From market at iospress.nl Thu Dec 6 08:46:04 2012 From: market at iospress.nl (Mads Kaern) Date: Thu, 6 Dec 2012 08:46:04 -0500 Subject: [BiO BB] Relaunch and Call for Papers of In Silico Biology Message-ID: <50c0a19cc751_176bd4213c734a2@worker11.madmimi.managedmachine.com.tmail> RELAUNCH AND CALL FOR PAPERS We are pleased to announce that _[In Silico Biology](http://www.insilicobiologyjournal.com/)_ is now a journal devoted exclusively to biological systems modeling and simulation, and we invite researchers working in this rapidly growing field to submit original research manuscripts for publication and proposals for reviews and special issues. _In Silico Biology_ has a new editorial team composed of internationally recognized, leading researchers in quantitative systems and synthetic biology, and aims to become one of the leading journals of research on modeling and simulation in these areas. We offer: * Immediate online publication upon acceptance * Rapid editorial decisions * Traditional in-print publication * No publication fee * Low Open Access fee OPEN ACCESS FEE WILL BE WAIVED FOR ALL MANUSCRIPTS SUBMITTED IN RESPONSE TO THIS CALL **About the Journal** _In Silico Biology_ is a scientific research journal for the advancement of computational models and simulations in studies of complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e., "in silico") modeling and analysis tools are developed and applied to generate new knowledge about biological systems dynamics, their design and control and their evolution. Studies published in _In Silico Biology_ generally use mechanistic models to gain quantitative insights into molecular processes regulatory networks, cell physiology and morphology, tissue dynamics and organ systems. Specific areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, differentiation and morphogenesis, among others. **Submission of Papers** Authors are requested to submit their manuscript to [isb_submissions at iospress.com](mailto:isb_submissions at iospress.com). For detailed instructions to authors, check our website [www.insilicobiologyjournal.com/submission-of-manuscript](http://www.insilicobiologyjournal.com/submission-of-manuscript). **Advisory Board** * Dennis Bray, University of Cambridge, UK * Roland Eils, University of Heidelberg, Germany * Hiroaki Kitano, The Systems Biology Institute, Japan * Michael Mackey, McGill University, Canada * John Tyson, Virginia Tech, USA * Hans Westerhoff, University of Manchester, UK **Editor-in-Chief** * Mads Kaern, University of Ottawa, Canada Email: [isb at iospress.com](mailto:isb at iospress.com) For the complete Editorial Board, visit our website: [www.insilicobiologyjournal.com/editorial-board](http://www.insilicobiologyjournal.com/editorial-board/). [Sign up now for ISB eTOC Alerts](https://iospress.metapress.com/content/105655/toc-alert) Automatically receive tables of contents as each new issue publishes View this email on the web here: http://mad.ly/ef5f43?pact=294327638876519082&fe=1 Unsubscribe: https://go.madmimi.com/opt_out?pact=294327638876519082&fe=1&amx=3600996658 You can also forward to a friend: https://go.madmimi.com/forward/294327638876519082?amx=3600996658 IOS Press | Nieuwe Hemweg 6B, 1013 BG, Amsterdam, The Netherlands, Tel: +31 20 688 3355, Fax: +31 20 687 0019, Email: market at iospress.nl From ICCS_CONF at NTU.EDU.SG Sat Dec 8 11:14:32 2012 From: ICCS_CONF at NTU.EDU.SG (International Conference on Computational Science) Date: Sun, 9 Dec 2012 00:14:32 +0800 Subject: [BiO BB] International Conference on Computational Science. One week to submit! December 15, 2012 Message-ID: <629B8F547581594A9B9760E372AA15771AFA54C1DE@EXCHANGE32.staff.main.ntu.edu.sg> Dear Colleagues, Please accept our apologies if you receive multiple copies of this email. One week to Main Track submission deadline. Workshop deadlines may differ. ****************************************************** * ICCS 2013 * International Conference on Computational Science * Barcelona, Spain * June 5-7, 2013 * Submission deadline: December 15, 2012 * http://www.iccs-meeting.org/iccs2013 ****************************************************** NEWS: 25 thematic workshops registered: http://www.iccs-meeting.org/iccs2013/workshop-list.php Keynote speakers: http://www.iccs-meeting.org/iccs2013/keynotes.html ? Prof. Steve Furber, University of Manchester ? Prof. David De Roure, Oxford e-Research Centre ? Dr. Thierry van der Pyl, DG CONNECT, European Commission ? Prof. Raimond Winslow, The Johns Hopkins University, ---------------------------------- Authors are invited to submit manuscripts reporting original unpublished research and recent developments in Computational Sciences by December 15, 2012. All accepted papers will be printed in the