From jdrugowitsch from bcs.rochester.edu Mon Feb 1 10:44:43 2010 From: jdrugowitsch from bcs.rochester.edu (Jan Drugowitsch) Date: Mon Feb 1 13:02:57 2010 Subject: [Computational-biology] CFP: IWLCS 2010, 13th International Workshop on Learning Classifier Systems Message-ID: <779ada561002010744w743003d0k6adb9978886c3ddc@mail.gmail.com> Our apologies if you receive multiple copies of this announcement. -------------------------------------------------------------------------- 13th International Workshop on Learning Classifier Systems to be held as part of the 2010 GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE (GECCO-2010) Sponsored by ACM SIGEVO http://www.sigevo.org/GECCO-2010 July 7-11, 2008 (Wednesday-Sunday) Portland Marriott Downtown Waterfront Hotel Portland, Oregon, USA PAPER SUBMISSION DEADLINE FOR WORKSHOP: Wednesday, March 25, 2010 Workshop Website: http://www.cs.nott.ac.uk/~jqb/IWLCS2010/ -------------------------------------------------------------------------- The Thirteenth International Workshop on Learning Classifier Systems (IWLCS 2010) will be held in Portland, Oregon, USA, Thursday, July 8, 2010 during the Genetic and Evolutionary Computation Conference (GECCO-2010), July 7-11, 2010. Originally, Learning Classifier Systems (LCSs) were introduced by John H. Holland as a way of applying evolutionary computation to machine learning and adaptive behavior problems. Since then, the LCS paradigm has broadened greatly into a framework that encompasses many representations, rule discovery mechanisms, and credit assignment schemes. Current LCS applications range from data mining, to automated innovation and the on-line control of cognitive systems. LCS research includes various actual system approaches: While Wilson's accuracy- based XCS system (1995) has received the highest attention and gained the highest reputation, studies and developments of other LCSs are usually discussed and contrasted. Advances in machine learning, and reinforcement learning in particular, as well as in evolutionary computation have brought LCS systems the necessary competence and guaranteed learning properties. Novel insights in machine learning and evolutionary computation are being integrated into the LCS framework. Thus, we invite submissions that discuss recent developments in all areas of research on, and applications of, Learning Classifier Systems. IWLCS is the event that brings together most of the core researchers in classifier systems. Moreover, a free introductory tutorial on LCSs is presented the day before the workshop at GECCO 2010. Tutorial and IWLCS workshop thus also provide an opportunity for researchers interested in LCSs to get an impression of the current research directions in the field as well as a guideline for the application of LCSs to their problem domain. Topics of interests include but are not limited to: - Paradigms of LCS (Michigan, Pittsburgh, ...) - Theoretical developments (behavior, scalability and learning bounds, ...) - Representations (binary, real-valued, oblique, non-linear, fuzzy, ...) - Types of target problems (single-step, multiple-step, regression/function approximation,...) - System enhancements (competent operators, problem structure identification and linkage learning, ...) - LCS for Cognitive Control (architectures, emergent behaviours, ...) - Applications (data mining, medical domains, bioinformatics, ...) Submissions and Publication --------------------------- Submissions will be short-papers up to 8 pages in ACM format. Please see the GECCO 2010 information for authors for further details. However, unlike GECCO, papers do not have to be submitted in anonymous format. All accepted papers will be presented at IWLCS 2010 and will appear in the GECCO workshop volume. Proceedings of the workshop will be published on CD-ROM, and distributed at the conference. Authors will be invited after the workshop to submit revised (full) papers that, after a thorough review process, are to be published in the next post-workshop proceedings volume (scheduled for 2012), in the Springer LNCS/LNAI book series. All papers should be submitted in PDF format and e-mailed to: jqb@cs.nott.ac.uk. Important dates --------------- * Paper submission deadline: Thursday, March 25, 2010 * Notification to authors: Thursday, April 1, 2010 * Submission of camera-ready material: by Tuesday, April 13, 2010 * Conference registration: by Monday, April 19, 2010 * Workshop date: Thursday, July 8, 2009 Committees ---------- - Organizing Commitee * Jaume Bacardit, University of Nottingham (UK). E-mail: jaume.bacardit@nottingham.ac.uk * Will Browne, Victoria University of Wellington (NZ). E-mail: will.browne@ecs.vuw.ac.nz * Jan Drugowitsch, University of Rochester (USA). E-mail: jdrugowitsch@bcs.rochester.edu - Advisory Committee * Ester Bernad-Mansilla, Universitat Ramon Llull (Spain). * Martin V. Butz, Universitat Wurzburg (Germany) * Tim Kovacs, University of Bristol (UK) * Pier Luca Lanzi, Politechnico de Milano (Italy) * Xavier Llora University of Illinois at Urbana-Champaign (USA) * Wolfgang Stolzmann, Daimler Chrysler AG (Germany) * Keiki Takadama, Tokyo Institute of Technology (Japan) * Stewart Wilson, Prediction Dynamics (USA) Further information ------------------- For more details, please visit the workshop website at: http://www.cs.nott.ac.uk/~jqb/IWLCS2010/ GECCO is sponsored by the Association for Computing Machinery Special Interest Group on Genetic and Evolutionary Computation (SIGEVO). SIG Services: 2 Penn Plaza, Suite 701, New York, NY, 10121, USA, 1-800-342-6626 (USA and Canada) or +212-626-0500 (Global). From jamieloc from yahoo-inc.com Mon Feb 1 16:54:36 2010 From: jamieloc from yahoo-inc.com (Jamie Lockwood) Date: