From prash from ruc.dk Wed Jul 2 11:46:54 2008 From: prash from ruc.dk (Prash) Date: Wed Jul 2 12:55:29 2008 Subject: [Computational-biology] The 9th International Conference on Systems Biology Message-ID: <20080702184654.qqjvzqvrtw880w4s@webmail-backend1.ruc.dk> ICSB 2008 The 9th International Conference on Systems Biology Gothenburg, Sweden Poster abstract submission deadline: July 23 www.icsb-2008.org From ozgun.harmanci from gmail.com Thu Jul 3 23:57:13 2008 From: ozgun.harmanci from gmail.com (ozgun.harmanci) Date: Fri Jul 4 10:45:16 2008 Subject: [Computational-biology] Interpolate missing residues in pdb files Message-ID: <9fc8b828-b200-4947-8110-03f9ce46b07a@f36g2000hsa.googlegroups.com> Hello, I am having trouuble with missing residues in pdb files and need to replace them (i.e. interpolate them) using a program. I think swiss- pdbviewer and pymol do that. My problem is that I am not very capable of using those programs and the person whom I asked for help told me that I have to check for missing residues in pdb file, open swiss- pdbviewer then add residue at correct place and finally she told me that I might need to do an energy minimization and I am thinking that I will definitely do a mistake there. I was wondering if anyone knows a more automated way to get the missing residues inserted for me because I am thinking that you can find missing residues in pdb and and programs can read that info and add these missing residues themselves automatically.. (but again maybe not..) Thanks. Sincerely, Arif. From icdm08-publicity from isti.cnr.it Fri Jul 4 16:29:23 2008 From: icdm08-publicity from isti.cnr.it (Maurizio Atzori) Date: Fri Jul 4 22:46:32 2008 Subject: [Computational-biology] Last reminder: CFP 8th IEEE International Conference on Data Mining (ICDM08) Message-ID: *** We apologize in advance if you receive multiple copies of this CFP *** CFP: LAST REMINDER for submitting a paper to IEEE ICDM08 ICDM '08: The 8th IEEE International Conference on Data Mining -------------------------------------------------------------- December 15-19, 2008 Pisa, Italy http://icdm08.isti.cnr.it/ Important Dates --------------- July 7, 2008 - 11:59pm PST Deadline for paper submission September 15, 2008 Notification to authors October 7, 2008 Deadline for camera-ready copies December 15-19, 2008 Conference Call for Papers --------------- The IEEE International Conference on Data Mining series (ICDM) has established itself as the world's premier research conference in data mining, providing a leading forum for presentation of original research results, as well as exchange and dissemination of innovative, practical development experiences. The conference covers all aspects of data mining, including algorithms, software and systems, and applications. In addition, ICDM draws researchers and application developers from a wide range of data mining related areas such as statistics, machine learning, pattern recognition, databases and data warehousing, data visualization, knowledge-based systems, and high performance computing. By promoting novel, high quality research findings, and innovative solutions to challenging data mining problems, the conference seeks to continuously advance the state-of-the-art in data mining. Besides the technical program, the conference will feature workshops, tutorials, panels, and the ICDM data mining contest. Paper Submissions ----------------- High quality papers in all data mining areas are solicited. Original papers exploring new directions will receive especially careful consideration. Papers that have already been accepted or are currently under review for other conferences or journals will not be considered for ICDM '08. Paper submissions should be limited to a maximum of 10 pages in the IEEE 2-column format, the same as the camera-ready format (see the IEEE Computer Society Press Proceedings Author Guidelines at http://www.computer.org/portal/pages/cscps/cps/final/icdm06.xml ). All papers will be reviewed by the Program Committee on the basis of technical quality, relevance to data mining, originality, significance, and clarity. A double blind review process will be adopted. Authors should avoid using identifying information in the text of the paper. A link to the Submission Form to submit your work is available at the following page: http://icdm08.isti.cnr.it/Paper-Submissions/19/paper-submissions Accepted papers will be published in the conference proceedings by the IEEE Computer Society Press and accorded oral presentation times in the main conference. Submissions accepted as regular papers will be allocated 10 pages in the proceedings. Submissions accepted as short papers will be allocated 6 pages in the proceedings and will have a shorter presentation time at the conference than regular papers. A selected number of IEEE ICDM '08 accepted papers will be invited for possible inclusion, in expanded and revised form, in the Knowledge and Information Systems journal (http://www.cs.uvm.edu/~kais/) published by Springer-Verlag. ICDM Best Paper Awards ---------------------- IEEE ICDM Best Paper Awards will be conferred at the conference on the authors of (1) the best research paper and (2) the best application paper. Strong, foundational results will be considered for the best research paper award and application-oriented submissions will be considered for the best application paper award. Workshops and Tutorials ----------------------- ICDM '08 will host short and long tutorials as well as workshops that focus on new research directions and initiatives. All accepted workshop papers will be included in a separate workshop proceedings published by the IEEE Computer Society Press. For further information on workshop and tutorial proposal submissions, please visit the conference website. ICDM Data Mining Contest ------------------------ ICDM '08 will host a data mining contest to challenge researchers and practitioners with a real practical data mining problem. For further details on proposals and expression of interest, please see: http://icdm08.isti.cnr.it/CallsFor/15/icdm-2008-data-mining-contest-call-for-proposals Topics of Interest ------------------ * Data mining foundations - Novel data mining algorithms in traditional areas (such as classification, regression, clustering, probabilistic modeling, pattern discovery, and association analysis) - Models and algorithms for new, structured, data types, such as arising in chemistry, biology, environment, and other scientific domains - Developing a unifying theory of data mining - Mining sequences and sequential data - Mining spatial and temporal datasets - Mining textual and unstructured datasets - Distributed data mining - High performance implementations of data mining algorithms - Privacy- and anonymity-preserving data analysis * Mining in emerging domains - Stream Data Mining - Mining moving object data, RFID data, and data from sensor networks - Ubiquitous knowledge discovery - Mining multi-agent data - Mining and link analysis in networked settings: web, social and computer networks, and online communities - Mining the semantic web - Data mining in electronic commerce, such as recommendation, sponsored web search, advertising, and marketing tasks * Methodological aspects and the KDD process - Data pre-processing, data reduction, feature selection, and feature transformation - Utility assessment, interestingness analysis, and post-processing - Statistical foundations for robust and scalable data mining - Handling imbalanced data - Automating the mining process and other process related issues - Dealing with cost sensitive data and loss models - Human-machine interaction for the KDD process - Visual analytics for data mining - Integration of data warehousing, OLAP and data mining - Data mining query languages - Security and data integrity * Integrated KDD applications, systems, and experiences - Bioinformatics, computational chemistry, ecoinformatics - Computational finance, online trading, and analysis of markets - Intrusion detection, fraud prevention, and surveillance - Healthcare, epidemic modeling, and clinical research - Customer relationship management - Telecommunications, network and systems management - Sustainable mobility and intelligent transportation systems Organization ------------ Conference Co-chairs: Franco Turini (KDD Lab, Univ. Pisa, Italy) Carlo Zaniolo (UCLA, USA) Naren Ramakrishnan (Virginia Tech, USA) Program Committee Chairs: Fosca Giannotti (KDD Lab, ISTI-CNR, Italy) Dimitrios Gunopulos (UC Riverside, USA) Vice Chairs: Gennady Andrienko (Fraunhofer Institute Autonomous Intelligent Systems) Ricardo Baeza-Yates (Yahoo! Research Barcelona) Elena Baralis (Politecnico di Torino) Roberto Bayardo (Google, Inc.) Toon Calders (Eindhoven Technical University) Gautam Das (University of Texas at Arlington) Luc De Raedt (Leuven) Amol Deshpande (University of Maryland) Carlotta Domeniconi (George Mason University) Charles Elkan (University of California, San Diego) Tapio Elomaa (University of Helsinki) Wei Fan (IBM) Johannes Gehrke (Cornell University) Aris Gionis (Yahoo! Research Barcelona) Hillol Kargupta (University of Maryland) Eamonn Keogh (University of California ? Riverside) Ravi Kumar (Yahoo! Research Silicon Valley) Laks V.S. Lakshmanan (University of British Columbia) Ling Liu, Georgia Institute of Technology) Nikos Mamoulis (University of Hong Kong) Giuseppe Manco (University of Calabria) Heikki Mannila (Helsinki University of Technology) Mirco Nanni (KDD Lab, ISTI ? CNR) Srinivasan Parthasarathy (The Ohio State University) Jian Pei (Simon Fraser University) Rajeev Rastogi (Yahoo! Labs - Bangalore) Yucel Saygin (Sabanci University) Kyuseok Shim (KAIST) Yannis Theodoridis (University of Piraeus) Michalis Vazirgiannis (Athens Univ. of Economics & Business) Zhi-Hua Zhou (Nanjing University) Steering Committee Chair: Xindong Wu (Univ. Vermont, USA) Tutorials Chairs: Dino Pedreschi (KDD Lab, Univ. Pisa, Italy) Arno Siebes (Uthrecht Univ., The Netherlands) Workshops Chairs: Francesco Bonchi (KDD Lab, ISTI-CNR, Italy) Bettina Berendt (Humbolt Univ. Berlin, Germany) Award Chair: Katharina Morik (Univ. Dortmund, Germany) Panels Chair: Jean-Francois Boulicaut (INSA Lyon, France) Exhibit and Demo Chairs: Michail Vlachos (IBM T. J. Watson Research Center, USA) Haixun Wang (IBM T. J. Watson Research Center, USA) Publicity Chairs: Maurizio Atzori (KDD Lab, ISTI-CNR, Italy) Yan-Nei Law (Bioinformatics Institute, Singapore) Sponsorship Chairs: Antonio Gulli (Ask.com, Italy) Raffaele Perego (HPC Lab, ISTI-CNR, Italy) Local Arrangements Chairs: Chiara Renso (KDD Lab, ISTI-CNR, Italy) Tiziana Mazzone (KDD Lab, ISTI-CNR, Italy) Local Arrangements Team: Miriam Baglioni, Michele Berlingerio, Andrea Mazzoni, Mirco Nanni, Ruggero Pensa, Fabio Pinelli, Simone Puntoni, Salvatore Rinzivillo, Salvatore Ruggeri, Roberto Trasarti (KDD Lab, Univ.Pisa and ISTI-CNR, Italy) Finance Chair: Dino Pedreschi (KDD Lab, Univ. Pisa, Italy) Further Information ------------------- icdm08-chair@isti.cnr.it icdm08-organizer@isti.cnr.it surface address: IEEE - ICDM08 KDD Lab, ISTI-CNR via A. Moruzzi, 1 56124 Pisa, Italy Phone: +39 050 3152999 - 3153000 - 3153001 Fax: +39 050 3152040 From icdm08-publicity from isti.cnr.it Fri Jul 4 17:00:52 2008 From: icdm08-publicity from isti.cnr.it (Maurizio Atzori) Date: Fri Jul 4 22:46:38 2008 Subject: [Computational-biology] CFP: First IEEE International Workshop on Semantic Aspects in Data Mining (SADM'08) Message-ID: *** We apologize in advance if you receive multiple copies of this CFP *** First International Workshop on Semantic Aspects in Data Mining (SADM'08) In conjunction with the 2008 IEEE International Conference on Data Mining (ICDM 2008) Pisa, Italy, December 15 - 19, 2008 http://www-kdd.isti.cnr.it/SADM/ Preliminary Call For Papers Knowledge Discovery is generally described as a process of automatic extraction of interesting useful, and previously unknown knowledge from data. It is expected that data characteristics, data semantics as well as the knowledge that already exists about the data can be directly incorporated into the knowledge discovery process. However, semantic and reasoning aspects may intervene in several steps of the discovery process, and now the questionis how these aspects interact within the process, and the forms that this can take. In data pre-processing, semantic aspects may