From jeff at bioinformatics.org Mon Nov 5 16:32:31 2012 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 05 Nov 2012 16:32:31 -0500 Subject: [BiO BB] Course on NGS data analysis with open source software next week Message-ID: <5098306F.1000908@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BI231 NGS Data Analysis November 12-16, 2012 Online at Bioinformatics.Org http://www.bioinformatics.org/wiki/BI231_NGS_Data_Analysis http://www.bioinformatics.org/edu/AGGG -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics to be covered include the description of sequencing strategies and platforms, experiment types, data formats, and command line tools for various workflows, such as quantification of transcripts, alternative splice forms, copy number variants, single nucleotide polymorphisms, etc. INSTRUCTOR: Shailender Nagpal, M.Sc. is a data analysis consultant in the biotechnology and pharmaceutical industries and specializes in the interpretation of data generated from various platforms in drug discovery, such as genomics and proteomics. CV: http://www.bioinformatics.org/wiki/Shailender_Nagpal SYLLABUS: The course is divided into 4 sessions, with live lectures scheduled for 17:00 to 18:00 GMT (12:00 PM to 1:00 PM US EDT), Monday through Thursday (Friday will be a reserve day). Homework assignments will involve running computationally intensive tools. Recorded lectures on Linux will also be provided. Session 1: Fundamentals of NGS technologies - strategies, platforms and types of experiments that can be done (whole genome, transcriptome, targeted, ChIP-Seq, etc.) Session 2: Data formats and overview of algorithms, workflows and command line tools Session 3: Whole genome sequencing workflow used for CNV and SNP discovery Session 4: Transcriptomics workflow for quantifying abundance of transcripts and alternative splicing junctions REGISTRATION: If you haven't already done so, please create an on-line account to access the educational section of our website (http://www.bioinformatics.org/edu/). You may register for the course directly by making a payment using the on-line registration form (use this form only for PayPal and credit card payments for the base tuition listed below.): http://www.bioinformatics.org/edu/AGGG Tuition: For-profit & government: $1,000 USD Non-profit & self-pay: $600 USD Additional discounts are available as follows: * Professional members: 20% discount (please inquire) * Limited scholarships may also be available for those in low-income economies (please inquire). Additional fee: A one month subscription to our high performance Linux server: $50 lab fee. For alternative payment methods, please write to edu at bioinformatics.org. FOR MORE INFORMATION: For more information, please visit: http://www.bioinformatics.org/wiki/BI231_NGS_Data_Analysis or contact edu at bioinformatics.org. From german.terrazas at nottingham.ac.uk Mon Nov 12 16:45:55 2012 From: german.terrazas at nottingham.ac.uk (German Terrazas) Date: Mon, 12 Nov 2012 21:45:55 +0000 Subject: [BiO BB] CFP NICSO 2013 - The VI International Workshop on Nature Inspired Cooperative Strategies for Optimization Message-ID: <50A16E13.8050801@nottingham.ac.uk> ******** PLEASE APOLOGIZE FOR MULTIPLE COPIES ******** *********************************************************** The VI International Workshop on Nature Inspired Cooperative Strategies for Optimization - NICSO 2013 September 2nd - 4th, 2013 Canterbury, United Kingdom http://modo.ugr.es/nicso2013 *********************************************************** CALL FOR PAPERS * * * IMPORTANT DATES * * * Full paper submission: April 15, 2013 Acceptance notification: May 15, 2013 Final camera ready: June 5, 2013 NICSO: September 2-4, 2013 NICSO 2013 will be the sixth edition of the International Workshop on Nature Inspired Cooperative Strategies for Optimization. This workshop aims at bringing together international researchers and practitioners from different disciplines in order to discuss recent advances and exchange ideas on the current state of the art of cooperative problem solving strategies. All submitted papers will be blind reviewed by at least two reviewers from the Program Committee. Selection criteria will be based on relevance, originality, significance, impact, technical soundness and quality of the presentation. Contributions are expected to provide original results, insights and experimental innovations. Manuscripts must be in PDF, not exceeding 12 pages and conforming to the Latex template at Instructions for Authors page for the book series Studies in Computational Intelligence (http://www.springer.com/series/7092). Contributions are welcome to