Mon Feb 1 17:34:40 2010 Subject: [Computational-biology] Announcing Yahoo!'s 2nd Annual Key Scientific Challenges Program Message-ID: <0F467378C540D046B688A63E911907B7075B3CE7@SNV-EXVS03.ds.corp.yahoo.com> INVENT THE FUTURE OF THE INTERNET What are the big problems Yahoo! is working on? What are the major challenges facing our industry today? What will the next generation of the Internet look like and how will we get there? Yahoo! Labs scientists are asked these questions every day. The questions, and answers, have created some big opportunities for PhD students around the globe. We are thrilled to announce Yahoo!'s second annual Key Scientific Challenges Program. This is your chance to get an inside look at-and help tackle-the big challenges that Yahoo! and the entire Internet industry are facing today. As part of the Key Scientific Challenges Program you'll gain access to Yahoo!'s world-class scientists, some of the richest and largest data repositories in the world, and have the potential to make a huge impact on the future of the Internet while driving your research forward. THE CHALLENGES AREAS INCLUDE: - Search Experiences - Machine Learning - Data Management - Information Extraction - Economics - Statistics - Multimedia - Computational Advertising - Social Sciences - Green Computing - Security - Privacy KEY SCIENTIFIC CHALLENGES AWARD RECIPIENTS RECEIVE: - $5,000 unrestricted research seed funding which can be used for conference fees and travel, lab materials, professional society membership dues, etc. - Access to select Yahoo! datasets - The unique opportunity to collaborate with our industry-leading scientists - An invitation to this summer's exclusive Key Scientific Challenges Graduate Student Summit where you'll join the top minds in academia and industry to present your work, discuss research trends and jointly develop revolutionary approaches to fundamental problems CRITERIA: To be eligible, you must be currently enrolled in a PhD program at any accredited institution. We're accepting applications from January 25th - March 5th 2010 and winners will be announced by early April 2010. To learn more about the program and how to apply, visit http://labs.yahoo.com/ksc. From tekaia from pasteur.fr Tue Feb 2 06:00:41 2010 From: tekaia from pasteur.fr (Fredj Tekaia) Date: Tue Feb 2 09:01:22 2010 Subject: [Computational-biology] Bioinformatics and Comparative Genome Analysis course in Institut Pasteur Paris Message-ID: Announcement and Call for applications: "Bioinformatics and Comparative Genome Analysis course" July 5 – July 17, 2010 Institut Pasteur Paris - France http://www.pasteur.fr/~tekaia/BCGA2010.html With financial support from: Institut Pasteur International Network. Aim of the course: The main objectives of the course are to familiarize young scientists (Biologists/Computer Scientists/Mathematicians) with bioinformatics and genome data analysis skills and to encourage multi-disciplinarity by introducing: 1- advanced fundamental algorithms in bioinformatics; 2- their application in genome analyses; 3- and recent knowledge acquired from genomes studies and perspectives. The course is aimed at motivated Ph.D and Post-doctoral students, as well as young assistant professors and junior scientists in Academic Institutions, with background in Mathematics, Statistics, Biology or Computing, and who are involved in Bioinformatics and Genomes studies. Duration: Full time from July 5 to July 17, 2010. Location: Institut Pasteur Paris, 28 rue du Dr Roux, 75724 cedex 15 Paris, France. Accommodation and meals: Selected students from developed countries will be charged a participation of 1300€. There will be no charge for students from developing countries and Institut Pasteur International Network. Applications Deadline: March 20, 2010. More information about the course, the preliminary draft programme, how to apply and application form can be found at the following link: http://www.pasteur.fr/~tekaia/BCGA2010.html Thank you for circulating this announcement. Best regards The Organizers: Odile Kalogeropoulos, Institut Pasteur Paris - France. Julie Thompson, IGBMC Strasbourg – France. Hugo Naya, Institut Pasteur de Montevideo - Uruguay. Fredj Tekaia, Institut Pasteur Paris - France. From jmheralds from gmail.com Tue Feb 2 18:33:15 2010 From: jmheralds from gmail.com (James Heralds) Date: Tue Feb 2 18:58:56 2010 Subject: [Computational-biology] Draft paper submission deadline is extended : BCBGC-10 Message-ID: <239d7edb-5444-46e0-90e0-0b51a25944da@n7g2000yqb.googlegroups.com> Draft paper submission deadline is extended : BCBGC-10 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. • International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) • International Conference on Automation, Robotics and Control Systems (ARCS-10) • International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) • International Conference on Computer Communications and Networks (CCN-10) • International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) • International Conference on High Performance Computing Systems (HPCS-10) • International Conference on Information Security and Privacy (ISP-10) • International Conference on Image and Video Processing and Computer Vision (IVPCV-10) • International Conference on Software Engineering Theory and Practice (SETP-10) • International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely James Heralds Publicity committee From jpezaris from gmail.com Wed Feb 3 12:49:04 2010 From: jpezaris from gmail.com (John Pezaris) Date: Wed Feb 3 13:38:58 2010 Subject: [Computational-biology] AREADNE 2010 Call for Abstracts Message-ID: CONFERENCE ANNOUNCEMENT -- and -- CALL FOR ABSTRACTS AREADNE 2010 Research in