From sdua at coes.latech.edu Wed Feb 4 15:24:05 2009 From: sdua at coes.latech.edu (Sumeet Dua) Date: Wed, 4 Feb 2009 14:24:05 -0600 Subject: [BiO BB] CfP:- Bioinformatics Track: International Conference on Contemporary Computing (IC3-09). Message-ID: Apologies for duplicate transmission. ** International Conference on Contemporary Computing August 17-19, 2009, NCR Delhi, India Special Track on Bioinformatics Papers due: February 28, 2009 Biology and Biomedicine have become increasingly data-driven sciences. The emerging research in this area is producing vast quantities of data daily from clinical trials, as well as statistics population genetics, imaging, gene sequencing, gene expression analysis, and protein identification projects. This data is inherently high dimensional and uniquely combines enormity with fine granularity, and the rate of accumulation of this data far exceeds our capacity to analyze it and to discover novel and significant knowledge embedded in it. Bioinformatics is a relatively new science of storing, extracting, organizing, analyzing, interpreting, and utilizing information from biological sequences and molecules. The goal of this conference special track is to explore, report, and share novel and significant research solutions using advanced algorithmic approaches of contemporary areas of computing to various bioinformatics challenges. Authors are invited to submit original papers to the special track exploring algorithmic theories, techniques, and applications for bioinformatics. Papers are invited (but not limited) to the following topics: Phylogenetics and Comparative Genomics Computational Proteomics Modeling of Biochemical Pathways Computational Biomarker Discoveries Microarray Data Analysis System Biology and Pathways Phylogenetics Computational Drug Discoveries RNAi and microRNA Analysis Biomedical Text Mining Protein/RNA Structure Prediction Biological Data Visualization Gene Ontologies Biological Data Management Techniques Sequence and Structural Motif Finding Biomedical and Clinical Image Analysis Modeling of Biological Networks and Pathways Feature Selection and Pattern Discovery in Biological Data Statistical Learning Methods in Bioinformatics Semantic Webs and Ontology-Driven Biological Data Integration Methods 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 conference web site: http://www.jiit.ac.in/jiit/ic3/. Location: Jaypee Institute of Information Technology University, Noida, U.P. (15kms from New Delhi), India. Proceedings: Conference Proceedings will be published by Springer in Communications in Computer and Information Science ISSN: 1865-0929 Submission deadline: February 28, 2009 For further information regarding the session please contact: Session Chair: Dr. Sumeet Dua ? Department of Computer Science, Louisiana Tech University, LA, USA. sdua at coes.latech.edu Conference General Co-Chairs: Dr. Sartaj Sahni ? University of Florida, FL, USA and Sanjay Goel, Jaypee Institute of Information Technology University, India. ************* -------------------------------- Sumeet Dua, Ph.D. Associate Professor of Computer Science Upchurch Endowed Professor, Coordinator of IT Research, College of Engineering and Science, Louisiana Tech University. Adjunct Associate Professor of Research, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA ? 70112 USA. Data Mining Research Laboratory: http://dmrl.latech.edu Mailing Address: 235 Nethken Hall, 600 W. Arizona Avenue, Ruston, LA - 71272 USA. Ph. 318-257-2830 Fax. 318-257-4922 E-mail. sdua at coes.latech.edu Web. http://www.latech.edu/~sdua -------------------------------- From barry.hardy at vtxmail.ch Thu Feb 5 04:03:43 2009 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 05 Feb 2009 10:03:43 +0100 Subject: [BiO BB] Predictive ADME and Toxicology Workshop, Oxford July 2009, Bursary awards available Message-ID: <498AAB6F.2000606@vtxmail.ch> We are running a Predictive ADME and Toxicology workshop week at Oxford University 27 ? 31 July 2009. We will take a hands-on case study approach using a variety of methods applied to ADME and Tox datasets and endpoints. More information on program can be found at: Blog: http://barryhardy.blogs.com/cheminfostream/ Pdf: http://barryhardy.blogs.com/files/echeminfoadmetprogramoxford09-1.pdf Web: http://echeminfo.com/COMTY_oxfordadmet09 A Bursary Award will be used to support the attendance of a selection of academic participants, who may be working in any area of research related to predictive ADME and toxicology. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 20 February 2009. best regards Barry Hardy eCheminfo Community of Practice Douglas Connect GmbH Switzerland barry.hardy -[at]- douglasconnect.com Tel: +41 61 851 0170 From jeff at bioinformatics.org Sun Feb 8 21:32:58 2009 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 08 Feb 2009 21:32:58 -0500 Subject: [BiO BB] African Virtual Conference on Bioinformatics (Afbix '09) Message-ID: <498F95DA.40908@bioinformatics.org> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= African Virtual Conference on Bioinformatics (Afbix '09) February 19-20, 2009 Online at Bioinformatics.Org =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= TARGET AUDIENCE: Graduate students and researchers in computational biology, molecular biology and medicine. The conference theme is "Tropical Bioinformatics." While most of the presenters are either in Africa or studying African species, attendance is open to everyone. MOTIVATION: In addition to research on tropical diseases, pathogenesis and their vectors, the field of bioinformatics has become an important part of life science studies in Africa. But, with the great geographical expanse of the continent, it is often impractical or uneconomical for African researchers to come together for conferences. That is, in person. The Bioinformatics Organization (Bioinformatics.Org) has therefore collaborated with Regional Student Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in Africa as "virtual hubs." Participating African RSGs and the hub institutions: - RSG East Africa (ILRI) - RSG East Africa (ICIPE) - RSG South Africa (SANBI) - RSG Morocco (SMBI) - RSG West Africa (Covenant University, Ota) Other hub institutions: - Notre Dame University, Indiana, USA VIRTUAL ATTENDANCE: Individual registrations cost only $10-30, depending on location. Please see the conference description page (URL below). PHYSICAL ATTENDANCE: For more information about attending this conference via one of the aforementioned hubs, please contact afbixx at gmail.com. FOR MORE INFORMATION: Please visit the conference description page: http://wiki.bioinformatics.org/Afbix09 From idoerg at gmail.com Mon Feb 9 18:36:58 2009 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 09 Feb 2009 15:36:58 -0800 Subject: [BiO BB] Call fro abstracts: METAGENOMICS, METADATA AND METAANALYSIS Message-ID: <1234222618.29512.27.camel@lafa> CALL FOR ABSTRACTS AND POSTERS: METAGENOMICS, METADATA AND METAANALYSIS An ISMB 2009 Special Interest Group (SIG) Date: June 27, 2009 Location: Stockholm, Sweden URL: http://gensc.org/gc_wiki/index.php/M3 There are now thousands of genomes and metagenomes available for study. Interest in improved sampling of diverse environments (e.g. ocean, soil, sediment, and a range of hosts) combined with advances in the development and application of ultra-high throughput sequence methodologies are set to vastly accelerate the pace at which new metagenomes are generated. At the same time, we have entered the era of large-scale sequencing projects, which include funded projects like the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project and the Human Microbiome Initiative, with many more visionary projects on the horizon. The M3 SIG will explore the latest concepts, algorithms, tools, informatic pipelines, databases and standards that are being developed to cope with the analysis of vast quantities of metagenomic data. Through a series of invited and contributed talks, a panel discussion, and flash talks associated with a poster session, we aim to highlight scientific advances in the field and identify core computational challenges facing the wider community. We invite you to submit extended abstracts to be considered as talks or posters for the M3 SIG. The abstracts will be reviewed by the SIG program committee for suitability and quality. Selected abstracts will be published in a special issue of the open access online journal Standards in Genomic Sciences http://standardsingenomics.org/ Topics include, but are not limited to: Metagenome and microbiome studies of biological interest Metagenome annotation Consistent contextual (meta)data acquisition and storage in metagenomics Contextual (meta)data and sequence data correlation studies Computational infrastructures for metagenomic data processing Algorithms, data structures and database architectures Important dates: April 1, 2009: Talk and poster abstracts due. April 20, 2009: notification of acceptance May 1, 2009: final abstracts due June 27th, 2009: M3 SIG alongside ISMB 2009 in Stockholm, Sweden Invited speakers include: Owen White, Genome Sciences, UMB Nikos Krypides Joint Genome Institute Michael Ashburner, University of Cambridge Susanna Sansone, EBI Peer Bork, EMBL For more information including submission: http://gensc.org/gc_wiki/index.php/M4 -- Iddo Friedberg, Ph.D. CALIT2 Atkinson Hall MC #0446 University of California San Diego 9500 Gilman Drive La Jolla, CA 92093-0446 USA +1 (858) 534-0570 http://iddo-friedberg.org From landman at scalableinformatics.com Sun Feb 15 20:22:08 2009 From: landman at scalableinformatics.com (Joe Landman) Date: Sun, 15 Feb 2009 20:22:08 -0500 Subject: [BiO BB] question: what is your rate limiting computational step? Message-ID: <4998BFC0.7090808@scalableinformatics.com> Hi folks: (purely non-commercial purpose question) We are looking to get feedback from informatics users and researchers where your computational bottlenecks are. Basically, we are trying to understand which programs or algorithms are the most time/resource consuming. The groups we speak to frequently often have their own particular needs, so I would like to make sure we are addressing the larger community of informatics users and researchers. The goal of this effort is to explore whether or not acceleration of some of these codes is possible or beneficial on GPU based systems. Part of my reason for asking is that I see a number of dynamic programming algorithms have been accelerated on FPGAs and other platforms, but I am not seeing large usage of these accelerators. This suggests that the barriers to obtaining/using these accelerators may be larger than the benefit of using them ... either because the costs are too high, or the wrong thing is being accelerated, and bottlenecks are elsewhere. The GPU-HMMer work recently announced does seem to have good uptake, and we want to see what else we should be looking at. We would like to know where the computational rate limiting steps are today, and what you need to run faster, and what the benefit of additional speed would be (as well as how much additional speed is needed to positively impact your research). Please feel free to email me offline, if there is interest, we will summarize. Again, strictly non-commercial in nature. Regards, Joe -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com http://jackrabbit.scalableinformatics.com phone: +1 734 786 8423 x121 fax : +1 866 888 3112 cell : +1 734 612 4615 From pac at lifeformulae.com Wed Feb 18 12:29:19 2009 From: pac at lifeformulae.com (Pam Culpepper) Date: Wed, 18 Feb 2009 11:29:19 -0600 Subject: [BiO BB] NCBI ASN.1 Cross Reference Guide Message-ID: <1234978159.2821.10.camel@localhost.localdomain> Those of you working with, or just interested in, the NCBI ASN.1 Data Model should check out our freely available NCBI ASN.1 Cross Reference page at - http://www.lifeformulae.com/pages/products_ncbi_xref.aspx This is a clickable map of all of the NCBI ASN.1 data structures, allowing the user to drill down or up to the object of interest by means of the Uses and Used By links accompanying each ASN.1 data structure definition. The NCBI XREF Help Section will guide to the top-level NCBI ASN.1 data structures associates with GenBank, EntrezGene, BlastOutput, and SNPdb data. Thanks, Pam -- Pamela A. Culpepper LifeFormulae, LLC 410 Pierce St., Suite 318 Houston, TX 77002 Phone: 713-357-9559 Email: pac at lifeformulae.com URL: http://www.lifeformulae.com From tcan at ceng.metu.edu.tr Fri Feb 20 07:25:30 2009 From: tcan at ceng.metu.edu.tr (Tolga Can) Date: Fri, 20 Feb 2009 14:25:30 +0200 Subject: [BiO BB] CFP: ISCIS-2009 -- Bioinformatics and Bioengineering Message-ID: <8ad607cb0902200425t22bbb9a6q9767fb10c5db397@mail.gmail.com> Call for Papers 24th International Symposium on Computer and Information Sciences :: Bioinformatics and Bioengineering Track September 14-16, 2009 Guzelyurt, North Cyprus http://iscis.metu.edu/ Authors are invited to submit original papers to the "Bioinformatics and Bioengineering" track of the "24th International Symposium on Computer and Information Sciences" (ISCIS-2009). ISCIS is a large annual gathering of researchers from a broad spectrum of Computer and Information Sciences. The interdisciplinary fields of Bioinformatics and Bioengineering will especially benefit from the interface of many research areas participating in ISCIS. The event will be composed of research presentations, keynote speeches, invited talks, and poster presentations. This year, ISCIS will be held on Sep 14-16, 2009, in North Cyprus, which combines beautiful bays with a sunny climate all year around. The submitted papers are expected to be in broad areas of Bioinformatics and Bioengineering, including - Biomedical Data Mining and Engineering - Molecular Sequence/Structure Databases - Sequence/Structure Search and Alignment - Functional Genomics, Proteomics - Medical Informatics - Drug Discovery - Protein folding and fold recognition - Microarray Technologies - Data Visualization - Bio-imaging - Biomedical & Biological Sensors - Tissue Engineering - Novel applications The submitted papers must be original and currently not under review elsewhere. The accepted articles will be published in IEEE Proceedings and will be included in the IEEE digital library. Accepted papers will be presented at the symposium. Papers should be prepared following IEEE format, double column, minimum 10pt fonts, and up to 6 pages. The submissions will be through electronic submission system available on http://iscis.metu.edu.tr/submission IMPORTANT DATES: - Submission of papers: April 17, 2009 - Notification of acceptance: June 15. 