From jeedward from gmail.com Mon Nov 3 07:06:42 2008 From: jeedward from gmail.com (john) Date: Mon Nov 3 12:35:22 2008 Subject: [Computational-biology] BCBGC-09 call for papers Message-ID: BCBGC-09 call for papers The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. 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 John Edward Publicity committee From stevet from bio.fsu.edu Mon Nov 3 15:56:23 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Mon Nov 3 21:18:19 2008 Subject: [Computational-biology] Other: Re - GCG non-support In-Reply-To: <46B83135.7050107@ebi.ac.uk> References: <46B1AEA8.2040308@ebi.ac.uk><20070802081845.D3246@epsilon.bio.fsu.edu><46B2F2E3.4020305@ebi.ac.uk><20070803131050.H7747@epsilon.bio.fsu.edu><1186251135.996351.149470@g12g2000prg.googlegroups.com> <46B721F0.8050407@ebi.ac.uk> <7930EE6CD7CA354D93B444D0433C061103A8C70D@NIHCESMLBX6.nih.gov> <46B83135.7050107@ebi.ac.uk> Message-ID: <20081103121427.E74728@epsilon.bio.fsu.edu> Hi Peter - I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG 'retirement.' Since that time several developments, only a few positive in my opinion, have clarified the situation. One - my online petition at www.petitiononline.com was very successful (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering signatures, almost 200 in a month, and in fostering international exposure, as the BioInform article from April 2008 attests (http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains committed to not releasing any GCG code, due to exhorbiant and without profit legal expense. So be it and understood - we tried. Two - Accelryrs did distirbute the 'perpetual' licenses to all valid license holders that were entitled to it, as I announced in this forum April 2008, and they worked great, even across multiple nodes in a cluster. Thany you Accelrys. However . . . Three - We (FSU) upgraded our Linux cluster that supports GCG and many other bioinformatics tools to CentOS version 5. Unfortunately, almost half of the GCG package now fails due to unresolvable library conflicts (as I warned would happen - unfortunately sooner than I had hoped). Our systems operations folk initially thought they could fix this but the solution has remained ellusive. The affected programs are all the oldest 'legacy' programs in the package, although some longtime GCG pragrams like Pearson's FastA package remain viable. Four - SeqLab continues to operate just fine, but without access to many of the analytic tools of the package, its usefullness is quite impacted, though I still think it's one of the best multiple sequence alignment editors around. This is where you come back in Peter. It may seem odd to ask, but the need is actually larger now that so much of the package no longer works in an Enterprise (or CentOS) Linux version 5 environment. I'm sure that I am not alone in this situation. So here goes - I've asked it many time before, and I've begun to do the work myself starting with PlotCon, but has anybody built SeqLab extension configuration files to launch EMBOSS programs? Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From orry.molsoft from gmail.com Mon Nov 10 19:08:36 2008 From: orry.molsoft from gmail.com (Andrew Orry) Date: Mon Nov 10 19:40:11 2008 Subject: [Computational-biology] Protein Structure and Drug Design Workshop - MolSoft February 5-6 2009 Message-ID: <4918CD04.4050602@molsoft.com> **MolSoft ICM Workshop: "Protein Structure and Drug Discovery" February 5th to 6th 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on February 5th to 6th 2009 in La Jolla, California USA. Please see www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft). The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing molecular movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy@molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest Newsletter: http://www.molsoft.com/news.