Encoding and Decoding of Neural Ensembles June 17 - 20, 2010 Nomikos Conference Center Santorini, Greece http://www.areadne.org info@areadne.org INTRODUCTION One of the fundamental problems in neuroscience today is to understand how the activation of large populations of neurons give rise to higher order functions of the brain including learning, memory, cognition, perception, action and ultimately conscious awareness. Electrophysiological recordings in behaving animals over the past forty years have revealed considerable information about what the firing patterns of single neurons encode in isolation, but it remains largely a mystery how collections of neurons interact to perform these functions. Recent technological advances have provided a glimpse into the global functioning of the brain. These technologies include functional magnetic resonance imaging, optical imaging methods including intrinsic, voltage-sensitive dye, and two-photon imaging, high-density electroencephalography and magnetoencephalography, and multi-microelectrode array electrophysiology. These technologies have expanded our knowledge of brain functioning beyond the single neuron level. At the same time, our understanding of how neuronal ensembles carry information has allowed the development of brain-machine interfaces (BMI) to enhance the capabilities of patients with sensory and motor deficits. Knowledge of how neuronal ensembles encode sensory stimuli has made it possible to develop perceptual BMIs for the hearing and visually impaired. Likewise, research in how neuronal ensembles decode motor intentions has resulted in motor BMIs by which people with severe motor disabilities can control external devices. CONFERENCE MISSION First and foremost, this conference is intended to bring scientific leaders from around the world to present their recent findings on the functioning of neuronal ensembles. Second, the meeting will provide an informal yet spectacular setting on Santorini in which attendees can discuss and share ideas outside of the presentations at the conference center. Third, this conference continues our long term project to form a systems neuroscience research institute within Greece to conduct state-of-the-art research, offer meetings and courses, and provide a center for visiting scientists from around the world to interact with Greek researchers and students. FORMAT AND SPEAKERS The conference will span four days, in morning and early evening sessions. Confirmed speakers include experts in the field of multi-neuron experiment and analysis (in alphabetic order): David Anderson (Caltech), Helen Barbas (Boston University), Carlos Brody (Princeton University), Matteo Carandini (University College London), Jose Carmena (University of California Berkeley), Bob Desimone (MIT), Tim Ebner (University of Minnesota), Adrienne Fairhall (University of Washington), Eb Fetz (University of Washington), Tamar Flash (The Weizmann Institute of Science), David Freeman (University of Chicago), Georgia Gregoriou (University of Crete), Melina Hale (University of Chicago), Michael Hausser (University College London), Jeff Lichtman (Harvard University), Nikos Logothetis (Max Planck Institute for Biological Cybernetics), John O'Keefe (University College London), Cathy Ojakangas (University of Chicago), Bijan Pesaran (New York University), Hans Scherberger (German Primate Center), Maneesh Sahani (UCL Gatsby Institute), Alcino Silva (University of California Los Angeles), Wolf Singer (Max Planck Institute for Brain Research ), Mike Shadlen (University of Washington), Irini Skaliora (Biomedical Research Foundation, Academy of Athens). CALL FOR ABSTRACTS We are currently soliciting abstracts for poster presentation. Submissions will be accepted electronically, and must be received by March 12, 2010. Automated email acknowledgment of submission will be provided, and manual verification will be made a few days after submission. Notification of acceptance will be provided by March 30, 2010. Please see our on-line Call for Abstracts at http://areadne.org/call-for-abstracts.html for additional details. ORGANIZING COMMITTEE Nicho Hatsopoulos, Co-Chair John Pezaris, Co-Chair Catherine Ojakangas Yiota Poirazi Thanos Siapas Andreas Tolias FOR FURTHER INFORMATION For further information please see the conference web site http://www.areadne.org or send email to info@areadne.org. -- Dr. J. S. Pezaris AREADNE 2010 Co-Chair Massachusetts General Hospital 55 Fruit Street Boston, MA 02114, USA john@areadne.org From Heather.Vincent from manchester.ac.uk Wed Feb 10 05:45:20 2010 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Wed Feb 10 10:06:14 2010 Subject: [Computational-biology] Mathematics for metabolic modelling Message-ID: <4B728E40.5080803@manchester.ac.uk> Applications are invited for this new distance learning course in mathematical methods for the biosciences. It is a Masters-level course, designed to provide professional development for employees working in the pharmaceutical and the biotechnology industries. It can be studied as an individual unit, or can be accredited towards a qualification from the University of Manchester, UK. The course will provide an introduction to the mathematical skills and concepts needed for modelling biological systems. Students will be using R, an increasingly important language for data analysis for the life sciences. For those beginning to use metabolic modelling in their research, it will also prepare you for our core modelling course 'Computational simulation and analysis of biochemical networks'. The key course themes are : Descriptive Statistics and Graphics with R Introduction to Probability Kinetics and Ordinary Differential Equations Inference