Jens Meiler (Vanderbilt University), Devleena Shivakumar (Schrodinger), Zsolt Zsoldos and Orr Ravitz (SimBioSys). Data Analysis and Visualisation Applications in Chemical Biology Chaired by Brian Marsden (Structural Genomics Consortium, University of Oxford) Dimitris Agrafiotis (Johnson & Johnson PR&D), Warren DeLano (DeLano Scientific LLC), Bob Hanson (St. Olaf College), Ajit Jadhav (National Chemical Genomics Center), Wen Hwa Lee (Structural Genomics Consortium Oxford), THURSDAY, OCTOBER 15 PDB Ligands, Chaired by John Westbrook (Rutgers University) Howard Feldman (Research Scientist, Chemical Computing Group), Paul Hawkins (OpenEye Scientific Software), Kim Henrick, (PDBe, European Bioinformatics Institute), Gerard J. Kleywegt (Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Cambridge), Nigel W. Moriarty (Lawrence Berkeley National Laboratory), Marc Nicklaus (National Institutes of Health), Gregory L Warren (OpenEye Scientific Software, Inc.), Antony Williams (Royal Society of Chemistry), François Delfaud (MEDIT). Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences). Speakers include Richard Judson (US EPA), Ellen Berg (BioSeek), Jonathan Dordick (Rensselaer Polytechnic Institute), Barry Hardy (Douglas Connect), Sanji Bhal (ACD/ Labs), Christodoulos Floudas (Princeton University), Robert Fraczkiewicz (Simulations Plus), Kyoung Tai No (Yonsei University), and Stephen Bryant (NIH). FRIDAY, OCTOBER 15 Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences). Speakers include Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences), Fangping Mu (Los Alamos National Laboratory), Katya Tsaioun (Apredica), Grace Patlewicz (DuPont), Michael Pelekis (Simulations Plus), and Anil Aswani (University of California at Berkeley). Contact: Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas Connect. Tel: +41 61 851 0170. email: echeminfo -[at]- douglasconnect.com Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo - [at]- douglasconnect.com Meeting Support: Rob Reedijk, eCheminfo Community of Practice, Douglas Connect. email: rob.reedijk -[at]- douglasconnect.com From Rob.Reedijk from douglasconnect.com Wed Sep 23 07:51:59 2009 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Sep 23 10:00:32 2009 Subject: [Computational-biology] InnovationWell 2009 Meeting; Philadelphia Oct 09: Program available Message-ID: The InnovationWell 2009 community of practice meeting program with abstracts is now complete and available at http://innovationwell.com/comty_conferencesprog09 The InnovationWell program will cover discussion of topics on Collaboration in Discovery and Development, Translational Bioinformatics, Systems Biology, Biomarkers, Blood-Brain Barrier Modeling and Predictive Toxicology. More detailed program below. This annual community of practice meeting is taking place for the fifth time and brings together a unique combination of pharmaceutical and healthcare industry experts, principal investigators and researchers from the academic and government sectors, and leaders from innovative enterprises. The smaller and more intimate meeting format pursued has fostered the type of collaboration not always found at large conferences. Registration fees include food (lunch, dinner, breaks and evening refreshments) for the days attended. Furthermore, arrangements have been made for some affordable accommodations (preferred rates), making the meeting economical to attend. We now have a great deal of information on preferred rates and travel directions available at http://innovationwell.com/comty_conferencelocation Innovation in Life Science & Healthcare R&D InnovationWell 2009 InterAction Meeting October 13-16, 2009 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Format: Seminars, Roundtables, Presentations, Panel Q&As, Discussions, Break-out Workshops, Web-supported. Evening Poster sessions, networking, social activities. This meeting will take place concurrently with the eCheminfo 2009 drug discovery community of practice meeting: http://echeminfo.com/comty_conferencesprog09 Call for Abstracts: If you wish to submit