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From lvannesc from disco.unimib.it Thu Nov 13 06:13:15 2008 From: lvannesc from disco.unimib.it (Vanneschi Leonardo) Date: Thu Nov 13 11:06:06 2008 Subject: [Computational-biology] EuroGP 2009 - submission deadline extended to 30 November 2008 Message-ID: <301E01E95DB8684CAFA9EC28E1032FF207C6FCE3@disco-exchange.disco.local> *** EuroGP 2009 additional submission deadline extension*** Due to a number of requests by individual authors for a further deadline extension, we have decided to grant an extension of the EuroGP 2009 submission deadline to 30 November 2008 --------------------------------------------------------------------- EuroGP 2009 12th European Conference on Genetic Programming T?bingen, Germany April 15-17 2009 ---------------------------------------------------------------------- EuroGP 2009 will take place in conjunction with EvoCOP 2009 (9th European Conference on Evolutionary Computation in Combinatorial Optimization), EvoBIO 2009 (7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics), and EvoWorkshops 2009 (the specialist workshops on a range of evolutionary computation topics and applications), in a joint event collectively intituled EvoStar 2009. EuroGP 2009 important dates are: *** Extended Submission deadline: 30 November 2008 *** Notification to authors: 9 January 2009 Camera-ready deadline: 28 January 2009 Conference: 15-17 April 2009 To submit a paper you can directly access the page: http://myreview.csregistry.org/eurogp09/ or otherwise find all instructions and information about the EvoStar 2009 events at the page: http://www.evostar.org EuroGP 2009 topics include but are not limited to: * Theoretical developments * Empirical studies of GP performance and behavior * Algorithms, representations and operators * Applications of GP to real-life problems * Hybrid architectures including GP components * Unconventional evolvable computation * Evolutionary design * Evolutionary robotics * Grammar-based GP * Evolvable hardware * Linear GP * Self-reproducing programs * Evolution of tree or graph structures * Evolution of various classes of automata or machines (e.g. cellular automata, finite state machines, pushdown automata, Turing machines) * Object-oriented genetic programming EuroGP 2009 Program Chairs: - Leonardo Vanneschi, University of Milano-Bicocca, Italy vanneschi(at)disco(dot)unimib(dot)it - Steven Gustafson, GE Global Research, USA steven(dot)gustafson(at)research(dot)ge(dot)com From evostar from na.icar.cnr.it Thu Nov 13 07:21:38 2008 From: evostar from na.icar.cnr.it (Evostar 2009) Date: Thu Nov 13 11:06:16 2008 Subject: [Computational-biology] Evostar 2009 - submission deadline extended to 30 November 2008 Message-ID: <491C1BD2.4010006@na.icar.cnr.it> ***Evostar 2009 additional submission deadline extension*** Due to a number of requests by individual authors for a further deadline extension, we have decided to grant an extension of the submission deadline for all the Evo* 2009 events to 30 November 2008 --------------------------------------------------------------- EVO* 2009 including EuroGP, EvoCOP, EvoBIO and EvoWorkshops 15-17 April, 2009 Eberhard Karls University T?bingen, Germany http://www.evostar.org --------------------------------------------------------------- The EuroGP, EvoCOP and EvoBIO conferences and the workshops collectively entitled EvoWorkshops compose EVO*: Europe's premier co-located events in the field of Evolutionary Computing. Featuring the latest in theoretical and applied research, EVO* topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimization, evolutionary algorithms, machine learning and data mining techniques in the biosciences, in numerical optimization, in music and art domains, in image analysis and signal processing, in hardware optimization and in a wide range of applications to scientific, industrial, financial and other real-world problems. Important dates for all events are: *** Extended Submission deadline: 30 November 2008 *** Notification to authors: 9 January 2009 Camera-ready deadline: 28 January 2009 Conference: 15-17 April 2009 If you are interested in submitting a paper please either go the "Submission" page in the official site http://www.evostar.org, or directly access the event submission pages: http://myreview.csregistry.org/eurogp09/ for EuroGP http://myreview.csregistry.org/evocop09/ for EvoCOP http://myreview.csregistry.org/evobio09/ for EvoBIO http://myreview.csregistry.org/evoworkshops09/ for the EvoWorkshops Scope of the events: EuroGP: Twelfth European Conference on Genetic Programming: high quality papers are sought on topics strongly related to the evolution of computer programs, ranging from theoretical work to innovative applications. EvoCOP: Ninth European Conference on Evolutionary Computation in