submission through the system available at http://www.easychair.org/conferences/?conf=nicso2013 The accepted papers will be published in the book series on STUDIES IN COMPUTATIONAL INTELLIGENCE (Springer) (http://www.springer.com/series/7092) indexed by ISI Web of Science Conference Proceedings, DBLP, Ulrichs, SCOPUS, MathSciNet, Current Mathematical Publications, Mathematical Reviews, Zentralblatt Math: MetaPress and Springerlink. The authors of a selection of the best accepted papers will be invited to revise and extend their contributions for publication in a special issue in the JOURNAL OF MEMETIC COMPUTING (Springer) (http://www.springer.com/engineering/computational+intelligence+and+complexity/journal/12293). Target topics (but not limited to): Adaptive Behaviour Ants Colonies Amorphous Computing Artificial Life Artificial Immune Systems Bioinformatics Bio-inspired architecture Complex Systems Distributed Computing Evolutionary Algorithms Evolutionary Robotics Evolvable Systems Games and Game Theory Genetic Algorithms Genetic Programming Hyperheuristics Membrane Computing Memetic Algorithms Quantum Computing Software Self-Assembly Systems Coevolution Swarm Intelligence * Programme Committee * Bel?n Melian, University of La Laguna, Spain Carlos Cruz Corona, University of Granada, Spain Cecilio Angulo, Technical University of Catalunya, Spain Christof Teuscher, Portland State University, US Colin Johnson, University of Kent, UK Dario Landa-Silva, University of Nottingham, UK Enrique Onieva, University of Granada, Spain Evelyne Lutton, INRIA, France Francisco Herrera, University of Granada, Spain Gabriela Ochoa, University of Stirling, UK Gianluigi Folino, Istituto di Calcolo e Reti ad Alte Prestazioni, Italy Giuseppe Scollo, University of Catania, Italy J. Marcos Moreno, University of La Laguna, Spain Jaume Bacardit, University of Nottingham, UK Jean-Louis Giavitto, Universit? d'Evry, France Jim Smith, University of the West of England, UK Jon Timmis, University of York, UK Jos? A. Moreno, University of La Laguna, Spain Jos? Alejandro Castillo, Instituto Nacional de Investigaciones Nucleares, Mexico Jos? Luis Verdegay, University of Granada, Spain Marco Dorigo, Universit? Libre de Bruxelles, Belgium Mar?a Teresa Lamata, University of Granada, Spain Mario Pavone, University of Catania, Italy Natalio Krasnogor, University of Nottingham, UK Oliver Korb, Cambridge Crystallographic Data Centre, UK Paolo Arena, University of Catania, Italy Ren? Doursat, Complex Systems Institure, France Roberto Battiti, University of Trento, Italy Shengxiang Yang, University of Leicester, UK Stefano Pizzuti, Energy, New Technologies & Envir. Agency, Italy Steven Gustafson, General Electric Global Research Center, US Vincenzo Cutello, University of Catania, Italy Vitorino Ramos, Technical University of Lisbon, Portugal Vittorio Maniezzo, University of Bologna, Italy * Workshop Organizers * Fernando Esteban Barril Otero German Terrazas Antonio D. Masegosa * Steering Committee * Natalio Krasnogor David A. Pelta This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From icbo2013 at gmail.com Tue Nov 13 10:03:52 2012 From: icbo2013 at gmail.com (ICBO 2013) Date: Tue, 13 Nov 2012 11:03:52 -0400 Subject: [BiO BB] CFP: ICBO2013 - International Conference on Biomedical Ontology - Call for Papers In-Reply-To: References: Message-ID: FIRST CALL FOR PAPERS - ICBO2013 The Fourth International Conference on Biomedical Ontologies 2013 (ICBO2013) http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ will be held at Concordia University, Montreal, Quebec, on July 8th - 9th 2013. The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience. The event is part of the Semantic Trilogy2013 featuring: * International Conference on Biomedical Ontologies (ICBO 2013) * Canadian Semantic Web Symposium (CSWS 2013) * Data Integration in the Life Sciences (DILS 2013) Call for Submissions: http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html ================ Ontologies are increasingly used in the semantic description of biological and medical data from creation to publication and consumption by semantically enabled applications. To be effective ontologies must be of high quality and work well together. Techniques for ontology use, good ontology design, ontology maintenance, and ontology coordination. Research papers in the areas of the application of ontologies to biomedical problems, ontology design and ontology interoperability, at any stage in the process of data creation to its use in applications. Approaches to ontology building and use. Use of such ontologies in knowledge management, knowledge discovery and next-generation