From azade.mohammadi from gmail.com Wed Apr 1 12:35:40 2009 From: azade.mohammadi from gmail.com (Azade Mohammadi) Date: Wed Apr 1 12:54:34 2009 Subject: [Computational-biology] feature selection problem,urgent help need Message-ID: <137dae570904011035q106a675ficfe003ec4966ff3f@mail.gmail.com> Hello, I have a problem in feature selection I would be thankful if you can help me. I have a dataset with limited samples (for example 100) and a lot of features (for example 3000) and i have to do feature selection. if i use cross validation (for example *10 fold*) i rank the features based on 90 samples (using svmrfe method) i achieve ranked feature for example {f2,f4,f1,f3,...} (it means f2 is ranked first with svmrfe) now, I want to know how many features i should use? so i should compute the performance for n feature selected from first of the ranked list and compute the performance of it. for example train learner with f2, another time with f2,f4, another time with f2,f4,f1 ... and see which is better , but my problem is: 1) first of all,for comparison should i use the performance of 9 fold that has been used for ranking or the performance of learner on the fold which has been left out?I mean in the *feature selection* *step (not in the final evaluation)*,for example to see I should select only f2 or select {f2 , f4} how should I compare? 2) in each stage of cross validation different feature subset will be created . i can compute for each feature the number of times it has repeated in each folding result, but after that how can i conclude the final feature set? can you please help me? I need your urgent help. thanks in advance Azadeh From jprudhomme from healthtech.com Thu Apr 2 14:11:26 2009 From: jprudhomme from healthtech.com (Jim Prudhomme) Date: Thu Apr 2 15:25:30 2009 Subject: [Computational-biology] Structure-Based Drug Design Message-ID: <002e01c9b3c6$d3494260$79dbc720$@com> ***Advanced Registration Discounts End May 1st*** CHI?s Structure-Based Drug Design: Sophisticated Approaches to Drug Discovery June 4-5, 2009 Royal Sonesta Hotel - Cambridge, Massachusetts www.healthtech.com/SBD Topics of discussion include: - Target Structure-Guided Drug Discovery - Feeding SBDD with Biochemical and Biophysical Information - Ligand-Based Predictions Applied to Drug Design - SBDD and Computational Chemistry Methods: A Marriage of Innovation - SBDD of Pharmacological Chaperons Distinguished Faculty: Alex Aronov, Ph.D., Vertex Pharmaceuticals, Inc. Xavier Barril, Ph.D. , ICREA Research Universitat de Barcelona Alex Burgin, Ph.D., deCODE Biostructures Miles Congreve, Ph.D., Heptares Therapeutics Ltd. Jos? Duca, Ph.D., Schering Plough Research Institute Stefan Geschwindner, Ph.D., AstraZeneca R&D M?lndal Ajay N. Jain, Ph.D., University of California, San Francisco Paul Labute, Ph.D., Computing Group (CCG) Dr. Richard J. Law, Evotec AG Brian B. Masek, Ph.D., Tripos International Mark Murcko, Ph.D., Vertex Pharmaceuticals, Inc. Sander Nabuurs, Ph.D., Radboud University Nijmegen Enrico O. Purisima, Ph.D., National Research Council of Canada Dagmar Ringe, Ph.D., Brandeis University Suo-Bao Rong, Ph.D., Pfizer Global R&D Tomi Sawyer, Ph.D., AILERON Therapeutics; Editor-in-Chief, Chemical Biology & Drug Design Andrew D. Scott, Ph.D., Pfizer Global Research and Development Suresh Singh, Ph.D., Vitae Pharmaceuticals Raymond C. Stevens, Scripps Research Institute Gergely Toth, Ph.D., Elan Pharmaceuticals Marcel Verdonk, Ph.D., Astex Therapeutics, Ltd. Markus Wagener, Ph.D., Schering-Plough Research Institute W. Patrick Walters, Ph.D., Vertex Pharmaceuticals, Inc. Plus! Pre-Conference Workshop, Wednesday, June 3 Designing Kinase Inhibitors* Topics Discussed: - Challenges of Crystal Structures - X-Ray Crystallography - Target Immobilized NMR Screening *Separate registration is required. Arrive early to attend... Protein Kinase Targets Conference June 1-3 Interested in Presenting a Poster? CHI welcomes you to share your research by displaying a poster in front of an international delegation. Poster abstracts are due May 7, 2009. Interested in Sponsorships and Exhibit Opportunities? Contact: Katelin Fitzgerald Manager, Business Development Tel: 781-972-5458 E-mail: kfitzgerald@healthtech.com Special Pricing is Available to Attend Both the Structure-Based Drug Design and Protein Kinase Conferences. Learn more , register and submit a poster abstract at www.healthtech.com/SBD Otherwise, call CHI at 781-972-5400. From paolo.romano from istge.it Fri Apr 3 10:16:32 2009 From: paolo.romano from istge.it (Paolo Romano) Date: Fri Apr 3 11:26:44 2009 Subject: [Computational-biology] CFP: NETTAB 2009 on Collaborative Bioinformatics Research and Development (social networks, wiki, ...) Message-ID: <200904031516.n33FGX7N002149@clus2.istge.it> Apologies if you receive more copies. =========================== Announce and Preliminary Call for Papers NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ Submissions deadlines: - April 28, 2009: Oral communication submission - May 15, 2009: Posters submission Submissions must be short papers of around 3 pages or 12.000 characters long. Special Issues in peer-review journals on workshop's topics planned: post-workshop ad hoc Call for papers will be issued. RATIONALE Advent of Wide Area Networks (WAN) allowed the availability of distributed information and prompted the need for searching and retrieving this data (Network Information Retrieval tools, NIR), as well the development of unprecedented communications between users (Computer Mediated Communication tools, CMC). Initially, CMC was asynchronous and based on electronic mail and newsgroups. From email systems, mailing lists and newsletter were soon derived, while newsgroups generated, shortly after, electronic fora. Synchronous communication were introduced through the advent of chat services. On this line, current multimedia teleconference systems were then set up. Virtual reality was first introduced for educational purposes by means of MUD (Multi-users Domain) systems, and especially by means of MOO (MUD Object-oriented). This line produced current virtual reality environment, like the emerging Second Life system. Life Sciences researchers largely took profit from CMC tools. The bionet newsgroups hierarchy remains one of the most famous and useful CMC system supporting life science research. Many mailing lists that were born in that context are still used. The development of open source software was largely made possible by the possibility of exchanging, in an effective way, knowledge, practices and skills among researchers. Web sites of communities of scientists were set up and often constituted the base for a real collaborative development and research. The most recent developments of collaborative development tools are impressive. Researchers can now collaboratively develop software (open source systems), discuss and compare development strategies (social networks), write documents (google docs, wiki systems), build knowledge bases. So, it may now be the time for presenting current technologies, tools and applications for collaborative work and for discussing perspectives of their utilization in support of Bioinformatics. For these reasons, NETTAB 2009 will be devoted to "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development". Moreover, there will be a special session on "Methods and Tools for RNA Structure and Functional Analysis". The transcription of almost all genomes generates a great number of coding and non-coding RNAs (ncRNAs). Although RNA is central to the synthesis of proteins, it is not only a messenger of genetic information: many cellular functions depend on ncRNAs, which exert their functions by their sequence and structure. In particular, small silencing RNAs (miRNAs, siRNAs and piRNAs) play a crucial role in many physiological processes and their aberrant expression is a common feature of human diseases including cancer. Models and tools able to increase our understanding of RNAs functions and their involvement in diseases