From Rob.Reedijk from douglasconnect.com Wed Sep 3 08:47:49 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Sep 3 09:03:23 2008 Subject: [Computational-biology] CFP - InnovationWell Autumn Community of Practice Meeting Message-ID: I am posting details for the InnovationWell Autumn Community of Practice Meeting in October 2008 in Bryn Mawr, Philadelphia. Please note that abstracts are still being accepted for posters. Innovation in Life Science & Healthcare Research and Product Development InnovationWell Autumn Community of Practice Meeting October 14-17, 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: http://innovationwell.net/comty_conferences The InnovationWell program will be covering topics in systems biology, computational biology, knowledge management, translational medicine, metabolomics, and predictive toxicology. The eCheminfo program will be covering topics in drug discovery informatics. Abstracts (300-500 words) should be submitted to innovationwell -[at]- douglasconnect.com or echeminfo -[at]- douglasconnect.com as soon as possible, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place. Speakers Keith Elliston (Genstruct), Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.), Stephen W. Edwards (U.S. Environmental Protection Agency), Paul McDonagh (Gene Network Sciences), Christopher M.L.S. Bouton (Pfizer), James R. Brown (GlaxoSmithKline), John Wilbanks (Creative Commons), Barry Bunin (Collaborative Drug Discovery), Michael Liebman (Windber Research Institute), Jerry Wright (Johns Hopkins Medical Institutions), Anastasia Christianson (AstraZeneca), James Golden (Science Applications International Corporation), John Speakman (National Cancer Institute), William Hayes (Biogen Idec), Andrew McMurray (Harvard University), Eugene Clark (Partners Healthcare), Alvin Berger (Metabolon), John Newman (USDA), Bruce Kristal (Brigham and Women’s Hospital), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Alex Tropsha (UNC), Barry Hardy (Douglas Connect), Weida Tong (FDA) Pre-Conference Workshop, October 13. Knowledge Management in R&D chaired by John Conway (Accelrys) and Frank Hollinger (FRESH Directions Consulting) We gratefully acknowledge the sponsorship support of the Chemical Computing Group, Merck Research Laboratories, SimBioSys, Tibotec, Tripos and MEDIT. More information at: InnovationWell Program http://innovationwell.net/COMTY_conferences http://innovationwell-bm810.eventsbot.com/ eCheminfo Program http://echeminfo.com/COMTY_conferences http://echeminfoBM810.eventsbot.com Rob Reedijk InnovationWell Community of Practice From rapacki from cbs.dtu.dk Wed Sep 3 09:27:30 2008 From: rapacki from cbs.dtu.dk (Kristoffer Rapacki) Date: Wed Sep 3 14:53:39 2008 Subject: [Computational-biology] Workshop Oct '08 on R and BioConductor for Genomic Data Analysis Message-ID: CBS/BioSys Workshop on R and BioConductor for Genomic Data Analysis October 7-10, 2008 (optional introduction to R October 6-7) Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark The focus will be the use of BioConductor for working with microarrays - - Gene Expression as well as Genomic Variation. Examples during the workshop will include SNP and CNV microarray chips. Data visualisation in R will also be covered in the workshop. Course language is English. The workshop assumes some programming experience, and basic familiarity with microarrays, statistics and their biological contexts. An optional introduction to R precedes the course and is open to all workshop participants. More information, including application form: http://www.biosys.dk/index.php?option=com_content&task=view&id=94&Itemid= Deadline for applying: Sep 12, 2008. The applicants will be notified by email of the status of their applications not later than Monday, September 22, 2008. Yours sincerely Kristoffer Rapacki ------------------------------------------------------------------------ Kristoffer Rapacki Center for Biological Sequence Analysis phone: +45 4525 2483 Department of Systems Biology fax: +45 4593 1585 Technical University of Denmark Building 208 e-mail: rapacki@cbs.dtu.dk DK-2800 Lyngby Denmark ------------------------------------------------------------------------ From lvannesc from disco.unimib.it Wed Sep 3 10:29:17 2008 From: lvannesc from disco.unimib.it (Vanneschi Leonardo) Date: Wed Sep 3 14:53:44 2008 Subject: [Computational-biology] CFP: European Conference on Genetic Programming (EuroGP 2009) Message-ID: <301E01E95DB8684CAFA9EC28E1032FF215E8A8@disco-exchange.disco.local> * Our apologies if you receive multiple copies of this announcement * -------------------------------------------------------------------------- C A L L F O R P A P E R S EuroGP 2009 12th European Conference on Genetic Programming T?bingen, Germany, April 15-17 2009 -------------------------------------------------------------------------- EuroGP 2009 will take place in conjunction with EvoCOP 2009 (9th European Conference on Evolutionary Computation in Combinatorial Optimization), EvoBIO 2009 (7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics), and EvoWorkshops 2009 (the specialist workshops on a range of evolutionary computation topics and applications) in a joint event collectively entitled EVO* 2009. High quality papers are sought on topics strongly related to the evolution of computer programs, ranging from theoretical work to innovative applications. A double-blind review process will be adopted. EuroGP 2009 will feature a mixture of oral presentations and poster sessions. Important dates are: Submission deadline: November 5, 2008 Conference: April 15-17, 2009 All information about EuroGP 2009 and all the other events of EVO* 2009 can be found at the page: http://www.evostar.org EuroGP topics include but are not limited to: * Theoretical developments * Empirical studies of GP performance and behavior * Algorithms, representations and operators * Applications of GP to real-life problems * Hybrid architectures including GP components * Unconventional evolvable computation * Evolutionary design * Evolutionary robotics * Grammar-based GP * Evolvable hardware * Linear GP * Self-reproducing programs * Evolution of tree or graph structures * Evolution of various classes of automata or machines (e.g. cellular automata, finite state machines, pushdown automata, Turing machines) * Object-oriented genetic programming EuroGP 2009 Program Chairs Leonardo Vanneschi, University of Milano-Bicocca, Italy Vanneschi (at) disco (dot) unimib (dot) it Steven Gustafson, GE Global Research, NY, USA Steven (dot) gustafson (at) research (dot) ge (dot) com From Rob.Reedijk from douglasconnect.com Wed Sep 3 18:24:06 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Thu Sep 4 10:42:11 2008 Subject: [Computational-biology] eCheminfo Community of Practice InterAction Meeting, October 14-17, Philladelphia - Latest Advances in Drug Discovery Informatics Message-ID: <6607ac21-ea45-4d43-a86e-8387489eee29@b38g2000prf.googlegroups.com> I am posting details for the eCheminfo Community of Practice InterAction Meeting in October 2008 in Bryn Mawr, Philadelphia. Please note that abstracts are still being accepted for posters. Latest Advances in Drug Discovery Informatics eCheminfo Autumn Community of Practice InterAction Meeting October 14-17, 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: http://echeminfo.com/comty_conferences Themes: Cheminformatics, Bioinformatics, Medicinal Chemistry, Drug Discovery Innovation, Structure-based Drug Design, Screening, Docking, Structural Biology, Predictive Toxicology, Predictive ADME, Chemogenomics Program