Combinatorial Optimization: practical and theoretical contributions are invited, related to evolutionary computation techniques and other meta-heuristics for solving combinatorial optimization problems. EvoBIO: Seventh European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: the emphasis is on evolutionary computation and other advanced techniques addressing important problems in molecular biology, proteomics, genomics and genetics, that have been implemented and tested in simulations and on real-life datasets. EvoWorkshops: The twelve workshops which make up this event are focused on the use of Evolutionary Computation in different application areas: EvoCOMNET: Telecommunication networks and other parallel and distributed systems EvoENVIRONMENT: Environmental issues EvoFIN: Finance and economics EvoGAMES: Games EvoHOT: Design automation EvoIASP: Image analysis and signal processing EvoINTERACTION: Interactive evolution and humanized computational intelligence EvoMUSART: Music, sound, art and design EvoNUM: Continuous parameter optimization EvoPHD: Graduate student workshop on evolutionary computation EvoSTOC: Stochastic and dynamic environments (EvoSTOC has organized the "yellow submarine challenge" competition for dynamic optimization, further information can be found in the workshop page) EvoTRANSLOG: Transportation and logistics In 2009, the event will take place in T?bingen, a traditional university town in Baden-W?rttemberg, Germany, situated on a ridge between the Neckar and Ammer rivers in the southwest of the country, about 30 kms southwest of Stuttgart. EVO* 2009 will be hosted at Eberhard Karls University in T?bingen, founded in 1477 and one of the oldest universities in Germany. Evo* 2009 proceedings will be published by Springer Verlag in the Lecture Notes in Computer Science series. The website http://www.evostar.org offers information relevant to all events, including calls for papers, deadlines, organizing committees, submission requirements, local information and a thorough view on the previous editions. From lvannesc from disco.unimib.it Thu Nov 13 06:13:15 2008 From: lvannesc from disco.unimib.it (Vanneschi Leonardo) Date: Thu Nov 13 11:06:22 2008 Subject: [Computational-biology] EuroGP 2009 - submission deadline extended to 30 November 2008 Message-ID: <301E01E95DB8684CAFA9EC28E1032FF207C6FCE3@disco-exchange.disco.local> *** EuroGP 2009 additional submission deadline extension*** Due to a number of requests by individual authors for a further deadline extension, we have decided to grant an extension of the EuroGP 2009 submission deadline to 30 November 2008 --------------------------------------------------------------------- EuroGP 2009 12th European Conference on Genetic Programming T?bingen, Germany April 15-17 2009 ---------------------------------------------------------------------- EuroGP 2009 will take place in conjunction with EvoCOP 2009 (9th European Conference on Evolutionary Computation in Combinatorial Optimization), EvoBIO 2009 (7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics), and EvoWorkshops 2009 (the specialist workshops on a range of evolutionary computation topics and applications), in a joint event collectively intituled EvoStar 2009. EuroGP 2009 important dates are: *** Extended Submission deadline: 30 November 2008 *** Notification to authors: 9 January 2009 Camera-ready deadline: 28 January 2009 Conference: 15-17 April 2009 To submit a paper you can directly access the page: http://myreview.csregistry.org/eurogp09/ or otherwise find all instructions and information about the EvoStar 2009 events at the page: http://www.evostar.org EuroGP 2009 topics include but are not limited to: * Theoretical developments * Empirical studies of GP performance and behavior * Algorithms, representations and operators * Applications of GP to real-life problems * Hybrid architectures including GP components * Unconventional evolvable computation * Evolutionary design * Evolutionary robotics * Grammar-based GP * Evolvable hardware * Linear GP * Self-reproducing programs * Evolution of tree or graph structures * Evolution of various classes of automata or machines (e.g. cellular automata, finite state machines, pushdown automata, Turing machines) * Object-oriented genetic programming EuroGP 2009 Program Chairs: - Leonardo Vanneschi, University of Milano-Bicocca, Italy