may lead to the design of new RNA-based therapeutics. The RNA community is also taking advantage of collaborative research tools such as Wikis and other virtual environments. The RNA WikiProject contains now over 600 articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct those articles. Therefore, the NETTAB 2009 special session will focus on collaborative research project, computational methods and tools for the analysis of RNA structures and functions, with a special emphasis on ncRNAs. KEYNOTE SPEAKER # Alex Bateman Wellcome Trust Sanger Institute Hinxton, Cambridge, UK # Tim Clark Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA # Duncan Hull School of Chemistry, University of Manchester, Manchester, UK # Michael Levitt Stanford University, USA # Debora Marks Systems Biology Department, Harvard Medical School Boston, USA TOPICS - Collaborative Web sites (bioinformatics.org, biojava, bioperl, ) - Communities of Practices (CoPs) Scientific practices in scientific communities Automatic detection / gathering / modelling of scientific practices Implementations of CoPs - Social networking (myExperiment, Annotea, myScience) Social Bookmarking Semantic Document Markup Relationships mining from literature - Open Source development Sharing of data models, libraries, interfaces - Social software for collaborative documentation development Wikis, blogs, google docs Knowledge Wikis Social-software-mediated collaborative scientific research Social-software-mediated collaborative tools' development Knowledge base collaborative development Ontologies collaborative development - Education and training tools E-learning Virtual environments Methods and Tools for RNA Structure and Functional Analysis - RNA structure prediction - Collaborative studies of RNAs - ncRNAs functional analysis and classification - miRNAs and networks - Genome-wide functional studies - Identification of ncRNAs - Databases of ncRNAs and miRNA targets - miRNA targets prediction - Synthetic miRNA and siRNA design - Gene expression analysis - Analysis of viral RNAs - RNAi therapeutics - Identification of ncRNAs biomarkers - RNA-protein interaction prediction DEADLINES Submissions for both oral communications and posters must be short papers of around THREE A4 pages or 12.000 characters long. - April 28, 2009: Oral communication submission Acceptation communication: May 12, 2009 - May 15, 2009: Posters submission - May 17, 2009: Early registration - June 10-13, 2009: Tutorials and Workshop Calls for SPECIAL ISSUES We plan to launch Calls for Special Issues on the themes of the workshop in peer-review journals with associated Impact factor around July for submission in September 2009. Best regards. Paolo Romano on behalf of NETTAB 2009 Chairs Paolo Romano (paolo.romano@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 AIUTACI AD AIUTARE: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From frist from coe01.ucalgary.ca Sat Apr 4 20:38:23 2009 From: frist from coe01.ucalgary.ca (Brian Fristensky) Date: Sat Apr 4 22:08:19 2009 Subject: [Computational-biology] Applied Computational Genomics Course Message-ID: <200904050138.n351cNmo023671@coe01.ucalgary.ca> Genome Canada APPLIED COMPUTATIONAL GENOMICS COURSE (ACGC) Led by Dr. Brian Fristensky WESTERN CANADA- JULY 14 TO JULY 20, 2009 - Calgary, Alberta, Canada EASTERN CANADA- AUGUST 25 TO AUGUST 31, 2009 - Montreal, Quebec, Canada www.gcbioinformatics.ca/training Since 2003, the ACGC courses have helped laboratory biologists become power users of the latest software tools. Through mastery of fundamental bioinformatics skills, this week-long course enables working biologists to take charge of their data and their projects. The ACGC course utilizes a wide array of popular software, within the context of a portable and comprehensive bioinformatics system. 1. BIRCH (Biological Research Computer Heirarchy) (http://home.cc.umanitoba.ca/~psgendb): o Provides a complete bioinformatics suite for analysis of sequences, molecular markers, phylogenetic trees, mircoarrays, and data mining and management. o Automates use of a wide range of programs (for example, BLAST, FASTA, clustalw, Phylip and many others) through a highly accessible graphic interface. o Fosters a unique environment for experimentation with data. 2. The Bluejay genome browser (http://bluejay.ucalgary.ca/) o Creates a means for visualization of the wealth of information hidden within the complexity of the genomes. o Permits comparisons of the organization of two or more chromosomes. o Allows for visualization of hot spots of gene expression. o Facilitates the annotation of new genomes. 3. Genome Canada Bioinformatics Help Desk (http://gchelpdesk.ualberta.ca/) o Beginner-level introduction to Perl scripting . o Gives consultation on bioinformatics problems on a fee-for-service basis. o Offers a repository of software. o Provides web tools, including BASys (Bacterial Annotation System), PlasMapper, BacMap CGView and others. 4. BioMoby (http://www.biomoby.org/) o Automatically discovers web services worldwide that work with almost any kind of biological data. o Facilitates the learning of Perl Scripts for leveraging web services for maximizing research outcomes. o Creates high-throughput data pipelines through implementation of the Taverna workbench. Proficiency with bioinformatics tools raises the bar with success in pure and applied research activity, thesis supervisory roles, publication potential, career placement opportunities, and the viability of funding avenues. After the course, attendees of the ACGC will have FREE internet access to all the Bioinformatics Platform tools and databases used in this course. All software is also freely downloadable. Faculty Faculty for the ACGC include some of the best recognized bioinformaticians from across Canada, including Drs. Christoph Sensen, Brian Fristensky, David Wishart, and Mark Wilkinson. Dr. Christoph Sensen was recently featured in international media for his breakthrough research on degenerative disorders linked to chronic wasting disease (CWD) in elk and Mad Cow Disease. Dr. Mark Wilkinson has recently been profiled in publications from a diverse range of international research organizations such as the Heart and Stroke Foundation of Canada, Microsoft Research, and the National E-Science Centre of the UK for his groundbreaking work into data and knowledge representation in the biological sciences, and in cardiovascular research in particular. Dr. David Wishart has been actively involved in teaching and developing bioinformatics training programs across Canada and the United States for more than 10 years. He has published more than 150 papers on bioinformatics and various "omics! " technologies. Dr. Fristensky has been a contributor to the fields of bioinformatics and plant molecular biology since the early 1980's. Publications span a range of interests, including resistance to biotic and abiotic stress in crops, software for DNA and protein sequence analysis, management of biological databases, and improving software usability in bioinformatics. Registration and further information Early Bird enrolment in the week-long course extends now to June 1, 2009 for the Calgary course and to July 1, 2009 for the Montreal course, at a reduced fee of $1,250 Cdn. for Canadian participants and $1,500 Cdn. for international participants. To register, and for further information, please visit our website at www.gcbioinformatics.ca/training Enquiries can be made to Susanne Cardwell in Canada at 403-210-6661, email smcardwe@ucalgary.ca Also, it would be greatly appreciated by BIP if you would consider sending out this message to your mailing lists and/or posting the information on your websites (a sponsorship agreement can be arranged for interested parties). From masulli from disi.unige.it Mon Apr 6 00:08:04 2009 From: masulli from disi.unige.it (Francesco Masulli) Date: Mon Apr 6 09:12:46 2009 Subject: [Computational-biology] LAST CFP: CIBB 2009 - 6th INT. MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS Genova (Italy) 15-17 October, 2009 Message-ID: <200904060708.05413.masulli@disi.unige.it> Please, accept our apologies for multiple postings. Paper submission deadline for CIBB 2009 is 15 April 2009 ========================================================================================= CIBB 2009 SIXTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS Genova (Italy) 15-17 October, 2009 Conference Website: http://cibb09.