2009 - Camera ready and registration due: July 1, 2009 - Symposium date: September 14-16, 2009 TRACK CHAIRS: Hakan Ferhatosmanoglu, The Ohio State University, USA Ambuj Singh, University of California, Santa Barbara, USA PROGRAM COMMITTEE: Mehmet Serkan Apaydin, Sabanci University, Turkey Tolga Can, Middle East Technical University, Turkey Ramana Davuluri, The Wistar Institute, USA Ugur Dogrusoz, Bilkent University, Turkey Werner Dubitzky, University of Ulster, UK Attila Gursoy, Koc University, Turkey Tamer Kahveci, University of Florida, USA Daisuke Kihara, Purdue University, USA Tao Li, Florida International University, USA Jie Liang, University Illionis at Chicago, USA Li Liao, University of Delaware, USA John Rose, University of South Carolina, USA Ahmet Sacan, Ohio State University, USA Cenk Sahinalp, Simon Fraser University, Canada Sinan Sarac, Technical University of Dresden, Germany Ugur Sezerman, Sabanci University, Turkey Saurabh Sinha, University of Illionis Urbana Champaign, USA Anna Tramontano, Sapienza University, Italy Metin Turkay, Koc University, Turkey Yusu Wang, Ohio State University, USA From kiekyon.huang at gmail.com Sat Feb 21 02:44:06 2009 From: kiekyon.huang at gmail.com (Kie Kyon Huang) Date: Sat, 21 Feb 2009 15:44:06 +0800 Subject: [BiO BB] orthologs inference Message-ID: What methods do you use to infer orthology? I use best reciprocal blast hit with similarity more than 30%. Any comment on that? From gorrieri at cs.unibo.it Sat Feb 21 05:31:37 2009 From: gorrieri at cs.unibo.it (Roberto Gorrieri) Date: Sat, 21 Feb 2009 11:31:37 +0100 (CET) Subject: [BiO BB] Computational Methods in Systems Biology (CMSB'09) -- call for papers Message-ID: <49287.79.50.115.197.1235212297.squirrel@ssl.cs.unibo.it> *********************************************************************** ** CMSB 2009 ** ** The 7th Conference on Computational Methods in Systems Biology ** ** Bologna, Italy, August 31st - September 1st, 2009 ** ** http://cmsb09.cs.unibo.it/ ** *********************************************************************** Call for papers The CMSB (Computational Methods in Systems Biology) conference series was established in 2003 to help catalyze the convergence of modellers, physicists, mathematicians, and theoretical computer scientists (from fields such as language design, concurrency theory, program verification) with molecular biologists, physicians and neuroscientists interested in a systems-level understanding of cellular physiology and pathology. CMSB 2009 solicits original research articles, surveys of current research and posters. These may cover theoretical or applied contributions that are motivated by a biological question and can demonstrate actual or potential usefulness towards answering that question. Additionally, they may cover models of computation inspired by biological processes; of which the motivation may be either computational or biological. In particular, relevant case studies and open biological questions that demand modelling of systems are of significant interest. Topics of interest (biological systems and networks: inference, properties, modelling, dynamics, simulation and reverse engineering) include, but are not limited to: * Modelling: o Re-engineering and synthesis of biological systems and networks o Definition and study of theoretical properties of biologically-inspired formal languages o Qualitative and quantitative languages and calculi o Theoretical comparisons between different formal models of cellular processes o Models including symbolic evolution and learning o Spatial, multi-level, and multi-formalism modeling * Simulation / Analysis: o Simulation and analysis methods for computational biology o Biologically-inspired extensions to concurrency theory, constraint programming, logical methods or language equivalences o Emergence of properties in complex biological systems o Parallel, distributed, and multi-resolution simulation methods o Methods to predict biological network behavior from