and Fitting of Data to Mathematical Models Markov Chain Monte Carlo (MCMC) Bayesian Inference Mathematical Inference Informing Modelling For details of Mathematics for metabolic modelling : http://octette.cs.man.ac.uk/bioinformatics/modules/maths.html For information on our distance Masters programmes in Computational Biology : http://octette.cs.man.ac.uk/bioinformatics/index.html If have any questions about the options, please contact Heather.Vincent@manchester.ac.uk From masulli from disi.unige.it Fri Feb 12 09:16:32 2010 From: masulli from disi.unige.it (Francesco Masulli) Date: Fri Feb 12 11:09:45 2010 Subject: [Computational-biology] School on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Message-ID: <201002121516.32938.masulli@disi.unige.it> *Our apologies if you receive multiple copies of this announcement* CALL FOR PARTICIPATION ===================================================================== International Course on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Vietri sul Mare, Salerno (Italy) - May 24-29, 2010 School Website: http://ciob10.disi.unige.it/ Joint course of the International School on Neural Nets "E.R. Caianiello" and of the Italian Network for Oncology Bioinformatics ===================================================================== * Please pass this Call for Participation to interested Colleagues * PURPOSE OF THE COURSE The Twentieth century is often referred as the Century of Biology, as evidenced by the extraordinary development of this scientific area who concluded that century with the great success of the Human Genome Project and the subsequent complete sequencing of human DNA. Currently we are at the beginning of the so-called Post-Genomic Era, characterized on one hand by the availability of a huge amount of Bioinformatics data (often in the public domain), and on the other hand by the need for new and efficient mathematical methods and algorithms capable of distill the information contained in these data. As a matter of fact the emphasis of research in Bioinformatics is shifting from the development of efficient storing and handling data methods, to the one of methods able to extract useful information from data. Computational Intelligence methodologies (that is, neural networks, evolutionary algorithms and fuzzy logic), partly inspired by natural systems, are a family of powerful methods for data analysis, able to transform the available heterogeneous data into biological knowledge. In recent years, these algorithms have been successfully applied in Bioinformatics to the solution of complex problems concerning signal analysis, classification, clustering, feature selection, and data mining and visualization. Nowadays, their applications encompass almost all areas of Bioinformatics. The course covers the applications of Computational Intelligence methods to the analysis of Bioinformatics data, with particular focus on applications in oncology. It is addressed to PhD students and researchers in Bioinformatics, Computer Science, Mathematics and Engineering, and includes: - theoretical lectures introducing the main aspects of Bioinformatics and Computational Intelligence methodologies; - lectures aimed to analyze some significant case studies of data analysis in oncology bioinformatics; - practical classes showing some relevant applications of Computational Intelligence methods to Bioinformatics data. LIST OF LECTURERS * Pierre Baldi, University of California, Irvine, CA, USA * Michele Ceccarelli, University of Sannio, Benevento, Italy * Raffaele Giancarlo, University of Palermo, Italy * Antonio Giordano, University of Siena, Italy and Director Sbarro Institute for Cancer research & Molecular Medicine, Philadelphia PA, USA * Paulo Lisboa, Liverpool John Moores University, Liverpool, UK * Francesco Masulli, University of Genoa, Italy & Temple University, PA, USA * Alfredo Petrosino, University Parthenope, Naples, Italy * Stefano Rovetta, University of Genoa, Italy * Giuseppe Russo, Temple University, Philadelphia, PA, USA * Roberto Tagliaferri, University of Salerno, Italy * Giorgio Valentini, University of Milan, Italy THE COURSE IS JOINTLY ORGANIZED BY International Institute for Advanced Scientific Studies (IIASS) Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC) Italian Network for Oncology Bioinformatics (RNBIO) THE COURSE IS SPONSORED BY GNCS, Gruppo Nazionale per il Calcolo Scientifico INNS, International Neural Network Society S.I.G. on Bioinformatics SIREN, Italian Neural Networks Society DISI - University of Genoa, Italy University of Salerno, Italy APPLICATION Deadline: March 30-th 2010 (forms will be soon available at http://ciob10.disi.unige.it/application.html) The course is open to all motivated students and research scientists, of any nationality. Applicants with few experience should include a recommendation letter of their supervisor. Places are limited to a maximum of 60 participants in addition to the lecturers. These will be allocated on a first come, first served basis. FOR ANY FURTHER INFORMATION please visit the website http://ciob10.disi.unige.it ------------------------------------------------------- -- <--------------------------------------------------------------------> Dr. Francesco Masulli Associate Professor of Computer Science DISI - Dept. Computer and Information Sciences University of Genova - Via Dodecaneso 35, 16146 Genoa - ITALY tel. +39 010 353 6604 fax. +39 010 353 6699 and Adjunct Associate Professor Center for Biotechnology - College of Science and Technology -Temple University - Philadelphia - PA, USA. email: masulli@disi.unige.it skype id: masulli url: http://www.disi.unige.it/person/MasulliF <--------------------------------------------------------------------> From jmheralds from gmail.com Fri Feb 12 13:58:55 2010 From: jmheralds from gmail.com (James Heralds) Date: Fri Feb 12 14:59:46 2010 Subject: [Computational-biology] Draft paper submission deadline is extended: BCBGC-10, Orlando, USA Message-ID: <5cb88afe-46e0-4c3b-bf70-5074fd7265f6@z19g2000yqk.googlegroups.