From dan.bolser at gmail.com Thu Jul 1 04:31:48 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 1 Jul 2010 09:31:48 +0100 Subject: [BiO BB] BioWikis - NETTAB 2010 Call for Contributions Message-ID: Blatantly not sorry for cross-posting, Dan. ---------- Forwarded message ---------- From: Date: 30 June 2010 17:15 Subject: [Nettab-Announce] NETTAB 2010 Call for Contributions To: nettab-announce at istge.it NETTAB 2010 on "Biological Wikis" November 29 - December 1, 2010, Naples, Italy http://www.nettab.org/ CALL FOR PAPERS See below for Topics, Contributions sought, Deadlines, Instructions and Committees. RATIONALE It is now clear that wiki systems offer a variety of advantages for the management of biological data and information. Some of the specific aims of wikis for biology (bio-wikis) include: ? ?* Collaborative development and sharing of knowledge ? ?* Collaborative annotation of database contents ? ?* Collaborative creation of database contents The collaborative development and sharing of documentation and knowledge allows communities to promote, exploit, discuss and reach consensus on procedures, data, experiences, news, and other varied information. Indeed valuable expertise and interests in special topics are usually distributed, and are rarely concentrated in a unique site or research group. The collaborative annotation of biological databases is increasingly under consideration because extended and accurate curation of an ever increasing volume of data is extremely costly and time consuming. Such distributed networks can help to improve and extend databases curation beyond that which is possible with, typically, limited numbers of curation staff. It allows users to contribute their expertise and observations ?independently of database central organizations. Although the contents of the database are collaboratively annotated, the underlying databases themselves are left unchanged. Furthermore, collaborative creation of community databases can capture emerging structure in rapidly developing fields. These database-wikis are indexes of biologically relevant data that emerge from focused and rapidly developing communities. They form a stopgap between unstructured discussion in fora and on mailing lists and the 'mature' databases that emerge subsequently. Hence they can be useful for discerning trends and promoting best practices, as well as ?collect unique and timely information. In the future, collaborative 'wiki' updates of almost all database contents can be envisaged. However several important issues need to be addressed: ? ?* How reliable are user contributions? ? ?* What format should annotations take? ? ?* How is this information feed back into 'authoritative' databases? Procedures should be implemented to support assessment of users' contributions, extraction of structured data from annotations, uptake of original data into reference databases. The authoritativeness of contributions is essential: how can quality be assessed? How do we deal with contributions from casual end users, since these are usually not considered adequate when compared with professional annotation at service centers. Can the open edition model of many wiki systems, e.g. Wikipedia, be as successful in life sciences? ?Alternatively, should the usual criteria for assessing quality of research be applied, including peer-evaluation of contributions and identification of users? Crediting users for their contributions (e.g. authorship assignment) may be necessary to stimulate ?the broadest possible participation. ?Which further benefits may be imagined to acknowledge user investment (subscriptions to services, journals, ...)? Special features may be required to cater for the specificity of biological data: textual information is only a small part of biological data, how can the numerous and heterogeneous biological data types be catered for, e.g. ?images, plots, diagrams? An adaptation of current wiki systems is needed. A survey of existing systems as well as current development efforts will be useful, so that possible synergies can be identified and supported, as well as ensure a coherent set of interoperable biological wikis. TOPICS The following list is not meant to be exclusive of any further topics as stated above. Submitted contributions should address one or more of the following topics: ? ?* Wiki development tools ? ? ? ? ?o Wikimedia ? ? ? ? ?o Wikimedia extensions ? ? ? ? ?o Semantic Wikis ? ? ? ? ?o Wiki-coupled CMSs ? ? ? ? ?o Other wikis ? ?* Arising issues for the biomedical domain: ? ? ? ? ?o Authoritativeness of contributions and sites ? ? ? ? ?o Quality assessment ? ? ? ? ?o Users acknowledgement ? ? ? ? ?o Stimulatation of quality contributions ? ? ? ? ?o Authorships management and reward ? ? ? ? ?o 'Scientific production' value for contributions ? ? ? ? ?o Management of bioinformatics data types ? ?