Summary Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline) Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College) Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group) In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT) PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health) Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery) Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia) Pre-Conference Workshop, 13 October Best Practices Virtual Screening Workshop chaired by Barry Hardy (Douglas Connect) Speakers John Irwin (UCSF), Georgia McGaughey (Merck), Johannes H. Voigt (Schering Plough), Lance Westerhoff (Quantum Bio), Zsolt Zsoldos (SimBioSys), Alexey Ornufriev (Virginia Tech), David Case (Rutgers University), Rommie Amaro (USCD), Peter Coveney (Univ. College London), Anna Kohlmann (Ariad Pharmaceuticals), Scott Brown (Abbott), Emil Alexov (Clemson University), Jens Erik Nielsen (University College Dublin, Ireland), Darren Flower (Jenner Institute, UK), Maja Mihajlovic (City College of New York), Michael Keiser (UCSF), Brian Marsden (University of Oxford, UK), Alex Tropsha (UNC), John Westbrook (Rutgers), Howard J Feldman (CCG), Igor V. Filippov (NCI), Raul Cachau (ATP, SAIC- Frederick), Vincent T. Moy (University of Miami), Paul Hawkins (OpenEye), Yulia Borodina (NCBI), Gerhard Wolber (Inte:Ligand, Austria), Marc Nicklaus (NCI), James P. Snyder (Emory), Anne Chaka (NIST), Esther Kellenberger (Univ. Strasbourg, France), Renxiao Wang (SIOC, Shanghai, PR China), Jim Dunbar (University of Michigan), Janna Wehrle (NIGMS), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI) CFP **Abstracts are still being considered for posters** Poster Session All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy - [at]- douglasconnect.com Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted as soon as possible. Contact: Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo - [at]- douglasconnect.com More information at: InnovationWell Program http://innovationwell.net/COMTY_conferences http://innovationwell-bm810.eventsbot.com/ eCheminfo Program http://echeminfo.com/COMTY_conferences http://echeminfoBM810.eventsbot.com Rob Reedijk eCheminfo Community of Practice From pag from intl-pag.org Thu Sep 4 20:42:56 2008 From: pag from intl-pag.org (PAG-XVII Conference) Date: Fri Sep 5 10:31:51 2008 Subject: [Computational-biology] CALL FOR ABSTRACTS - Plant & Animal Genome XVII Conference Message-ID: <200809050142.m851gur4006833@www.intl-pag.org> Dear Colleague: You are invited to attend the Plant & Animal Genome XVII Conference (PAG-XVII), January 10-14, 2009 taking place at the Town & Country Convention Center in San Diego, California. This is a call for abstracts and pre-registration. Everyone who submits an abstract is required to pay the registration fee prior to the meeting to be included in the Final Abstract Guide and posted on the website. You must be registered by December 1, or your abstract will NOT be printed or posted on the website. Please update us if you cannot attend so we may free up poster space in the Grand Exhibit Hall where exhibits and coffee breaks are just steps from the Atlas Foyer. Don't forget to check out the Travel Grant Applications; the deadlines are closing soon. The meeting will again offer the satellite sessions and workshops as presented in earlier conferences. A couple of new workshops this time are "Genomics of Plant Disease Resistance" and "Recombination". There will be over 100 technical, industry, and computer training workshops. The meeting draft for PAG-XVII and abstracts from PG-I through PAG-XVI are available on the PAG website at: http://intl-pag.org/ We are requesting that all abstracts be submitted electronically. Point your browser to the address below and click on the "Abstracts Submission" link when ready to submit your abstract at: http://intl-pag.org/ Due to severe delays in getting VISAs to enter the US, we recommend that you plan ahead and begin the process now. DO NOT WAIT! See the information link at the web site as updates are provided. All researchers presenting posters must pre-register for the meeting to have their abstract printed in the final meeting program. The abstract DEADLINE is Friday, October 3, 2008. Registration is available via the internet using our secure on-line registration form. Full Conference (Univ/Non-Profit/Govt) Registration for ALL attendees: Pre-Registration (deadline November 1, 2008): $550 Late Registration (after November 1, 2008): $650 On-site Registration: $750 Full Conference (Industry) Registration for ALL attendees: Pre-Registration (deadline November 1, 2008): $750 Late Registration (after November 1, 2008): $850 On-site Registration: $950 Weekend Only (Univ/Non-Profit/Govt) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 1, 2008): $375 Late Registration (after November 1, 2008): $425 On-site Registration: $475 Weekend Only (Industry) Registration (Fri/Sat/Sun) for ALL attendees: Pre-Registration (deadline November 1, 2008): $475 Late Registration (after November 1, 2008): $525 On-site Registration: $575 Student Registration (proof required): Pre-Registration (deadline November 1, 2008): $350 Late Registration (after November 1, 2008): $400 All questions regarding Plant & Animal Genome XVII should be directed to Scherago Int'l at Tel: 201-653-4777 ext. 20, Fax: 201-653-5705 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 XVII Conference ---------------- January 10-14, 2009 -------------------------------------------------------------------------- From dannynorrey from hotmail.com Mon Sep 8 05:29:41 2008 From: dannynorrey from hotmail.com (Danny Norrey) Date: Mon Sep 8 10:29:36 2008 Subject: [Computational-biology] Comparing densities Message-ID: Dear list / comp-bio@net.bio.net I am currently undertaking a project on small Madeiran passerines using distance sampling. I was wondering whether anyone can help me, I have chosen models based on AIC; Goodness of fit, etc, however, each species is more suited to a different model. Is it therefore possible to compare densities between species? (Using different models), as the difference may be a function of the choice of model not a difference in population size. Thanks in advance and sorry if this has appeared in a previous thread John Norrey _________________________________________________________________ Make a mini you and download it into Windows Live Messenger http://clk.atdmt.com/UKM/go/111354029/direct/01/ From frederic.fleche from gmail.com Wed Sep 10 03:37:18 2008 From: frederic.fleche from gmail.com (Fred) Date: Wed Sep 10 08:38:55 2008 Subject: [Computational-biology] Bioinformatics Jobs Listing Message-ID: Dear all, Just to let you know that a Bioinformatics jobs listing is availableat the following url :http://www.bioinformatics.fr/jobs.php A google map, a RSS feed and an email alert service are associated to this listing. Kind Regards, Fred From paolo.romano from istge.it Mon Sep 15 08:44:03 2008 From: paolo.romano from istge.it (Paolo Romano) Date: Mon Sep 15 11:38:40 2008 Subject: [Computational-biology] CFP: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) Message-ID: <200809151359.m8FDxQjH024542@ibm43p.biotech.ist.unige.it> International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 28th November 2008, Edinburgh, UK http://www.swat4ls.org/ CALL FOR PAPERS Overview -------- The workshop is organized in sessions and open discussions. Invited speakers will present state-of-the-art, provocative lectures on the workshop's main topic, while a number of submissions will be accepted as oral presentations and posters on all workshop's topics. Workshop Description -------------------- Semantic Web technologies, tools and applications are starting to emerge in Life Sciences. In recent years, systems have been introduced and an increasing interest among researchers is arising. 