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Draft paper submission deadline is extended: BCBGC-10, Orlando, USA The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. • International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) • International Conference on Automation, Robotics and Control Systems (ARCS-10) • International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) • International Conference on Computer Communications and Networks (CCN-10) • International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) • International Conference on High Performance Computing Systems (HPCS-10) • International Conference on Information Security and Privacy (ISP-10) • International Conference on Image and Video Processing and Computer Vision (IVPCV-10) • International Conference on Software Engineering Theory and Practice (SETP-10) • International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney Worldฎ Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining — all situated on 10 tropically landscaped acres. Here, guests can experience a full- service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely James Heralds From thkim7 from buffalo.edu Mon Feb 15 17:40:14 2010 From: thkim7 from buffalo.edu (Taehyong Kim) Date: Tue Feb 16 13:46:16 2010 Subject: [Computational-biology] Updates- ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB 2010) Message-ID: Due to holidays and many requests, we are extending the submission deadline to March 15, 2010. Call for Papers and Proposals ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB 2010) August 2-4, Niagara Falls, New York, USA http://www.cse.buffalo.edu/ACM-BCB2010 ACM is pleased to announce that it has taken over sponsorship of the former International Joint Conference on Bioinformatics, Systems Biology, and Intelligent Computing (IJCBS), and will be holding the newly renamed International Conference On Bioinformatics and Computational Biology (ACM-BCB) in August 2010 in Niagara Falls, NY. This conference builds on the success of IJCBS 2009 in Shanghai, and is the start of ACM's efforts to better support the bioinformatics and computational biology community. We invite you to submit papers with unpublished, original research describing recent advances on all aspects of Bioinformatics and Computational Biology. All papers will undergo peer review by the conference program committee; accepted papers will be published in the conference proceedings (in CD) and in the ACM Digital Library. Authors of selected papers will be invited to extend their papers for submission to several journals. Papers should not exceed 10 pages in ACM template on 8.5 x 11 inch paper (see ACM templates at http://www.acm.org/sigs/publications/proceedings-templates). Papers should be submitted via the link (https://cmt.research.microsoft.com/BCB2010/). The topics of relevance for the conference papers include but are not limited to the following: ? Assembly algorithms for the next generation sequencing ? Genome annotations via mass spectrometry ? Gene discovery and protein function prediction ? Functional genomics algorithms for high throughput data generation methods ? DNA and protein motif discovery ? Models of gene expression regulation at RNA level ? Algorithms for comparative and evolutionary genomics ? Molecular evolution and phylogeny reconstruction ? Multiple genome alignment ? Computational genomics for plant and animal genomes ? Engineering of bioinformatic databases ? Models of gene expression networks ? Computational proteomics and methabolomics ? Prediction of protein-protein interactions ? Protein structure prediction and molecular dynamics ? Visualization of biomolecular and cellular structure, dynamics and interactions ? Modeling of methabolic pathways ? Computational epigenomics ? Models of cellular and multicellular systems ? Prediction of cellular network dynamics from incomplete information ? Clinical genomics and proteomics ? Data mining in biomolecular databases ? High performance computing for complex biomolecular and cellular systems . Biomedical imaging Proposals for Tutorials and Workshops: We also invite you to submit tutorial/workshop proposals focusing on problems and new challenges of Bioinformatics and Computational Biology. Submit the proposals by e-mail to Tutorial/Workshop Chairs. Key Dates Paper Submission deadline March 15, 2010 Author Notification May 1, 2010 Workshop proposal Jan. 1, 2010 Tutorial Proposal Jan. 1, 2010 Conference Date 2-4 August, 2010 Organizing Committee *Steering Committee* Joydeep Ghosh, University of Texas at Austin Vipin Kumar, University of Minnesota Meral Ozsoyoglu, Case Western Reserve University Yi Pan, Georgia State University Dong Xu, University of Missouri-Columbia Aidong Zhang, SUNY at Buffalo (co-chair) Joe Zhang, University of Southern Mississippi (co-chair) *General Chairs* Aidong Zhang, SUNY at Buffalo Mark Borodovsky, Georgia Tech *Program Chairs* Gultekin Ozsoyoglu, Case Western Reserve University Armin Mikler, University of North Texas *Treasurer* Joe Zhang, University of Southern Mississippi *Workshop Chairs* Michael Buck, SUNY at Buffalo Vasant Honavar, Iowa State University Zhongming Zhao, Vanderbilt University Medical Center Jason Wang, New Jersey Institute of Technology *Poster Chairs* Tony Hu, Drexel University Sun Kim, Indiana University *Publicity Chairs* Mary Qu Yang, NIH Kebin