* Wikis and collaborative systems for: ? ? ? ? ?o Genomics, proteomics, metabolomics, any -omics ? ? ? ? ?o Proteins analysis and visualization ? ? ? ? ?o gene and proteins interactions ? ? ? ? ?o metabolic pathways ? ? ? ? ?o oncology research ? ?* Issues to be tackled by wiki and collaborative research for: ? ? ? ? ?o Genomics, proteomics, metabolomics, any -omics ? ? ? ? ?o Proteins analysis and visualization ? ? ? ? ?o gene and proteins interactions ? ? ? ? ?o metabolic pathways ? ? ? ? ?o oncology research TYPE OF CONTRIBUTIONS The following possible contributions are sought: ? ?* Oral communications ? ?* Posters ? ?* Software demos All accepted contributions will be published in the proceedings of the workshop. DEADLINES * ?September 24, 2010: Oral communications submission ? ? ? ? ?o Decisions announced: October 24, 2010 * October 17, 2010: Posters submission ? ? ? ? ?o Decisions announced: October 24, 2010 * October 29, 2010: Early registration ends * November 29 - December 1, 2010: Workshop and Tutorials INSTRUCTIONS Kindly follow the instructions carefully when preparing your contribution and submit your contribution through the EasyChair system at http://www.easychair.org/conferences/?conf=nettab2010. All contributions should follow the same format, as specified here: font type: Times New Roman, font size: 12 pti, page size: A4, left and right margins: 2.0 cm, upper margin: 2.5 cm, lower margin: 2.0 cm. The lenght of contributions for oral communications should be between 3 and 5 pages, including tables and figures. They should include: Abstract, Introduction, Methods, Results and Discussion, References. All contributions for oral communications will be evaluated by at least three referees. The length of contributions for posters should be no more then 3 pages, including tables and figures. They should include: Introduction, Methods, Results, References. All posters will be evaluated on the basis of their relevance fot the workshop's topics only. For any further information or clarification, please contact the organization by email at info at nettab.org. ORGANIZATION Co-chairs ? ?* Angelo Facchiano, CNR-ISA, Avellino, Italy ? ?* Paolo Romano, National Cancer Research Institute, Genoa, Italy Scientific Committee ? ?* Claudia Angelini, IAC, National Research Council, Napoli, Italy ? ?* Roland Barriot, Universit? Paul Sabatier - CNRS, Toulouse, France ? ?* Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, United Kingdom ? ?* Dan Bolser, University of Dundee, Scotland, United kingdom ? ?* Philip E. Bourne, University of California, San Diego UCSD, La Jolla, USA ? ?* Mike Carasio, Keygene N.V., Wageningen, The Netherlands ? ?* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy ? ?* Italia De Feis, IAC, National Research Council, Napoli, Italy ? ?* Angelo Facchiano, ISA, National Research Council, Avellino, Italy ? ?* Carl Herrmann, Universit? de la M?diterran?e, Marseille, France ? ?* Pascal Hingamp, Universit? de la M?diterran?e, Marseille, France ? ?* Eran Hodis, Weizmann Institute of Science, Rehovot, Israel ? ?* Robert Hoffmann, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, USA ? ?* Thomas Kelder, BiGCaT Bioinformatics, University of Maastricht, The Netherlands ? ?* Alexander Pico, The Gladstone Institutes, University of California, San Francisco, USA ? ?* Jaime Prilusky, Bioinformatics, Weizmann Institute of Science, Rehovot, Israel ? ?* Paolo Romano, Bioinformatics, National Cancer Research Institute, Italy ? ?* Andrew Su, Bioinformatics, Genomics Institute of the Novartis Research Foundation, San Diego, USA ? ?* Joel Sussman, Weizmann Institute of Science, Rehovot, Israel ? ?* Tim Vickers, Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, USA ? ?* Wyeth Wasserman, Department of Medical Genetics, University of British Columbia, Vancouver, Canada ? ?* and further members yet to be confirmed Organizing Committee ? ?* Claudia Angelini, IAC, National Research Council, Napoli, Italy ? ?* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, Italy ? ?* Italia De Feis, IAC, National Research Council, Napoli, Italy ? ?* Angelo Facchiano, ISA, National Research Council, Avellino, Italy ? ?