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. Keynote Speakers ------------------------ + Semantic web technology in translational cancer research, Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA + Using Ontologies to bring Web Services on to the Semantic Web Mark Wilkinson, Dept. of Medical Genetics, University of British Columbia, Canada Workshop Venue and Format ------------------------ The workshop will take place in Edinburgh, Scotland, on 28 November 2008, and is hosted by the e-Science Institute of the UK's National e-Science Centre (NeSC). SWAT4LS will be a one-day workshop and will consist of two invited talks, regular paper and poster presentations. The workshop will conclude with a panel discussion on the strength and weaknesses of the Semantic Web for the Life Sciences. Deadlines --------- * Submission deadline (both papers and posters): 30 September 2008 * Notification of acceptance: 20 October 2008 * Camera-ready submission: 3 November 2008 (Authors who are interested in submitting a paper/poster to the workshop, but may require a short extension to the deadline, should get in touch with the organisers.) Topics of Interest ------------------ Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards (RDF, OWL, ...) o RDF/OWL, SKOS, .... and their applicability to bioinformatics o RDF Schemas and Query systems o Biomedical Ontologies and related tools o Formal approaches to large biomedical controlled terminologies and vocabularies * Systems for a Semantic Web for Bioinformatics o Bio-ontologies, RDF stores, Semantic Web Services o RDF repositories and query systems for life sciences o Semantically aware biomedical Web Services o Semantic Biological Data Integration Systems * Existing and perspective applications of the Semantic Web for Bioinformatics o Semantic browsers, Semantic collaborative research o Case studies, use cases, and scenarios o Semantic Web applications in life sciences Type of contributions ---------------------- The following possible original contributions are sought: * Oral communications (regular papers) * Posters * Software demos All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Furthermore, a selection of papers will be published in a special issue of the BMC Bioinformatics journal devoted to the SWAT4LS workshop. 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. Workshop Chairs ---------------- + Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, United Kingdom + Adrian Paschke, Biotechnology Centre, TU Dresden, Dresden, Germany + Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy + Andrea Splendiani, Medical Informatics Department, University of Rennes 1, Rennes, France ===================================================================== In Co-operation with: - National Cancer Research Institute, Genova, Italy - Biotechnology Centre, TU Dresden, Dresden, Germany - School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, United Kingdom - Universit? de Rennes 1, Rennes, France - e-Science Institute, Edinburgh, Scotland, United Kingdom - SeaLife Project, European Commission Information Society and Media - Laboratory for Interdisciplinary Technologies in Bioinformatics (LITBIO), Italy ===================================================================== For any information, refer to info@swat4ls.org . Paolo Romano (paolo.romano@istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From finocchi from di.uniroma1.it Wed Sep 17 02:38:25 2008 From: finocchi from di.uniroma1.it (Irene Finocchi) Date: Wed Sep 17 12:32:40 2008 Subject: [Computational-biology] ALENEX'09: last call for papers Message-ID: <5e953910809170038u4902e205i4519df1c12446c75@mail.gmail.com> ************************************************************************ 11th Workshop on Algorithm Engineering and Experiments ALENEX 2009 - CALL FOR PAPERS January 3, 2009 New York City, New York http://www.siam.org/meetings/alenex09/ ************************************************************************ SCOPE The aim of the ALENEX workshop is to provide a forum for presentation of original research in the implementation and experimental evaluation of algorithms and data structures. We invite submissions that present significant case studies in experimental analysis (such studies may tighten, extend, or otherwise improve current theoretical results) or in the implementation, testing, and evaluation of algorithms for realistic environments and scenarios, including specific applied areas (databases, networks, operations research, computational biology and physics, computational geometry, and the world wide web) that present unique challenges in their underlying algorithmic problems. We also invite submissions that address methodological issues and standards in the context of empirical research on algorithms and data structures. The scientific program will include time for discussion and debate of topics in this rapidly evolving research area. The workshop is supported by SIAM (Society for Industrial and Applied Mathematics) and by SIGACT (ACM Special Interest Group on Algorithms and Computation Theory). It precedes the ACM-SIAM Symposium on Discrete Algorithms (SODA09), being held on January 4-6, 2009, and takes place on the same day as the Workshop on Analytic Algorithmics and Combinatorics (ANALCO09). Since researchers in both fields are approaching the problem of learning detailed information about the performance of particular algorithms, we expect that interesting synergies will develop. IMPORTANT DATES Deadline for submission: October 1, 2008 Notification to authors: mid-November, 2008 Final version: mid-December, 2008 Workshop: January 3, 2009 SUBMISSIONS Authors are invited to submit an extended abstract electronically by October 1, 2008 (11:59 EDT PM, strict deadline). The electronic submission server is at: http://www.easychair.org/conferences/?conf=alenex09 The abstract must consist of at most 10 pages. Results omitted due to space constraints can be put into a clearly marked appendix, which will be read at the discretion of the program committee. Simultaneous submission to other conferences with published proceedings is not allowed. The proceedings of ALENEX will be published openly and electronically by SIAM. A special issue of the ACM Journal of Experimental Algorithmics (JEA) will be dedicated to selected papers from ALENEX09. Authors of accepted papers are also strongly encouraged to submit publicly available code and data to JEA Research Code Repository (http://www.jea.acm.org/repository/). PROGRAM COMMITTEE Susanne Albers, Universitat Freiburg, Germany Mark de Berg, Technische Universiteit Eindhoven, the Netherlands Kenneth Clarkson, IBM Research Mike Fellows, University of Newcastle, Australia Irene Finocchi (co-chair), Sapienza University of Rome, Italy Efi Fogel, Tel Aviv University, Israel Stefan Funke, Universitat Greifswald, Germany John Hershberger (co-chair), Mentor Graphics Corporation, Calibre Division Jyrki Katajainen, University of Copenhagen, Denmark Piyush Kumar, Florida State University Rina Panigrahy, Microsoft Research CONTACT ADDRESSES For further information please visit http://www.siam.org/meetings/alenex09/ From chinmaydwibedi from gmail.com Wed Sep 17 23:19:59 2008 From: chinmaydwibedi from gmail.com (chinmay) Date: Thu Sep 18 11:57:02 2008 Subject: [Computational-biology] RSG-India at HGM - Notice Message-ID: <3a79d013-b98f-4b4a-a7f0-d71c53213071@i20g2000prf.googlegroups.com> RSG-India at HGM 2008! We are very happy to inform you all that RSG-India has been given an opportunity to have a booth at the Human Genome Meeting 2008 to be held at Hyderabad from 27th-31st September 2008! Regional Student Group – India (RSG-India) is a student organization dedicated to the development of the Bioinformatics and Computational Biology student community in India. RSG-India is part of an initiative by the Student Council of the International