vanneschi(at)disco(dot)unimib(dot)it - Steven Gustafson, GE Global Research, USA steven(dot)gustafson(at)research(dot)ge(dot)com From knobbe from cs.uu.nl Sat Nov 15 18:05:27 2008 From: knobbe from cs.uu.nl (knobbe@cs.uu.nl) Date: Sun Nov 16 13:45:20 2008 Subject: [Computational-biology] CfP DMKD Special Issue on Global Modeling using Local Patterns Message-ID: <200811152305.mAFN5ff5004427@fire02.rbg.informatik.tu-darmstadt.de> [ please distribute - apologies for multiple postings ] ------------------------------------------------------------------------ Global Modeling Using Local Patterns Special Issue Of Data Mining And Knowledge Discovery Submission Deadline: March 21, 2009 ------------------------------------------------------------------------ Over the last decade, research in local pattern discovery has developed rapidly, and a range of techniques is available for producing extensive collections of patterns. Because of the exhaustive nature of most techniques, the pattern collections provide a fairly complete picture of the information content of the database. However, in many cases this is where the process stops. The local patterns represent fragmented knowledge, and often it is not clear how the pieces of the puzzle can be combined into a global model, which is often the expected result of a data mining process. Consequently, the question of how to turn large collections of patterns into global models has received considerable attention. In data mining, the probably bestknown line of work that follows this approach are various approaches for associative classification, such as CBA and its successors. Similar problems also occur in propositionalization approaches to relational learning, where the goal is to discover propositional features that may be relevant for a propositional global model, or in related areas such as bioinformatics, text mining and computer vision, where the process of discovering complex features may be viewed as a local pattern discovery search. In general, all these approaches follow three different phases: 1. Local Pattern Discovery: finding a collection of local patterns in a given database that satisfy a set of inductive constraints, such as frequency or correlation with the target variable. 2. Pattern Subset Selection: selecting from the set of discovered patterns a small but informative subset of patterns that shows little redundancy. 3. Global Modeling: turning the set of selected patterns into an actionable global model by combining patterns effectively and dealing with potential conflicts between the patterns found. While each of these phases has been studied well in isolation, their dependencies are not yet well understood. Research areas that are of interest to this special issue include: * Associative Classification * Combination Strategies * Compression-based Pattern Selection * Constraint-based Pattern Set Mining * Efficient Pattern Set Discovery * Ensembles of Patterns * Feature Construction and Selection * Generalilty of Local Pattern Constraints * Global Modeling with Patterns * Iterative Local Pattern Discovery * KDD Process-models for Building Global Models from Local Patterns * Metrics for Pattern Set Selection * Pattern Ordering * Patterns and Information Theory * Pattern Set Selection * Pattern Teams * Propagation of Global Modeling Constraints to Local Pattern Discovery * Propositionalisation * Quality Measures for Pattern Sets * Resolution of Conflicting Predictions * Subgroup Discovery The full text of the call for papers can be found at: http://www.springer.com/cda/content/document/cda_downloaddocument/CFP_10618_20081111.pdf You can also reach this page from the DMKD journal site of Springer (http://www.springer.com/computer/database+management+%26+information+retrieval/journal/10618, click on "Call for Papers - Special Issue on ..."). Please don't hesitate to contact us for any further questions. Kind regards, Arno Knobbe, Johannes Fuernkranz Guest editors special issue From kannan from bmb.uga.edu Tue Nov 18 12:42:13 2008 From: kannan from bmb.uga.edu (Natarajan Kannan) Date: Tue Nov 18 13:47:03 2008 Subject: [Computational-biology] post-doc position at UGA Message-ID: <216d58830811180942o65248e21u6cfbbdd0ff0bd346@mail.gmail.com> Computational Biology Postdoctoral Position: One post-doctoral position is available to investigate