Jia, Beijing University of Technology *Student Awards Chairs* Susan Bridges, Mississippi State University Parthasarathy Srinivasan, Ohio State University *Best Paper Awards Chairs* Joydeep Ghosh, University of Texas at Austin Wei Wang, University of North Carolina at Chapel Hill *Panel Chair* Vipin Kumar, University of Minnesota *Keynote Chair* Dong Xu, University of Missouri-Columbia *Proceedings Chairs* Li Liao, University of Delaware Guo-zheng Li, Tongji University *Tutorials Chairs* Mohammed Zaki, Rensselaer Polytechnic Institute Bo Yuan, Shanghai Jiaotong University *Registrations Chair* Preetam Ghosh, University of Southern Mississippi *Local Arrangements* Zihua Hu, SUNY at Buffalo Marianne Sullivan, SUNY at Buffalo From jprudhomme from healthtech.com Wed Feb 17 16:01:47 2010 From: jprudhomme from healthtech.com (Jim Prudhomme) Date: Wed Feb 17 18:30:46 2010 Subject: [Computational-biology] CHI's 10th Structure-Based Design Conference Message-ID: <018201cab014$6ba37770$42ea6650$@com> Join us for CHI's 10th Anniversary Event... STRUCTURE-BASED DRUG DESIGN: Multidisciplinary Innovations and Structural Insights to Enhance Drug Discovery June 23-25, 2010 Royal Sonesta Hotel, Cambridge, MA Register by March 26 and Save up to $350 www.healthtech.com/sbd In this program, we wish to highlight some recent breakthrough stories and successes using SBDD driven by medicinal chemistry, computational and biophysical approaches. This conference continues to offer both new attendees and alumni insights into the latest work of community thought-leaders as well as invaluable networking opportunities. Topics Include: - Selectivity Optimization: Using Structure to Optimize Selectivity - In Silico Discovery of Small Molecule Binders - New Computational Methods in SBDD - Targeting of Protein-Protein Interactions - New Advances in Docking - Impact of SBDD on Small Molecule Drug Discovery - GPCR Drug Discovery - Workshop: Therapeutic Target Space: Methods for Druggability Assessment View the full agenda and register at www.healthtech.com/SBD or call 781-972-5400. Interested in Sponsoring and/or Exhibiting? Contact Katelin Fitzgerald at 781-972-5458, kfitzgerald@healthtech.com From tekaia from pasteur.fr Fri Feb 19 08:57:47 2010 From: tekaia from pasteur.fr (Fredj Tekaia) Date: Fri Feb 19 09:09:49 2010 Subject: [Computational-biology] Bioinformatics and Comparative Genome Analysis course in Institut Pasteur Paris Message-ID: <0C1594A4-2ADD-4DF0-BE45-1FA35AE967FA@pasteur.fr> Call for applications: "Bioinformatics and Comparative Genome Analysis course" July 5 – July 17, 2010 Institut Pasteur Paris - France Applications Deadline: March 20, 2010. More information about the course, the preliminary programme, how to apply and application form can be found at the following link: http://www.pasteur.fr/~tekaia/BCGA2010.html The Organizers: Odile Kalogeropoulos, Institut Pasteur Paris - France. Julie Thompson, IGBMC Strasbourg – France. Hugo Naya, Institut Pasteur de Montevideo - Uruguay. Fredj Tekaia, Institut Pasteur Paris - France. From info from ices2010.org Fri Feb 19 12:02:16 2010 From: info from ices2010.org (ICES) Date: Fri Feb 19 14:21:23 2010 Subject: [Computational-biology] [icescfp] ICES 2010 - 9th International Conference on Evolvable Systems Message-ID: <4B7EC418.2080908@ices2010.org> Just a small reminder that the deadline for ICES 2010 is fast approaching. http://www.ices2010.org/ Meanwhile, we have some exciting news: we have secured two great keynote speakers: Prof. Andrew Turberfield, from the Clarendon Laboratories at the University of Oxford will present a keynote on "Using DNA to construct molecular systems", while Prof. Steve Furber, from the University of Manchester, will speak on "Biologically-Inspired Massively-Parallel Architectures - computing beyond a million processors". We are hard at work to secure a third keynote speaker that we hope will be as interesting and relevant to our research. So get those papers in! We are really looking forward to seeing you in York this September! Gianluca Tempesti ICES 2010 General Chair ======================================================== 9th International Conference on Evolvable Systems (ICES) - From Biology to Hardware St. William's College, York, UK, 5th-8th September 2010 http://www.ices2010.org/ ======================================================== *** Submission Deadline: 5th March 2010 *** Held without interruption since 1995, ICES has become the leading conference in the field of evolvable hardware and systems. The 9th ICES conference, to be held in York, UK, in September 2010, hopes to build on the success of its predecessors by bringing together researchers who combine biologically inspired concepts with hardware and presenting the latest developments in the field. Topics include, but are not limited to: * Evolutionary hardware design * Co-evolution of hybrid systems * Embryonic hardware * Intrinsic and extrinsic evolution * Hardware/software co-evolution * On-line hardware evolution * Evolutionary robotics * Autonomic and organic computing * Evolutionary circuit diagnostics and testing * Self-repairing and fault tolerant systems * Self-reconfigurable and adaptive hardware * Generative and developmental approaches * Real-world applications of evolvable hardware * MEMS and nanotechnology in evolvable hardware * Formal models for bio-inspired hardware systems * Novel devices/testbeds/tools for evolvable hardware === Paper Submission === Prospective authors are cordially invited to submit original papers using the electronic submission form on the conference webpage. All accepted papers will be included in the conference proceedings. === Conference Venue === The conference will be held in