conference proceedings published by Elsevier Science in the open-access Procedia Computer Science. The ICCS conference is the prime annual event in Computational Science. This interdisciplinary conference on modelling and simulation of real-world phenomena will draw academic and industry leaders from all relevant fields. ICCS intends to provide a forum to disseminate world-leading research in the field of (scientific) Computational Science and in particular to highlight the role which modelling and simulation plays in future scientific discovery. ICCS 2013 invites original contributions on all topics related to Computational Science, including, but not limited to: * Scientific Computing * Problem Solving Environments * Advanced Numerical Algorithms * Complex Systems: Modelling and Simulation * Hybrid Computational Methods * Web- and Grid-based Simulation and Computing * Parallel and Distributed Computing * Advanced Computing Architectures and New Programming Models * Visualization and Virtual Reality as Applied to Computational Science * Applications of Computation as a Scientific Paradigm * New Algorithmic Approaches to Computational Kernels and Applications * Computational Humanities * Education in Computational Science * Large Scale Scientific Instruments * Computational Sociology The submitted paper must be camera-ready and formatted according to the rules of Procedia Computer Science, not exceeding 10 pages. Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the paper submission system http://www.iccs-meeting.org/iccs2013/papers/upload.php Papers must be based on unpublished original work and must be submitted to ICCS only. After the conference, selected papers will be invited for a special issue of the Journal of Computational Science. ICCS is an ERA 2010 A-ranked conference series. For further details please visit http://www.iccs-meeting.org/ ---------------------------------- IMPORTANT DATES: Paper submission deadline: December 15, 2012 Notification of acceptance: February 10, 2013 ---------------------------------- ORGANIZERS: Conference Local Organizers: Vassil Alexandrov and Rosa Badia Workshop Chair: Michael Lees Publicity Chair: Valeria Krzhizhanovskaya Scientific Co-chair: Jack Dongarra Scientific Chair: Peter Sloot ----- To unsubscribe please send an email to LISTSERV at MLIST.NTU.EDU.SG with the following command in the body of your email: SIGNOFF ICCS or UNSUBSCRIBE ICCS From sandra.sendra.upv at gmail.com Mon Dec 10 16:52:45 2012 From: sandra.sendra.upv at gmail.com (Sandra Sendra) Date: Mon, 10 Dec 2012 22:52:45 +0100 Subject: [BiO BB] CFP: The 3rd IEEE International Workshop of Smart Communication Protocols and Algorithms (IEEE SCPA 2013) Message-ID: <201212102152.qBALqj4a026004@smtp.upv.es> Apologies for crossposting -------------------- CALL FOR PAPERS ----------------- The 3rd IEEE International Workshop of Smart Communication Protocols and Algorithms (SCPA 2013) June 9-13, 2013, Budapest, HUNGARY In conjunction with IEEE ICC 2013 http://scpa.it.ubi.pt/2013/ Selected papers will be invited to the Special Issue on Smart Protocols and Algorithms of the International Journal Network Protocols and Algorithms (ISSN 1943-3581) or to the Special Issue on Recent Patents on Telecommunications Journal ((Online)ISSN 2211-7415, (Print) ISSN 2211-7407) Communication protocols and algorithms are needed to communicate network devices and exchange data between them. The appearance of new technologies usually comes with a protocol procedure and communication rules that allows data communication while taking profit of this new technology. Recent advances in hardware and communication mediums allow proposing new rules, conventions and data structures which could be used by network devices to communicate across the network. Moreover, devices with higher processing capacity let us include more complex algorithms that can be used by the network device to enhance the communication procedure. Smart communication protocols and algorithms make use of several methods and techniques (such as machine learning techniques, decision making techniques, knowledge representation, network management, network optimization, problem solution techniques, and so on), to communicate the network devices to transfer data between them. They can be used to perceive the network conditions, or the user behavior, in order to dynamically plan, adapt, decide, take the appropriate actions, and learn from the consequences of its actions. The algorithms can make use of the information gathered from the protocol in order to sense the environment, plan actions according to the input, take consciousness of what is happening in the environment, and take the appropriate decisions using a reasoning engine. Goals such as decide which