the structural mechanisms of signaling proteins using computational and bioinformatics approaches. Candidates should have a Ph.D. in molecular or structural biology and experience in applying standard computational tools in a Linux/Unix environment. Preference will be given to candidates with experience in molecular modeling and molecular dynamics simulations. Interested candidates should send their CV including names of three references to: kannan@bmb.uga.edu -- Natarajan Kannan, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602-7229 E-mail: kannan@bmb.uga.edu Office phone: 706-542-7326 From alemmon from evotutor.org Thu Nov 20 19:22:57 2008 From: alemmon from evotutor.org (Alan Lemmon) Date: Thu Nov 20 22:43:54 2008 Subject: [Computational-biology] Graduate student position at FSU Message-ID: ////////////////////////////////////////// Accepting Graduate Students for Fall 2009 The new lab of Alan R. Lemmon in the Department of Scientific Computing at Florida State University (Tallahassee) is now accepting Ph.D. students interested in studying phylogenetics, phylogeography, speciation, bioinformatics, and/or population genetics. Members of the lab are encouraged (but not required) to develop independent projects that combine aspects of theoretical (statistical/computational) and empirical evolutionary biology. The current focus of the Lemmon lab is to develop statistical methods for phylogeography and phylogenetics using genomic data, as well as to development large numbers of nuclear markers using pyrosequencing techniques. The Department of Scientific Computing at Florida State University (http://www.csit.fsu.edu/) is a unique, interdisciplinary group of faculty and students who test scientific questions and develop methods by applying computational and statistical techniques to interesting problems in Biology, Physics, Mathematics, Geology, and Chemistry. Dr. Lemmon is also a member of the Department of Biology, which allows him to advise students with primarily empirical projects. Members of the Lemmon Lab have access to the following resources: Top-ranked High Performance Computing Facility (1500+ cores) State of the art genetics lab Reduced rate at University of Florida Genome Center Certified Nimblegen Microarray Facility State of the art equipment for behavioral experiments State of the art live animal facility Apalachicola National Forest (minutes from campus!) Interested individuals should visit the lab website ( http://www.evotutor.org/LemmonLab/), as well as contact Dr. Lemmon directly (alemmon@evotutor.org). ////////////////////////////////////////// -- Alan R. Lemmon CPB Postdoctoral Fellow UC Davis From icdm08-publicity from isti.cnr.it Fri Nov 21 07:10:17 2008 From: icdm08-publicity from isti.cnr.it (Maurizio Atzori) Date: Fri Nov 21 09:19:33 2008 Subject: [Computational-biology] 2008 IEEE Int. Conference on Data Mining (ICDM08) - Call for Participation Message-ID: Call for Participation IEEE International Conference on Data Mining (ICDM 2008) Pisa, Italy, December 15-19, 2008 http://icdm08.isti.cnr.it The 2008 edition of the IEEE International Conference on Data Mining series (ICDM 2008) will be held in Pisa, Italy, on December 15 thru 19, 2008. IEEE ICDM is well established as a top ranked research conference in data mining, providing a premier forum for presentation of original research results, as well as exchange and dissemination of innovative, practical development experiences. PROGRAM: More information on the program, including a list of accepted papers, is now available at http://icdm08.isti.cnr.it/ . Highlights are: three invited talks by Serge Abiteboul (INRIA Saclay and University Paris-Sud), Ravi Kumar (Yahoo! Inc.), and Harvey J. Miller (University of Utah); four tutorials, a panel on Social Networks and Data Mining, 8 demos, the ICDM contest and 10 workshops. All this in addition to 70 regular papers and 74 short papers accepted out of 724 submissions from 53 countries. VENUE & ACCOMMODATION: The conference venue is located in the historical city center of Pisa. Multiple hotels in all price categories are within walking distance of the venue; see http://icdm08.isti.cnr.it/Accomodation/ for details. SOCIAL EVENTS: ICDM 2008 offers a rich and varied social program. All participants are invited to the Welcome Party at the Teatro Verdi on December 16 and an