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2009 is jointly organized by: *INNS International Neural Network Society SIG Bioinformatics *GNCS Gruppo Nazionale Calcolo Scientifico *HHF Human Health Foundation Onlus *SIREN Italian Neural Networks Society *RNBIO The Italian Network for Oncology Bioinformatics *DISI Dept. Computer and Information Sciences - Univ. Genova (Italy) *DMI Dipartimento di Matematica e Informatica - Univ. Salerno (Italy) Technical areas addressed by CIBB 2009 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Key-note lecturers: Taishin Nomura, Osaka University, Japan L. Gwenn Volkert, Kent State University, Kent, OH, USA Gilles Bernot, University of Nice Sophia Antipolis,France Leif E. Peterson, Methodist Hospital Research Institute Houston, TX, USA The scientific program will include, besides the key-note lectures, some tutorials (included in the registration fee) and contributed papers that will be presented in oral or poster sessions. The following Special Sessions will be included in the program: Combining Bayesian and Machine Learning Approaches in Bioinformatics: State of Art and Future Perspectives, organized by Claudia Angelini, Pietro Lio', Luciano Milanesi . ISMDS - Intelligent Systems for Medical Decisions Support, organized by Alexandru Floaresand Florin Manolache . Using game-theoretical tools in Bioinformatics, organized by Fioravante Patrone . Data Clustering and Bioinformatics, organized by Vassilis P. Plagianakos Dimitris K. Tasoulis . Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2009 will be published in revised extended form as a post conference volume of Lecture Notes in Bioinformatics LNBI/LNCS series of Springer Verlag. We are also planning to edit a special issue of an international journal containing contributions of the authors of the best papers presented to CIBB 2009. Chairs: Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Leif E. Peterson, Methodist Hospital Research Institute, Houston, TX, USA Roberto Tagliaferri, University of Salerno, Italy Scientific Program Committee: Klaus-Peter Adlassnig, Medical University of Vienna, Austria Gilles Bernot, University of Nice Sophia Antipolis, France Domenico Bordo, National Cancer Research Institute, Genova, Italy Giovanni Cuda, University of Magna Graecia, Catanzaro, Italy Joaquin Dopazo, Centro de Investigacion Principe Felipe, Valencia, Spain Enrico Formenti, University of Nice Sophia Antipolis, France Antonio Giordano, University of Siena, Italy & Temple Univ, Philadelphia, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Nicolas Le Novere, Wellcome-Trust Genome Campus, Hinxton, UK Pietro Lio', University of Cambridge, UK Giancarlo Mauri, University of Milano Bicocca, Italy Oleg Okun, Precise Biometrics AB, Sweden Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Jagath Rajapakse, Nanyang Technological University, Singapore Volker Roth, University of Basel, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Anna Tramontano, Sapienza University, Rome, Italy Giorgio Valentini, University of Milan, Italy Gennady M. Verkhivker, University of Kansas, KS & UC San Diego, CA, USA L. Gwenn Volkert, Kent State University, Kent, OH, USA Steering Commitee: 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, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Paper submission deadline: 15 April 2009 Notification of acceptance: 15 June 2009 Final paper due: 15 July 2009 Conference: 15-17 October 2009 Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and should be not longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. <--------------------------------------------------------------------> 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 oscadd from gmail.com Wed Apr 1 13:44:50 2009 From: oscadd from gmail.com (Raghava) Date: Mon Apr 6 11:57:53 2009 Subject: [Computational-biology] Bioinformatics Suite Message-ID: <96acd60f-c5e2-426d-9560-87b401dfb085@v23g2000pro.googlegroups.com> Dear Colleagues Our group have developed number of webservers (http:// www.imtech.res.in/raghava/ ) over th\ e years. I got lot of request related to i) availability of source code; ii) perl scripts\ used to build software; iii) standalone version of methods. In order to help our bioinfo\ rmatics users particularly young developers who wish to develop bioinformatics programs; f\ irst time we are releasing source code (written in PERL) for public. I hope these perl scr\ ipts will be useful for bioinformatics community. Codes are available from http://www.imtech.res.in/raghava/gpsr/ https://sourceforge.net/projects/gpsraghava/ This is just starting, we will release all software to public in next one year. I will app\ reciate you comment/suggestion/feedback on this package GPSR. Regards Raghava ====================================================== # Dr G P S Raghava, Scientist and Head Bioinformatics Centre # # Institute of Microbial Technology, Sector-39A, Chandigarh, India # # Phone: +91-172-2690557, Fax: +91-172-2690632 # # Eadd: http://www.imtech.res.in/raghava/ raghava@imtech.res.in # #===================================================== From jqb from Cs.Nott.AC.UK Tue Apr 7 10:05:25 2009 From: jqb from Cs.Nott.AC.UK (Jaume Bacardit) Date: Tue Apr 7 10:44:53 2009 Subject: [Computational-biology] [Extended Deadline] CFP: Memetic Computing Journal special issue on Metaheuristics for Large Scale Data Mining Message-ID: <49DB6BB5.3010506@cs.nott.ac.uk> [Apologies if you receive multiple times this announcement] Call for Papers: Memetic Computing Journal special issue on Metaheuristics for Large Scale Data Mining - Extended Deadline Guest editors: Jaume Bacardit School of Computer Science and School of Biosciences University of Nottingham jaume.bacardit@nottingham.ac.uk Xavier Llora National Center for Supercomputing Applications University of Illinois at Urbana-Champaign xllora@illinois.edu Submission deadline: May 31st , 2009 Aim and Scope Data mining and knowledge discovery are crucial techniques across many scientific disciplines. Recent developments such as the Genome Project (and its successors) or the construction of the Large Hadron Collider have provided the scientific community with vast amounts of data. Metaheuristics and other evolutionary algorithms have been successfully applied to a large variety of data mining tasks. Competitive metaheuristic approaches are able to deal with rule, tree and prototype induction, neural networks synthesis, fuzzy logic learning, and kernel machines -to mention but a few. Moreover, the inherent parallel nature of some metaheuristics (e.g. evolutionary approaches, particle swarms, ant colonies, etc) makes them perfect candidates for approaching very large-scale data mining problems. Although a number of recent techniques have applied these methods to complex data mining domains, we are still far from having a deep and principled understanding of how to scale them to datasets of terascale, petascale or even larger scale. In order to achieve and maintain a relevant role in large scale data mining, metaheuristics need, among other features, to have the capacity of processing vast amounts of data in a reasonable time frame, to use efficiently the unprecedented computer power available nowadays due to advances in high performance computing and to produce when possible- human understandable outputs. Several research topics impinge on the applicability of metaheuristics for data mining techniques: (1) proper scalable learning paradigms and knowledge representations, (2) better understanding of the relationship between the learning paradigms/representations and the