scenario fits best its end-to-end purpose, or environment prediction, can be achieved with smart protocols and algorithms. Moreover, they could learn from the past and ! use this knowledge to improve futur e decisions. In this workshop, researchers are encouraged to submit papers focused on the design, development, analysis or optimization of smart communication protocols or algorithms at any communication layer. Algorithms and protocols based on artificial intelligence techniques for network management, network monitoring, quality of service enhancement, performance optimization and network secure are included in the workshop. We welcome technical papers presenting analytical research, simulations, practical results, position papers addressing the pros and cons of specific proposals, and papers addressing the key problems and solutions. The topics suggested by the conference can be discussed in term of concepts, state of the art, standards, deployments, implementations, running experiments and applications. Topics of interest: Authors are invited to submit complete unpublished papers, which are not under review in any other conference or journal, including, but are not limited to, the following topic areas: - Smart network protocols and algorithms for multimedia delivery - Application layer, transport layer and network layer cognitive protocols - Cognitive radio network protocols and algorithms - Automatic protocols and algorithms for environment prediction. - Algorithms and protocols to predict data network states. - Intelligent synchronization techniques for network protocols and algorithms - Smart protocols and algorithms for e-health - Software applications for smart algorithms design and development. - Dynamic protocols based on the perception of their performance - Smart protocols and algorithms for Smartgrids - Protocols and algorithms focused on building conclusions for taking the appropriate actions. - Smart Automatic and self-autonomous ad-hoc and sensor networks. - Artificial intelligence applied in protocols and algorithms for wireless, mobile and dynamic networks. - Smart security protocols and algorithms - Smart cryptographic algorithms for communication - Artificial intelligence applied to power efficiency and energy saving protocols and algorithms - Smart routing and switching protocols and algorithms - Cognitive protocol and algorithm models for saving communication costs. - Any kind of intelligent technique applied to QoS, content delivery, network Monitoring and network management. - Smart collaborative protocols and algorithms - Problem recognition and problem solving protocols Genetic algorithms, fuzzy logic and neural networks applied to communication protocols and algorithms Important Dates Registration of abstracts: January 4, 2013 Submission Deadline: January 11, 2013 Acceptance Notification: February 22, 2013 Camera Ready Deadline: March 8, 2013 Submission guidelines: All submissions must be full papers in PDF format and uploaded on EDAS (http://edas.info/N13469). All submissions should be written in English with a maximum paper length of five (5) printed pages (10-point font) including figures without incurring additional page charges. General Chairs Jaime Lloret, Univ. Politecnica Valencia, Spain Joel Rodrigues, Inst. of Telecommunications, Univ. of Beira Interior, Pt TPC Chairs Ivan Stojmenovic, University of Ottawa, Canada Yevgeni Koucheryavy, University of Tampere, Finland Panel Chairs Mario Proen?a Jr, State University of Londrina Sabu M. Thampi, Institute of Information Technology and Management - Kerala (IIITM-K), India Industry Chairs Felix Gomez-Marmol, NEC Laboratories Europe, Germany Publicity Chairs Sandra Sendra, Univ. Politecnica Valencia, Spain Web Chair Emilio Granell, Univ. Politecnica Valencia, Spain From cannataro at unicz.it Wed Dec 12 17:01:52 2012 From: cannataro at unicz.it (Mario Cannataro) Date: Wed, 12 Dec 2012 23:01:52 +0100 (CET) Subject: [BiO BB] ICCS Workshop on Biomedical and Bioinformatics Challenges for Computer Science (BBC 2013) In-Reply-To: References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> <29b4f0ef371de5adb52505f83a1d153a.squirrel@email.unicz.it> Message-ID: <8a9b80c485a3eac1ad09c3134eb1841d.