Society of Computational Biology [ISCB-SC] to improve Computational Life sciences’ research and learning around the world at a closer and more involved level. HGM is the annual conference organized by the Human Genome Organization HUGO, designed to update and increase knowledge in the field of Human Genome research. HGM is one of the ‘must-attend’ conferences in the international conference calendar. We at RSG-India are very excited about this opportunity. As far as we know, this is the first time a student organization has been allowed its own booth at an international Conference of this stature. If you are a student interested in Computational Biology or Bioinformatics, and will be attending HGM 2008, we would really like to meet you and discuss any ideas that you might have regarding the future development of Bioinformatics and Computational Biology in India. Please do drop in at the RSG-India booth at HGM 2008. For further details about RSG-India please visit our website www.iscbsc.org/rsg/rsg-india or the RSG-India message board http://groups.google.co.in/group/rsg-india. If you have any questions regarding this, or would like to contact us, please do drop in an e- mail at rsg-india@iscbsc.org. Best regards, Team RSG-India From lbcao from it.uts.edu.au Thu Sep 18 02:59:00 2008 From: lbcao from it.uts.edu.au (Longbing Cao) Date: Thu Sep 18 11:57:11 2008 Subject: [Computational-biology] Regarding the Special Issue on Agents and Data Mining on IEEE Intelligent Systems Message-ID: <48D20A44.2010303@it.uts.edu.au> Dear colleagues and authors, [Apologize if this is not related to you.] With regard to the Special Issue on Agents and Data Mining on IEEE Intelligent Systems, www.computer.org/portal/pages/intelligent/content/AgentsDMCFP.html I recently received plenty of requests from Asia, Europe and America asking for extension of the deadline. In addition, I was informed that some of submissions have been sent back by IEEE IS for modification due to inconsistency with the submission guidelines, and there are plenty of submissions still under checking by IEEE IS and haven't gone into the special issue paper management system. To solve the above two issues, I have asked special approval from the IEEE IS to extend the due date to 24 September for both incoming submissions and those requested to be modified. If you have been asked by IEEE IS to change your submission to fit in the guideline, you may find the above due date in the email you received. For those who requested the extension and will submit the paper before the new deadline, please make sure your submission is aligned with IEEE IS submission guideline. Please note the above date is the hard cutting point. Regards, Longbing From evostar from na.icar.cnr.it Thu Sep 18 09:03:39 2008 From: evostar from na.icar.cnr.it (Evostar 2009) Date: Thu Sep 18 11:57:25 2008 Subject: [Computational-biology] Evostar 2009 - third Call for Papers Message-ID: <48D25FBB.9050700@na.icar.cnr.it> * Our apologies if you receive multiple copies of this announcement * --------------------------------------------------------------- THIRD CALL FOR PAPERS --------------------------------------------------------------- EVO* 2009 including EuroGP, EvoCOP, EvoBIO and EvoWorkshops 15-17 April, 2009 Eberhard Karls University Tübingen, Germany http://www.evostar.org --------------------------------------------------------------- The EuroGP, EvoCOP and EvoBIO conferences and the workshops collectively entitled EvoWorkshops compose EVO*: Europe's premier co-located events in the field of Evolutionary Computing. Featuring the latest in theoretical and applied research, EVO* topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimization, evolutionary algorithms, machine learning and data mining techniques in the biosciences, in numerical optimization, in music and art domains, in image analysis and signal processing, in hardware optimization and in a wide range of applications to scientific, industrial, financial and other real-world problems. EuroGP: Twelfth European Conference on Genetic Programming: high quality papers are sought on topics strongly related to the evolution of computer programs, ranging from theoretical work to innovative applications. EvoCOP: Ninth European Conference on Evolutionary Computation in Combinatorial Optimization: practical and theoretical contributions are invited, related to evolutionary computation techniques and other meta-heuristics for solving combinatorial optimization problems. EvoBIO: Seventh European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: the emphasis is on evolutionary computation and other advanced techniques addressing important problems in molecular biology, proteomics, genomics and genetics, that have been implemented and tested in simulations and on real-life datasets. EvoWorkshops: The twelve workshops which make up this event are focused on the use of Evolutionary Computation in different application areas: EvoCOMNET: Telecommunication networks and other parallel and distributed systems EvoENVIRONMENT: Environmental issues EvoFIN: Finance and economics EvoGAMES: Games EvoHOT: Design automation EvoIASP: Image analysis and signal processing EvoINTERACTION: Interactive evolution and humanized computational intelligence EvoMUSART: Music, sound, art and design EvoNUM: Continuous parameter optimization EvoPHD: Graduate student workshop on evolutionary computation EvoSTOC: Stochastic and dynamic environments (EvoSTOC has organized the “yellow submarine challenge” competition for dynamic optimization, further information can be found in the workshop page) EvoTRANSLOG: Transportation and logistics In 2009, the event will take place in Tübingen, a traditional university town in Baden-Württemberg, Germany, situated on a ridge between the Neckar and Ammer rivers in the southwest of the country, about 30 kms southwest of Stuttgart. EVO* 2009 will be hosted at Eberhard Karls University in Tübingen, founded in 1477 and one of the oldest universities in Germany. Important Dates for all events are: *** Submission deadline: 5 November 2008 *** Notification to authors: 9 January 2009 Camera-ready deadline: 21 January 2009 Conference: 15-17 April 2009 Evo* 2009 proceedings will be published by Springer Verlag in the Lecture Notes in Computer Science series. The website http://www.evostar.org offers information relevant to all events, including calls for papers, deadlines, organizing committees, submission requirements, local information and a thorough view on the previous editions. From stoermer from disi.unitn.it Tue Sep 23 03:07:38 2008 From: stoermer from disi.unitn.it (Heiko Stoermer) Date: Tue Sep 23 10:57:11 2008 Subject: [Computational-biology] Second Call For Papers - Semantic Web Applications and Perspectives (SWAP 2008) Message-ID: Second Call For Papers - http://swapconf.it/2008/callforpapers.php 5th Workshop on Semantic Web Applications and Perspectives (SWAP 2008) FAO-UN, Roma, Italy 15-17 December 2008 http://swapconf.it/2008/ SWAP 2008 aims at giving an overview of work performed by the Semantic Web community, and aims to attract researchers, developers and interested practitioners alike. The setting for the workshop is highly interactive, and presentations are expected to focus on practical aspects and open problems. The workshop will cover either theoretical or implementation issues that anyway relate to Semantic Web applications. The following is a partial list of topics of interests: # Applications of Semantic Web technologies # Data Semantics and Linked Data # Semantic Social Networks # Semantic Portals # Semantic Web for e-business, e-science, e-government, and e-learning # Languages, tools and methodologies for representing and managing Semantic Web data # Robust and scalable knowledge