From Heather.Vincent from manchester.ac.uk Mon Feb 2 11:42:27 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Mon Feb 2 12:27:16 2009 Subject: [Bio-matrix] Introduction to Ontologies for the Biosciences Message-ID: <49872273.2020005@manchester.ac.uk> Introduction to Ontologies for the Biosciences (http://octette.cs.man.ac.uk/bioinformatics/modules/cs847.html) is one of a number of online courses from The University of Manchester. It is designed mainly for biologists, but it will also be of interest to computer scientists. An awareness of bioinformatics tools and resources will be essential for anyone taking the course. (Our 'Introduction to Bioinformatics' (http://octette.cs.man.ac.uk/bioinformatics/modules/bs6061.html) would provide suitable preparation.) The courses will begin again on 2 March 2009. The application deadline is 13 February 2009. Bio-ontologies now play a crucial role, both in the indexing of experimental data and in the provision of conceptual abstractions for aggregating results. This means that there is a need for domain experts to be trained in the formal and conceptual bases underlying ontology languages and modelling principles. Understanding of the underlying principles of ontology development is necessary if domain experts are to be enabled to develop ontologies that support inference, which is critical for automated verification. Our distance courses are delivered in a Virtual Learning Environment, which allows us to extend the classroom into the web. We use a range of tools to support our online teaching activities. Each course, which is paced to suit those in full-time employment, runs over 16 teaching weeks. Teaching and learning are focussed around tutor-supported exercises. In this course, the course tasks are :- 1 Ontology ice breaker. This will be an exercise to make people aware of the issues, and of the need for a common vocabulary. 2 Compare and contrast two bio-ontologies. 3 MCQ on what OWL statements mean. 3 Short ontology building project. 4 Advanced OWL as a project. You will find information on all our courses, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk From ijcbs from isibm.org Tue Feb 3 16:58:44 2009 From: ijcbs from isibm.org (ijcbs@isibm.org) Date: Tue Feb 3 17:12:34 2009 Subject: [Bio-matrix] The Second Call for Papers: IJCBS09 Message-ID: <6CFDE26A1B5A4B3D8E52358772C4E80C@AVOCADO> Apologies if you receive a duplicate copy. ********************************************************** The International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS'09) will take place in Shanghai, China on August 3rd - 6th, 2009. You are invited to submit papers with unpublished original work describing recent advances on all aspects of Bioinformatics, Systems Biology and Intelligent Computing, including, but not restricted to the following topics: Bioinformatics: Bio-molecular and phylogenetic databases, bio-languages, interoperability in bio-databases, bio-ontology and data mining; identification and classification of genes; sequence search and alignment; protein structure prediction and molecular simulation; molecular evolution and phylogeny; functional genomics, proteomics; drug discovery; gene expression analysis; bioinformatics engineering; bio-data visualization; algorithms, modeling and simulation of bio-sets; biomarkers of toxicity; bio-imaging; signaling and computation, genetics and genomics. Systems Biology: Modeling and simulation of biological processes, pathways, networks, pipelines, mathematical and quantitative models of cellular and multicellular systems, emergence of properties in complex biological systems, methods to predict biological network behavior from incomplete information, statistical modeling of biological data, prediction and validation, synthetic biological systems, high performance bio-computing, self-organization in living systems (cells, organisms, swarms, ecosystems, etc.), platforms for computational modeling of living systems (parallel, distributed, and multi-resolution simulation methods), differential, discrete and/or stochastic modeling-language frameworks, applications of systems biology towards understanding disease mechanisms, pharmaceutical drug discovery and drug target validation. Intelligent Computing: Machine learning, data mining, pattern recognition, agents, neural computing, kernel methods, evolutionary computing, swarm intelligence and optimization; feature selection/extraction; ensemble methods; manifold learning theory; artificial life and artificial immune systems; technology to develop artificial components, systematization methodology for intelligent systems, and scientific principles related to artificial life. Important Dates Workshop/Special Session Proposals: February 1, 2009 Paper Submission (maximum 8 pages with IEEE/CS conference format): February 15, 2009 Notification to Authors: March 15, 2009 Camera-Ready, Full Papers: April 5, 2009 Paper Submission and Publication IJCBS09 invites authors to submit papers using the linkhttp://www.isibm.org/IJCBS/submission.html. By submitting your paper to IJCBS'09, you implicitly state that the paper is based on your own original research and that it was not and will not be submitted elsewhere. Papers should not exceed 7 pages with standard IEEE CS formats. All submitted papers should be written in English. Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted. All submitted papers will be peer-reviewed. All accepted papers of registered authors will be included in the proceedings published by IEEE Computer Society and indexed in EI. Selected papers will be invited to adapt their papers for their publication in several journals, including BMC Genomics, International Journal of Data Mining & Bioinformatics, International Journal of Pattern Recognition and Artificial Intelligence, Journal of Supercomputing, International Journal of Computational Biology and Drug Design, IJFIPM and other SCI and PubMed indexed journals. Other Information Awards will be granted to the best paper of those presented at the conference. The IJCBS'09 will award a number of travel fellowships for students and authors of outstanding papers. Please find conference organization, workshops, special sessions, tutorials, keynotes, paper submission, author instructions and registration information at the IJCBS websitehttp://www.isibm.org/IJCBS. If you have any questions, please contact Dr. Joe Zhang (USA) or Dr. Guozheng Li (China) by email ijcbs09@orca.st.usm.edu . IJCBS 2009 Program Committee and Organizing Committee Sponsors/Supporters: ISIBM, NSF, IEEE, IEEE Computer Society, Chinese Academy of Science and Tongji University in Shanghai From wcom from worldcomp.cviog.uga.edu Fri Feb 20 18:50:17 2009 From: wcom from worldcomp.cviog.uga.edu (WORLDCOMP'09 Congress Conferences) Date: Sat Feb 21 13:54:47 2009 Subject: [Bio-matrix] Call For Papers: Computer Science & Computer Engineering Conferences, USA, WORLDCOMP'09, Submission Deadline: Feb. 25, 2009 Message-ID: <20090220235017.30C608193D@worldcomp.cviog.uga.edu> CALL FOR PAPERS ================= Paper Submission Deadline: February 25, 2009 WORLDCOMP'09 The 2009 World Congress in Computer Science, Computer Engineering, & Applied Computing Date and Location: July 13-16, 2009, Las Vegas, USA http://www.world-academy-of-science.org You are invited to submit a paper; see below for submission instructions. All accepted papers will be published in the respective conference proceedings (in printed books/proceedings). WORLDCOMP'09 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. In recent past, keynote and/or tutorial speakers included: Prof. David A. Patterson (U. of California, Berkeley); Prof. Michael J. Flynn (Stanford U.); Prof. John H. Holland (U. of Michigan, Ann Arbor); Prof. H. J. Siegel (Colorado State U.); Prof. Barry Vercoe (MIT); Prof. Ruzena Bajcsy (U. of California, Berkeley); Prof. Jun Liu (Harvard U.); Dr. Jim Gettys (OLPC + developer of X Window); and many other distinguished speakers. For this year's conference, the keynote speakers include: Prof. Ian Foster (Father of Grid Computing), Dr. Eric Drexler (Father of Nanotechnology), Prof. Brian Athey (Head, NIH National Center for Computational Medicine & Biology), Dr. Jose Munoz (Deputy Director, National Science Foundation Office of Cyberinfrastructure), and many other distinguished speakers. The 2009 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'09) is composed of the following conferences (all will be held simultaneously, same location and dates: July 13-16, 2009, USA). A link to each conference's URL can be found at http://www.world-academy-of-science.org BIOCOMP'09: International Conf. on Bioinformatics & Computational Biology CDES'09: International Conf. on Computer Design CGVR'09: International Conf. on Computer Graphics & Virtual Reality CSC'09: International Conf. on Scientific Computing DMIN'09: International Conf. on Data Mining EEE'09: International Conf. on e-Learning, e-Business, Enterprise Information Systems, & e-Government ERSA'09: International Conf. on Engineering of Reconfigurable Systems and Algorithms ESA'09: International Conf. on Embedded Systems & Applications FCS'09: International Conf. on Foundations of Computer Science FECS'09: International Conf. on Frontiers in Education: Computer Science & Computer Engineering GCA'09: International Conf. on Grid Computing & Applications GEM'09: International Conf. on Genetic & Evolutionary Methods ICAI'09: International Conf. on Artificial Intelligence ICOMP'09: International Conf. on Internet Computing ICWN'09: International Conf. on Wireless Networks IKE'09: International Conf. on Information & Knowledge Engineering IPCV'09: International Conf. on Image Processing, Computer Vision, & Pattern Recognition MSV'09: International Conf. on Modeling, Simulation & Visualization Methods PDPTA'09: International Conf. on Parallel and Distributed Processing Techniques & Applications SAM'09: International Conf. on Security and Management SERP'09: International Conf. on Software Engineering Research and Practice SWWS'09: International Conf. on Semantic Web and Web Services SUBMISSION OF PAPERS: Prospective authors are invited to submit their draft papers by uploading them to http://worldcomp.cviog.uga.edu/ . Submissions must be received by Feb. 25, 2009 and they must be in either MS doc or pdf formats (about 5 to 7 pages - single space, font size of 10 to 12). All reasonable typesetting formats are acceptable (later, the authors of accepted papers will be asked to follow a particular typesetting format to prepare their papers for publication.