publishing. Topics: http://www.unbsj.ca/sase/csas/data/ws/icbo2013/themes.html ===== Ontologies for biomedical research and clinical applications Reports on ontologies for, and their application in, high throughput omics data and systems biology, toxicology and environmental health, disorders, diseases, phenotypes and physiology, SNP variation and pharmacogenomics, translational research and personalized medicine, public health and electronic health care, are invited. Foundations and methodology Papers on foundational and methodological issues pertaining to biomedical ontology are invited. Eligible topics are, though not limited to, the following; knowledge representation and reasoning, philosophical foundations of ontology, upper-level ontologies, topics in ontology engineering including design and life cycle, methodologies for knowledge elicitation and capture, ontology-oriented text mining techniques, ontology modularity, mapping, merging, and alignment of ontologies, and ontology evaluation. Biomedical ontologies and the Semantic Web Research on formal representation of biomedical knowledge using RDF and OWL, Identifiers, mappings & normalization, biomedical research using linked data, integration strategies using the linked open data cloud, visualization and manipulation of ontology, federation of online resources, workflows and semantic web services for biomedical knowledge discovery. Social aspects of biomedical ontologies Perpectives from biomedical ontologists on community standards, adoption, and proliferation of semantics, use of semantic wikis, bio-curation & crowdsourcing techniques, user engagement and feedback, semantic publishing and provenance, governance, evolution and sustainability. Submissions: http://www.unbsj.ca/sase/csas/data/ws/icbo2013/submissions.html ========== All accepted submissions will be published as part of the Conference Proceedings. Papers are to be prepared using templates (available on website) and submitted via EasyChair. Details will follow in the full Call for Papers in December 2012. 1. Long Research Paper (up to 15 pages) should satisfy the following criteria: original research; novelty in methodology and/or in research results; significant development with large potential for impact; theoretical soundness and/or strong evaluation with demonstration of utility in applications. 2. Short Research Paper (up to 8 pages) should satisfy the following criteria: original research; methodological soundness with either novel methodology & application, or demonstrated improvement over existing methods (with appropriate validation), or the use of existing methodology but in novel application. Short papers are appropriate for applied research or systems, or the development of new approaches. 3. Systems Paper (up to 4 pages) must describe the functionality, availability, and an application of the system. The system itself must be demonstrated at the conference. 4. Early Career Track (up to 8 pages) is to support the work of young investigators. There will be an Early Career Track session for the presentation of the papers. The ECT paper review and acceptance criteria are the same as the short research papers. The staggered submission dates allows submissions (from young investigators) that are not accepted as long or short research papers to be revised and re-submitted; as well as allow first time submissions from young investigators to the Early Career Track directly. 5. Late Breaking Report (up to 2 pages) This track is for extended abstracts of posters. A limited set of the peer-reviewed reports will be selected to be presented as a flash talk. All reports must be presented as posters. Late breaking reports should address a clearly defined problem that is of interest to the DILS community. A late breaking report is appropriate for interesting preliminary results; and systems updates. 6. Highlights (up to 500 words) This track highlights original peer-reviewed research with significant impact on data integration research or life sciences research that is published between May 1, 2012 and May 1, 2013. The submission is a short abstract highlighting the importance of the work for the DILS community. If the publication is not open access, then the authors must make the paper available to the review committee. 7. Workshops Workshops are half-day or full-day scientific events intended to provide a forum for the discussion of a specific topic through individual paper presentations. The workshop organizers will be responsible for advertising the workshop and reviewing and selecting the contributions. Workshops can be events focusing on a specific topic; they can also include interest group meetings, or meetings designed to disseminate the results of a research project on a specific topic. 