help in (1) identifying source data of interest, (2) enriching the data with additional domain information, and (3) generating more meaningful and human understandable patterns, once the generated patterns are directly related to the input data. During the mining task, semantics may be used as constraints, thus allowing (1) search space reduction, (2) pattern pruning, and (3) the development of more efficient algorithms. Background knowledge may intervene in the post-processing step helping in the explanation of large amounts of patterns, typically difficult to interpret. The objective of SADM is to introduce standardized formal methods which can explicitly consider data semantics, background knowledge, or reasoning in the mining process. This knowledge has to be represented/formalized in a knowledge repository, such as ontologies, conceptual schemas, knowledge bases, etc. The main aspect is that this knowledge has to be explicitly incorporated into the KDD process, where the algorithms for data preprocessing, data mining or post-processing make use of this knowledge to improve the KDD process. The key idea is to develop a more general understanding about how to exploit data semantics and background knowledge, and to create standardized procedures for designing more intelligent data mining methods. We believe that such an effort can lead to the development of the science of semantic data mining. Invited Talk: Prof. Jean Francois Boulicaut from University of Lyon, will give a talk. The preliminary title is: "If constraint-based mining is the answer, what is the constraint?" Special Issue The organizers intend to publish a selected and extended paper (the Best Paper) as a special issue of an international journal (to be confirmed). . Topics of Interest: The workshop will seek submissions where semantic information plays an explicit role in the knowledge discovery process. The intent of the workshop is to bring together researchers and practitioners interested in semantic aspects in data mining from a wide range of possible data mining subareas, including: web mining, medical data mining, spatio-temporal data mining, ubiquitous knowledge discovery, and privacy-preserving data mining. The aim of the workshop is to receive contributions in the following topics, which are not exclusive: - Techniques to embed semantics into the discovery process - Semantics in data pre-processing and post-processing - Semantic-based pruning - Knowledge-based data mining algorithms - Semantic-based techniques for feature selection - Ontologies and data pre-processing - Ontology-based evaluation of discovered patterns - Data Mining Query Languages - Constraint-based data mining - Semantics for Knowledge representation, interpretation, and reasoning - Semantics in SBIA Spatial and Spatio-temporal data mining - Conceptual modeling and data mining - Semantic-based KDD processes and frameworks - Semantics in biological data mining - Semantics for uncertainty handling in data mining - Semantics in Privacy-Preserving Data Mining - Semantics in Social Network Data Mining Researchers interested in domain-driven data mining may want to submit their papers to DDDM'08 workshop on Domain Driven Data Mining (DDDM'08). Important Dates: - Submission Deadline: 1 August 2008 - Notification acceptance: 15 September 2008 - Camera-ready: 7 October 2008 - Workshop day: 15 or 19 december 2008 Preliminary Program Committee List (***to be completed***): * Luis Otavio Alvares, UFRGS, Brazil * Maurizio Atzori, - ISTI-CNR, Italy * Miriam Baglioni, Dept of Computer Science, University of Pisa, Italy * Toon Calders, Eindhoven Technical University, The Netherlands * Saso Dzeroski, Jozef Stefan Institute, Dept. of Knowledge Technologies, Slovenia Oracle * Baris Kazar, Oracle, USA * Vipin Kumar University of Minnesota USA * Jin Soung Yoo, Indiana University, USA * Jose Antonio de Macedo, EPFL, Switzerland * Mirco Nanni, ISTI CNR, Italy * Giuseppe Psaila, University of Bergamo, Italy * Yucel Saygin, Sabanci University, Turkey * Yannis Theodoridis, Univ Pireus, Athens, Greece * Monica Wachowicz, UPM, Madrid, Spain * Mohammed Zaki, Department of Computer Science Rensselaer Polytechnic Institute, USA Submission Guidelines and Review Process: High quality research papers in the relevant areas are solicited. Original papers exploring new directions will receive especially careful consideration. Papers that have already been accepted or are currently under review for other conferences or journals will not be considered. All accepted workshop papers will be included in the IEEE ICDM Workshop Proceedings, to be published by the IEEE Computer Society Press. Therefore, at least one author of the accepted paper must register to attend the workshop. Paper submissions should be limited to a maximum of 8 pages in PDF format, in the IEEE 2-column style (see the IEEE Computer Society Press Proceedings Author Guidelines at http://www.computer.org/portal/pages/cscps/cps/final/icdm06.xml). All papers will be reviewed by the Program Committee on the basis of technical quality, relevance to workshop topics, originality, significance, and clarity. We will follow the double blind review process. Authors must hence not use identifying information in the text of the paper and bibliographies must be referenced to preserve anonymity. Please use the Submission Form on the ICDM'08 website to submit your paper. Organization: Chairs: Dr. Vania Bogorny, Instituto de Informatica, Universidade Federal do Rio Grande do Sul, E-mail: vbogorny [at] inf.ufrgs.br Dr. Hui Xiong, Management Science and Information Systems Department, Rutgers, the State University of New Jersey, Email: hxiong [at] rutgers.edu Dr. Chiara Renso, KDD Laboratory, ISTI-CNR Pisa, Italy, Via G. Moruzzi 156124 PISA - Italy Email: chiara.renso [at] isti.cnr.it From yanlinlin82 from gmail.com Fri Jul 4 19:46:51 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Fri Jul 4 22:46:43 2008 Subject: [Computational-biology] Re: Interpolate missing residues in pdb files References: Message-ID: On Jul 4, 12:57?pm, "ozgun.harmanci" wrote: > Hello, > I am having trouuble with missing residues in pdb files and need to > replace them (i.e. interpolate them) using a program. I think swiss- > pdbviewer and pymol do that. My problem is that I am not very capable > of using those programs and the person whom I asked for help told me > that I have to check for missing residues in pdb file, open swiss- > pdbviewer then add residue at correct place and finally she told me > that I might need to do an energy minimization and I am thinking that > I will definitely do a mistake there. I was wondering if anyone knows > a more automated way to get the missing residues inserted for me > because I am thinking that you can find missing residues in pdb and > and programs can read that info and add these missing residues > themselves automatically.. (but again maybe not..) > > Thanks. > > Sincerely, > Arif. Even if an automatic way to do that could be found, the theoretical models used in the methods must be understood clearly. In addition, all results from computation and/or software need be verified by experiments, since they just give hints or guides for that. From tavares from fe.up.pt Thu Jul 10 07:51:26 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Thu Jul 10 11:53:16 2008 Subject: [Computational-biology] Symposium "Image Processing and Data Visualization" within the SEECCM 2009, Greece - Announce & Call for Papers Message-ID: <831d878b-e351-41a2-a13b-9f9bfc549cbe@f36g2000hsa.googlegroups.com> (Our apologies for cross-posting. We appreciate if you kindly distribute this information by your co- workers and colleagues.) *************************************************************************** Symposium “Image Processing and Data Visualization” 2nd South-East European Conference on Computational Mechanics (SEECCM 2009) Island of Rhodes, Greece, 22-24 June 2009 http://www.seeccm2009.org (A special interest conference of the European Community on Computational Methods in Applied Sciences (ECCOMAS) and of the International Association for Computational Mechanics (IACM)) *************************************************************************** Dear Colleague, Within the 2nd South-East European Conference on Computational Mechanics (SEECCM 2009), to be held in Island of Rhodes, Greece, in 22-24 June 2009, we are organizing the Symposium “Image Processing and Data Visualization”. The main goal of the Symposium “Image Processing and Data Visualization” is to provide a platform for communications among specialists from complementary fields such as mechanics, computational vision, mathematics, physics, informatics, computer graphics, bio- medical-practice, psychology, clinicians and industry. Participants in this symposium should present and discuss their proposed methods in the corresponding fields that are related to the symposium topics and explore the translational potentials of this emerging technological field. Hence, this symposium should be an excellent opportunity to refine ideas for future work and to establish constructive cooperation. Due to your research activities in the related fields, we are pleased to invite you to submit your work and participate in the Symposium “Image Processing and Data Visualization”. Topics of interest include (but are not restricted to): - Image Analysis; - Image Restoration, Compression, Segmentation and Description; - Object Tracking, Matching, Registration, Recognition and Reconstruction; - Visual Inspection; - 3D Vision; - Medical Imaging; - Data Processing, Modelling and Analysis; - Scientific Visualization; - Enhanced Visualization; - Human Computer Interaction; - Enhanced and Virtual Reality; - Simulation and Animation; - Software Development for Image Processing and Data Visualization; - Grid Computing in Image Processing and Data Visualization; - Applications of Image Processing and Data Visualization. Important dates and Instructions: - Deadline for submission one page abstract: 30 November 2008; - Authors notification: 31 December 2008; - Final contribution submission: 28 February 2009. - To submit your contribution, you should access the conference website at www.seeccm2009.org and select the Symposium “Image Processing and Data Visualization” or send your file by email to the organizers (tavares@fe.up.pt, ceconst@stanford.edu). With kind regards, Yours sincerely, The Organizers, João Manuel R. S. Tavares (tavares@fe.up.pt) Faculty of Engineering of University of Porto, Porto, Portugal Christos E. Constantinou (ceconst@stanford.edu) Stanford University, USA From prash from ruc.dk Sun Jul 13 16:02:29 2008 From: prash from ruc.dk (Prash) Date: Sun Jul 13 17:30:02 2008 Subject: [Computational-biology] BSB '08 live on July 14, 2008 Message-ID: <20080713230229.06ja3h4ry8808kkc@webmail-backend1.ruc.dk> Dear All, The virtual conference: BSB '08 which we are organizing would go live tomorrow at http://www.ustream.tv/channel/bioinformatics.org The above link is a free streaming with low resolution. Should you need to go for good resolution, please register at http://wiki.bioinformatics.org/Bioinformatics_to_Systems_Biology_2008 Sincerely Prash Director, Bioinformatics.org Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ ?Never let your sense of morals get in the way of doing what's right.? ~~ Isaac Asimov From reddy from cs.wayne.edu Sun Jul 13 20:27:06 2008 From: reddy from cs.wayne.edu (Chandan K. Reddy) Date: Mon Jul 14 11:29:56 2008 Subject: [Computational-biology] CFP: 1st Workshop on Data Mining in Functional Genomics In-Reply-To: References: Message-ID: 1st Workshop on Data Mining in Functional Genomics in Conjunction with IEEE International Conference on Bioinformatics and Biomedicine Philadelphia, PA, USA, Nov. 5-7, 2008 http://www.cs.wayne.edu/~reddy/Workshop/DMFG08/ Workshop Description: Functional genomics is a sub-field of molecular biology that makes use of the enormous amounts of data produced by genomic projects to describe some dynamic aspects such as gene transcription, translation, and protein-protein interactions. Because these phenomena are typically characterized by large and increasing amounts of data, diverse and unusual data types, and complex relationships, interpreting such data requires novel approaches that include multiple tools, new algorithms, resources, etc. in an