management and reasoning on the Web # Ontology Design, Extraction, and Evolution # Ontology Mapping, Merging, and Alignment # Semantic Web technology for collaboration and cooperation # Semantic Multimedia # Semantics in P2P systems and grids # Searching, Querying, Visualizing and Interpreting the Semantic Web # Evaluation of Semantic Web techniques # Languages, Tools and Methodologies for Semantic Web Data # Large Scale Knowledge Management # Semantic Brokering # Semantic Coordination, Integration, Matching and Interoperability # Semantic Web Mining # Semantic Information Retrieval # Visualization and Modeling # Semantic Web Personalization # Semantic Web middleware # Machine learning and human language technologies for the Semantic Web # Semantic Web services # Tools and Methodologies for Semantic Web Agents # Semantic Web Trust, Privacy, Security and Intellectual Property Rights # Systems of annotation extraction # Social aspects of distributed cooperative annotation # Presentation and discussions of application scenarios # Analysis of social online communities # Web 2.0 personalization # Web 2.0 technologies for recommender systems # Web 2.0-based ontology learning # Assistive technologies and the Semantic Web Important Dates: October 17th - Paper Submission November 14th - Notifications November 21st - Camera Ready December 15th - Tutorial Day December 16-17 - SWAP 2008 Please, find the detailed call for papers and submission requirements at http://swapconf.it/2008/callforpapers.php. Jointly organized by: * Istituto di Scienze e Tecnologie della Cognizione (Consiglio Nazionale delle Ricerche), Roma - http://www.istc.cnr.it * Food and Agricultural Organization of the United Nations, Roma - http://www.fao.org In collaboration with: * W3C (World Wide Web Consortium) Office in Italy, * Semedia Group (DEIT, Universita' Politecnica delle Marche), * University of Trento. General Chairs Aldo Gangemi (ISTC-CNR) Johannes Keizer (FAO-UN) Program Chairs Valentina Presutti (ISTC-CNR) Heiko Stoermer (Universit? di Trento) -- Heiko Stoermer University of Trento, Italy Dept. of Information Science and Engineering (DISI) http://disi.unitn.it/~stoermer OKKAM id: http://www.okkam.org/entity/ok5f23a5ce-a683-4c4d-ae73-b78cdc17aec1 From gbonte from ulb.ac.be Tue Sep 23 10:01:35 2008 From: gbonte from ulb.ac.be (gbonte) Date: Tue Sep 23 11:32:56 2008 Subject: [Computational-biology] PhD research position in Bioinformatics & Machine Learning in ULB-MLG, Brussels, Belgium In-Reply-To: References: <9aebbd80-3d9c-4cd3-8351-bf9c958ab80e@f36g2000hsa.googlegroups.com> <8623a936-eaad-4735-9187-41bf92832bde@i24g2000prf.googlegroups.com> Message-ID: ***PhD research position in Bioinformatics*** Functional Genomics Unit, IJB & Machine Learning Group, ULB Brussels, Belgium *Position description Applications are invited for a full-time PhD research position at the Functional Genomics Unit (FGU), Medicine Department, Institut jules Bordet (IJB), Belgium. The researcher will get his/her PhD in the Machine Learning Group (MLG), Computer Science Department, Universit? Libre de Bruxelles (ULB), Belgium. The vacancy available to be filled in soon offers tenure of four years. The researcher is expected to carry out fundamental research in Machine Learning (MLG) and to take an active role in the applied research projects of the FGU, which is funding the position. The Functional Genomics Unit is a research group that carries out applied research on genomics in breast cancer. Cutting-edge bio- technologies are used to bring new insights in breast cancer biology. These new discoveries are then brought to clinic (translational research) in order to improve the management of breast cancer patients. The Machine Learning Group is a research group that carries out theoretical research on statistical machine learning, predictive modeling and computational statistics, and takes part in several applied research projects in domains as diverse as data mining, bioinformatics to biomedical engineering and wireless sensor networks. This inter-disciplinary position provides unique opportunities in bioinformatics. Previous studies involving microarray and survival data in breast cancer led to high impact publications (see http://www.ulb.ac.be/di/map/bhaibeka/research.html for an overview). The machine learning methods introduced in these articles deal specifically with the high dimensionality of the microarray data and the fitting/validation of models for survival prediction of the patients. *Qualifications Candidates are expected to attach their transcripts and a letter of recommendation from their MSc supervisor or any other relevant person. Applicants are expected to have strong programming skills, the ability to work independently, strong interpersonal skills, good writing and oral communication. Any research experience on data mining, machine learning, and statistical analysis will be an asset as well as an experience in microarray data analysis. Upon offer of a position, the candidates who are non-EU citizens are required to obtain an appropriate long-term Schengen visa; further information is available from their nearest Belgian embassy. *Deadline Applicants are encouraged to apply as soon as possible as positions will remain open until filled in by a suitable candidate. *Contact Candidates are invited to send their CV with the detailed list of publications and a research statement in .pdf format by email to gbonte@ulb.ac.be . The subject field of your email must include MLG-JOB: research position. *Equal Opportunity Employer ULB is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. ULB wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply. -- Gianluca Bontempi Machine Learning Group Computer Science Department - D?partement d'Informatique Universit? Libre de Bruxelles Boulevard du Triomphe - CP212 1050 Bruxelles, Belgium email: gbonte@ulb.ac.be Office Phone: +32-2-650 55 91 Fax: +32 2 650.56.09 web: http://www.ulb.ac.be/di/mlg From oksayakh from cs.iastate.edu Tue Sep 23 16:12:40 2008 From: oksayakh from cs.iastate.edu (Oksana Yakhnenko) Date: Tue Sep 23 17:26:19 2008 Subject: [Computational-biology] Call for papers: NIPS 2008 Workshop on Cost-Sensitive Learning Message-ID: <06E269EAE81E42D6A49C17116270DEE3@OksanaPC> Dear Moderator, can you please forward the following CFP to the Computational Biology mailing list? Thank you. ==Call for Papers: NIPS 2008 Workshop on Cost-Sensitive Learning== http://www.cs.iastate.edu/~oksayakh/cslworkshop_nips2008.html Description and background ------------------------ The goal of cost-sensitive learning is to minimize data acquisition costs while maximizing the accuracy of the learner/predictor. Many fields in machine learning attempt to solve cost-sensitive learning with strong simplifying assumptions. For example, in semi-supervised learning, class-labels are assumed to be expensive and features are implicitly assumed to have zero cost. In active learning, labels are again assumed to be expensive; however the learner may ask an oracle to reveal a label for unlabeled data for selected examples. Active feature acquisition assumes that obtaining features is expensive (but typically all features are assumed to be equally expensive), and the learner identifies instances for which complete information is most informative to classify a particular test sample. Inductive transfer learning and domain adaptation methods assume that training data for a particular task is expensive or but other data from other domains may be cheaper (although relative costs are usually not explicitly modeled). Cascaded classifier architectures are primarily designed in order to reduce the cost of acquiring features to classify a sample (a sample may be classified the moment the available data is sufficient to