a poster abstract for the meeting which will be placed on the program, please send to Barry Hardy (barry.hardy –(at)- douglasconnect.com) for review. Attractive poster prizes will be awarded for best posters at the meeting (subject to peer review). A special peer-reviewed issue of Future Medicinal Chemistry with a focus on collaboration in discovery and development is being published from the meeting. Accepted poster and presentation abstracts are eligible for consideration. Please contact Barry Hardy if interested in submitting a paper for review. Pre-Conference Workshop, October 12 Forum on Collaboration in Discovery and Development To register for the meeting right now, please visit: http://InnovationWell-BM09.eventsbot.com To download a pdf of the program including the registration form: http://barryhardy.blogs.com/files/innovationwell-bm09-90812.pdf InnovationWell 2009 Program Summary MONDAY, OCTOBER 12 Forum on Collaboration in Discovery and Development, Co-chaired by Peter Gates (Johnson & Johnson PR&D) and Barry Hardy (Douglas Connect). Speakers include Barry Hardy (Douglas Connect), Shree Nath (Pointcross), Simson Alex (Johnson & Johnson), Chris Waller (Pfizer), Michael Liebman (Strategic Medicine), Jeff Spitzner (Rescentris), and Bob O’Hara (ResultWorks). TUESDAY, OCTOBER 13 Translational Bioinformatics: Bridging Bioinformatics and Biomedical Informatics in Translational Medicine, Chaired by Jake Chen (Indiana University). Speakers include Jessica Tenenbaum (Duke Translational Medicine Institute, Duke University), Steve Naylor (Predictive Physiology and Medicine, Inc.), Javed Mostafa (University of North Carolina), Jay Zhang (Myriad Genetics), Maricel Kann (University of Maryland), Iya Khalil (Gene Network Sciences), Hai Hu (Windber Research Institute), Jake Chen (Indiana University – Purdue University), and Susan Stephens (Johnson & Johnson). WEDNESDAY, OCTOBER 14 Systems Biology and Biomarkers, Chaired by Darius Dziuda (Central Connecticut State University). Speakers include Anamika Sarkar (Novartis), Darius Dziuda (Central Connecticut State University), Frank Tobin (Tobin Consulting LLC), Andreas Matern (Thomson Reuters Healthcare and Science), and Usha Reddy (Merck). Modeling of the Blood–Brain Barrier in Drug Discovery and Development, Chaired by Roméo Cecchelli (Université d'Artois, France). Speakers include Stefan Lundquist (AstraZeneca), Reinhard Gabathuler (AngioChem), Maxime Culot (University of Lille), Damir Janigro (Cleveland Clinic), Marie-Pierre Dehouck (University of Lille), Pierre- Olivier Couraud (Institut Cochin), and Anna Seelig (University of Basel). THURSDAY, OCTOBER 15 Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences). Speakers include Richard Judson (US EPA), Ellen Berg (BioSeek), Jonathan Dordick (Rensselaer Polytechnic Institute), Barry Hardy (Douglas Connect), Sanji Bhal (ACD/ Labs), Christodoulos Floudas (Princeton University), Robert Fraczkiewicz (Simulations Plus), Kyoung Tai No (Yonsei University), and Stephen Bryant (NIH). FRIDAY, OCTOBER 15 Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences). Speakers include Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences), Fangping Mu (Los Alamos National Laboratory), Katya Tsaioun (Apredica), Grace Patlewicz (DuPont), Michael Pelekis (Simulations Plus), and Anil Aswani (University of California at Berkeley). Contact: Program: Dr. Barry Hardy, InnovationWell Community of Practice, Douglas Connect. Tel: +41 61 851 0170. email: innovationwell -[at]- douglasconnect.com Blog: http://barryhardy.blogs.com/ Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. innovationwell - [at]- douglasconnect.com Meeting Support: Rob Reedijk, eCheminfo Community of Practice, Douglas Connect. email: rob.reedijk -[at]- douglasconnect.com From karen.morris from bbsrc.ac.uk Thu Sep 24 08:30:21 2009 From: karen.morris from bbsrc.ac.uk (karen morris (RRes-Roth)) Date: Thu Sep 24 11:40:28 2009 Subject: [Computational-biology] IB2010 - Integrative Bioinformatics Symposium - Cambridge UK March 2010 Message-ID: CALL FOR PAPERS The Integrative