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== ICCS 2013 6th Workshop on Biomedical and Bioinformatics Challenges for Computer Science (BBC 2013) http://staff.icar.cnr.it/cannataro/bbc2013/ held in conjunction with International Conference on Computational Science (ICCS 2013) Barcelona, Spain June 5 - June 7, 2013 http://www.iccs-meeting.org/iccs2013/ ===================================================================== * * * CALL FOR PAPERS - Deadline EXTENDED January 2, 2013 * * * ===================================================================== CALL FOR PAPERS AIMS & SCOPE Emerging technologies in genomics, proteomics, interactomics and other life science areas are generating an increasing amount of complex data and information. The evolving data and information ecosystem includes large experimental ?omics? data sets, natural language text from the scientific literature and the Web, and highly connected heterogeneous information networks, such as open linked data distributed on the Internet. Integrating and analysing this information in the context of modern life science research problems and biomedical applications poses a considerable challenge for bioinformatics and computational biology. Traditionally, bioinformatics has concentrated on methods and technologies facilitating the acquisition, storage, organization, archiving, analysis and visualization of biological and medical data. Computational biology, on the other, hand, has emphasized mathematical and computational techniques facilitating the modelling and simulation of biomedical processes and systems. In recent years the distinction between these two fields has become increasingly blurred. In order to tackle the growing complexity associated with emerging and future life science challenges, bioinformatics and computational biology researchers and developers need to explore, develop and apply novel computational concepts, methods, tools and systems. Many of these new approaches are likely to involve advanced and large-scale computing techniques, technologies and infrastructures such as: * High-performance architectures and systems (e.g., multicore, GPU); * Distributed computing (e.g. grid, cloud, peer-to-peer, Web services, e-infrastructures); * Data and information management and integration (e.g., databases, data warehousing, data fusion); * Knowledge discovery/management (e.g., knowledge bases, data mining, ontologies, workflow); * Computational simulation (mechanistic, stochastic, multi-model); * Artificial and computational intelligence (machine learning, agents, evolutionary techniques). Together, these topics cover the key bioinformatics and computational biology techniques and technologies encountered in modern life science environments: (1) Advanced computing architectures/infrastructures; (2) Data/information management and integration; (3) Data/information analysis and knowledge discovery; (4) Integration of quantitative/symbolic knowledge into executable biomedical ?theories? or models. The aim of this workshop is to bring together computer and life scientists to discuss emerging and future directions in these areas. This is the 6th edition of this workshop, which was previously held in Krak?w (2008), Baton Rouge (2009), Amsterdam (2010), Singapore (2011), and Omaha (2012). This 6th edition has been modified to incorporate the advanced and large-scale bioinformatics and computational biology challenges associated with executable ?theories? or models. TOPICS OF INTEREST The workshop is seeking original research contributions presenting innovative bioinformatics and computational biology concepts and solutions in the areas outline above. The topics of interest include but are not limited to the following: Computer Science Bioinformatics Computational Biology * Dedicated hardware & architectures * High performance & distributed computing * Parallelisation techniques * Grid/cloud computing * Service-orientation * Volunteer computing * Peer-to-peer computing * (Distributed) workflows * E-infrastructures * Data management/integration/fusion * Biological sequence & structure analysis * Genomics, proteomics, metabolomics, interactomics, etc. * Analysis of biological networks * Biomedical image analysis * Neuroimaging * Data visualization * Data mining & knowledge discovery * Simulation of biological systems/processes * Multi-model approaches * Systems biology * Knowledge-based techniques * Knowledge management * Artificial / computational intelligence techniques * Executable theories and models PAPER SUBMISSION AND PUBLICATION The manscripts submitted to this workshop must be camera-ready and formatted according to the rules of Procedia Computer Science (http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description). Please use this file for a Latex template plus instructions (http://www.iccs-meeting.org/iccs2013/procedia/ecrc-procs.zip) and click here for an MS word template file (http://www.iccs-meeting.org/iccs2013/procedia/ProcediaComputerScience_template.dot). Submission implies the willingness of at least one of the authors to register and present the paper at the workshop. PostScript and source versions of your paper must be submitted electronically through the paper submission system (http://www.iccs-meeting.org/iccs2013/papers/upload.php) indicating the workshop title 6th Workshop on Biomedical and Bioinformatics Challenges for Computer Science (BBC 2013) A copyright form (http://www.iccs-meeting.org/iccs2013/procedia/ProcediaComputerScience_copyrightform.doc) is only needed after the paper has been accepted for publication in the proceedings. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. Dates of deadlines for manuscript submission (full paper), notification of acceptance, deadline for camera-ready paper submission and registration may be found in the Important Dates (http://www.iccs-meeting.org/iccs2013/important-dates.html) section of the ICCS Web site, unless otherwise specified on this workshop site. Manuscripts submitted to this workshop must be based on unpublished, mature and original work and must be submitted to ICCS only. ICCS is an ERA 2010 A-ranked conference series. JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of the Journal of Computational Science. Selected papers (extended and revised version) accepted on the 1st edition of this workshop have been published on a special section of Future Generation Computer Systems, Elsevier. IMPORTANT DATES Full papers submission: January 2, 2013 (EXTENDED) Notification of acceptance: February 10, 2013 Camera-ready papers: March 1, 2013 Authors registration: February 10 - March 10, 2013 Participant early registration: February 10 - April 25, 2013 Tutorials, welcome reception: June 4, 2013 Conference/Workshop sessions: June 5 - June 7, 2013 WORKSHOP CO-ORGANIZERS Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy Werner Dubitzky, University of Ulster, United Kingdom Joakim Sundnes, Simula Research Laboratory, Norway Rodrigo Weber dos Santos, Federal University of Juiz de Fora, Brazil PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Dave Angulo, DePaul University, Chicago, USA 2. Francisco Azuaje, CRP-Sant?, Luxembourg 3. Daniel Berrar, Tokyo Institute of Technology, Tokyo, Japan 4. Eun Bo Shim, Kangwon National University, Chuncheon, Republic of Korea 5. Rui Brito, University of Coimbra, Portugal 6. Kevin Burrage, University of Oxford, Oxford, United Kingdom 7. Nagasuma Chandra, Indian Institute of Science, Bangalore, India 8. Bastien Chopard, University of Geneva, Geneva, Switzerland 9. Tim Clark, Harvard Medical School, USA 10. Attila Csik?sz-Nagy, King?s College London, UK, and Fondazione Edmund Mach, Trento, Italy 11. Giuseppe Di Fatta, University of Reading, UK 12. Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI, Orsay, France 13. Alan Garny, University of Oxford, Department of Physiology, Anatomy & Genetics 14. Concettina Guerra, University of Padova, Italy 15. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 16. Ulrich Hansmann, Research Centre Juelich, Germany 17. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 18. Pilar Herrero, Universidad Polit?cnica de Madrid, Madrid, Spain 19. Alfons Hoekstra, University of Amsterdam, Amsterdam, The Netherlands 20. Ela Hunt, Bundesamt f?r Statistik BFS / Office Federal de la Statistique OFS, Switzerland 21. Glenn Terje Lines, Simula Research Laboratory, Norway 22. Marcelo Lobosco, Federal University of Juiz de Fora, Brazil 23. Uko Maran, University of Tartu, Estonia 24. Wagner Meira Jr., Federal University of Minas Gerais, Brazil 25. Maria Mirto, University of Salento, Italy 26. Hartmut Mix, University of Technology Dresden, Germany 27. Igor Mozeti?, Jo?ef Stefan Institute, Ljubljana, Slovenia 28. Salvatore Orlando, University of Venezia, Italy 29. Mar?a S. P?rez, Universidad Polit?cnica de Madrid, Madrid, Spain 30. Gernot Plank, University of Graz, Austria 31. Omer F. Rana, Cardiff University, UK 32. Osbaldo Resendis-Antonio, Universidad Nacional Aut?noma de M?xico, Mexico 33. Blanca Rodriguez, University of Oxford, UK 34. Insik Shin, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea 35. Luis Paulo da Silva Barra, Federal University of Juiz de Fora, Brazil 36. Fabrizio Silvestri, ISTI-CNR, Italy 37. Raymond Spiteri, University of Saskatchewan, Canada 38. Martin Swain, Aberystwyth Universith, Aberystwyth, United Kingdom 39. Roberto Tagliaferri, University of Salerno, Italy 40. El-Ghazali Talbi, Universit? des Sciences et Technologies de Lille, France 41. Paolo Trunfio, University of Calabria, Italy 42. Pierangelo Veltri, University Magna Gr?cia of Catanzaro, Italy 43. Edward J. Vigmond, University of Calgary, Canada 44. Jordi Vill? i Freixa, Universitat de Vic, Vic, Spain 45. Giovanni Vozzi, University of Pisa, Pisa, Italy 46. Chong Wang, Technical University of Wildau, Wildau, Germany 47. Huiru Zheng, University of Ulster, Jordanstown, United Kingdom 48. Albert Zomaya, University of Sydney, Australia 49. Bla? Zupan, University of Ljubljana, Ljubljana, Slovenia From dan.bolser