the historic centre of York, a walled riverside city in the north of England, around two hours by rail from London, Edinburgh and Manchester. York is a small city with a rich 2000 years history, a popular tourist destination with a lively caf? bar and restaurant culture, offering a number of museums and galleries set around the Minster, one of Europe's largest Gothic cathedrals. === Organising Committee === General Chair: Gianluca Tempesti, University of York, UK Programme Co-Chairs: Julian F. Miller, University of York, UK Andy Tyrrell, University of York, UK Publicity Chairs: Andy Greensted, University of York, UK Michael Lones, University of York, UK Local Chairs: Stephen L. Smith, University of York, UK James Walker, University of York, UK Steering Committee: Pauline Haddow, NTNU, Norway Tetsuya Higuchi, AIST, Japan Julian F. Miller, University of York, UK Jim Torresen, NTNU, Norway Andy Tyrrell, University of York, UK From jmheralds from gmail.com Sat Feb 20 17:08:10 2010 From: jmheralds from gmail.com (James Heralds) Date: Sat Feb 20 17:39:16 2010 Subject: [Computational-biology] Call for papers: BCBGC-10, Orlando, USA, July 2010 Message-ID: It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, Orlando, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. • International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) • International Conference on Automation, Robotics and Control Systems (ARCS-10) • International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) • International Conference on Computer Communications and Networks (CCN-10) • International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) • International Conference on High Performance Computing Systems (HPCS-10) • International Conference on Information Security and Privacy (ISP-10) • International Conference on Image and Video Processing and Computer Vision (IVPCV-10) • International Conference on Software Engineering Theory and Practice (SETP-10) • International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney Worldฎ Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining — all situated on 10 tropically landscaped acres. Here, guests can experience a full- service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely James Heralds From jbdundas from gmail.com Mon Feb 22 16:49:08 2010 From: jbdundas from gmail.com (jitesh dundas) Date: Mon Feb 22 17:01:18 2010 Subject: [Computational-biology] population dynamics problem Message-ID: <326ea8621002221349g6e1a721ah2df1b84f318d000f@mail.gmail.com> Sir, I wanted to know if we could consider miRNA signatures for the cancer cells . I have been studying the group dynamics of cells with specifically the content of? mRNAs (or miRNA signatures or other measures..I am interested in looking at miRNA signatures within each cell ) in the cells. Cells have dynamic behavior and the way they behave and react to pathogen attacks is really interesting..Till date, not much work has been done on understanding how cells react to viral attack or cancer cells. here we look at the concentration of mRNAs and their associated change and try to find out exactly how the concentration of mRNAs is changing as the behaviour of cells change.. This is a little complicated as the number of cells, eac hof different type, environment factors, internal factors. age and health needs to be considered.. CHanges in MRNA content have been noticed for cancer cells and normal cells..Is there any pattern in the cells and their associated environment when we considered the mRNA of the cells. We will try looking at other factors too as mRNA alone cannot affect the cancer trigger.. Subsequently, we aim to deploy self-evolving networks and find if any patterns are found.. I went through many databases like NCBI,EMBL, SAGE and specific mRNA databases too but the content didnt give us a clear picture of how mRNA changes with cancer cell bahviour or its content in normal cells.. This will be interesting and can have good impact in cancer and drug-discovery. This will also mean studying specific behaviour patterns of dynamic cells as static cells do not show much change or resistance.. We have till now studied cell behaviour, collected data of mRNA and other factors and tried to find exactly how cells are affected by cancer attack..The trigger can be understood with this experiment.. dynamics of different types of cells, working together for a common purpose has not been studied in depth..Data from databases and group dynamics theory will help us understand all these better.. Any comments Sir.any experimental data that I could use for this..is there anyone interested in working with me on this.. Thanks & Regards, Jitesh Dundas http://openwetware.org/wiki/Jitesh_Dundas_Lab Phone:- +91-9561527190 From masulli from disi.unige.it Thu Feb 25 08:53:04 2010 From: masulli from disi.unige.it (Francesco Masulli) Date: Thu Feb 25 09:28:04 2010 Subject: [Computational-biology] 2nd call -School on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Message-ID: <201002251453.04519.masulli@disi.unige.it> *Our apologies if you receive multiple copies of this announcement* Application deadline: March 20, 2010 CALL FOR PARTICIPATION ===================================================================== International Course on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Vietri sul Mare, Salerno (Italy) - May 24-29, 2010 School Website: http://ciob10.disi.unige.it/ Joint course of the International School on Neural Nets "E.R. Caianiello" and of the Italian Network for Oncology Bioinformatics ===================================================================== * Please forward this Call for Participation to interested Colleagues * PURPOSE OF THE COURSE The