Bioinformatics Symposium is being held on 22nd to 24th March 2010 in Cambridge, United Kingdom. web site: http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010 This sixth meeting on Integrative Bioinformatics will be of interest to Bioinformaticians, Computer Scientists and others working in, or interested in finding out more about, the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We are now inviting submission of manuscripts to be considered for presentation at IB2010. The deadline for online submissions is 1st December 2009. Accepted papers will appear in a special issue of the Journal of Integrative Bioinformatics (http://journal.imbio.de) which will be available as the printed conference proceedings. To submit a paper, please visit the symposium web site where further details can be found. Topics of interest include: Data integration and knowledge management Errors and inconsistencies in biological databases Combined dry- and wet-lab studies Prediction and integration of metabolic and regulatory networks Genotype-phenotype linkage Protein-protein interactions Integrative microarray modelling and analyses Integrative approaches for drug design Virtual cell modelling Tool integration and workflow systems Computational systems biology Integrative modelling and simulation frameworks Integrative data and text mining approaches Network analysis Data visualisation and visual analytics Further information can be obtained from Paul Verrier (paul.verrier@bbsrc.ac.uk) or Chris Rawlings (chris.rawlings@bbsrc.ac.uk) From fbtc2010 from disi.unitn.it Thu Sep 24 13:46:55 2009 From: fbtc2010 from disi.unitn.it (FBTC 2010) Date: Thu Sep 24 17:19:05 2009 Subject: [Computational-biology] Cfp FBTC 2010, From Concurrency To Biology and back Message-ID: <200909241846.n8OIks5U027436@disi.unitn.it> _Apologies for multiple posting_ ================================================================ CALL FOR PAPERS FBTC 2010 3rd Int. Workshop "From Biology To Concurrency and back" March 27, 2010, Paphos, Cyprus Satellite event of ETAPS 2010, http://www.etaps10.cs.ucy.ac.cy/ http://www.disi.unitn.it/~fbtc2010/ ================================================================ AIM: As in its previous editions, the workshop aims at gathering researchers with special interest at the convergence of life and computer science, with particular focus on the application of techniques and tools from concurrency. We solicit the submission of unpublished results reporting on both modelling, analysis, and validation of biological behaviours using concurrency-inspired methods and platforms, and on bio-inspired models and tools for describing distributed interactions. Topics of interest include, but are not limited to: applications of techniques from rewriting logics, process calculi, Petri Nets, graph grammars, hybrid systems, and model checking to the representation and testing of scenarios from life sciences. IMPORTANT DATES: Title and abstract submission: Sunday, November 8, 2009 Paper submission: Sunday November 15, 2009 Author notification: Sunday January 17, 2010 Camera-ready papers: Friday February 12, 2010 SUBMISSION: We solicit the submission of unpublished papers reporting on original research on the topics of interest to FBTC. Authors will have to submit their papers via EasyChair (https://www.easychair. org/login.cgi?conf=fbtc2010). Papers should take the form of a pdf file in EPTCS style (http://www.eptcs.org/), and should not exceed 15 pages. If necessary, detailed proofs or other additional material can be added in a clearly-labelled section "Applendix for referees". Referees might review it at their discretion. PUBLICATION: The proceedings will be a volume of the open-access journal EPTCS. A soft-copy of the proceedings will be distributed at the workshop. Full versions of selected papers may later on be invited for an archival journal special issue dedicated to FBTC 2010. PROGRAM COMMITTEE: Marco Antoniotti (University of Milan Bicocca, IT) Chiara Bodei (University of Pisa, IT) Luca Bortolussi (University of Trieste, IT) Luca