incomplete information * Tools / Frameworks / Libraries: o Modelling, analysis and simulation tools o Differential, discrete and/or stochastic modeling-language frameworks o Visualization methods for computational biology o Biological databases and exchange formats for biological data and standards * Applications: o Detailed biological case-studies on which formal models successfully apply o Computer models in nano-sciences applied to biological domains o Model-driven analysis of biological systems Submission The CMSB 2009 conference solicits high quality papers reporting research results and/or experience reports related to the topics mentioned above. All papers must be original, unpublished, and not submitted for publication elsewhere. Contributions should be submitted electronically as PDF via Easychair at * http://www.easychair.org/conferences/?conf=cmsb09 using the Springer LNCS style. Papers should not exceed 15 pages in length. If necessary, the paper may be supplemented with a clearly marked appendix, which will be reviewed at the discretion of the program committee. The proceedings of the conference will be published with Springer under the series named Lecture Notes in Bioinformatics, sub-series of Lecture Notes in Computer Science. The best papers presented at the Conference will be selected for a special issue of a Journal. Important Dates March, 16: Submission of abstracts March, 23: Submission of full papers May, 18: Notification of paper acceptance June, 15: Revised version of papers August 31 ? September 1: Conference Invited speakers * Rita Casadio, Universit? di Bologna, Italy * John K. Heath, University of Birmingham, UK * Corrado Priami, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (Italy) Steering Committee * Finn Drabl?s, Norwegian University of Science and Technology, Trondheim (Norway) * Fran?ois Fages, INRIA Rocquencourt, France * David Harel, Weizmann Institute of Science, Israel * Monika Heiner, TU Cottbus (Germany) * Michael H?rnquist , Link?ping University, Sweden * Satoru Miyano, University of Tokyo, Japan * Gordon Plotkin, University of Edinburgh, UK * Corrado Priami, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (Italy) * Adelinde M. Uhrmacher, University of Rostock, Germany Program Committee * Pierpaolo Degano, Universit? di Pisa, Italy (co-chair) * Finn Drabl?s, Norwegian University of Science and Technology, Trondheim, Norway * Fran?ois Fages, INRIA Rocquencourt, France * Stephen Gilmore, University of Edinburgh, UK * Roberto Gorrieri, Universit? di Bologna, Italy (co-chair) * Monika Heiner, TU Cottbus, Germany * Adaoha Elizabeth C. Ihekwaba, CoSBI, Italy * Marta Kwiatkowska, University of Oxford, UK * Pietro Li?, Computing Lab Cambridge, UK * Satoru Miyano, University of Tokyo, Japan * Mark van Rossum, University of Edinburgh, UK * Grzegorz Rozenberg, Leiden University, Leiden, NL * Carolyn Talcott, Stanford Research Institute, USA * Adelinde M. Uhrmacher, University of Rostock, Germany Organizing Committee * Cinzia Di Giusto, Universit? di Bologna, Italy * Roberto Gorrieri, Universit? di Bologna, Italy * Cristian Versari, Universit? di Bologna, Italy (chair) * Antonio Vitale, Universit? di Bologna, Italy * Gianluigi Zavattaro, Universit? di Bologna, Italy From christoph.gille at charite.de Mon Feb 23 17:48:41 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 23 Feb 2009 23:48:41 +0100 (CET) Subject: [BiO BB] orthologs inference In-Reply-To: References: Message-ID: <0c5f2af9f2f62fbb6f2418d0626037b1.squirrel@webmail.charite.de> > What methods do you use to infer orthology? It is tricky to exclude paralogy. If the sequence similarity is significantly below of that for other known othologous pairs it might be a case of paralogy? Conversely, the evolutionary clock may run at a higher pace for this protein. From jeedward at yahoo.com Fri Feb 27 07:17:34 2009 From: jeedward at yahoo.com (John Edward) Date: Fri, 27 Feb 2009 04:17:34 -0800 (PST) Subject: [BiO BB] Paper submission deadline just less than a week: MULTICONF-09 Message-ID: <679090.61415.qm@web45912.mail.sp1.yahoo.com> ? Paper submission deadline just less than a week: MULTICONF-09 ? The deadline for draft paper submission at the 2009 Multi Conference in Computer Science, Information Technology and Control systems and Computational Science and Computer Engineering (MULTICONF-09) (website: http://www.PromoteResearch.org) is just less than a week from now. ? The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The event consists of the following conferences: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-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 John Edward Publicity committee