integrated fashion. Data Mining is the process of automatic discovery of novel, understandable and potentially useful models from such massive amounts of data. Organized in conjunction with BIBM 2008, the objective of this workshop is to facilitate collaboration between data mining researchers and bioinformaticians by presenting cutting-edge research topics and methodologies in the areas of functional genomics and data mining. While such research has an interdisciplinary character, this workshop emphasizes on the application of various data mining techniques such as data pre-processing, data visualization, model evaluation, classification and cluster analysis to research problems that arise in functional genomics. We encourage papers that employ data mining techniques for tasks related to functional genomics. Research papers are solicited in, but not limited to the following topics: • Microarray Expression Analysis • Protein Structure Prediction • Protein-Protein Interactions • Sub-cellular Localization • Proteomics • Mass spectrometry • Integration of Heterogeneous data • Gene Ontology Paper Submission: Papers should be at most 8 pages long, including all figures, tables, and references. Papers should be submitted electronically by email to the workshop chairs in .pdf format. All papers accepted for this workshop will be included in the Workshop Proceedings published by the IEEE Computer Society Press, which are indexed by EI. Important Dates: Paper Submission Deadline: August 15, 2008 Notification of Acceptance: September 10, 2008 Final Camera-ready Paper Due: September 17, 2008 Workshop Day: November 5, 6, or 7, 2008 Workshop Organizers: Chandan K. Reddy Wayne State University Jiong Yang Case Western Reserve University From phoebe from deakin.edu.au Sun Jul 13 20:34:52 2008 From: phoebe from deakin.edu.au (Phoebe Chen) Date: Mon Jul 14 11:30:01 2008 Subject: [Computational-biology] APBC2009 Deadline Approaching Message-ID: <7.0.1.0.2.20080714112651.047d1ec8@deakin.edu.au> ************************************************************************************************************ APBC2009 Deadline Approaching - Full Paper Submission on 20 July ( 6 days) this SUNDAY ************************************************************************************************************ ============================================= CALL FOR PAPERS - APBC2009 Please help us to distribute this CFP as wide as possible. The Seventh Asia-Pacific Bioinformatics Conference (APBC2009) Beijing, China, 13-16 January 2009 http://bioinfo.au.tsinghua.edu.cn/apbc2009/ ============================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Seventh Asia-Pacific Bioinformatics Conference, APBC2009 will be held in Beijing, China, following the 2008 Olympic Games. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. --------------------------------------------------------------- Important Dates Paper submission deadline July 20, 2008 Paper acceptance decision Sep 10, 2008 Camera-ready copy of papers and Author registration Oct 10, 2008 Poster submission open July 20, 2008 Poster submission deadline Sept 20, 2008 Poster acceptance decision Oct 1, 2008 Registration open Sept 20, 2008 Early-bird registration Nov 20, 2008 Conference Jan 13-16, 2009 ---------------------------------------------------------- Confirmed Invited Speakers * (Keynote) David J. Lipman, M.D., Director, NCBI, NLM, NIH, USA * (Keynote) David Botstein, Ph.D., Anthony B. Evnin Professor of Genomics, Director, Lewis Sigler Institute for Integrative Genomics, Princeton University, USA * Martin Vingron, Ph.D., Director at the Max Planck Institute for Molecular Genetics, Head of Computational Molecular Biology Department, Germany * John Mattick, Ph.D., Professor and ARC Federation Fellow at the Institute for Molecular Bioscience, University of Queensland, Australia * Michael B. Eisen, Ph.D., Scientist, Lawrence Berkeley National Lab and Adjunct Assistant Professor, University of California at Berkeley, USA * Pavel Pevzner, Ph.D., Ronald R. Taylow Professor of Computer Science, Director, Center for Algorithmic and Systems Biology at UCSD, USA * Bailin Hao, Ph.D., Professor, Fudan University and Institute of Theoretical Physics, CAS, China * Chunting Zhang, Ph.D., Professor, Tianjin University, China ---------------------------------------------------------- Conference Co-Chairs * Michael Q. Zhang, Cold Spring Harbor Laboratory, USA * Yanda Li, Tsinghua University, China * Xuegong Zhang, Tsinghua University, China -------------------------------------------------------------- Program Committee Co-Chairs * Michael S. Waterman, University of Southern California, USA * Michael Q. Zhang, Cold Spring Harbor Laboratory, USA * Xuegong Zhang, Tsinghua Unviersity, China ---------------------------------------------------------------- APBC Steering Committee * Yi-Ping Phoebe Chen (Chair), Deakin University, Australia * Sang Yup Lee, KAIST, Korea * Satoru Miyano, University of Tokyo, Japan * Mark Ragan, University of Queensland, Australia * Limsoon Wong, National University of Singapore * Michael Q. Zhang, CHSL, USA and Tsinghua University, ChinaTopics of Interest ----------------------------------------------------------------- Papers are solicited on, but not limited to, the following topics: * Sequence Analysis * Motif Finding * Recognition of Genes and Functional Elements * RNA Analysis * Physical and Genetic Mapping * Molecular Evolution and Phylogeny * Protein Structure Analysis * Microarray Design and Data Analysis * Deep Sequencing Data Processing * Transcriptome, Gene Expression * Epigenomics * Proteomics and Post-Translational Modifications * Pathways, Networks and Systems * Ontologies * Databases and Data Integration * Biomedical Literature Mining and Understanding * Population Genetics, SNP and Haplotyping * Comparative Genomics ---------------------------------------------------------------- Program Committee Members (Confirmed): * Tatsuya Akutsu,Kyoto University, Japan * Joel Bader, Johns Hopkins University, USA * Harmen Bussemaker, Columbia University, USA * Andrea Califano, Columbia University, USA * Francis Y.L. Chin, Hong Kong University, Hong Kong * Phoebe