* Paolo Romano, Bioinformatics, National Cancer Research Institute, Genoa, Italy Supporting Institutes, Scientific Societies and Projects This list is still under definition. ? * National Research Council (CNR), Italy ? * National Cancer Research Institute (IST), Genoa, Italy ? * Italian Network for Oncology Bioinformatics (RNBIO) Sponsors Sponsorships are still under definition. You are welcome to email us for further information if you are interested in sponsoring this workshop. We look forward to meeting you in Naples! Paolo Romano and Angelo Facchiano ?on behalf of the Scientific Committee Paolo Romano (paolo.romano at 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 ?Skype: p.romano Web: http://www.nettab.org/promano/ _______________________________________________ Nettab-Announce mailing list Nettab-Announce at istge.it http://webmail.istge.it/mailman/listinfo/nettab-announce From ngadewal at yahoo.com Fri Jul 2 07:33:18 2010 From: ngadewal at yahoo.com (nikhil gadewal) Date: Fri, 2 Jul 2010 04:33:18 -0700 (PDT) Subject: [BiO BB] Cathepsin Message-ID: <126034.93962.qm@web51505.mail.re2.yahoo.com> Dear Members, ?????????I am looking for?an online tool which predicts the cleavage site for the set of proteins using an enzyme "Cathepsin G". If anybody have a program (tool) please let me know. ???????? Thanks in advance. Regards, ? NIKHIL S. GADEWAL ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India From denguehost at gmail.com Sat Jul 3 07:57:44 2010 From: denguehost at gmail.com (Chris Baker) Date: Sat, 3 Jul 2010 08:57:44 -0300 Subject: [BiO BB] CFP: ECCB 2010 Workshop: Annotation, interpretation and management of Mutations (AIMM2010) , Ghent, Belgium, In-Reply-To: References: Message-ID: ========================================================================================= ECCB 2010 Workshop: Annotation, interpretation and management of Mutations (AIMM2010) - Call for Papers ========================================================================================= http://www.unbsj.ca/sase/csas/data/aimm2010/ This year's will workshop showcase the state of the art in extraction and reuse of genotype-phenotype information. Annotation of mutations with their impact on phenotypic expression is crucial to understanding genetic mechanisms involved in phenotypic processes and ultimately in complex diseases. Managing this knowledge is key to generating novel hypotheses. Despite the existence of literature and databases describing impacts of mutations, association studies fail to deliver linkage to phenotypes which is the most important contemporary research interest. Extraction of such information from scientific literature is a promising research field and existing solutions are ready to be deployed as services and as semantic web services. Keynote Speakers: Michael Schroeder - Professor BIOTEC Technical University Dresden, DE. Joost Schymkowitz - Professor VIB Switch Laboratory, Vrije Universiteit Brussel. Submissions: We invite short papers (3000 words / 8 pages) and demonstrations on the following topics: * Issues related to storage and representation of mutation information, including traditional databases, RDF triple stores, semantic knowledgebases and mutation ontologies. * NLP tools and systems for recognition and grounding of entities related to mutations and their annotations: including mutation impacts and mutation grounding. Also evaluations of these NLP tools and systems. * Systems for mutation impact prediction, reusing existing mutation databases and text extracted data. * Bioinformatics data integration, discoverable semantic web services and workflows, and semantic assistants for mutation annotation integration. Submissions can be made through the EasyChair submission page: https://www.easychair.org/account/signin.cgi?conf=aimm2010 Submission guidelines can be found on our website http://www.unbsj.ca/sase/csas/data/aimm2010/ Organizers Christopher J.O. Baker Ph.D., Associate Professor / Innovatia Research Chair, Department of Computer Science and Applied Statistics, University of New Brunswick, Saint John, Canada. Email: bakerc at unb.ca Dietrich Rebholz-Schuhmann MD, Ph.D., Research Group Leader, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. Email: Rebholz at ebi.ac.uk Ren? Witte Dr.-Ing., Assistant Professor, Group Leader, Semantic Software Lab, Concordia University, Department of Computer Science and Software Engineering, Montreal, Canada. Email: rwitte at cse.concordia.ca Important Deadlines: Abstract submission: July 20 Full paper submission: July 26 Acceptance notification: August 12 Final manuscript submission: September 2 AIMM2010 workshop: September 26 Venue: ECCB2010 @ Ghent, Belgium. http://www.eccb2010.org/ Previous Events: http://www.ebi.ac.uk/Rebholz-srv/aimm.html http://www.biomedcentral.com/content/pdf/1471-2105-10-S8-info.pdf 2010 Session Topics: http://www.unbsj.ca/sase/csas/data/aimm2010/ ===================================================== Mutation Databases and Metadata: Design, Content, Accuracy ----------------------------------------------------- Over 