at gmail.com Fri Dec 14 09:51:38 2012 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 14 Dec 2012 14:51:38 +0000 Subject: [BiO BB] Fwd: Elixir-UK GOBLET Trainers Workshop In-Reply-To: References: Message-ID: Time to train! ---------- Forwarded message ---------- From: Vicky Schneider-Gricar Date: 14 December 2012 14:29 Subject: Elixir-UK GOBLET Trainers Workshop To: Vicky Schneider-Gricar Dear Colleague ELIXIR-UK and GOBLET under the auspices of BBSRC and TGAC would like to invite you to the ELIXIR-UK/GOBLET Trainers workshop that will take place at the Genome Analysis Centre (TGAC) in Norwich on the 25th-26th March 2013. The aims, structure and programme of the workshop can be found here: http://www.tgac.ac.uk/tgac-training-programme-elixir-uk-goblet-trainers-workshop/ As workshop participants you will only need to cover your own travel expenses, BBSRC sponsorship will be funding the workshop, including two nights? accommodation and meals for participants! The Organizing Committee has specifically expressed an interest to invite you as a participant. If you are able to come, please register here as soon as possible: http://www.tgac.ac.uk/tgac-training-programme-elixir-uk-goblet-trainers-workshop/registration/ Topics will include: What is the 'training landscape' (UK, Europe, the globe). Successful initiatives: learning from each other. Sharing best practice (technologies, approaches, courses materials, etc.). Trainers: their value, recognition and career development. Collaborative training. The workshop has a limited place for participants, and we will be opening participation to all if there are any places available (as on first come first serve basis). So please, make sure you register as soon as possible. We are looking forward to seeing you at the ELIXIR-UK/GOBLET Trainers workshop 2013. On behalf of the Organizing committee: Vicky Schneider-Gricar (TGAC) Teresa Attwood (GOBLET) Dawn Field (NERC EOS) Carole Goble (ICT Sector Manchester) Chris Ponting (CGAT) Best regards and please do not hesitate to contact me should you need more information. Helen Helen Tunney PA to Directorate The Genome Analysis Centre (TGAC) Norwich Research Park Colney Norwich NR4 7UH Tel: 01603 450809 Fax: 01603 450021 Email: helen.tunney at tgac.ac.uk From mkrallinger at cnio.es Mon Dec 17 06:07:26 2012 From: mkrallinger at cnio.es (Martin Krallinger) Date: Mon, 17 Dec 2012 12:07:26 +0100 Subject: [BiO BB] CALL FOR PARTICIPATION: CHEMDNER task: Chemical compound and drug name recognition task Message-ID: CALL FOR PARTICIPATION: CHEMDNER task: Chemical compound and drug name recognition task (http://www.biocreative.org/tasks/biocreative-iv/chemdner) (1) TASK GOAL AND MOTIVATION The goal of this task is to promote the implementation of systems that are able to detect mentions in text of chemical compounds and drugs. The recognition of chemical entities is also crucial for other subsequent text processing strategies, such as detection of drug-protein interactions, adverse effects of chemical compounds or the extraction of pathway and metabolic reaction relations. A range of methods have been explored to the recognition of chemical compound mentions, including machine learning techniques, rule-bases approaches and different dictionary-lookup strategies. We foresee a considerable interest in the result of this task by the NLP/text mining community on one side, as well as by the bioinformatics, drug discovery/biomedicine and chemoinformatics communities on the other side. As has been the case in previous BioCreative efforts (resulting in high impact papers in the field), we expect that successful participants will have the opportunity to publish their system descriptions in a journal article. (2) CHEMDNER TRACK DESCRIPTION The CHEMDNER is one of the tracks posed at the BioCreative IV community challenge (http://www.biocreative.org). We invite participants to submit results for the CHEMDNER task providing predictions for one or both of the following subtasks: a) Given a set of documents, return for each of them a ranked list of chemical entities described within each of these documents [Chemical document indexing sub-task] b) Provide for a given document the start and end indices corresponding to all the chemical entities mentioned in this document [Chemical entity mention recognition sub-task]. For these two tasks the organizers will release training and test data collections. The task organizers will provide details on the used annotation guidelines; define a list of criteria for relevant chemical compound entity types as well as selection of documents for annotation. (3) REGISTRATION Teams can participate in the CHEMDNER task by registering for track 2 of BioCreative IV. You can register additionally for other