Chen, Deakin University, Australia * Runsheng Chen, Institute of Biophysics, CAS, China * Xue-wen Chen, University of Kansas, USA * Nadia El-Mabrouk, University of Montreal, Canada * Mikhail Gelfand, Russian Academy of Science, Russia * Roderic Guigo, Centre de Regulacio Genomica, Barcelona, Spain * Jing-Dong Jackie Han, CAS, China * Jenn-Kang Hwang, National Chiao Tung University, Taiwan * Sridhar Hannenhalli, University of Pennsylvania, USA * Daniel Huson, University of T?bingen, Germany * Tao Jiang, University of California Riverside, USA * Uri Keich, Cornell University, USA * Luhua Lai, Peking University, China * Tak Wah Lam, University of Hong Kong, Hong Kong * Charles Lawrence, Brown University, USA * Chris Lee, UCLA, USA * Doheon Lee, KAIST, Korea * Sang Yup Lee, KAIST, Korea * Cheng Li, DFCI/HSPH, USA * Hao Li, UCSF, USA * Jinyan Li, Nanyang Technological University, Singapore * Wen-Hsiung Li, University of Chicago, USA * Wentian Li, Feinstein Institute for Medical Research, USA * Yixue Li, CAS and Shanghai Jiaotong University, China * Jun S. Liu, Harvard University, USA * Jingchu Luo, Peking University, China * Bin Ma, University of Western Ontario, Canada * Hiroshi Mamitsuka, Kyoto University, Japan * Satoru Miyano, University of Tokyo, Japan * Kenta Nakai, University of Tokyo, Japan * Jurg Ott, Rockefeller University, China * Laxmi Parida, IBM Watson Research Center, USA * Pavel A. Pevzner, UCSD, USA * John Quackenbush, Harvard School of Public Health, USA * Mark Ragan, University of Queensland, Australia * Nikolaus Rajewsky, MDC-Berlin, Germany * Ron Shamir, Tel Aviv Univ, Israel * Steven Skiena, State University of New York at Stony Brook, USA * Yun S. Song, UC Berkeley, USA * Paul Spellman, Lawrence Berkeley National Laboratory, USA * Fengzhu Sun, USC, USA * Zhirong Sun, Tsinghua University, China * Masaru Tomita, Keio University, Japan * Martin Vingron, Max Planck Institute for Molecular Genetics, Germany * Lusheng Wang, City University of Hong Kong, Hong Kong * Zhiping Weng, Boston University, USA * Limsoon Wong, National University of Singapore * Wing H. Wong, Stanford University, USA * Eric Xing, Carnegie Mellon University, USA * Ying Xu, University of Georgia, USA * Hong Xue, HKUST, Hong Kong * Ueng Cheng Yang, National Yang Ming University, Taiwan * Weichuan Yu, Hong Kong University of Science and Technology, Hong Kong * Luoxin Zhang, National University of Hong Kong, Hong Kong * Hongyu Zhao, Yale University, USA * Qing Zhou, UCLA, USA -------------------------------------------------------------- Tutorial Co-Chairs * Eric P. Xing, Carnegie Mellon University, USA * Rui Jiang, Tsinghua University, China -------------------------------------------------------------- Organizing Committee * Xuegong Zhang (Chair), Tsinghua University * Luhua Lai, Peking University * Zhirong Sun, Tsinghua University * Jingchu Luo, Peking University * Jingdong Jackie Han, Inst of Genetics & Development, CAS * Shao Li (Poster Co-Chair), Tsinghua University * Rui Jiang, Tsinghua University * Xiaoyan Zhu (Poster Co-Chair), Tsinghua University * Yonglong Zhuang (Publicity Chair), Bioknow Co. ----------------------------------------------------------------- APBC2009 invites high-quality original papers and posters on any topic related to Bioinformatics and Computational Biology. Accepted papers will be invited to be published in the journal BMC Bioinformatics. The conference will be held at Tsinghua University three months after the Beijing 2008 Olympic Games and two weeks before the traditional Chinese New Year. Post-conference tours will be arranged to major scenery and historical cities in Northern and Southern China. ------------------------------------------------------------------- Call for Papers APBC2009 invites high-quality original full papers on any topic related to Bioinformatics and Computational Biology. The submitted papers must have not been published or under the consideration for publication in any other journals or conferences with formal proceedings. All accepted papers will be arranged for oral presentation at the conference. Accepted papers will be invited to be published in the journal BMC Bioinformatics, following the journal?s publication policy. Papers should not be more than 10 pages in length, including the title, authors and addresses, abstract, text, figures and tables, and references. The manuscripts can be prepared with any of the popular word-processing tools but should be submitted as PDF files. The main text font should not be single-column, single-spaced, with fonts not smaller than 10pt. Tables and figures should be placed among the texts. Color figures are allowed at submission. Authors can provide supplementary materials at their own website if necessary, and can submitted as an attachment when their papers are accepted to be included on the journals. The online submission system will be open from May 1 to July 20, 2008. --------------------------------------------------------------- From gfogel from natural-selection.com Fri Jul 18 18:45:24 2008 From: gfogel from natural-selection.com (Gary Fogel) Date: Fri Jul 18 21:01:29 2008 Subject: [Computational-biology] IEEE CIBCB 2009 Call for Papers Message-ID: <20080718234526.7C9E31C2A4@renown.xo.com> --------------------------------------------------------------------------------------------- Call for Papers: IEEE CIBCB 2009 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology March 30-April 2, Nashville, TN, USA --------------------------------------------------------------------------------------------- This symposium will bring together top researchers, practitioners, and students from around the world to discuss the latest advances in the field of Computational Intelligence and its application to real world problems in biology. Computational Intelligence includes artificial neural networks, fuzzy logic, evolutionary algorithms, and other emerging techniques. Topics of interest include but are not limited to: gene expression array analysis, structure prediction and folding, drug design, molecular sequence alignment and analysis, metabolic pathway analysis, medical imaging and pattern recognition, analysis of large