400 mutation databases have been produced in the past (determined via ?google? search). Many are no longer maintained and cover very specific data sets. In total, these repositories have been designed to support a wide range of features including listings of SNPs, point mutations, insertions, deletions, and observed phenotypes. Furthermore they incorporate a wide range of modified protein features and metrics in the accompanying annotations to the mutation descriptions. In the main these databases are manually curated however mutation annotations are frequently inaccurate e.g. in the PDB, inaccurate to the degree of 40 % of all PDB records. In addition to assessing content and coverage issues this session will explore issues related to storage and representation of mutations information showcasing a spectrum of mutation repositories types from traditional databases to RDF triple stores semantic knowledgebases and mutation ontologies. ======================================================= Extraction of mutations and annotations from literature ------------------------------------------------------- AI techniques such as text mining and natural language processing have been used in BioNLP to enable the extraction and grounding of named entities (mutations, protein, organisms) and impact annotations (protein properties, directions and scale of impact) from the mutation literature, with high levels of precision and recall, albeit prototype in scale. To facilitate their adoption it is necessary to measure the accuracy, recreation and update of existing mutation databases as we as their incorporation into semi manual annotation pipelines - the next milestone. In addition there is continuing discussion over the appropriate metrics for individual tasks within these systems which requires community involvement. This emergent technology now needs standardization. For the workshop we will solicit presentations, posters and demos of NLP tools, evaluations of mutation pipelines, mutation ontology population, and invite suggestions for a database reconstruction challenge to illustrate state of the art performance. ===================================================== Impacts of Mutations: Prediction and Bootstrapping ----------------------------------------------------- The ability to predict the impact of a mutation or the consequence of a sequence variant is central to the diagnosis of genetic diseases. Non-synonymous mutations may impact translational regulation, mRNA stability, mRNA splicing and rates of translation. Proteins affected by nsSNPs may have altered; catalytic sites, stability, ability to aggregate, and or post-translational modifications. Moving from SNP to sequence to structure and function has been addressed with varying degrees of accuracy with sequence and structure based (molecular mechanism, empirical energy function or machine learning) methods. Applying such techniques at a genome scale requires that robust approaches are identified, benchmarked with standard metrics in order to assign valid significance to ns mutations. Reuse of existing mutation databases and text extracted data for training prediction algorithms and checking quality of predictions is pivotal. ===================================================== Mutation Data Integration and Reuse ----------------------------------------------------- For scientists to make rapid advances in our understanding of living systems our infrastructures and techniques for knowledge translation are insufficient. Hypothesis generation based on the reuse of extracted information and in-silico predictions remains a distant capability for most scientists. Furthermore building the derived insights of mutational studies into robust models of a specific biological domain also seems far off. A multi level approach to biology must be accompanied by integrated infrastructures build from a diverse toolset. Integration with information from different systems will require the adoption of rich metadata for semantic knowledge integration, such as provided by existing phenotype ontologies and ontologies specific to impacts, sequence rearrangements and in vitro methodologies to construct mutants. For integration of bioinformatics data, discoverable semantic web services and workflows for mutation integration are emerging paradigms and this session will host examples of reusable mutation extraction and data integration workflows. Semantic assistant clients facilitating real time mutation annotation integration to desktop applications e.g. when browsing pubmed abstracts will be also be showcased. -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker From alexandru.floares at