provide sufficient classification confidence, without waiting for all features to be obtained). There is an important but neglected common thread linking all of these different research communities. In particular, all these learning methods are motivated by the need to minimize the cost of data acquisition in many different application domains such as computer-aided medical diagnosis, computational linguistics, computational biology, and computer vision. Although all of these areas have felt the need for a principled solution to the problem, the partial solutions that have tried to solve the problem (eg semi-supervised learning, active learning, multi-task inductive transfer etc) rarely model the cost explicitly, and very little effort has been expended on modeling application specific characteristics. Recently to some papers have started modeling the acquisition costs directly, but there is a lot of scope for theoretically rigorous work on this topic. It is also important to explicitly model the requirements from real world application communities and to bridge it with the work on theory/algorithms. Goals --------------- The goal of the workshop is to bring together researchers interested in the application of cost-sensitive learning (computer vision, natural language processing, computer-aided diagnostics, computational biology) with researchers interested in theory & algorithms for learning when data acquisition is costly. The main aim is to focus attention on a practically important problem where practitioners have long sought theoretically sound algorithms but which has not been sufficiently addressed in the literature. A secondary goal is to bring together ideas from semi-supervised learning, active learning, feature acquisition, inductive transfer learning and other areas, in order that there may be more exchange of ideas across these (extremely active) communities. Topics of Interest ------------------------ We welcome both novel theory/algorithms and papers that highlight open problems and challenges in real-world applications which call for cost sensitive learning. Submissions on following topics are particularly encouraged: Algorithms/Theory: -active learning -semi-supervised learning -transfer learning -reinforcement learning -domain adaptation, -cascaded classifier learning -...and related. Applications which call for cost-sensitive learning: -computer vision -computational linguistics -natural language processing -computer-aided diagnosis -differential medical diagnosis -...and others. Paper submission ------------------------ We welcome papers of up to 8 pages in the NIPS 2008 format. The accepted papers will be available for downloading from the workshop website. Accepted papers will be either presented as a talk or poster (with poster spotlight). Papers should be emailed to the organizers at cslworkshop.nips.2008@gmail.com. Please indicate whether you only wish to present a poster. Important Dates ------------------------ Deadline for submissions: October 17, 2008 Notification of acceptance: November 7, 2008 Workshop date: December 13, 2008 Organizers ------------------------ Balaji Krishnapuram (Siemens Medical Solutions USA) Shipeng Yu (Siemens Medical Solutions USA) Oksana Yakhnenko (Iowa State University) R. Bharat Rao (Siemens Medical Solutions USA) Lawrence Carin (Duke University) Invited Speakers ------------------------ John Shawe-Taylor (University College, London) Volker Tresp (University of Munich) Program Committee ------------------------ Chiru Bhattacharya (IISc, Bangalore) Rich Caruana (Cornell) Mario Figueiredo (IST, Portugal) Yves Grandvalet (UTC, France) Yan Liu (IBM) Prem Melville (IBM) Sunita Sarawagi (IIT Bombay) Fei Sha (USC & Yahoo research) Volker Tresp (Siemens) Kai Yu (NEC Research) Ulf Brefeld (Technische Universitaet, Berlin) Steffen Bickel (Max Planck Institute of Computer Science) Vikas Sindhwani (IBM) Johannes F?rnkranz (Darmstadt University) John Shawe-Taylor (University College, London) Sanjoy Dasgupta (University of California, San Diego) Steven Abney (University of Michigan) From pratyarth08 from gmail.com Fri Sep 26 02:44:04 2008 From: pratyarth08 from gmail.com (pratyarth08@gmail.com) Date: Fri Sep 26 13:41:53 2008 Subject: [Computational-biology] A National Level Technical Symposium On Bioinformatics - PRATYARTH '08 Message-ID: HEY FRIENDS, Want to explore Bioinformatics? An awesome chance coming up your way... A National Level Technical Symposium- PRATYARTH '08! Watch out for this at the SASTRA University campus on 11th and 12th of October '08! Have your pick from the latest diversified research topics. START REGISTERING @ www.combigs.bioinfosastra.com From skiadas from chaos2009.net Fri Sep 26 17:20:48 2008 From: skiadas from chaos2009.net (Christos Skiadas) Date: Fri Sep 26 17:50:54 2008 Subject: [Computational-biology] 2nd Chaotic Modeling and Simulation International Conference (CHAOS2009) , Abstract/Paper submission Message-ID: <243265085712296317487@PC100855613103> Dear Colleague, =20 This is a call for Abstract/Paper submission to the forthcoming Nonlinear C= onference titled: =20 2nd Chaotic Modeling and Simulation International Conference (CHAOS2009), C= hania, Crete, Greece, June 1-5, 2009. =20 The forthcoming International Conference (Chaos2009) on Chaotic Modeling, S= imulation and Applications will take place at the MAICh Conference Centre, = Chania, Crete, Greece (June 1-5, 2009). The general topics and the special sessions proposed for the Conference (Ch= aos2009) include but are not limited to: Chaos and Nonlinear Dynamics, Stochastic Chaos, Chemical Chaos, Data Analys= is and Chaos, Hydrodynamics, Turbulence and Plasmas, Optics and Chaos, Cha= otic Oscillations and Circuits, Chaos in Climate Dynamics, Geophysical Flow= s, Biology and Chaos, Neurophysiology and Chaos, Hamiltonian Systems, Chaos= in Astronomy and Astrophysics, Chaos and Solitons, Micro- and Nano- Elect= ro-Mechanical Systems, Neural Networks and Chaos, Ecology and Economy. For more information and submission details please visit the conference web= site at: http://www.chaos2009.net =20 Kind regards =20 Christos H. Skiadas Conference Chair Data Analysis and Forecasting Laboratory Technical University of Crete Chania, Crete, Greece skiadas@chaos2009.net =20 =20 =20 =20 =20 If you don't like to receive messages regarding the CHAOS2009 Conference, p= lease click here: Remove From lawyn from bii.a-star.edu.sg Tue Sep 30 02:09:31 2008 From: lawyn from bii.a-star.edu.sg (lawyn@bii.a-star.edu.sg) Date: Tue Sep 30 08:51:45 2008 Subject: [Computational-biology] Call for Participation: 8th IEEE International Conference on Data Mining (ICDM08) In-Reply-To: <33479.202.156.8.12.1212414865.squirrel@webmail.bii.a-star.edu.sg> References: <33479.202.156.8.12.1212414865.squirrel@webmail.bii.a-star.edu.sg> Message-ID: <63784.172.18.3.132.1222758571.squirrel@webmail.bii-sg.org> ====================== CALL FOR PARTICIPATION ====================== The 8th IEEE International Conference on Data Mining (ICDM'08) Polo Didattico G. Carmignani ? Piazza dei Cavalieri, Pisa, Italy December 15-19, 2008 http://icdm08.isti.cnr.it/ Sponsored by: Yahoo! Research Wind Microsoft Exeura Ask.com IBM Research IEEE IEEE Computer Society Software Products Italia Consiglio Nazionale delle Ricerche Istituto di Scienze e Tecnologie dell?Informazione Universit? di Pisa ================= HIGHLIGHTS ========================= * 70 Regular Papers and 74 Short Papers * 9 workshops * 3 invited talks * 4 tutorials * 1 panel All main conference and workshop proceedings will be published in the conference proceedings by the IEEE Computer Society Press. Best paper awards will be conferred at the conference on the authors of (1) the best research paper and (2) the best application paper. Several