biological data sets, and a variety of other topics. The use of computational intelligence must play a substantial role in submitted papers. Submissions will be peer reviewed and accepted papers will be published in the conference proceedings. Paper Submission: Prospective authors are invited to submit papers of no more than eight (8) pages including results, figures and references; submission details can be found on the symposium web site: www.ieee-ssci.org. Authors are expected to present their paper at the symposium. IEEE CIBCB 2009 will be held in conjunction with the IEEE Symposium Series on Computational Intelligence 2009 (IEEE SSCI 2009). Over 20 such conferences will be co-located at this event. Special Sessions and Tutorials: It is anticipated that the symposium will have a number of special sessions and tutorials. Consult the SSCI symposium web site for instructions on proposing a special session or tutorial. Papers for special sessions must have significant computational intelligence content. Location: Nashville, Tennessee is well known for its cultural events and moderate climate. It is considered a global music center. Nashville is the capital of Tennessee and located on the beautiful Cumberland River. ---------------------------------------------------------------------- Important Dates: Special session and tutorial proposal deadline: August 30, 2008 Paper submission deadline: October 31, 2008 Author notification: November 30, 2008 Camera-ready paper deadline: January 15, 2009 Conference: March 30-April 2, 2009 ---------------------------------------------------------------------- Program Chair: Kay C. Wiese Technical Co-Chairs: Madhu Chetty, Mihail Popescu Publicity Chair: Gary B. Fogel Proceedings Chair: L. Gwenn Volkert Special Sessions Chair: Scott F. Smith Tutorials Chair: Dan Ashlock ---------------------------------------------------------------------- For further inquires: IEEE SSCI 2009 Enquiries: Vincenzo Piuri ? piuri@dti.unimi.it SSCI Symposium Chair IEEE CIBCB 2009 Enquiries: Kay C. Wiese ? wiese@cs.sfu.ca CIBCB Program Chair http://www.ieee-ssci.org http://www.ieee-ssci.org/files/SSCI2009cfp.pdf From Rob.Reedijk from douglasconnect.com Wed Jul 23 16:10:34 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Thu Jul 24 20:44:27 2008 Subject: [Computational-biology] Call for Papers/InnovationWell Autumn Community of Practice Meeting Oct 2008 Philadelphia Message-ID: <2b88bd2e-f719-464f-bcb6-6cbf31547c4f@e39g2000hsf.googlegroups.com> Hello, I am posting details for the InnovationWell Autumn Community of Practice Meeting in October 2008 in Bryn Mawr, Philadelphia. Please note that the deadline to apply for bursaries is July 31, 2008. Innovation in Life Science & Healthcare Research and Product Development InnovationWell Autumn Community of Practice Meeting 14-17 October 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: http://innovationwell.net/comty_conferences Themes: Critical Path Advances in Drug Development, Innovation & Knowledge Management in R&D and Translational Medicine, Computational Biology, Predictive ADME, Predictive Toxicology, Metabolomics, Biomarkers, Systems Biology Program Summary Systems Biology, chaired by Keith Elliston (Genstruct) Computational Biology, chaired by Debraj Guhathakurta (Merck) Knowledge Management in Translational Medicine, David Bousfield (Ganesha Associates) Applications of Metabolomics to Drug Discovery & Development, chaired by Bruce Kristal (Brigham and Women’s Hospital) Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery) Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia) Pre-Conference Workshop, 13 October Knowledge Management in R&D chaired by John Conway (Accelrys) and Frank Hollinger (FRESH Directions Consulting) Speakers Keith Elliston (Genstruct), Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.), Stephen W. Edwards (U.S. Environmental Protection Agency), Paul McDonagh (Gene Network Sciences), Christopher M.L.S. Bouton (Pfizer), James R. Brown (GlaxoSmithKline), John Wilbanks (Creative Commons), Barry Bunin (Collaborative Drug Discovery), Michael Liebman (Windber Research Institute), Jerry Wright (Johns Hopkins Medical Institutions), Anastasia Christianson (AstraZeneca), James Golden (Science Applications International Corporation), John Speakman (National Cancer Institute), William Hayes (Biogen Idec), Andrew McMurray (Harvard University), Eugene Clark (Partners Healthcare), Alvin Berger (Metabolon), John Newman (USDA), Bruce Kristal (Brigham and Women’s Hospital), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Alex Tropsha (UNC), Barry Hardy (Douglas Connect), Weida Tong (FDA) CFP We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation relevant to innovation and knowledge management in the life sciences. The work presented should involve innovative new method development or application in the areas of systems biology, translational medicine, knowledge management, computational biology, metabolomics, predictive ADME, predictive toxicology or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome. Abstracts (300-500 words) should be submitted to innovationwell - [at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008. Bursary Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants should be working in a relevant area of research related to life science, healthcare, and drug product discovery and development at the postdoctoral, graduate student and senior undergraduate levels. To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to R&D (300-500 words) to innovationwell -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008. Poster Session All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy [at] douglasconnect.com Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted at the very latest by 31 August 2008. Contact: Program: Dr. Barry Hardy, InnovationWell Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. InnovationWell -[at]- douglasconnect.com From mgjvanleeuwen from gmail.com Fri Jul 25 07:18:33 2008 From: mgjvanleeuwen from gmail.com (Matthijs van Leeuwen) Date: Fri Jul 25 12:07:55 2008 Subject: [Computational-biology] Computational Biologist / Bioinformatician Sought for Biotech