nature of the problems to be solved, (3) efficiency enhancement techniques, and (4) visualization tools that expose as much insight as possible to the domain experts based on the learned knowledge. We would like to invite researchers to submit contributions on the area of large-scale data mining using metaheuristics. Potentially viable research themes are: * Learning paradigms based on metaheuristics, evolutionary algorithms, learning classifier systems, particle swarm, ant colonies, tabu search, simulated annealing, etc * Hybridization with other kinds of machine learning techniques including exact and approximation algorithms * Knowledge representations for large-scale data mining * Advanced techniques for enhanced prediction (classification, regression/function approximation, clustering, etc.) when dealing with large data sets * Efficiency enhancement techniques * Parallelization techniques * Hardware acceleration techniques (vectorial instuctions, GPUs, etc.) * Theoretical models of the scalability limits of the learning paradigms/representations * Principled methodologies for experiment design (choosing methods, adjusting parameters, etc.) * Explanatory power and visualization of generated solutions * Data complexity analysis and measures * Ensemble methods * Online data mining and data streams * Examples of real-world successful applications Instructions for authors Papers should have approximately 20 pages (but certainly not more than 24 pages). The papers must follow the format of the Memetic Computing journal: http://www.springer.com/engineering/journal/12293?detailsPage=contentItemPage&CIPageCounter=151543 Papers should be submitted following the Memetic Computing journal guidelines. When submitting the paper please select this special issue as the article type. Important dates Manuscript submission: May 31st, 2009 Notification of acceptance: July 31st, 2009 Submission of camera-ready version: Sep 30th, 2009 -- ------------------------------------------------------------------- Jaume Bacardit, PhD Lecturer in Bioinformatics University of Nottingham Automated Scheduling, Planning and Optimisation research group, School of Computer Science, Jubilee Campus, Nottingham, NG8 1BB, UK Multidisciplinary Centre for Integrative Biology, School of Biosciences, Sutton Bonington, LE12 5RD, UK Tel: +441159516276 Fax: +44 1159516292 Email: jaume _dot_ bacardit _at_ nottingham _dot_ ac _dot_ uk Web: http://www.cs.nott.ac.uk/~jqb -------------------------------------------------------------------- -- ------------------------------------------------------------------- Jaume Bacardit, PhD Lecturer in Bioinformatics University of Nottingham Automated Scheduling, Planning and Optimisation research group, School of Computer Science, Jubilee Campus, Nottingham, NG8 1BB, UK Multidisciplinary Centre for Integrative Biology, School of Biosciences, Sutton Bonington, LE12 5RD, UK Tel: +441159516276 Fax: +44 1159516292 Email: jaume _dot_ bacardit _at_ nottingham _dot_ ac _dot_ uk Web: http://www.cs.nott.ac.uk/~jqb -------------------------------------------------------------------- This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From tekaia from pasteur.fr Tue Apr 7 12:33:06 2009 From: tekaia from pasteur.fr (Fredj Tekaia) Date: Tue Apr 7 16:15:41 2009 Subject: [Computational-biology] Last call: Bioinformatics and Comparative Genome Analysis EMBO course in Hong Kong Message-ID: <55806DE2-884E-467F-BF4C-AAFC10788086@pasteur.fr> Last Call for application to the : Bioinformatics and Comparative Genome Analysis course August 17 - August 29, 2009 HKU-Pasteur Research Centre - Hong Kong Deadline for application: April 15, 2009. Course program: http://www.pasteur.fr/~tekaia/BCGA2009/ BCGA2009_Prog.html Duration: Full time from August 17 to August 29, 2009. Location: Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. Accommodation and social: Acceptance to the course includes free accommodation (double room based) breakfast, lunch and dinner. More information about the course, how to apply and application form can be found at the course web page: http://www.pasteur.fr/~tekaia/ BCGA2009.html Organizers/Contact: Roberto Bruzzone, HKU-Pasteur Research Centre - Hong Kong. Si Lok, Genome Research Center The University of Hong Kong - Hong Kong. Tin Wee Tan, National University of Singapore - Singapore. Ueng-Cheng Yang, National Yang-Ming University, Taipei - Taiwan. Fredj Tekaia, Institut Pasteur Paris - France. With financial support from: EMBO - Institut Pasteur Paris. From masulli from disi.unige.it Fri Apr 10 14:15:16 2009 From: masulli from disi.unige.it (Francesco Masulli) Date: Sat Apr 11 12:38:01 2009 Subject: [Computational-biology] CIBB 2009: Paper deadline extended to 30 April 2009 Message-ID: <200904102115.17301.masulli@disi.unige.it> Please, accept our apologies for multiple postings. After several requests, the paper submission deadline for CIBB 2009 has been extended to 30 April 2009 ========================================================================================= CIBB 2009 SIXTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS Genova (Italy) 15-17 October, 2009 Conference Website: http://cibb09.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2009 is jointly organized by: *INNS International Neural Network Society SIG Bioinformatics *GNCS Gruppo Nazionale Calcolo Scientifico *HHF Human Health Foundation Onlus *SIREN Italian Neural Networks Society *RNBIO The Italian Network for Oncology Bioinformatics *DISI Dept. Computer and Information Sciences - Univ. Genova (Italy) *DMI Dipartimento di Matematica e Informatica - Univ. Salerno (Italy) Technical areas addressed by CIBB 2009 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Key-note lecturers: Taishin Nomura, Osaka University, Japan L. Gwenn Volkert, Kent State University, Kent, OH, USA Gilles Bernot, University of Nice Sophia Antipolis,France Leif E. Peterson, Methodist Hospital Research Institute Houston, TX, USA The scientific program will include, besides the key-note lectures, some tutorials (included in the registration fee) and contributed papers that will be presented in oral or poster sessions. The following Special Sessions will be included in the program: Combining Bayesian and Machine Learning Approaches in Bioinformatics: State of Art and Future Perspectives, organized by Claudia Angelini, Pietro Lio', Luciano Milanesi . ISMDS - Intelligent Systems for Medical Decisions Support, organized by Aaron Baughman, Alexandru Floares, and Florin Manolache . Using game-theoretical tools in Bioinformatics, organized by Fioravante Patrone . Data Clustering and Bioinformatics, organized by Vassilis P. Plagianakos Dimitris K. Tasoulis . Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2009 will be published in revised extended form as a post conference volume of Lecture Notes in Bioinformatics LNBI/LNCS series of Springer Verlag. We are also planning to edit a special issue of an international journal containing contributions of the authors of the best papers presented to CIBB 2009. Chairs: Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Leif E. Peterson, Methodist Hospital Research Institute, Houston, TX, USA Roberto Tagliaferri, University of Salerno, Italy Scientific Program Committee: Klaus-Peter Adlassnig, Medical University of Vienna, Austria Gilles Bernot, University of Nice Sophia Antipolis, France Domenico Bordo, National Cancer Research Institute, Genova, Italy Giovanni Cuda, University of Magna Graecia, Catanzaro, Italy Joaquin Dopazo, Centro de Investigacion Principe Felipe, Valencia, Spain Enrico Formenti, University of Nice Sophia Antipolis, France Antonio Giordano, University of Siena, Italy & Temple Univ, Philadelphia, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Nicolas Le Novere, Wellcome-Trust Genome Campus, Hinxton, UK Pietro Lio', University of Cambridge, UK Giancarlo Mauri, University of Milano Bicocca, Italy Oleg Okun, Precise Biometrics AB, Sweden Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Jagath Rajapakse, Nanyang