student travel grants will be available. Application details will appear in the ICDM'08 website soon. *********************************************** *********************************************** !!! Early Registration by 31st October!!! ----------------------------------------------- On-line registration (and more information) at http://icdm08.isti.cnr.it/Registration/25/registration Regular registration covers all the events of ICDM'08 during the five conference days including workshops and tutorials, and covers proceedings for the conference and the workshops. *********************************************** *********************************************** Tutorials include: +++++++++++++++++++++++++ T1 ? Integration of Classification and Pattern Mining: A Discriminative and Frequent Pattern-based Approach Hong Cheng and Jiawei Han (UIUC), Xifeng Yan (IBM T.J. Watson Research Center), Philip S. Yu (UIC) T2 ? Privacy-Preserving Location Services Mohamed F. Mokbel (University of Minnesota, Twin Cities) T3 ? Sample Selection Bias ? Covariate Shift: Problems, Solutions, and Applications Wei Fan (IBM T.J. Watson Research), Masashi Sugiyama (Tokyo Institute of Technology) T4 ? Mining Ubiquitous Data Streams: From Theory to Applications Joao Gama (University of Porto), Shonali Krishnaswamy and Mohamed Medhat Gaber (Monash University) Workshops include: +++++++++++++++++++++++++ RIKD?08 ? Reliability Issues in Knowledge Discovery DDDM?08 ? The Second International Workshop on Domain Driven Data Mining MCD?08 ? Mining complex data SSTDM?08 ? Spatial and Spatio-temporal data mining HPDM?08 ? 10th International workshop on high performance data mining FDM?08 ? Foundations of Data Mining SADM?08 ? First International Workshop on Semantic Aspects in Data Mining DMDM?08 ? Data Mining for Design and Marketing VM?08 ? Video mining ADN?08 ? Analysis of dynamic networks SOCIAL PROGRAM +++++++++++++++ ICDM'08 offers an exciting social program, including the conference welcome reception, outdoor activities, and the conference banquet. The conferences will be held at the Polo Didattico G. Carmignani ? Piazza dei Cavalieri, newly renovated conference center of the University of Pisa, located in Piazza dei Cavalieri, in the historical center of Pisa (200 m. from Piazza dei Miracoli and the tower). This beautiful square is at walking distance from most hotels. More information about attractions is available from the conference webpage: http://icdm08.isti.cnr.it/ -------------- *** Further Information *** icdm08-chair@isti.cnr.it icdm08-organizer@isti.cnr.it --------------- Organization ------------ Conference Co-chairs: Franco Turini (KDD Lab, Univ. Pisa, Italy) Carlo Zaniolo (UCLA, USA) Naren Ramakrishnan (Virginia Tech, USA) Program Committee Chairs: Fosca Giannotti (KDD Lab, ISTI-CNR, Italy) Dimitrios Gunopulos (UC Riverside, USA) Tutorials Chairs: Dino Pedreschi (KDD Lab, Univ. Pisa, Italy) Arno Siebes (Uthrecht Univ., The Netherlands) Workshops Chairs: Francesco Bonchi (KDD Lab, ISTI-CNR, Italy) Bettina Berendt (Humbolt Univ. Berlin, Germany) Award Chair: Katharina Morik (Univ. Dortmund, Germany) Panels Chair: Jean-Francois Boulicaut (INSA Lyon, France) ICDM Steering Committee Chair: Xindong Wu (Univ. Vermont, USA) From suchismi from gmail.com Tue Sep 30 03:58:33 2008 From: suchismi from gmail.com (bioinformatica) Date: Tue Sep 30 08:51:59 2008 Subject: [Computational-biology] On job computational training in Bioinformatics Message-ID: Dear Students, The Bioinformatica Solutions is providing training in all the fields of Bioinformatics like vaccine design, siRNA design, Gene identification, Structure based rational Drug designing, genomics, proteomics, QSAR, metabolomics, new metabolic pathway design ,bioperl, biopython, pharma informatics, etc. We are also giving training in Bio-Perl. bio-Phython,ASP.Net etc.whic are the industry oriented course in IT. Accommodation is available here nearby our institute & we assist in accommodation finding also. Many papers are published from this institute in reputated journal from the students which was doing dissertation work from TBS. You can download the application form from the site: www.thebioinformatica.com and registration can be done by sending your CV and form. Shuchi Smita Director The Bioinformatica Solutions From gal.chechik from gmail.com Tue Sep 30 15:22:55 2008 From: gal.chechik from gmail.com (Gal Chechik) Date: Tue Sep 30 17:43:06 2008 Subject: [Computational-biology] Call for papers: NIPS-08 Workshop on Machine Learning in Computational Biology In-Reply-To: <8f229dfc0809301300o6c3d42beu40c88e8c9db02a3a@mail.gmail.com> References: <8f229dfc0809301300o6c3d42beu40c88e8c9db02a3a@mail.gmail.com> Message-ID: <8f229dfc0809301322i74afd45y7e53fcd05c27b819@mail.gmail.com> Call for contributions New Problems and Methods in Computational Biology http://www.mlcb.org A workshop at the Twenty-Second Annual Conference on Neural Information Processing Systems (NIPS 2008) Whistler, BC, Canada, December 12, 2008. Deadline for submission of extended abstracts: October 12, 2008 WORKSHOP DESCRIPTION The field of computational biology has seen dramatic growth over the past few years, in terms of newly available data, new scientific questions and new challenges for learning and inference. In particular, biological data is often relationally structured and highly diverse, and thus requires combining multiple weak evidence from heterogeneous sources. These sources include sequenced genomes of a variety of organisms, gene expression data from multiple technologies, protein sequence and 3D structural data, protein interaction data, gene ontology and pathway databases, genetic variation data (such as SNPs), and an enormous amount of text data in the biological and medical literature. These new types of scientific and clinical problems require novel supervised and unsupervised learning approaches that can use these growing resources. The workshop will host presentations of emerging problems and machine learning techniques in computational biology. We encourage contributions describing either progress on new bioinformatics problems or work on established problems using methods that are substantially different from standard approaches. Kernel methods, graphical models, feature selection and other techniques applied to relevant bioinformatics problems would all be appropriate for the workshop. This year the workshop will follow a mini-symposium on Computational Biology that will take place in Vancouver on the afternoon of Thursday Dec 11th. SUBMISSION INSTRUCTIONS Researchers interested in contributing should upload an extended abstract of 1-6 pages in PDF format to the MLCB submission web site http://www.easychair.org/conferences/?conf=mlcb2008 by October 12, 2008, 11:59pm (Samoa time). No special style is required. Authors may use the NIPS style file, but are also free to use other styles as long as they use standard font size (11-12 pt) and standard margins (same as the NIPS style file). All submissions will be anonymously peer reviewed and will be evaluated on the basis of their technical content. A strong submission to the workshop typically presents a new learning method that yields new biological insights, or applies an existing learning method to a new biological problem. However, submissions that improve upon existing methods for solving previously studied problems will also be considered. Examples of research presented in previous years can be found online at www.fml.tuebingen.mpg.de/nipscompbio/previous. Please note that accepted abstracts will be posted online at www.mlcb.org. Authors may submit two versions of their abstract, a longer version for review and a shorter version for posting to the web page. In addition, presentations will be video taped and published