oncopredict.com Sat Jul 3 10:11:02 2010 From: alexandru.floares at oncopredict.com (Alexandru Floares) Date: Sat, 3 Jul 2010 07:11:02 -0700 (PDT) Subject: [BiO BB] CFP CIBB 2010 & i-CDSS 2010 Message-ID: <52260.188.24.83.133.1278166262.squirrel@secure82.inmotionhosting.com> [apologies for multiple posts] Special Session Intelligent Clinical Decision Support Systems (i-CDSS) CIBB 2010 - SEVENTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS Web site: http://cibb10.pa.icar.cnr.it/ Date: September 16-18, 2010 Location: Palermo, Italy Description and Scope Medicine and its scientific and technological background are rapidly and profoundly changing in the Information Age. The impact of the biomedical equipment used to produce and collect laboratory data, signals and images is impressive. New high-throughput technologies have appeared and existing technologies have been radically transformed. For example, techniques such as electroencephalography or radiography, which two decades ago seemed to reach a bottleneck, came to a new life, and their importance as diagnostic tools is continuously increasing. As a result, our capacity to produce and record huge amount of complex biomedical data - patient conditions, diagnostic tests, treatments, outcomes, different kind of "omics" data (genomics/proteomics, etc.), biosignals and images ? have dramatically increased. These data provide an unprecedented source of information that can lead to potential improvements in medical diagnostic, prognostic, and individualized, optimized treatment strategy. However, much more work is required. Although technology has brought about tremendous new sources of important biomedical data, we have not moved very far with regard to extracting the knowledge that lies latent in this data. In recent years, modern computer science has brought forth tremendous new tools such as artificial neural networks, decision trees, fuzzy logic, evolutionary computing, support vector machines, and the like. Also, the prevailing reductionist view by its own result seems to lead biomedicine to the systemic view. In some recent studies, omics data are placed in a pathways/networks context, but most often only the structure of these networks is investigated ? leaving the more complex dynamics as an unresolved challenge for dynamical systems analysis and control theoretic applications. Yet the professional, political, and social issues that separate the medical community and the intelligent computing and dynamical systems communities have delayed the serious application of these tools to accelerate progress in translational medicine, genome-to-phenome, bench-to-bedside and clinical trials, ultimately hindering implementation in public health programs. The mission of these annually held special sessions is to develop a foundation for Knowledge Based Medicine (KBM), the next step beyond Evidence Based Medicine (EBM), combining computational intelligence and dynamical systems. Topics We encourage papers describing new or applying existing intelligent computing methods to real and practical medical and health-care problems in which the biomedical problems are central. The topics of interest include, but are not limited to: ? disease modeling, diagnosis and prevention ? prognostic and treatment outcome predictions ? patient monitoring and alarm systems ? optimization of patient-management workflows ? biomedical data\text\web mining and data visualization ? integration of biomedical data sources and domain knowledge ? translational bioinformatics (genomics, proteomics, etc.) ? biomedical signals and images processing ? design of clinical trials Submissions addressing theoretical problems should clearly outline the expected impact of the proposed solution to the medical field. Audience ? Medical informaticians ? Bioinformaticians ? Neuroinformaticians ? Computer scientists ? Statisticians ? Molecular biologists and medical doctors ? Biomedical and electrical engineers ? Other researchers and developers Session Chairs Alexandru Floares, SAIA ? OncoPredict & Solutions of Artificial Intelligence Applications, Cluj-Napoca, Email: alexandru _ dot _ floares _ at _ iocn _ dot _ ro Leif Peterson, Center for Biostatistics, The Methodist Hospital Research Institute, Houston, Texas USA, E-mail: peterson _ dot _ leif _ at _ ieee _ dot _ org Important Dates Manuscript submission deadline: July 10, 2010 Notification of acceptance: July 15, 2010 Camera-ready papers due: July 30, 2010 Conference: September 16-18, 2010 Submissions (Instructions to Authors) Papers submitted for this session should be submitted by July 15, 2010. To submit a paper, please use the following steps: 1. Prepare your paper in LATEX following the guidelines available at http://cibb10.pa.icar.cnr.it/images/cibb-sample-v.1.2.zip. The size of the paper should not exceed 10 pages in that format. 