Technological University, Singapore Volker Roth, University of Basel, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Anna Tramontano, Sapienza University, Rome, Italy Giorgio Valentini, University of Milan, Italy Gennady M. Verkhivker, University of Kansas, KS & UC San Diego, CA, USA L. Gwenn Volkert, Kent State University, Kent, OH, USA Steering Commitee: 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, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Paper submission deadline: 30 April 2009 (extended) Notification of acceptance: 15 June 2009 Final paper due: 15 July 2009 Conference: 15-17 October 2009 Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and should be not longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. <--------------------------------------------------------------------> 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 oscadd from gmail.com Fri Apr 10 11:22:24 2009 From: oscadd from gmail.com (Raghava) Date: Sat Apr 11 12:38:07 2009 Subject: [Computational-biology] Prediction of guide strand of microRNAs Message-ID: Dear Colleagues We have developed a method for predicting "guide strand of microRNAs from its sequence and secondary structure" it is published in BMC Bioinformatics see http://www.biomedcentral.com/1471-2105/10/105 . Though it is developed to discriminate for guide and passenger strand of miRNA but it can be used to design siRNA. I hope this information will be useful for bioinformatics community. With Regards Raghava #====================================================== # Dr G P S Raghava FASc, FNASc, Scientist and Head Bioinformatics Centre # # Institute of Microbial Technology, Sector-39A, Chandigarh, India # # Phone: +91-172-2690557, Fax: +91-172-2690632 # # Eadd: http://www.imtech.res.in/raghava/ raghava@imtech.res.in # #=====================================================- From db60 from st-andrews.ac.uk Tue Apr 14 07:19:09 2009 From: db60 from st-andrews.ac.uk (Daniel Barker) Date: Tue Apr 14 09:56:31 2009 Subject: [Computational-biology] Course: St Andrews, Scotland, Bioinformatics and Comparative Genomics, 15-18 August 2009 Message-ID: The University of St Andrews and the Scottish Bioinformatics Forum will be hosting: Summer School - Bioinformatics and Comparative Genomics Start Date: 15th August 2009, 09:00 am End Date: 18th August 2009 Location: The University of St Andrews, Scotland http://www.genome-bioinformatics.org Confirmed Speakers: Prof Ziheng Yang FRS, University College London, UK Prof Neil Hall, University of Liverpool, UK Dr Zemin Ning, Wellcome Trust Sanger Institute, UK Dr David Martin, University of Dundee, UK Prof Geoff Barton, University of Dundee, UK Dr Daniel Barker, University of St Andrews, UK Prof Ian Korf, UC Davis Genome Center, USA Prof Dannie Durand, Carnegie Mellon University, USA Dr Chris Janssen, SBF and University of Glasgow, UK Dr David Ferrier, University of St Andrews, UK The summer school on bioinformatics and comparative genomics will address practical bioinformatics for sequence analysis and comparative genomics for use in biological and biomedical research. Internationally renowned invited speakers will discuss current challenges, applications, and future outlook in the field. The school will consist of a series of lectures, seminars and practical classes, allowing participants both insight into theory and the opportunity to learn practical skills in data analysis and interpretation. Registration for the summer school includes attendance at a one-day international conference on 18th August, "Comparative Genomics". Four nights of accommodation (14th-17th August) are optionally available on registration. Full details and registration please see: http://www.genome-bioinformatics.org We look forward to seeing you in August. Best regards, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From devipsrs from gmail.com Sat Apr 18 07:35:48 2009 From: devipsrs from gmail.com (devipsrs@gmail.com) Date: Sat Apr 18 10:58:21 2009 Subject: [Computational-biology] Extended deadline: BCBGC-09 call for papers Message-ID: Extended deadline: BCBGC-09 call for papers The extended deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is very close from now. The conference will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: • International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) • International Conference on Automation, Robotics and Control Systems (ARCS-09) • International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) • International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) • International Conference on Information Security and Privacy (ISP-09) • International Conference on Recent Advances in Information Technology and Applications (RAITA-09) • International Conference on Software Engineering Theory and Practice (SETP-09) • International Conference on Theory and Applications of Computational Science (TACS-09) • International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely Susan Publicity committee From jprudhomme from healthtech.com Tue Apr 21 14:41:09 2009 From: jprudhomme from healthtech.com (Jim Prudhomme) Date: Tue Apr 21 15:46:47 2009 Subject: [Computational-biology] Structure-Based Drug Design Message-ID: <002301c9c2b9$1e719bb0$5b54d310$@com> ***Advanced Registration Discounts End May 1st*** CHI?s Structure-Based Drug Design: Sophisticated Approaches to Drug Discovery June 4-5, 2009 Royal Sonesta Hotel - Cambridge, Massachusetts www.healthtech.com/SBD Topics of discussion include: - Target Structure-Guided Drug Discovery - Feeding SBDD with Biochemical and Biophysical Information - Ligand-Based Predictions Applied to Drug Design - SBDD and Computational Chemistry Methods: A Marriage of Innovation - SBDD of Pharmacological Chaperons Distinguished Faculty: Alex Aronov, Ph.D., Vertex Pharmaceuticals, Inc. Xavier Barril, Ph.D. , ICREA Research Universitat de Barcelona Alex Burgin, Ph.D., deCODE Biostructures Miles Congreve, Ph.D., Heptares Therapeutics Ltd. Jos? Duca, Ph.D., Schering Plough Research Institute Stefan Geschwindner, Ph.D., AstraZeneca R&D M?lndal Ajay N. Jain, Ph.D., University of California, San Francisco Paul Labute, Ph.D., Computing Group (CCG) Dr. Richard J. Law, Evotec AG Brian B. Masek, Ph.D., Tripos International Mark Murcko, Ph.D., Vertex Pharmaceuticals, Inc. Sander Nabuurs, Ph.D., Radboud University Nijmegen Enrico O. Purisima, Ph.D., National Research Council of Canada Dagmar Ringe, Ph.D., Brandeis University Suo-Bao Rong, Ph.D., Pfizer Global R&D Tomi Sawyer, Ph.D., AILERON Therapeutics; Editor-in-Chief, Chemical Biology & Drug Design Andrew D. Scott, Ph.D., Pfizer Global Research and Development Suresh Singh, Ph.D., Vitae Pharmaceuticals Raymond C. Stevens, Scripps Research Institute Gergely Toth, Ph.D., Elan Pharmaceuticals Marcel Verdonk, Ph.D., Astex Therapeutics, Ltd. Markus Wagener, Ph.D., Schering-Plough Research Institute W. Patrick Walters, Ph.D., Vertex Pharmaceuticals, Inc. Plus! Pre-Conference Workshop, Wednesday, June 3 Designing Kinase Inhibitors* Topics Discussed: - Challenges of Crystal Structures - X-Ray Crystallography - Target Immobilized NMR Screening *Separate registration is required. Arrive early to attend... Protein Kinase Targets Conference June 1-3 Interested in Presenting a Poster? CHI welcomes you to share your research by displaying a poster in front of an international delegation. Poster abstracts are due May 7, 2009. Interested in Sponsorships and Exhibit Opportunities? Contact: Katelin Fitzgerald Manager, Business Development Tel: 781-972-5458 E-mail: kfitzgerald@healthtech.com Special Pricing is Available to Attend Both the Structure-Based Drug Design and Protein Kinase Conferences. Learn more , register and submit a poster abstract at www.healthtech.com/SBD Otherwise, call CHI at 781-972-5400. From Rob.Reedijk from douglasconnect.com Wed Apr 22 10:23:02 2009 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Apr 22 11:37:27 2009 Subject: [Computational-biology] Predictive ADMET Workshop: Application of Predictive ADME and Toxicology methods to drug discovery and development, Oxford July 27-31, 2009 Message-ID: <921f9187-7d91-4666-9ee5-1b4be225a08e@37g2000yqp.googlegroups.com> I am posting information on a 5 day workshop taking place at Oxford University in July 2009. 