Start-up Message-ID: <66b705550807250518r522ca2fo8cbb0c403960691c@mail.gmail.com> Dear comp bio member, Looking to spend time in an interesting location? SimuGen is a toxicogenomics company originating in Cambridge (UK), now establishing some operations in Kuala Lumpur (Malaysia) with the aim of launching the first product from Malaysia within a year. It'll be a web-based tool using proprietary dose-response models of gene expression phenotypes from human cell cultures exposed to chemicals. The aim being to help pharma develop safer drugs. This has already attracted significant attention internationally, and the intention is to begin a collaboration with a large pharma company in the near future. The company is looking for a highly driven, independent bioinfomatician / computational biologist to conduct the R&D through to product implementation in Malaysia. This post will last 8 months and may be suited to somebody who is technically very good but still junior in industry, looking for a shorter-term challange. However we would also consider somebody with more experience and ambitions of eventually leading much of the company's R&D as a 'product architect' in the UK or internationally. This has the potential to grow into an exciting position, with highly competitive rewards for achieving crucial company milestones. In the first instance the core expectations would be: (1) Manage the quality control of all data (from benchtop to analysis). (2) Do extensive literature and database searches for toxicicologically relevant candidate genes. (3) Format and manage gene expression data for analysis. (4) Work closely with the Chief Scientific Officer (based in the UK) and the S-plus server team to set up the web-tool for customers. (5) Help manage the collaboration with the pharma company. In terms of basic skills we are looking for: (1) Gene expression analysis (microarrays, qPCR) - crucial (2) Ability to do database and literature searches for candidate genes - crucial (3) R programming skills - highly valued The intention is to start this position in September, with a competitive salary based on experience. Interested persons can contact Dr Wills (CSO) with informal inquiries at quin.wills@simugen.co.uk. A brief list of questions they might have, in addition to a very brief CV clearly demonstrating skill sets, project management and research potential would be most useful.We regret that we will not respond to queries where the candidate clearly does not have the correct background/skills. From mckenzie.tobias from gmail.com Sun Jul 27 13:54:34 2008 From: mckenzie.tobias from gmail.com (mckenzie.tobias@gmail.com) Date: Mon Jul 28 12:45:23 2008 Subject: [Computational-biology] Betweenness Calculation Message-ID: <1a16e56a-9e8a-4f4d-8b0d-125acb004d20@a70g2000hsh.googlegroups.com> Hi, I'm doing a project on residue networks and I have to calculate betweenness of the residues. However I have to use a slightly different betweenness definition. I don't have to use a all-pairs shortest path approach. In other words I have to calculate the shortest paths using some destination nodes, ie from node 1 to node t, from node 2 to node t etc.. I don't have an idea on how to do that. Can you help me? Thanks. Tobias From calibrii.arthur3 from gmail.com Mon Jul 28 20:37:54 2008 From: calibrii.arthur3 from gmail.com (Art) Date: Mon Jul 28 21:01:13 2008 Subject: [Computational-biology] Biology and Bioinformatics Search Engine Message-ID: <7f325bac-9cd5-48b1-85e3-ac11fcd15311@l42g2000hsc.googlegroups.com> Hi, I wanted to share with you this new search engine. www.Vadlo.com Or Google the word "Vadlo", and check the first link. I am sure you will like it! -Art From inesdesantiago from gmail.com Wed Jul 30 05:32:57 2008 From: inesdesantiago from gmail.com (ines santiago) Date: Wed Jul 30 12:45:39 2008 Subject: [Computational-biology] Re: Comp-bio Digest, Vol 38, Issue 9 In-Reply-To: <200807291704.m6TH4LO24026@net.bio.net> References: <200807291704.m6TH4LO24026@net.bio.net> Message-ID: <7f52bad90807300332m474bce81td831d564139221b3@mail.gmail.com> The cartoons are hilarious :) Thanks Art On Tue, Jul 29, 2008 at 6:04 PM, wrote: > Send Comp-bio mailing list submissions to > comp-bio@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/comp-bio > or, via email, send a message with subject or body 'help' to > comp-bio-request@net.bio.net > > You can reach the person managing the list at > comp-bio-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Comp-bio digest..." > > > Today's Topics: > > 1. Betweenness Calculation (mckenzie.tobias@gmail.com) > 2. Biology and Bioinformatics Search Engine (Art) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 Jul 2008 11:54:34 -0700 (PDT) > From: mckenzie.tobias@gmail.com > Subject: [Computational-biology] Betweenness Calculation > To: bionet-biology-computational@net.bio.net > Message-ID: > <1a16e56a-9e8a-4f4d-8b0d-125acb004d20@a70g2000hsh.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I'm doing a project on residue networks and I have to calculate > betweenness of the residues. However I have to use a slightly > different betweenness definition. I don't have to use a all-pairs > shortest path approach. In other words I have to calculate the > shortest paths using some destination nodes, ie from node 1 to node t, > from node 2 to node t etc.. > > I don't have an idea on how to do that. Can you help me? > > Thanks. > Tobias > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Jul 2008 18:37:54 -0700 (PDT) > From: Art > Subject: [Computational-biology] Biology and Bioinformatics Search > Engine > To: bionet-biology-computational@net.bio.net > Message-ID: > <7f325bac-9cd5-48b1-85e3-ac11fcd15311@l42g2000hsc.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I wanted to share with you this new search engine. > > www.Vadlo.com > > Or Google the word "Vadlo", and check the first link. I am sure you > will like it! > > -Art > > > > ------------------------------ > > _______________________________________________ > Comp-bio mailing list > Comp-bio@net.bio.net > http://www.bio.net/biomail/listinfo/comp-bio > > End of Comp-bio Digest, Vol 38, Issue 9 > *************************************** >