tracks too. To register your team, go to the following page that provides more detailed instructions: http://www.biocreative.org/news/biocreative-iv/team/ Mailing list and contact information: You can post questions related to the CHEMDNER task to the BioCreative mailing list. To register for the BioCreative mailing list, please visit the following page: http://biocreative.sourceforge.net/mailing.html (4) WORKSHOP CHEMDNER is part of the BioCreative evaluation effort. The BioCreative Organizing Committee will host the BioCreative IV Challenge evaluation workshop (http://www.biocreative.org/events/biocreative-iv/CFP/) at NCBI, National Institutes of Health, Bethesda, Maryland, on October 7-9, 2013 (5) CHEMDNER TASK ORGANIZERS Martin Krallinger, Spanish National Cancer Research Center (CNIO) Obdulia Rabal, University of Navarra, Spain Julen Oyarzabal, University of Navarra, Spain Alfonso Valencia, Spanish National Cancer Research Center (CNIO) (6) REFERENCES - Vazquez, M., Krallinger, M., Leitner, F., & Valencia, A. (2011). Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications. Molecular Informatics, 30(6?7), 506-519. - Krallinger M, et al. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 2011;12 Suppl 8:S3 - Corbett, P., Batchelor, C., & Teufel, S. (2007). Annotation of chemical named entities. BioNLP 2007: Biological, translational, and clinical language processing, 57-64. - Klinger, R., Kol??ik, C., Fluck, J., Hofmann-Apitius, M., & Friedrich, C. M. (2008). Detection of IUPAC and IUPAC-like chemical names. Bioinformatics, 24(13), i268-i276. - Hettne, K. M., Stierum, R. H., Schuemie, M. J., Hendriksen, P. J., Schijvenaars, B. J., Mulligen, E. M. V., ... & Kors, J. A. (2009). A dictionary to identify small molecules and drugs in free text. Bioinformatics, 25(22), 2983-2991. - Yeh, A., Morgan, A., Colosimo, M., & Hirschman, L. (2005). BioCreAtIvE task 1A: gene mention finding evaluation. BMC bioinformatics, 6(Suppl 1), S2. - Smith, L., Tanabe, L. K., Ando, R. J., Kuo, C. J., Chung, I. F., Hsu, C. N., ... & Wilbur, W. J. (2008). Overview of BioCreative II gene mention recognition. Genome Biology, 9(Suppl 2), S2. From jprudhomme at healthtech.com Wed Dec 19 13:24:49 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Wed, 19 Dec 2012 13:24:49 -0500 Subject: [BiO BB] R&D Informatics Collaboration/Bioinformatics in Molecular Medicine Message-ID: <007c01cdde16$21a8cd90$64fa68b0$@com> Dear Colleague, The Informatics Channel at CHI's Molecular Med TRI-CON 2013 is coming up and advanced registration discounts will be offered until January 11. Come to San Francisco to network with senior level informatics experts and IT professionals from pharma, biotech and academia. Please see the corresponding URLs for more information. Integrated R&D Informatics and Knowledge Management - Feb. 13-15 Leveraging IT and Informatics to Enable Global Information Sharing - Feb. 13-15 Featuring: Sebastien Lefebvre, Head, R&D Information Architecture Practice, AstraZeneca Pharmaceuticals Arturo Morales, Ph.D., Global Leader Data Federation Initiative, Informatics Systems Lead, Novartis Mark A. Musen, M.D., Ph.D., Professor of Medicine, Biomedical Informatics, Stanford Center for Biomedical Informatics Research Arun Nayar, Global Head, External Collaborations, R&D, Information, AstraZeneca Pharmaceuticals Phyllis Post, Executive Director, Merck & Co., Inc. More: http://www.triconference.com/discovery-informatics Register: http://www.triconference.com/mmtc_content.aspx?id=111101 Bioinformatics in the Genome Era: Understanding the Evolving Role of Bioinformatics in Molecular Medicine - Feb. 13-15 Featuring: William S. Dalton, Ph.D., M.D., CEO, M2Gen; Director, Personalized Medicine Institute, Moffitt Cancer Center Marcia Kean, Chairman, Strategic Initiatives, Feinstein Kean Healthcare Nathan Price, Ph.D., Associate Professor, Institute for Systems Biology Deepak Rajpal, Ph.D., Senior Scientific Investigator, Computational Biology, Medicines Discovery & Development, GlaxoSmithKline Joseph Szustakowski, Ph.D., Senior Group Head, Bioinformatics, Biomarker Discovery, Novartis Institutes for BioMedical Research More: http://www.triconference.com/bioinformatics-genome Register: http://www.triconference.com/mmtc_content.aspx?id=111101 Recommended Short Courses - Feb. 12 NGS Data and the Cloud Best Practices in Personalized and Translational Medicine Data Visualization Open Cloud & Data Science More: http://www.triconference.com/mmtc_content.aspx?id=99784 Register: http://www.triconference.com/mmtc_content.aspx?id=111101 Thank you, and please forward this information to those who may find it useful. James Prudhomme Senior Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Direct: 781-972-5486 jprudhomme at healthtech.com From