27-31 July, 2009 Predictive ADMET Workshop: Application of Predictive ADME and Toxicology methods to drug discovery and development, a Hands-on 5 Day eCheminfo Workshop. Case Study Approach on ADME and Tox endpoints and datasets. http://echeminfo.com/comty_oxfordadmet09 Medical Sciences Teaching Centre, Oxford University, Oxford, UK Bursarys award available (deadline February 20, 2009) facilitated by Barry Hardy eCheminfo Community of Practice These workshops are aimed to provide a set of stimulating workshops using latest advanced in silico techniques of relevance to chemists, life scientists, clinical researchers, toxicologists and modellers working in drug discovery and development. Participants should return to their labs with new ideas, best practices and software experiences to maximise productivity in their own drug discovery and development research activities. Workshop groups will study problems with hands-on examples using leading-edge software and discuss complex issues highlighted by examples and case studies presented by instructors. A case study set will be used to link all workshop activities through the week. Workshop Instructors Barry Hardy (Douglas Connect), Ismael Zamora (Pompeu Fabra University and Lead Molecular Design), Christoph Helma (in silico toxicology), David Leahy (University of Newcastle), Philip Judson (Lhasa), Anton Hopfinger (University of New Mexico), Mark Cronin (Liverpool John Moores University), Olga Obrezanova (BioFocus DPI), Glen Myatt (Leadscope), Judith Madden (Liverpool John Moores University), Arianna Bassan (S-IN) Software packages and an IT classroom will be used by instructors and participants to work through Predictive ADME and Toxicology problems. Participants may propose problems and issues to the faculty ahead of the workshop. Participants will also have ample opportunity to discuss their perspectives and criticisms of the methods studied and should take-away key nuggets of understanding from these intensive sessions. A related workshop will run the week before 20-24 July, 2009 Drug Discovery Design Methods & Applications: Virtual screening, structure-based drug design, cheminformatics and molecular modelling supporting drug discovery and design, a Hands-on 5 Day eCheminfo Workshop. Case Study approach including Kinases. http://echeminfo.com/comty_oxfordworkshop09 For further information and questions on the Workshop programs, please contact Dr. Barry Hardy at: barry.hardy -[at]- douglasconnect.com, Tel: +41 61 851 0170 For registrations, please contact Nicki Douglas, nicki.douglas -[at]- douglasconnect.com, Tel: +41 61 851 0461 From nir from rosettadesigngroup.com Sat Apr 25 10:13:37 2009 From: nir from rosettadesigngroup.com (Nir London) Date: Sat Apr 25 12:00:57 2009 Subject: [Computational-biology] What is your favorite journal in the field of computational structural biology? Message-ID: Following the success of our previous poll which was followed by an =20 extensive and interesting discussion, and in order to better our =20 Bi(Tri,..)-Weekly Digests, we present a new poll which will determine =20= once and for all, which is the best journal for the computational =20 structural biologist. = http://rosettadesigngroup.com/blog/353/what-is-your-favorite-journal-in-th= e-field-of-computational-structural-biology/ Of course we=92re all reading all of the journals mentioned, and =20 certainly each has its own benefits. There is also the question if by =20= =93favorite=94 journal we mean where would you like to publish, or which = =20 are you enjoying reading the most? We know the question isn=92t =20 adequately defined. Nontheless, we urge you to pick one and try to =20 explain in the comments what makes that journal special. Nir London. http://rosettadesigngroup.com/blog/= From allan.tucker from brunel.ac.uk Mon Apr 27 08:32:55 2009 From: allan.tucker from brunel.ac.uk (allan tucker (brunel)) Date: Mon Apr 27 08:58:59 2009 Subject: [Computational-biology] {Disarmed} Systems Biology Symposium 25 - 26 June at Brunel University Message-ID: <99CEB8928E3C436F928246BF4FD0346A@disc.stjohns.brunel.ac.uk> Symposium on Biological and Chemical Informatics for Health: Foundations for Systems Biology Brunel University, West London, UK 25-26 June 2009 Find out more and register for this free event here http://bcih-sb.brunel.ac.uk Integration of biological and chemical informatics presents a real opportunity to address some of the most exciting and challenging issues posed by systems biology. These diverse disciplines, and their interaction, play a crucial role in addressing key issues in drug design and discovery, environmental sustainability, health and disease processes, and disease prevention, diagnosis and treatment. Join us for a two day symposium sponsored by the BBSRC and Brunel University, where influential leaders in bioinformatics, chemoinformatics, systems biology and health, will present the latest developments that are helping to shape this interdisciplinary field. This symposium is open to those working in the field, including academics, researchers, students and industry and will provide an excellent environment for delegates to participate in networking activities and developing collaborative, interdisciplinary research partnerships. We are delighted that the following have already agreed to speak at the event: Bioinformatics Janet Thornton, Director of the European Bioinformatics Institute Marco Ramoni, Director of Biomedical Cybernetics Laboratory, Harvard Medical School Christine Orengo, Professor of Bioinformatics, University College London Health Sally Davies, Director General of Research and Development and Chief Scientific Adviser for the Department of Health and NHS Chemoinformatics Peter Willett, Professor of Information Science, Sheffield University Robert Glen, Director of Unilever Centre for Molecular Science Informatics, Cambridge University Peter Johnson, Professor of Computational Chemistry, Leeds University Systems Biology Tom Kirkwood, Director of the Newcastle Centre for Integrated Systems Biology of Ageing and Nutrition Simon Gaskell, Vice-President for Research, Manchester University Chris Rawlings, Head of Department of Biomathematics and Bioinformatics, Rothamsted Research, BBSRC David Gilbert, Head of School of Information Systems, Computing and Mathematics, Brunel University Colin Miles, Head of Systems Biology, BBSRC Stephen Muggleton, Director of Modelling, Centre for Integrative Systems Biology at Imperial College Peter Bramley, Head of School of Biological Sciences, Royal Holloway London For more details and free registration see: http://bcih-sb.brunel.ac.uk From zzhao from vcu.edu Mon Apr 27 12:27:38 2009 From: zzhao from vcu.edu (Zhongming Zhao) Date: Mon Apr 27 19:15:49 2009 Subject: [Computational-biology] Call for Abstracts/Papers, Third Summit on Systems Biology Message-ID: <49F5EB0A.105@vcu.edu> +++++++++++++++++++++++++++++++++++++++++++++ This email and the attached documents are intended to serve as an invitation for you and your colleagues to actively participate in a conference, the third Summit on Systems Biology, which will be held June 16-19, 2009 in Richmond, Virginia. This will be the third in a planned continuing series of Summits on System Biology, with different themes each year. In 2007, our theme was 'Basic, Clinical and Translational Research' with a focus on heart disease and cancer. We received broad support for the 2007 conference and the response from attendees was excellent. This year our focus is Microbial Systems Biology and we invite you to participate. details are provided below. Submit your abstract online and join us!! *Abstract submission deadline: May 7, 2009* *SUMMIT ON SYSTEMS BIOLOGY 2009: The Microbial World and Beyond June 16-19, 2009* The