Twentieth century is often referred as the Century of Biology, as evidenced by the extraordinary development of this scientific area who concluded that century with the great success of the Human Genome Project and the subsequent complete sequencing of human DNA. Currently we are at the beginning of the so-called Post-Genomic Era, characterized on one hand by the availability of a huge amount of Bioinformatics data (often in the public domain), and on the other hand by the need for new and efficient mathematical methods and algorithms capable of distill the information contained in the data. As a matter of fact, the emphasis of research in Bioinformatics is shifting from the development of efficient data storing and handling methods, to the one of methods able to extract useful information from data. Computational Intelligence methodologies (that is, neural networks, evolutionary algorithms and fuzzy logic), partly inspired by natural systems, are a family of powerful methods for data analysis, able to transform the available heterogeneous data into biological knowledge. In recent years, these algorithms have been successfully applied in almost all areas of Bioinformatics to the solution of complex problems concerning signal analysis, classification, clustering, feature selection, and data mining and visualization. The course covers the applications of Computational Intelligence methods to the analysis of Bioinformatics data, with particular focus on applications in oncology. It is addressed to PhD students and researchers in Bioinformatics, Computer Science, Mathematics and Engineering, and includes: - theoretical lectures introducing the main aspects of Bioinformatics and Computational Intelligence methodologies; - lectures aimed to analyze some significant case studies of data analysis in oncology bioinformatics; - practical classes showing some relevant applications of Computational Intelligence methods to Bioinformatics data. LIST OF LECTURERS * Pierre Baldi, University of California, Irvine, CA, USA * Michele Ceccarelli, University of Sannio, Benevento, Italy * Raffaele Giancarlo, University of Palermo, Italy * Antonio Giordano, University of Siena, Italy and Director Sbarro Institute for Cancer research & Molecular Medicine, Philadelphia PA, USA * Paulo Lisboa, Liverpool John Moores University, Liverpool, UK * Francesco Masulli, University of Genoa, Italy & Temple University, PA, USA * Panos M. Pardalos, University of Florida, Gainesville, FL, USA. * Alfredo Petrosino, University Parthenope, Naples, Italy * Stefano Rovetta, University of Genoa, Italy * Giuseppe Russo, Temple University, Philadelphia, PA, USA * Roberto Tagliaferri, University of Salerno, Italy * Andrea Tettamanzi,University of Milan, Italy * Giorgio Valentini, University of Milan, Italy THE COURSE IS JOINTLY ORGANIZED BY International Institute for Advanced Scientific Studies (IIASS) Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC) Italian Network for Oncology Bioinformatics (RNBIO) THE COURSE IS SPONSORED BY GNCS, Gruppo Nazionale per il Calcolo Scientifico INNS, International Neural Network Society S.I.G. on Bioinformatics SIREN, Italian Neural Networks Society DISI - University of Genoa, Italy University of Salerno, Italy IMPORTANT DATES: Application deadline: March 20, 2010 Notification of acceptance: March 25, 2010 Hotel reservation deadline: April 10, 2010 Registration fee payment deadline: April 15, 2010 School May 24-29, 2010 The application form is available at http://ciob10.disi.unige.it/application.html The course is open to all motivated students and research scientists, of any nationality. Applicants with few experience should include a recommendation letter of their supervisor. Places are limited to a maximum of 60 participants in addition to the lecturers. These will be allocated on a first come, first served basis. REGISTRATION FEE (taxes included) Master and PhD Students: 350,00 EURO Academic Participants (govt/univ) : 450,00 EURO Industrial Participants: 600,00 EURO The registration fee includes tuition only. Info on accommodation are available at http://ciob10.disi.unige.it/application.html Some scholarships are available for students who are otherwise unable to participate at the school. Payment details will be notified with acceptance of applications. FOR ANY FURTHER INFORMATION please visit the website http://ciob10.disi.unige.it From man_of_maggie from yahoo.com Fri Feb 26 00:38:35 2010 From: man_of_maggie from yahoo.com (Maggie's Man) Date: Fri Feb 26 07:49:06 2010 Subject: [Computational-biology] Looking for guidance on an alignment question Message-ID: <456954.67678.qm@web110514.mail.gq1.yahoo.com> I'm lookiing at a degenerate repeat promoter polymorphism. I have 43 sequences from 8 species (the polymorphism is found in humans/apes and old world monkeys). The sequences are 7 to 23 repeats in length. The repeats are 19-25 nucleotides in length. I would like to do a nucleotide alignment that is "repeat based". That is, it uses the repeats as the basic unit of the alignment. There are 112 distinct repeats in the whole sample. I can think of two ways to do this: Generate a matrix for all the repeats and find a piece of software that will allow me to input my own matrix AND allow me to use a 112-character alphabet for repeat-based sequences. (Unicode can handle this on the alphabet end). I have yet to find any such software. Globally align the repeats and insert gaps accordingly into each repeat of the sequences, then do a DNA alignment that would preserve the gaps and allow me to set the constant gapped repeat length as the minimum "chunk" size to be considered. Is there anything out there that can do this? Thank you. Bryan Maloney IUPUI.