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, and email address for each author. The first page should also identify the name of the Contact Author and a maximum of 5 topical keywords that would best represent the content of the paper. Finally, the name of the conference that the paper is being submitted to must be stated on the first page. Papers will be evaluated for originality, significance, clarity, impact, and soundness. Each paper will be refereed by two experts in the field who are independent of the conference program committee. The referees' evaluations will then be reviewed by two members of the program committee who will recommend a decision to the chair of the track that the paper has been submitted to. The chair will make the final decision. Lastly, the Camera-Ready papers will be reviewed by one member of the program committee. IMPORTANT DATES: Feb. 25, 2009: Submission of papers (about 5 to 7 pages) March 25, 2009: Notification of acceptance April 25, 2009: Camera-Ready papers and Registration due July 13-16, 2009: The 2009 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'09 - 22 joint conferences) COORDINATOR: H. R. Arabnia, PhD Professor, Computer Science Editor-in-Chief, The Journal of Supercomputing (Springer) Advisory Board, IEEE Technical Committee on TCSC Vice President, Int'l Society of Intelligent Biological Medicine The University of Georgia, USA Tel: (706) 542-3480 email: hra@cs.uga.edu SPONSORS (confirmed as of Feb. 20, 2009): Academic Sponsors include: United States Military Academy, Network Science Center, USA; Biomedical Cybernetics Laboratory, HST of Harvard University and MIT, USA; Argonne's Leadership Computing Facility of Argonne National Laboratory, USA; Functional Genomics Laboratory, University of Illinois at Urbana-Champaign, USA; Minnesota Supercomputing Institute, University of Minnesota, USA; Intelligent Data Exploration and Analysis Laboratory, University of Texas at Austin, Texas, USA; Harvard Statistics Department Genomics & Bioinformatics Laboratory, Harvard University, USA; Texas Advanced Computing Center, The University of Texas at Austin, Texas, USA; Center for the Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA; Bioinformatics & Computational Biology Program, George Mason University, Virginia, USA; Institute of Discrete Mathematics and Geometry, Vienna University of Technology, Austria; BioMedical Informatics & Bio-Imaging Laboratory, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA; Knowledge Management & Intelligent System Center (KMIS) of University of Siegen, Germany; National Institute for Health Research; Hawkeye Radiology Informatics, College of Medicine, University of Iowa, USA; Institute for Informatics Problems of the Russian Academy of Sciences, Moscow, Russia; Medical Image HPC & Informatics Lab (MiHi Lab), University of Iowa, USA; SECLAB of U. of Naples Federico II, U. of Naples Parthenope, and Second U. of Naples, Italy; U. of North Dakota, USA; Intelligent Cyberspace Engineering Lab., ICEL, Texas A&M University (Com./Texas), USA; International Society of Intelligent Biological Medicine; World Academy of Biomedical Sciences & Technologies; and European Commission. Other Sponsors include: High Performance Computing for Nanotechnology (HPCNano); HoIP - Health without Boundaries; The International Council on Medical and Care Compunetics; The UK Department for Business, Enterprise & Regulatory Reform; VMW Solutions Ltd.; Scientific Technologies Corporation; and others. TUTORIALS: 12 to 15 tutorials are currently being planned - all tutorials are free to conference registrants. Tutorial subjects include, ABET accreditation as it relates to computing, various aspects of supercomputing (parallel and distributed systems and processing), visualization, preparation for teaching online courses, various areas of security, sensor networks, bioinformatics for computer scientists, web services for mobile and wireless systems, ... PURPOSE / HISTORY: This set of joint conferences is the largest annual gathering of researchers in computer science, computer engineering and applied computing. Many of the joint conferences in WORLDCOMP are the premier conferences for presentation of advances in their respective fields. We anticipate to have 2,400 or more attendees from over 85 countries participating in the 2009 joint conferences. The motivation is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. The model used to form these annual conferences facilitates communication among researchers from all over the world in different fields of computer science, computer engineering and applied computing. Both inward research (core areas of computer science and engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications) will be covered during the conferences. WORLDCOMP'09 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. One registration fee provides full access to all events/sessions of all conferences (including tutorials). The registration fee is set at the low end of the academia range for Academic Conferences. MEMBERS OF PROGRAM AND ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; AI; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra@cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, a short biography together with research interests and the name of the conference offering to help with. Many who have already joined the committees of individual tracks are renowned leaders, scholars, researchers, scientists and practitioners of the highest ranks; many are directors of research laboratories, fellows of various societies, heads/chairs of departments, deans and provosts, and program directors of various funding agencies. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, health spa, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (recreational destinations, Golf courses, ...) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= This email was sent to: biomatrx@magpie.bio.indiana.edu To opt out of this email list: http://worldcomp.cviog.uga.edu/cgi-bin/rm/full.cgi?F46C9C5E-F790-11DD-8AA4-D7C9A53D19CC From marling from prime.cs.ohiou.edu Sat Feb 21 21:22:10 2009 From: marling from prime.cs.ohiou.edu (marling@prime.cs.ohiou.edu) Date: Sun Feb 22 11:07:23 2009 Subject: [Bio-matrix] Call for Papers: Workshop on CBR in the Health Sciences Message-ID: <200902220222.n1M2MAnL020813@p1.cs.ohiou.edu> Workshop on Case-Based Reasoning in the Health Sciences The Eighth International Conference on Case-Based Reasoning (ICCBR-09) Seattle, Washington, USA July 21, 2009 Call for Papers There has been an explosion of interest in health sciences applications of Case-Based Reasoning (CBR), not only in the traditional CBR in Medicine domain, but also in bioinformatics, enabling home health care technologies, CBR integration, and synergies between CBR and knowledge discovery. This is the seventh in a series of exciting workshops, which have been held at every ICCBR and ECCBR since 2003. This workshop will be held at ICCBR-09, in Seattle, Washington, USA, on July 21, 2009. The goals of this workshop are to: * provide a forum for identifying important contributions and opportunities for research on the application of CBR to the health sciences, * promote the systematic study of how to apply CBR to the health sciences, and * showcase applications of CBR in the health sciences. Some of the technical issues addressed, and potential outcomes of the workshop, are to identify challenges specific to applying CBR to the health sciences, required methodological improvements to fit this context needs, preferred types and domains of applications, and guidelines to better develop CBR systems in this domain. We welcome all those interested in the problems and promise of CBR in the health sciences, whether or not they have participated in past workshops. Topics of interest include (but are not limited to): * Integration of CBR in health care environments * CBR in medical decision-support systems * CBR in medical imaging * CBR in enabling technologies for those with physical disabilities or chronic health problems * CBR and knowledge discovery in medicine and the health sciences * Cognitive approaches to applying CBR to medicine * Theoretical framework for CBR in medical reasoning * CBR in bioinformatics * CBR and evidence-based medicine Paper presentations will be interspersed with discussions in which we characterize, categorize, and discuss the benefits of specific CBR applications in the health sciences. A wrap-up round table discussion will summarize the lessons learnt, issues identified, and future directions. Submission Requirements PDF paper submissions should be formatted according to Springer LNCS format, with a maximum of ten pages. Author's instructions along with LaTeX and Word macro files are available at the Information for LNCS Authors page, http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0 We will not accept papers that are exact duplicates of others, but we welcome papers that are modifications of them that focus on CBR in the Health Sciences. For example, submissions summarizing previously published material relating to this workshop's topic are welcomed. In your submissions and finalized papers, please cite the other publication and indicate clearly its relationship to this workshop's paper. Please upload submissions via the ICCBR-09 EasyChair Conference Site, https://www.easychair.org/login.cgi?conf=iccbr09 Important Dates * Submission Deadline: April 15, 2009 * Notification Date: May 18, 2009 * Camera-Ready Deadline: May 29, 2009 * Workshop date: July 21, 2009 Workshop Web Site http://oucsace.cs.ohiou.edu/~marling/iccbr09/workshop.html Organizing Committee Co-Chairs Cindy Marling Ohio University, USA marling@ohio.edu Stefania Montani University of Piemonte Orientale, Italy stefania.montani@unipmn.it Committee Members Klaus-Dieter Althoff, University of Hildesheim, Germany Isabelle Bichindaritz, University of Washington, USA Peter Funk, Malardalen University, Sweden Alec Holt, University of Otago, New Zealand Lakhmi Jain, University of South Australia, Australia Jean Lieber, Loria, France Stefan V. Pantazi, Conestoga College Institute of Technology, Canada Petra Perner, Institute of Computer Vision and Applied Computer Sciences, Germany Luigi Portinale, University of Piemonte Orientale, Italy Olga Vorobieva, Pavlov State Medical University, Russia