sandra.sendra.upv at gmail.com Sun Dec 23 04:44:30 2012 From: sandra.sendra.upv at gmail.com (Sandra Sendra) Date: Sun, 23 Dec 2012 10:44:30 +0100 Subject: [BiO BB] Deadline Extension: COMPUTATION TOOLS 2013 || May 27 - June 1, 2013 - Valencia, Spain Message-ID: <201212230944.qBN9iUdc027686@smtp.upv.es> INVITATION: ================= Please consider to contribute to and/or forward to the appropriate groups the following opportunity to submit and publish original scientific results to COMPUTATION TOOLS 2013. The submission deadline is extended to January 22, 2013. Authors of selected papers will be invited to submit extended article versions to one of the IARIA Journals: http://www.iariajournals.org ================= ============== COMPUTATION TOOLS 2013 | Call for Papers =============== CALL FOR PAPERS, TUTORIALS, PANELS COMPUTATION TOOLS 2013, The Fourth International Conference on Computational Logics, Algebras, Programming, Tools, and Benchmarking May 27 - June 1, 2013 - Valencia, Spain General page: http://www.iaria.org/conferences2013/COMPUTATIONTOOLS13.html Call for Papers: http://www.iaria.org/conferences2013/CfPCOMPUTATIONTOOLS13.html - regular papers - short papers (work in progress) - posters Submission page: http://www.iaria.org/conferences2013/SubmitCOMPUTATIONTOOLS13.html Submission deadline: January 22, 2013 Sponsored by IARIA, www.iaria.org Extended versions of selected papers will be published in IARIA Journals: http://www.iariajournals.org Print proceedings will be available via Curran Associates, Inc.: http://www.proceedings.com/9769.html Articles will be archived in the free access ThinkMind Digital Library: http://www.thinkmind.org Please note the Poster and Work in Progress options. The topics suggested by the conference can be discussed in term of concepts, state of the art, research, standards, implementations, running experiments, applications, and industrial case studies. Authors are invited to submit complete unpublished papers, which are not under review in any other conference or journal in the following, but not limited to, topic areas. All tracks are open to both research and industry contributions, in terms of Regular papers, Posters, Work in progress, Technical/marketing/business presentations, Demos, Tutorials, and Panels. Before submission, please check and conform with the Editorial rules: http://www.iaria.org/editorialrules.html COMPUTATION TOOLS 2013 Topics (topics and submission details: see CfP on the site) Logics Reasoning logics; Fuzzy logics; Semantic logics; Temporal logics; Emotion logics; Ambiant logics; Modal logics; Description logics; Computational tree logic; Computational logics and constraints; Quantum computational logics; Executable computational logics; Monadic computational logics; Many-valued computational logics; Computability logic Algebras Computational algebras; K-theories, C*-algebras, Index theory; Algebraic and topological K-theory; Geometric group theory and group C*-algebras; Noncommutative geometry and topology; Pseudodifferential operators on singular manifolds; Topological invariants of non-simply connected manifolds; Deformation quantization; Lambda calculus; Relation algebra; Algebras for symbolic computation; Constructive algebras Advanced computation techniques Machine learning; Fuzzy theory/computation/logic; (Artificial) neuronal networks; Distributed artificial intelligence; Genetic algorithms; Analytic tableaux; Autonomous agent-based techniques; Knowledge-based systems and automated reasoning; Logical issues in knowledge representation /non-monotonic reasoning/belief; Dempster-Shafer theory; Concurrent computation and planning; Deduction and reasoning Specialized programming languages Logic programming; Specialized computation languages; Real-time computation languages; Embedded-computing languages; Programming semantics; Content-driven programming; Multimedia-oriented programming; Context-driven programming; Service-oriented programming; Pattern-oriented programming; Regenerative programming; Progressive programming; Sensing-oriented programming; Mobile-ubiquity-oriented computing; Compilation issues Tools for distributed computation Platforms for distributed computing; Specification and verification of programs and systems; Techniques for cloud computing; On-request resource allocation mechanisms; Security and privacy techniques; Computational benchmarking metrics, criteria and methodologies; Distributed debug and on-fly repairing; Inference of schemas, integrity constraints in computational applications; Real-world applications, experiments, projects ------------------------------------------- Committee: http://www.iaria.org/conferences2013/ComCOMPUTATIONTOOLS13.html ================================================