Cardelli (Microsoft Research Cambridge, UK) Erik de Vink (Technische Universiteit Eindhoven, NL) Fran?ois Fages (INRIA Paris-Rocquencourt, F) Anthony Finkelstein (University College London, UK) Radu Grosu (Stony Brook University, US) Jane Hillston (University of Edinburgh, UK) Anna Ing?lfsd?ttir (Reykjavik University, IS) Emanuela Merelli (University of Camerino, IT) (Co-chair) Paola Quaglia (CoSBi and Trento University, IT) (Co-chair) Carolyn Talcott (SRI International, US) Adelinde Uhrmacher (University of Rostock, DE) Cristian Versari (University of Bologna, IT) INVITED SPEAKER: Alberto Policriti (University of Udine, IT) From conf from topaz.gatech.edu Fri Sep 25 18:21:26 2009 From: conf from topaz.gatech.edu (Georgia Tech Conference Announcement) Date: Fri Sep 25 19:21:10 2009 Subject: [Computational-biology] 7th Georgia Tech - ORNL Conference on Bioinformatics Message-ID: <20090925232126.8FDE37D489D@topaz.gatech.edu> The 7th Georgia Tech - ORNL Conference on Bioinformatics - In silico Biology: Genome Biology and Bioinformatics will be held in Atlanta, Georgia, November 12-14, 2009 http://www2.isye.gatech.edu/binf2009/ Georgia Tech continues the tradition of organizing bi-annual International Conference on Bioinformatics, bringing together leading researchers in genomics, bioinformatics and genome biology to present recent advances in the field and to discuss open problems. Important Dates Deadline for early registration: October 15, 2009 Deadline for poster abstract subsmission: October 1, 2009 Notification of acceptance of abstracts: October 11, 2009 We invite papers submissions in the following areas * genomics * transcriptomics * proteomics * reconstruction and modeling of gene networks * evolutionary biology SPEAKERS Margaret O. Dayhoff lecture: David Lipman , NCBI/NIH, Bethesda, MD, USA Plenary Speakers: Vineet Bafna, University of California at San Diego, USA Gill Bejerano, Stanford University, Stanford, CA, USA Jeffrey Bennetzen, University of Georgia, Athens, GA, USA Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA Nick Grishin, University of Texas, Dallas, TX, USA Curtis Huttenhower, Harvard University, Boston, MA, USA King Jordan, Georgia Tech, Atlanta, GA, USA Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA Eugene Koonin, NCBI/NIH, Bethesda, MD, USA Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA Boris Lenhard, University of Bergen, Norway Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel Joanna Masel, University of Arizona, Tucson, AZ, USA Andrey Mironov, Moscow State University, Russia Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA Natasa Przulj, University of California at Irvine, CA, USA John Reinitz, State Uiversity of New York at Stony Brook, NY, USA Pierre Rouze, Gent University, Gent, Belgium CONFERENCE CHAIRS Mark Borodovsky, Georgia Tech and Emory University Eva K. Lee, Georgia Tech and Emory University PROGRAM COMMITTEE Nicholas Bergman, Georgia Tech Dmitrij Frishman, Technische Universitaet Muenchen, Germany Andrey Gorin, Oak Ridge National Laboratory Andrzej M. Kierzek, University of Surrey, UK. Eileen Kraemer, University of Georgia Jun Liu, Harvard University Hannah Margalit, Hebrew University Andrey Rzhetsky, University of Chicago Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute Gary Stormo, Washington University Lance Waller, Emory University Ying Xu, University of Georgia and Oak Ridge National Laboratory Soojin Yi, Georgia Tech Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee ADMINISTRATION Harry Sharp, Georgia Tech CONFERENCE LOCATION The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus is located in Midtown Atlanta near the center of the 1996 Olympic development, close to the Fox Theatre and Margaret Mitchell house. From pag from intl-pag.org Mon Sep 28 04:21:53 2009 From: pag from intl-pag.org (PAG-XVIII Conference) Date: Mon Sep 28 07:41:34 2009 Subject: [Computational-biology] CALL FOR ABSTRACTS - Plant & Animal Genome XVIII Conference Message-ID: <200909280921.n8S9Lrjw013663@www.intl-pag.org> Dear Colleague: You are invited to attend the