Third Annual Summit on Systems Biology will be held on June 16-19, 2009, in historic Richmond, Virginia located two hours south of Washington, DC. The Summit is comprised of five scientific sessions and two workshops to bring together computational and experimental scientists in the area of microbial systems. The third summit will discuss research directions and latest findings in the "omics" domain, as well as promote collaborations in microbial systems biology and related disciplines. Dr. Leroy Hood, Director of the Institute for Systems Biology, and Dr. Stuart Kauffman, of the University of Calgary, and a recipient of the MacArthur Foundation Award, and Albert-L?szl? Barab?si, Director, Center for Complex Network Research, Northeastern University, all pioneers in Systems Biology, are members of the Summit Steering Committee. *The five scientific sessions are: * . Microbial Engineering . Metagenomics and Microbial Ecology . Host-Pathogen Interaction . Human Microbiome . Technological Advances in Systems Biology *The two workshops are:* . Tree of Life and Microbial Systems Biology . Gene Networks and Diseases *Program Design* The three day program is divided into five (5) main sessions and two (2) workshops. The workshops will be held on the day preceding the formal opening of the conference. Web will also host two poster sessions, one for students and one for more senior researchers. There will be a */New Technology Workshop /*as a pre-conference event, in concert with the student poster session on Tuesday evening, June 16. Instrument manufacturers will provide presentations and virtual demonstrations on the latest technology and applications. *Technical Symposia* *Session I: Microbial Engineering * The first session provides a broad overview of synthetic biology, systems biology and biological engineering and their applications to health, clean and renewable energy, and the environment. Specific topics include synthetic gene networks and the biosynthetic capacity of microbial systems. This session brings together a diverse group of participants from a variety of disciplines. *Session II: Metagenomics and Microbial Ecology* The second session of the summit highlights the latest developments in our understanding of the emergence and evolution of pathogenic and non-pathogenic microbes with a particular emphasis on insights gained through genomic analyses of microbial communities. *Session III: Host-Pathogen Interactions* The third session focuses on how innovative approaches and high-throughput techniques are used to study the complex interactions between bacterial pathogens and their eukaryotic hosts. Participants studying a range of pathogens using various host systems come together to discuss integrated systems approaches. *Session IV: Human Microbiome* The fourth session provides the opportunity to discuss the latest advances in sequencing the human microbiome. The session underlines the importance of the metabolic function of microbiota and the role of symbiosis in health and disease. *Session V: Technological Advances in Systems Biology * The final session focuses on how emerging technologies are driving advances in metagenomics, transcriptomics, proteomics and metabolomics at the microbial community level. The session features cutting-edge research on quantitative mass spectrometry and the latest advances in DNA sequencing. *Interactive Workshops* *New Technology Workshop *This event will involve presentations on the latest technology and applications by instrument manufacturers and active researchers on the opening evening of the conference, and will be held concurrently with the student poster session and reception. *Workshop I: Gene networks and disease *The past decade has witnessed an exponential growth of biological data including genomic sequences, gene annotations, expression and regulation, and protein-protein interactions. We will include discussions on the relationship between oral pathogens and cardiovascular disease, with special interest in the virulence of Streptococcus sanguinis. This workshop focuses on the reconstruction and analysis of gene networks and pathways of human pathogens and their application to disease. *Workshop II: Assembling the Microbial Tree of Life *During the 21^st century, the advances on microbial systems biology will be closely tied to phylogenomics approaches to unravel the evolutionary relationships of the microbial world. By involving an interdisciplinary group of scientists and students from outside the tree of life community, including mathematicians, statisticians, clinicians, computer scientists, chemists, physicists, and engineers, the workshop will foster the development of new questions and lines of research contributing to the generation of a robust microbial phylogenetic framework. *Venue and Accommodations:* The Omni Richmond Hotel 100 South 12th Street Richmond, Virginia 23219 Phone: (804) 344-7000, Fax: (804) 648-6704 Toll Free 1-888-444-OMNI The Omni Richmond Hotel, a luxury hotel, offers Southern hospitality in a contemporary setting. Overlooking the scenic James River in the heart of Richmond's financial and historical districts, the Omni Richmond is located in lively, historic Shockoe Slip. _http://www.omnihotels.com/FindAHotel/Richmond.aspx_ */Government rate for Summit attendees for early registration./* For conference information and registration, go to: _http://www.vcu.edu/csbc/systemsbiologysummit/_ Program contact: Zhongming Zhao, Ph.D., Assistant Professor Psychiatric Genetics Email: _zzhao@vcu.edu_ Gregory A. Buck, Ph.D.Chair, Steering Committee Director, Center for the Study of Biological Complexity, Virginia Commonwealth University. By phone: 804-827-0026 or email _sysbiosummit@vcu.edu_ -- ============================================ Zhongming Zhao, Ph.D. Asst. Professor of Bioinformatics Depts. Psychiatry and Human Genetics and Center for the Study of Biological Complexity Virginia Commonwealth University PO Box 980126, Richmond VA 23298-0126 Phone: (804) 828-8129 Fax: (804) 828-1471 http://bioinfo.vipbg.vcu.edu/ From paolo.romano from istge.it Tue Apr 28 08:14:35 2009 From: paolo.romano from istge.it (Paolo Romano) Date: Tue Apr 28 12:38:28 2009 Subject: [Computational-biology] NETTAB 2009: Deadline postponed to May 4, 2009, for Oral communications Message-ID: <200904281328.n3SDSkK9046168@ibm43p.biotech.ist.unige.it> Due to many requests for a new deadline for submission of contributions for oral communications, the related deadline has been postponed to: Monday May 4, 2009, at 12.00 (noon), EST (GMT+1). ===== Last Call for Oral communications NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ Deadline approaching: May 4, 2009: Oral communication submission Contributions must be short papers of around THREE A4 pages or 12.000 characters long. Submit through the EasyChair system at: http://www.easychair.org/conferences/?conf=nettab2009 . See web site for details. Motivation The most recent developments of collaborative development tools are impressive. Researchers can now collaboratively develop software (open source systems), discuss and compare development strategies (social networks), write documents (google docs, wiki systems), build knowledge bases. So, it may now be the time for presenting current technologies, tools and applications for collaborative work and for discussing perspectives of their utilization in support of Bioinformatics. For these reasons, NETTAB 2009 will be devoted to "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development". The RNA community is also taking advantage of collaborative research tools such as Wikis and other virtual environments. The RNA WikiProject contains now over 600 articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct those articles. Therefore, the NETTAB 2009 special session will focus on collaborative research project, computational methods and tools for the analysis of RNA structures and functions, with a special emphasis on ncRNAs. Invited Speakers (more to be announced) # Alex