8. Tutorials Tutorials are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. Tutorials can include hands-on training, in which case the proposal should specify the exact requirements (laptops, software to install, etc.). Important dates: http://www.unbsj.ca/sase/csas/data/ws/icbo2013/dates.html ============ 4 January 2013: Workshop and tutorial proposal submission deadline 18 January 2013: Notification of acceptance of workshops and tutorial proposals 1 February 2013: Conference (long & short) paper submission deadline 1 April 2013: Notification of conference paper acceptance 15 April 2013: System, early career and workshop paper submission deadline 15 May 2013: Notification of system, early career and workshop paper acceptance 20 May 2013: Submission of late breaking reports and highlight track papers 1 June 2013: Notification of acceptance of late breaking reports and highlight-track papers 15 June 2013: Deadline for all camera-ready copies for the proceedings Organizing Committee: http://www.unbsj.ca/sase/csas/data/ws/icbo2013/committees.html ================= Co-Scientific Chair: Michel Dumontier Co-Scientific Chair: Christopher Baker Local Organizer: Gregory Butler Program Chair: Robert Hoehndorf Workshop and Tutorial Chair: Chris Mungall Poster and Demonstration Chair: Trish Whetzel Proceedings and Special Issue Chair: Janna Hastings Early Career Chair: Melissa Haendle Publicity Chair: Sivaram Arabandi Sponsorship Chair: TBD From djwild at indiana.edu Wed Nov 14 12:26:23 2012 From: djwild at indiana.edu (David Wild) Date: Wed, 14 Nov 2012 12:26:23 -0500 Subject: [BiO BB] Introductory Cheminformatics PDF eBook available for $25 Message-ID: All, Just to let you know that the Introducing Cheminformatics PDF eBook is available until the end of the year for a reduced price of $25 at http://www.lulu.com/shop/david-wild/introducing-cheminformatics/ebook/product-20073569.html The eBook is in the form of a regular (unprotected) PDF, and is derived from learning materials used at Indiana University. It gives an intensive introduction to cheminformatics, including the history of the field, representing 2D and 3D chemical structures on computer, storing and using databases of chemical and related biological information, handling chemical information on the web and in the scholarly literature, and giving an overview of some advanced topics such as use of cheminformatics in chemistry libraries, clustering and diversity, QSAR and predictive modeling, 3D alignment and docking, and software toolkits cheminformatics software. The eBook is provided in PDF format, and is split into 12 lessons, each focusing on a particular area of cheminformatics. The first six are focused on the foundational aspects of the field, such as representing 2D structures, and the remaining six cover more advanced applications in the field. Each lesson details learning objectives and concludes with a set of questions that are designed to be thought provoking, with responses and answers in a final chapter. The text is hyperlinked to current resources on the web, with references to pertinent external articles where appropriate. The eBook is designed for computing, biology, bioinformatics, chemistry, library science and other students needing an introduction to the field, and also would be suitable for professional life science or computing practitioners who need a rapid, flexible introduction to cheminformatics. More information on the eBook is at http://slg.djwild.info. Please feel free to forward this to anyone who might be interested David _____________________________________________ Dr. David J. Wild, Assistant Professor Indiana University School of Informatics & Computing http://about.me/djwild http://djwild.info 901 E 10th St Rm 207, Bloomington, IN 47408 Tel. +1 812 856 1848 Email djwild at indiana.edu From rrwagner at faw.at Mon Nov 19 10:47:47 2012 From: rrwagner at faw.at (Prof. Roland Wagner) Date: Mon, 19 Nov 2012 16:47:47 +0100 Subject: [BiO BB] ITBAM 2013 Call for Papers Message-ID: <50AA54A3.9080802@faw.at> [Apologies for cross-posting] Call for Papers 4th International Conference on Information Technology in Bio- and Medical Informatics - ITBAM 2013 Prague (Czech Republic) August 26 - 30, 2013 Data intensive disciplines, such as life sciences and medicine, are promoting vivid research activities in the area of databases. Modern technologies, such as high-throughput mass- spectrometry and sequencing, micro-arrays, high-resolution imaging, etc. produce enormous and continuously increasing