2. E-mail manuscripts in pdf format to: a. alexandru _ dot _ floares _ at _ iocn _ dot _ ro b. peterson _ dot _ leif _ at _ ieee _ dot _ org Proceedings Accepted papers will be published in the compact disk of conference proceedings with ISBN. A selection of papers presented at CIBB 2010 will be published in revised extended form as a post conference volume. Revised papers of the previous editions of CIBB were published in the Springer Verlag LNBI/LNCS (see http://www.springer.com/series/538 General Chairs Paulo J. Lisboa, John Moores University, Liverpool, UK Riccardo Rizzo, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Biostatistics Technical Chair Elia Biganzoli, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy Bioinformatics Technical Chair Francesco Masulli, University of Genova, Italy and Temple Univ. Philadelphia, PA, USA Scientific Committee Sansanee Auephanwiriyakul, Department of Computer Engineering, Chiang Mai University, Chiang Mai, Thailand Federico Ambrogi, University of Milan Milan, Italy Claudia Angelini, Istituto per le Applicazioni del Calcolo "M. Picone" (IAC), sede di Napoli, IAC-CNR Naples, Italy Sanghamitra Bandyopadhyay, Indian Statistical Institute, Kolkata, India Gilles G. Bernot, University of Nice Sophia Antipolis, Nice, France Chengpeng Bi, Bioinformatics, Children?s Mercy Hosp., Kansas City, USA Mario Cannataro, University ?Magna Graecia? Catanzaro, Italy Xuewen Chen, Electrical Engineering and Computer Science, University of Kansas, Lawrence, Kansas, USA Giuseppe Di Fatta, Computer Science and Informatics School of Systems Engineering, The University of Reading Reading UK Enrico Formenti, University of Nice Sophia Antipolis, Nice, France Salvatore Gaglio, Dipartimento di Ingegneria Informatica, University of Palermo, Palermo, Italy Christoph Friedrich, Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany Antonio Giordano, University of Siena, Italy and Sbarro Institute for Cancer Research and Molecular Medicine and Center for Biotechnology, Temple Univ., Philadelphia, PA, USA Saman Halgamuge, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia Pietro Lio', Computer Laboratory, University of Cambridge, Cambridge, UK Michael Lones, Department of Electronics, University of York, York, UK Elena Marchiori, Department of Computer Science, Faculty of Science, Radboud University, Nijmegen, The Netherlands Giancarlo Mauri, Dipartimento di Informatica, Sistemistica e Comunicazione, University of Milano Bicocca Milan, Italy Luciano Milanesi, Istituto di tecnologie biomediche (ITB), sede di Milano, CNR, Milan, Italy David A. Pelta, Dept. of Computer Science and A.I. University of Granada, Granada Spain Leif E. Peterson, Methodist Hospital Research Institute Houston, TX, USA Gianluca Pollastri, Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Dublin Ireland Mihail Popescu, Health Management and Info. Dept., University of Missouri - Columbia, Columbia, Missouri, USA Volker Roth, Computer Science Dept., University of Basel, Basel, Switzerland Giuseppe Russo, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology Temple University Philadelphia, PA, USA Jennifer Smith, Electrical and Computer Engineering Dept., Boise State University, Boise, Idaho, USA Federico Mattia Stefanini, Department of Statistics "G. Parenti", University of Florence, Florence Italy Alfonso Urso, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Giorgio Valentini, University of Milan, Milan, Italy Kay Wiese, School of Computing Science, Simon Fraser University, Surrey, Canada Yanqing Zhang, Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA Local Organizing Committee Alfonso Urso, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Pietro Storniolo, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Giosu? Lo Bosco, University of Palermo, Italy Congress Management: Fabio Ferrara, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Giampiero Rizzo, Istituto di Calcolo e Reti ad Alte Prestazioni, (ICAR), sede di Palermo, CNR, Palermo Italy Steering Committee Pierre Baldi, University of California Irvine CA, USA Alexandru Floares, Oncological Institute Cluj-Napoca Romania Jon Garibaldi, University of Nottingham UK Francesco Masulli, University of Genova, Italy and Temple University Philadelphia, PA, USA Roberto Tagliaferri, University of Salerno Italy ===================================================================== Alexandru Floares, MD, PhD Head of Artificial Intelligence Department Cancer Institute Cluj-Napoca 400015, Str. Republicii, Nr. 34-36, Cluj-Napoca, Romania