Bateman Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK # Doron Betel MSKCC - Computational Biology Center New York, USA # Tim Clark Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA # Duncan Hull School of Chemistry, University of Manchester, Manchester, UK # Gabriel Valiente Technical University of Catalonia, Department of Software, Barcelona, Spain # Debora Marks Systems Biology Department, Harvard Medical School, Boston, USA # Gabriel Valiente Technical University of Catalonia, Department of Software, Barcelona, Spain Topics - Collaborative Web sites (bioinformatics.org, biojava, bioperl, ) - Communities of Practices (CoPs) Scientific practices in scientific communities Automatic detection / gathering / modelling of scientific practices Implementations of CoPs - Social networking (myExperiment, Annotea, myScience) Social Bookmarking Semantic Document Markup Relationships mining from literature - Open Source development Sharing of data models, libraries, interfaces - Social software for collaborative documentation development Wikis, blogs, google docs Knowledge Wikis Social-software-mediated collaborative scientific research Social-software-mediated collaborative tools' development Knowledge base collaborative development Ontologies collaborative development - Education and training tools E-learning Virtual environments Methods and Tools for RNA Structure and Functional Analysis - RNA structure prediction - Collaborative studies of RNAs - ncRNAs functional analysis and classification - miRNAs and networks - Genome-wide functional studies - Identification of ncRNAs - Databases of ncRNAs and miRNA targets - miRNA targets prediction - Synthetic miRNA and siRNA design - Gene expression analysis - Analysis of viral RNAs - RNAi therapeutics - Identification of ncRNAs biomarkers - RNA-protein interaction prediction Deadlines Contributions for both oral communications and posters must be short papers of around THREE A4 pages or 12.000 characters long. They must be submitted through the EasyChair system at: http://www.easychair.org/conferences/?conf=nettab2009 . - May 4, 2009: Oral communication submission - May 15, 2009: Posters submission - May 17, 2009: Early registration - June 10-13, 2009: Tutorials and Workshop Calls for SPECIAL ISSUES We plan to launch Calls for Special Issues on the themes of the workshop in peer-review journals with associated Impact factor around July for submission in September 2009. Best regards. Paolo Romano on behalf of NETTAB 2009 Chairs NETTAB '09 - Ninth International Workshop on Network Tools and Applications in Biology 10-13 June 2009, Catania, Italy http://www.nettab.org/2009/ Paolo Romano (paolo.romano@istge.it) Bioinformatics National Cancer Research Institute (IST) From jprudhomme from healthtech.com Wed Apr 29 12:00:11 2009 From: jprudhomme from healthtech.com (Jim Prudhomme) Date: Wed Apr 29 13:01:45 2009 Subject: [Computational-biology] Structure-Based Drug Design Message-ID: <009b01c9c8eb$f531ef50$df95cdf0$@com> ***Advanced Registration Discounts End May 1st*** CHI?s Structure-Based Drug Design: Sophisticated Approaches to Drug Discovery June 4-5, 2009 Royal Sonesta Hotel - Cambridge, Massachusetts www.healthtech.com/SBD Topics of discussion include: - Target Structure-Guided Drug Discovery - Feeding SBDD with Biochemical and Biophysical Information - Ligand-Based Predictions Applied to Drug Design - SBDD and Computational Chemistry Methods: A Marriage of Innovation - SBDD of Pharmacological Chaperons Distinguished Faculty: Alex Aronov, Ph.D., Vertex Pharmaceuticals, Inc. Xavier Barril, Ph.D. , ICREA Research Universitat de Barcelona Alex Burgin, Ph.D., deCODE Biostructures Miles Congreve, Ph.D., Heptares Therapeutics Ltd. Jos? Duca, Ph.D., Schering Plough Research Institute Stefan Geschwindner, Ph.D., AstraZeneca R&D M?lndal Ajay N. Jain, Ph.D., University of California, San Francisco Paul Labute, Ph.D., Computing Group (CCG) Dr. Richard J. Law, Evotec AG Brian B. Masek, Ph.D., Tripos International Mark Murcko, Ph.D., Vertex Pharmaceuticals, Inc. Sander Nabuurs, Ph.D., Radboud University Nijmegen Enrico O. Purisima, Ph.D., National Research Council of Canada Dagmar Ringe, Ph.D., Brandeis University Suo-Bao Rong, Ph.D., Pfizer Global R&D Tomi Sawyer, Ph.D., AILERON Therapeutics; Editor-in-Chief, Chemical Biology & Drug Design Andrew D. Scott, Ph.D., Pfizer Global Research and Development Suresh Singh, Ph.D., Vitae Pharmaceuticals Raymond C. Stevens, Scripps Research Institute Gergely Toth, Ph.D., Elan Pharmaceuticals Marcel Verdonk, Ph.D., Astex Therapeutics, Ltd. Markus Wagener, Ph.D., Schering-Plough Research Institute W. Patrick Walters, Ph.D., Vertex Pharmaceuticals, Inc. Plus! Pre-Conference Workshop, Wednesday, June 3 Designing Kinase Inhibitors* Topics Discussed: - Challenges of Crystal Structures - X-Ray Crystallography - Target Immobilized NMR Screening *Separate registration is required. Arrive early to attend... Protein Kinase Targets Conference June 1-3 Interested in Presenting a Poster? CHI welcomes you to share your research by displaying a poster in front of an international delegation. Poster abstracts are due May 7, 2009. Interested in Sponsorships and Exhibit Opportunities? Contact: Katelin Fitzgerald Manager, Business Development Tel: 781-972-5458 E-mail: kfitzgerald@healthtech.com Special Pricing is Available to Attend Both the Structure-Based Drug Design and Protein Kinase Conferences. Learn more , register and submit a poster abstract at www.healthtech.com/SBD Otherwise, call CHI at 781-972-5400. From tavares from fe.up.pt Tue Apr 21 12:03:30 2009 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Wed Sep 30 17:18:12 2009 Subject: [Computational-biology] (no subject) Message-ID: <1b972f8c-e0e8-4b75-9da5-f6fd4156b600@z9g2000yqi.googlegroups.com> ------------------------------------------------------------------------------------------------------------------------------------------ (Apologies for cross-posting) EURASIP Journal on Advances in Signal Processing Special issue on Image Processing and Analysis in Biomechanics http://www.hindawi.com/journals/asp/si/ipab.html 2nd Call for papers We would appreciate if you could distribute this information by your colleagues and co-workers. ------------------------------------------------------------------------------------------------------------------------------------------ Dear Colleague, A critical component for true realistic biomechanical analysis and simulations is to obtain accurately, from images, the geometric data and the behavior of the desired structures. For that, the use of automatic, efficient, and robust techniques of image processing and analysis is mandatory. The main objective of this Special Issue, of the EURASIP Journal on Advances in Signal Processing, on Image Processing and Analysis in Biomechanics is to bring together recent advances in the related fields (not limited to): - Signal processing in biomechanical applications; - Data interpolation, registration, acquisition and compression in biomechanics; - Segmentation of objects in images for biomechanical applications; - 3D reconstruction of objects from images for biomechanical applications; - 2D/3D tracking and object analysis in images for biomechanical applications; - 3D vision in biomechanics; - Biomechanical applications involving image processing and analysis algorithms; - Virtual reality in biomechanics; - Software development for image processing and analysis in biomechanics. Submission Instructions: Authors should follow the journal Author Guidelines (http:// www.hindawi.com/journals/asp/guidelines.html) and submit their manuscript through the journal Manuscript Tracking System (http:// mts.hindawi.com/), according to the following timetable: - Manuscript Due: May 1, 2009; - First Round of Reviews: August 1, 2009; - Publication Date: November 1, 2009. Lead Guest Editor Jo?o Manuel R. S. Tavares, University of Porto, Portugal (tavares@fe.up.pt) Guest Editor R. M. Natal Jorge, University of Porto, Portugal (rnatal@fe.up.pt)