online as part of the videolectures.net website supported by Pascal. The workshop allows submissions of papers that are under review or have been recently published in a conference or a journal. This is done to encourage presentation of mature research projects that are interesting to the community. The authors should clearly state any overlapping published work at time of submission. Authors of accepted abstracts will be invited to submit full length versions of their contributions for publication in a special issue of BMC Bioinformatics. ORGANIZERS Gal Chechik, Google Research Christina Leslie, Memorial Sloan-Kettering Cancer Center William Stafford Noble, Department of Genome Sciences, University of Washington Gunnar Raetsch, Friedrich Miescher Laboratory of the Max Planck Society (Tuebingen, Germany) Quaid Morris, Terrence Donnelley Centre for Cellular and Biomolecular Research, University of Toronto PROGRAM COMMITTEE Pierre Baldi, UC Irvine Kristin Bennett, Rensselaer Polytechnic Institute Mathieu Blanchette, McGill University Florence d'Alche, Universite d'Evry-Val d'Essonne, Genopole Eleazar Eskin, UCLA Brendan Frey, University of Toronto Nir Friedman, The Hebrew University of Jerusalem Michael I. Jordan, UC Berkeley Alexander Hartemink, Duke University David Heckerman, Microsoft Research Michal Linial, The Hebrew University of Jerusalem Klaus-Robert Mueller, Fraunhofer FIRST Uwe Ohler, Duke University Dana Pe'er, Columbia University Alexander Schliep, Max Planck Institute for Molecular Genetics Bernhard Schoelkopf, Max Planck Institute for Biological Cybernetics Eran Segal, The Weizmann Institute Jean-Philippe Vert, Ecole des Mines de Paris Eric Xing, Carnegie Mellon University From oksayakh from cs.iastate.edu Tue Sep 30 23:48:44 2008 From: oksayakh from cs.iastate.edu (Oksana Yakhnenko) Date: Wed Oct 1 14:51:11 2008 Subject: [Computational-biology] Call for papers: NIPS 2008 Workshop on Cost-Sensitive Learning Message-ID: <5E1828F7331645EAAD0EAEE21816908C@OksanaPC> Apologies if you are receiving multiple copies of this email, and please forward to interested parties. ----- Original Message ----- From: Oksana Yakhnenko To: colt@cs.uiuc.edu Sent: Friday, September 26, 2008 4:22 PM Subject: Call for papers: NIPS 2008 Workshop on Cost-Sensitive Learning ==Call for Papers: NIPS 2008 Workshop on Cost-Sensitive Learning== http://www.cs.iastate.edu/~oksayakh/cslworkshop_nips2008.html Description and background ------------------------ The goal of cost-sensitive learning is to minimize data acquisition costs while maximizing the accuracy of the learner/predictor. Many fields in machine learning attempt to solve cost-sensitive learning with strong simplifying assumptions. For example, in semi-supervised learning, class-labels are assumed to be expensive and features are implicitly assumed to have zero cost. In active learning, labels are again assumed to be expensive; however the learner may ask an oracle to reveal a label for unlabeled data for selected examples. Active feature acquisition assumes that obtaining features is expensive (but typically all features are assumed to be equally expensive), and the learner identifies instances for which complete information is most informative to classify a particular test sample. Inductive transfer learning and domain adaptation methods assume that training data for a particular task is expensive or but other data from other domains may be cheaper (although relative costs are usually not explicitly modeled). Cascaded classifier architectures are primarily designed in order to reduce the cost of acquiring features to classify a sample (a sample may be classified the moment the available data is sufficient to provide sufficient classification confidence, without waiting for all features to be obtained). There is an important but neglected common thread linking all of these different research communities. In particular, all these learning methods are motivated by the need to minimize the cost of data acquisition in many different application domains such as computer-aided medical diagnosis, computational linguistics, computational biology, and computer vision. Although all of these areas have felt the need for a principled solution to the problem, the partial solutions that have tried to solve the problem (eg semi-supervised learning, active learning, multi-task inductive transfer etc) rarely model the cost explicitly, and very little effort has been expended on modeling application specific characteristics. Recently to some papers have started modeling the acquisition costs directly, but there is a lot of scope for theoretically rigorous work on this topic. It is also important to explicitly model the requirements from real world application communities and to bridge it with the work on theory/algorithms. Goals --------------- The goal of the workshop is to bring together researchers interested in the application of cost-sensitive learning (computer vision, natural language processing, computer-aided diagnostics, computational biology) with researchers interested in theory & algorithms for learning when data acquisition is costly. The main aim is to focus attention on a practically important problem where practitioners have long sought theoretically sound algorithms but which has not been sufficiently addressed in the literature. A secondary goal is to bring together ideas from semi-supervised learning, active learning, feature acquisition, inductive transfer learning and other areas, in order that there may be more exchange of ideas across these (extremely active) communities. Topics of Interest ------------------------ We welcome both novel theory/algorithms and papers that highlight open problems and challenges in real-world applications which call for cost sensitive learning. Submissions on following topics are particularly encouraged: Algorithms/Theory: -active learning -semi-supervised learning -transfer learning -reinforcement learning -domain adaptation, -cascaded classifier learning -...and related. Applications which call for cost-sensitive learning: -computer vision -computational linguistics -natural language processing -computer-aided diagnosis -differential medical diagnosis -...and others. Paper submission ------------------------ We welcome papers of up to 8 pages in the NIPS 2008 format. The accepted papers will be available for downloading from the workshop website. Accepted papers will be either presented as a talk or poster (with poster spotlight). Papers should be emailed to the organizers at cslworkshop.nips.2008@gmail.com. Please indicate whether you only wish to present a poster. Important Dates ------------------------ Deadline for submissions: October 17, 2008 Notification of acceptance: November 7, 2008 Workshop date: December 13, 2008 Organizers ------------------------ Balaji Krishnapuram (Siemens Medical Solutions USA) Shipeng Yu (Siemens Medical Solutions USA) Oksana Yakhnenko (Iowa State University) R. Bharat Rao (Siemens Medical Solutions USA) Lawrence Carin (Duke University) Invited Speakers ------------------------ John Shawe-Taylor (University College, London) Volker Tresp (University of Munich) Program Committee ------------------------ Chiru Bhattacharya (IISc, Bangalore) Rich Caruana (Cornell) Mario Figueiredo (IST, Portugal) Yves Grandvalet (UTC, France) Yan Liu (IBM) Prem Melville (IBM) Sunita Sarawagi (IIT Bombay) Fei Sha (USC & Yahoo research) Volker Tresp (Siemens) Kai Yu (NEC Research) Ulf Brefeld (Technische Universitaet, Berlin) Steffen Bickel (Max Planck Institute of Computer Science) Vikas Sindhwani (IBM) Johannes F?rnkranz (Darmstadt University) John Shawe-Taylor (University College, London) Sanjoy Dasgupta (University of California, San Diego) Steven Abney (University of Michigan)