Email: alexandru.floares at iocn.ro President of SAIA Group 400310 Str. Al. Vlahuta, Bl. Lama C, Ap. 45, Cluj-Napoca, Romania Email: alexandru.floares at saia.ro From anthony.goldbloom at kaggle.com Tue Jul 6 02:49:39 2010 From: anthony.goldbloom at kaggle.com (Anthony Goldbloom | Kaggle) Date: Tue, 6 Jul 2010 16:49:39 +1000 Subject: [BiO BB] New machine learning Q&A site Message-ID: A new Q&A site has just launched for machine learning and statistics questions. http://metaoptimize.com/qa/ The site is not specific to bioinformatics. The idea is that there isn't enough cross-polination between adjacent fields like stats, machine learning, natural language processing, bioinformatics etc. The site aims to improve the communication between these fields. It hopes to allow people to come together and share knowledge, techniques and ideas in an informal online setting - and to discuss details that don't always make it into publications. From yvan.strahm at gmail.com Wed Jul 7 03:04:19 2010 From: yvan.strahm at gmail.com (yvan) Date: Wed, 07 Jul 2010 09:04:19 +0200 Subject: [BiO BB] Cathepsin In-Reply-To: <126034.93962.qm@web51505.mail.re2.yahoo.com> References: <126034.93962.qm@web51505.mail.re2.yahoo.com> Message-ID: <4C3426F3.3090804@gmail.com> On 07/02/2010 01:33 PM, nikhil gadewal wrote: > Dear Members, > > I am looking for an online tool which predicts the cleavage site for the set of proteins using an enzyme "Cathepsin G". If anybody have a program (tool) please let me know. > Thanks in advance. > Regards, > > NIKHIL S. GADEWAL > ACTREC, > Tata Memorial Centre, > Kharghar, > Navi Mumbai, > India > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > Hello, Did you try PoPS? http://pops.csse.monash.edu.au/pops-cgi/index.php Cheers, yvan From idoerg at gmail.com Fri Jul 23 12:13:34 2010 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 23 Jul 2010 12:13:34 -0400 Subject: [BiO BB] Announcing CAFA: Critical Assessment of protein Function Annotations In-Reply-To: References: Message-ID: Apologies for cross-posting Announcing CAFA: Critical Assessment of protein Function Annotations http://biofunctionprediction.org Genome sequencing and structural genomics projects have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function". The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations. About the CAFA experiment *The problem*: There are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are preforming? *The solution*: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function and Biological Process. A set of protein sequences is provided by the organizers. Participants are expected to submit their predictions by the submission deadline. The predictions will be evaluated during the Automated Function Prediction (AFP) meeting, which has been approved as a Special Interest Group (SIG) meeting, at ISMB 2011 conference (Vienna, Austria). How to participate in CAFA? 1. Register for the experiment at http://biofunctionprediction.org 2. (Recommended) Subscribe to the low-traffic announcement list http://groups.google.com/group/afp2011-announce 3. Download target proteins, available September 15, 2010 4. Submit predictions before January 15, 2011 5. Join us at the AFP-SIG at Vienna July 15-16, 2011 for the fifth protein function prediction meeting to hear the CAFA results, and about the latest research in computational protein function prediction More details at: http://biofunctionprediction.org Looking forward to hearing from you! The CAFA organizing Team: Predrag Radivojac, Michal Linial and Iddo Friedberg -- Iddo Friedberg http://iddo-friedberg.net/contact.html From cannataro at unicz.it Sat Jul 24 12:44:06 2010 From: cannataro at unicz.it (Mario Cannataro) Date: Sat, 24 Jul 2010 18:44:06 +0200 (CEST) Subject: [BiO BB] Advanced Computing Solutions for Health Care and Medicine - Special Issue Journal of Computational Science Message-ID: I apologize for any cross-posting of this announcement. ===================================================================== Special Issue of the Journal of Computational Science, Elsevier ?Advanced Computing Solutions for Health Care and Medicine? http://bioingegneria.unicz.it/HealthCareComputing/ http://ees.elsevier.com/jocs/ ===================================================================== * * * CALL FOR PAPERS - Deadline September 30, 2010 * * * ===================================================================== SCOPE It is undoubtful that Computer Science and Health Care are two research fields that, especially recently, are sharing common topics. Many conferences (e.g. see CBMS - Computer-Based Medical Systems and ICCS - International Conferences on Computational Science) have been organized