Plant & Animal Genome XVIII Conference (PAG-XVIII), January 9-13, 2010 taking place at the Town & Country Convention Center in San Diego, California. To view the pre-registration brochure please download the PDF file: http://www.scherago.com/pag/RegBrochure.pdf The meeting will again offer the satellite sessions and workshops which took place at Plant & Animal Genome XVII. The meeting draft for PAG-XVIII and abstracts from PG-I through PAG-XVII are available on the PAG website listed below. The exhibits and posters will now take place in the Grand Exhibit Hall, adjacent to the California room. We are no longer using the lower level parking facility. We are requesting that all abstracts be submitted electronically. The abstract deadline is MONDAY, November 2, 2009; extended to allow for the new registration process. The abstract submission website is now open. All attendees looking to submit an abstract will be required to pay the registration fee PRIOR to submitting their abstract. You will be assigned an attendee ID# which will be issued once you complete the on-line registration process. You can look up your ID# on the PAG website at: http://intl-pag.org You will be required to provide your attendee ID# to complete the on-line abstract submission process. Due to severe delays in getting VISAs to enter the United States, we recommend that you plan ahead and do NOT wait for your abstract acceptance to begin the process. DO NOT WAIT. All researchers presenting posters must pre-register for the meeting to have their abstract printed in the final meeting program. Tha abstract deadline is MONDAY, November 2, 2009. Registration is available via the Internet using our secure on-line registration form listed below. https://www.pagregistration.com/pag18reg.shtml Full Conference (Univ/Non-Profit/Govt) Registration for ALL attendees: Pre-Registration (deadline November 2, 2009): $550 Late Registration (after November 2, 2009): $650 On-site Registration: $750 Full Conference (Industry) Registration for ALL attendees: Pre-Registration (deadline November 2, 2009): $775 Late Registration (after November 2, 2009): $875 On-site Registration: $975 Weekend Only (Univ/Non-Profit/Govt) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 2, 2009): $400 Late Registration (after November 2, 2009): $450 On-site Registration: $500 Weekend Only (Industry) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 2, 2009): $500 Late Registration (after November 2, 2009): $550 On-site Registration: $600 Student Registration (proof required): Pre-Registration (deadline November 1, 2009): $375 Late Registration (after November 1, 2009): $425 On-site Registration: $475 All questions regarding Plant & Animal Genome XVIII should be directed to Scherago Int'l at Tel: 201-653-4777 ext. 20, Fax: 201-653-5705 or or Email: pag@scherago.com. Sincerely, Darrin Scherago - VP, Meeting Manager Scherago International, Inc. 525 Washington Blvd., Suite 3310, Jersy City, NJ 07310 -------------------------------------------------------------------------- Plant & Animal Genome XVIII Conference ---------------- January 9-13, 2010 -------------------------------------------------------------------------- From kennerqq from gmail.com Mon Sep 28 13:53:14 2009 From: kennerqq from gmail.com (kennerqq) Date: Mon Sep 28 14:28:32 2009 Subject: [Computational-biology] Perl script in miRanda microRNA data output Message-ID: Hi all, I used miRanda software to predict the microRNA target from 3'UTR. It come up with a large file which includes those "hits" and "no hits" lines. Since it is too big to handle, i want to remove the "no hits" lines. I heard that using a simple Perl Script can easily get rid of "no hits" lines in the document. Unfortunately, I do not know how to use it. Does anybody have a clue? Thanks a lot, Ken From chris.morris from stfc.ac.uk Tue Sep 29 05:44:00 2009 From: chris.morris from stfc.ac.uk (Morris, Chris (STFC,DL,CSE)) Date: Tue Sep 29 12:59:06 2009 Subject: [Computational-biology] Perl script in miRanda microRNA data output In-Reply-To: References: Message-ID: <3FACFB8AB0CA1B41A4B83670D0DEC1DE02F4871B@exchange08.fed.cclrc.ac.uk> You don't even need per perl. Just do: grep -v 'no hits' output.txt ____________________________________________ Chris Morris chris.morris@stfc.ac.uk Tel: +44 1925 603689 Fax: +44 1925 603825 Mobile: 07921-717915 http://pims.instruct-fp7.eu/ STFC, Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD > -----Original Message----- > From: comp-bio-bounces@oat.bio.indiana.edu [mailto:comp-bio- > bounces@oat.bio.indiana.edu] On Behalf Of kennerqq > Sent: 28 September 2009 19:53 > To: comp-bio@magpie.bio.indiana.edu > Subject: [Computational-biology] Perl script in miRanda microRNA data output > > Hi all, > > I used miRanda software to predict the microRNA target from 3'UTR. It come > up with a large file which includes those "hits" and "no hits" lines. Since > it is too big to handle, i want to remove the "no hits" lines. I heard that > using a simple Perl Script can easily get rid of "no hits" lines in the > document. Unfortunately, I do not know how to use it. Does anybody have a > clue? > > Thanks a lot, > > Ken > _______________________________________________ > Comp-bio mailing list > Comp-bio@net.bio.net > http://www.bio.net/biomail/listinfo/comp-bio -- Scanned by iCritical. From wiedeman from uci.edu Tue Sep 29 13:06:57 2009 From: wiedeman from uci.edu (Lyle Wiedeman) Date: Tue Sep 29 13:10:50 2009 Subject: [Computational-biology] Perl script in miRanda microRNA data output In-Reply-To: <3FACFB8AB0CA1B41A4B83670D0DEC1DE02F4871B@exchange08.fed.cclrc.ac.uk> References: <3FACFB8AB0CA1B41A4B83670D0DEC1DE02F4871B@exchange08.fed.cclrc.ac.uk> Message-ID: <026401ca412f$a287d640$e79782c0$@edu> It's also easy and sometimes faster to do with sed: sed -e '/no hits/d' output.txt Lyle Wiedeman UC Irvine -----Original Message----- From: comp-bio-bounces@oat.bio.indiana.edu [mailto:comp-bio-bounces@oat.bio.indiana.edu] On Behalf Of Morris, Chris (STFC,DL,CSE) Sent: Tuesday, September 29, 2009 3:44 AM To: kennerqq; comp-bio@magpie.bio.indiana.edu Subject: RE: [Computational-biology] Perl script in miRanda microRNA data output You don't even need per perl. Just do: grep -v 'no hits' output.txt ____________________________________________ Chris Morris chris.morris@stfc.ac.uk Tel: +44 1925 603689 Fax: +44 1925 603825 Mobile: 07921-717915 http://pims.instruct-fp7.eu/ STFC, Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD > -----Original Message----- > From: comp-bio-bounces@oat.bio.indiana.edu [mailto:comp-bio- > bounces@oat.bio.indiana.edu] On Behalf Of kennerqq > Sent: 28 September 2009 19:53 > To: comp-bio@magpie.bio.indiana.edu > Subject: [Computational-biology] Perl script in miRanda microRNA data output > > Hi all, > > I used miRanda software to predict the microRNA target from 3'UTR. It come > up with a large file which includes those "hits" and "no hits" lines. Since > it is too big to handle, i want to remove the "no hits" lines. I heard that > using a simple Perl Script can easily get rid of "no hits" lines in the > document. Unfortunately, I do not know how to use it. Does anybody have a > clue? > > Thanks a lot, > > Ken > _______________________________________________ > Comp-bio mailing list > Comp-bio@net.bio.net > http://www.bio.net/biomail/listinfo/comp-bio -- Scanned by iCritical. _______________________________________________ Comp-bio mailing list Comp-bio@net.bio.net http://www.bio.net/biomail/listinfo/comp-bio From HISHAM from uhcl.edu Wed Sep 30 16:07:48 2009 From: HISHAM from uhcl.edu (Al-Mubaid, Hisham) Date: Wed Sep 30 16:40:07 2009 Subject: [Computational-biology] BICoB-2010 CFP - Submission Deadline: October 23, 2009 Message-ID: <4B57CB6706E6144C9D5D960FEEDA8E8E0285A3FE@EXUHCL1.pclab.uhcl.edu> *** We apologize if you receive multiple copies of this CFP *** BICoB-2010 - Call for Papers http://sce.uhcl.edu/bicob10/ 2nd International Conference on Bioinformatics and Computational Biology (BICoB) March 24 - 26, 2010, Honolulu, Hawaii, USA Full paper Submission Deadline: ........................................October 23, 2009 Notification of Acceptance: ............................................... December 11, 2009 Pre-registration and Camera-ready paper due:................ January 8, 2010 Computational techniques have already enabled unprecedented advances in modern biology and medicine. This continues to be a vibrant research area with broadening of computational techniques and new emerging challenges. The Bioinformatics and Computational Biology (BICoB) conference was established by the ISCA to promote the advancement of computing techniques and their application to life sciences. T he BICoB conference will feature original unpublished research in all areas of bio-informatics and computational biology, and covering the entire spectrum of underlying computational techniques/models/paradigms. The topics of interest include (and are not limited to): * Genome analysis: Genome assembly, genome and chromosome annotation, gene finding, alternative splicing, EST analysis and comparative genomics. * Sequence analysis: Multiple sequence alignment, sequence search and clustering, function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences. * Phylogenetics: Phylogeny estimation, models of evolution, comparative biological methods, population genetics. * Structural Bioinformatics: Structure matching, prediction, analysis and comparison; methods and tools for docking; protein design * Analysis of high-throughput biological data: Microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS, proteomics, mass spectrometry. * Genetics and population analysis: Linkage analysis, association analysis, population simulation, haplotyping, marker discovery, genotype calling. * Systems biology: Systems approaches to molecular biology, multiscale modeling, pathways,gene networks. SUBMISSION PROCEDURES BICoB welcomes submissions in all areas of computing with impact on life sciences including (but not limited to) algorithms, databases, languages, systems, and high performance computing. For example: - Parallel and high-performance techniques - Unifying computational techniques - Data and image mining techniques - Approximation and randomized algorithms and systems - Computational biology on emerging architectures and hardware accelerators Papers will be accepted only by electronic submission (PDF only). A full paper, including title, author's name(s) and affiliation, mailing address, telephone, fax and email of the principal author, should be submitted by October 23, 2009 at the following web site: https://cmt.research.microsoft.com/BICOB2010/ The submitted manuscript should closely reflect the final paper as it will appear in the Proceedings which will be a maximum of 6 pages (+2 pages with additional page charge). ISCA double-column format will be used. See:See http://www.isca-hq.org/sample-isca-manuscript-format.pdf . If you encounter any difficulties during submission or if you require further information, please contact: isca@ipass.net. Authors wishing to have their papers reviewed for possible publication in the ISCA Journal of Computers and Applications should send by postal mail or email expanded versions of their papers directly to the Editor, Prof. David Jeff Jackson. (See Instructions to Authors at: http://www.isca-hq.org/j-authr.htm ) ................................................... IMPORTANT DATES Full paper Submission Deadline: ..........................................October 23, 2009 Notification of Acceptance: ............................................... December 11, 2009 Pre-registration and Camera-ready paper due:..................... January 8, 2010 CONFERENCE CHAIR George Karypis University of Minnesota karypis@cs.umn.edu PROGRAM CO-CHAIRS Hisham Al-Mubaid University of Houston-Clear Lake hisham@uhcl.edu If you would like to be removed from our distribution list, please reply to this email with the word 'REMOVE' in the Subject line. Mary Ann Sullivan Executive Director, ISCA International Society for Computers and Their Applications 975 Walnut Street, Suite 132 Cary, NC 27511 USA Phone: 919-467-5559 FAX: 919-467-3430 E-mail: isca@ipass.net