amounts of data. Huge public databases provide access to aggregated and consolidated information on genome and protein sequences, biological pathways, diseases, anatomy atlases, and scientific literature. There has never been more potentially available information to study biomedical systems, ranging from single cells to complete organisms. However, it is a non-trivial task to transform the vast amount of biomedical data into actionable information triggering scientific progress and supporting patient management. Major biomedical application scenarios for research in the database community include but are not limited to: * Systems biology * Genomics, proteomics, and metabolomics * Genome-wide association studies * Drug target discovery and personalized medicine * Neuroscience and neuroinformatics * Electronic patient records * Patient monitoring * Surgery planning and support * etc. Various emerging database technologies for coping with the challenges of these application scenarios have been developed and are an active area of research in information technology: * Administration of vast amounts of data * Integration of heterogeneous data sources * Federated and distributed databases * Data warehouses * Data mining techniques such as classification, clustering, association rule mining, etc. * Decision support systems * Information and image retrieval * Signal processing and streaming databases * Privacy protection and data security * Data quality assurance * Process management and collaborative work * User interfaces and visualization * Interoperability and standardization * etc. Designing database technology to support applications in life sciences and medicine is an inspiring field of interdisciplinary research. The path from an idea to a practical application is often long and laborious, involving intensive interactions between experts in information technology, life sciences and the medical field. ITBAM accompanies and supports this path by providing an excellent venue for the exchange of ideas, fruitful discussions, and effective interactions among interdisciplinary researchers. In addition to the regular conference program featuring presentations of full and short research papers published in the proceedings, ITBAM encourages the submission of posters reporting work in progress. All accepted posters will be displayed during the whole event and abstracts will also be included in the proceedings. IMPORTANT DATES * Submission of full papers (firm): February 25, 2013 * Notification of acceptance: May 6, 2013 * Submission of posters (firm): May 6, 2013 * Camera-ready copies due: June 7, 2013 Paper Submission Details: Authors are invited to submit electronically original contributions or experience reports in English. The submitted manuscript should closely reflect the final paper as it will appear in the proceedings. * Paper submissions should not exceed 15 pages in LNCS format. Poster submissions are expected to consist of 1 page Abstract (http://www.springer.de/comp/lncs/authors.html). * Any submission that exceeds length limits or deviates from formatting requirements may be rejected without review. * For paper registration and electronic submission see: https://confdriver.ifs.tuwien.ac.at/dexa2013 * Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. * Duplicate submissions are not allowed. Authors are expected to agree to the following terms: "I understand that the paper being submitted must not overlap substantially with any other paper that I am a co-author of and that is currently submitted elsewhere. Furthermore, previously published papers with any overlap are cited prominently in this submission." Accepted Papers: All accepted conference papers will be published in "Lecture Notes in Computer Science" (LNCS) by Springer Verlag. Accepted full papers will be of 15 pages length, short papers 8 pages. Authors of accepted papers must sign a Springer copyright release form. For further inquiries, please contact the Conference Organisation Office (gabriela at dexa.org). GENERAL CHAIRPERSON: * Christian B?hm, University of Munich, Germany PROGRAM COMMITTEE CO-CHAIRPERSONS: * Sami Khuri, San Jos? State University, USA * Miroslav Bursa, Czech Technical University Prague, Czech Republic * M. Elena Renda, IIT - CNR, Pisa, Italy PROGRAM COMMITTEE: tbd -- WARNING: Computer viruses can be transmitted via email. The recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. Warning: Although the company has taken reasonable precautions to ensure no viruses are present in this email, the company cannot accept responsibility for any loss or damage arising from the use of this email or attachments.