where both computer scientists and physicians discussed about research problems and results of common interests. Similarly, measurements, communication and electronic engineering communities are presenting their results to medical doctors and biologists communities for health care and life quality applications. There are research problems in computer science that are critical while addressing issues related to health care and there are research topics in biomedicine and in health care that cannot be addressed without computer science applications. For instance, in the first direction (computer science versus health care), high performance computing and communications, (large) data base management techniques, data quality and real time communications poses research problems that find application and validation in health care management systems where performances cannot accept any compromise. In other words, the health care domain can be considered as a realistic validation platform for many computer science solutions. On the other side, health care information and management systems are currently one of the main interests for health care actors. Significant improvement in efficiency and effectiveness in health care strategies have been improving by using information and communication technologies (ICT). High-performance and large-scale health care applications pose different challenges to computer science such as in distributed data management of medical images, high-performance simulation of organs or biological systems, data mining and warehousing of large health care data stores, just to name a few. The goal of this special issue is to collect high quality papers containing results in computer science applications for health care and medical environments. In particular, we invite papers on solutions and prototypes that already have found their utilization in clinical houses or in biomedical laboratories, both in patient front solutions (such as surgery room, electronic patient records improvements, medical doctor decision process) or in back office solutions (such as in biological laboratory, off line clinical data analysis). TOPICS OF INTEREST Research areas of relevance to this special issue would therefore include, but are not limited to, the following topics: - advanced solutions for clinical information system - bioinformatics applications for genomics and proteomics - bioinformatics applications for medical images - medical data and communication integration - high performance computation within health care applications - Peer-to-Peer and large scale social networks techniques for health care problems managements (e.g., epidemiological control and studies) - data management and communication improvements in large scale health care systems - large-scale Electronic Health Records - high-performance simulations of organs - high-performance simulations of biological systems - large-scale, trans-national health-care infrastructures and applications The special issue is also interested in computer science solutions integrated in electronic devices, or high performance communication solutions supporting health care management problems, as for instance: - telemedicine, - integrated Informatics Systems for Medicine, - high performance and portable clinical data management solutions. IMPORTANT DATES: Paper submission: 30 September, 2010 First Decision notification: 15 December, 2010 Revised Paper Submission: 31 January, 2011 Second Decision notification: 31 March, 2011 Final papers: 30 April, 2011 Tentative Publication Schedule: 2011 SUBMISSION GUIDELINE: All manuscripts and any supplementary material should be submitted through the Elsevier Editorial System (EES). The EES website is located at http://ees.elsevier.com/jocs/. Authors must select ?Special Issue: Healthcare Computing? when they reach the ?Article Type? step in the submission process. The Guide for Authors is located at http://www.elsevier.com/wps/find/journaldescription.cws_home/721195/authorinstructions More information about the Journal of Computational Science can be found here: http://www.elsevier.com/wps/find/journaldescription.cws_home/721195/description#description Please contact Mario Cannataro (cannataro at unicz.it) for further information GUEST EDITORS: - Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy - Joakim Sundnes, Simula Research Laboratory, Norway - Pierangelo Veltri, University Magna Gr?cia of Catanzaro, Italy - Rodrigo Weber dos Santos, Federal University of Juiz de Fora, Brazil Backup Web Site: http://staff.icar.cnr.it/cannataro/HealthcareComputing/ **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ ****************************************