orchestral concert will be performed for the occasion. In the afternoon of Wednesday, December 17, the social program offers a guided excursion followed by the Gala Dinner at Stazione Leopolda of Pisa, a socio-cultural center which was recently renovated from an old railway station. TRAVEL: Pisa enjoys excellent accessibility. Pisa Aiport http://www.pisa-airport.com/ is directly reachable from all major European airports and many other airports throughout the world. REGISTRATION: http://icdm08.isti.cnr.it/Registration/ . More information on location, accommodation and travel is available at http://icdm08.isti.cnr.it/ . Hoping to see you in Pisa, Fosca Giannotti and Dimitrios Gunopulos IEEE ICDM 2008 PC Co-chairs Naren Ramakrishnan, Franco Turini, Carlo Zaniolo IEEE ICDM 2008 Conference Co-chairs From nir from rosettadesigngroup.com Fri Nov 21 13:54:05 2008 From: nir from rosettadesigngroup.com (Nir London) Date: Fri Nov 21 16:17:46 2008 Subject: [Computational-biology] The Macromolecular Modeling Blog Message-ID: <007A40CF-DBBE-4CF8-B27F-DFE7682C6D62@rosettadesigngroup.com> Hi all, and a special hi to the structural biology fans :) We started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/ We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears. please check it out and tell me what you think... If any of you is interested in writing for the blog I'd be very happy if you contact me. Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com/ From shanbiogene from gmail.com Sat Nov 22 02:23:24 2008 From: shanbiogene from gmail.com (shan) Date: Sat Nov 22 12:29:03 2008 Subject: [Computational-biology] Bioinformatics Projects And Training Message-ID: NeoGen BioSolutions offers projects in various fields like Bioinformatics Biotechnology, Cheminformatics, and Pharmacogenomics for interested aspirants. The projects offered by NBS are live and industrial and designed keeping in mind the latest advancements in the respective fields. These projects are designed by our highly trained faculty who are having good industrial and research experience. The projects offered by NBS fall in to 2 categories ƒæ Academic projects as part of graduation / post graduation courses. ƒæ Projects for working Professional from pharma /biotech/ bioinformatics companies. Academic projects as part of graduate / post graduate courses. Academic projects, which are the part of the curriculum, for the fulfillment of the degree in different streams of life sciences are provided by NeoGen. The students can put forward their own ideas for the project work which shall be encouraged by us based on the feasibility and time span; else the students can also opt from the project list provided by us. However the list is provided only after registration. Partial list of the projects is provided for reference. * Annotations * Algorithm development * Bio programming * Primer designing * Protein modelling * Mutational analysis * Structure prediction * Computational Biology * Tool development * Metabolicpathway reconstruction * Data mining. Projects for working Professional from pharma /biotech/bioinformatics companies. The interested working aspirants can put forward their ideas and innovations and carry out their research cum project work at NeoGen. NBS provides the platform for the growth of the aspirants having sound knowledge and grip over the concepts. Certificates are issued after the successful completion of the project. The outstanding project works are encouraged for publications on the interest of the students. Contact Address: NeoGen BioSolutions No:12, M.E.S Road, Ganapathypuram, East Tambaram, Chennai- 600059. Ph: 044-22396384/ 044-64991544 9094019577/9940376674. Email: info@neogenbiosolutions.com From imarin from ibv.csic.es Mon Nov 24 09:47:50 2008 From: imarin from ibv.csic.es (imarin@ibv.csic.es) Date: Mon Nov 24 11:20:37 2008 Subject: [Computational-biology] Postdoctoral positions Message-ID: <89d2a928-2d9c-4f35-9388-f1a2dc24fd23@33g2000yqm.googlegroups.com> We are seeking two highly motivated postdoctoral researchers to work in our group at the Instituto de Biomedicina de Valencia (IBV-CSIC) Lab website: http://www.uv.es/~genomica/eng/index.htm Topics: 1)Comparative genomics and bioinformatics of genes involved in human diseases 2)Development of new methods of network analysis The positions require individuals with a PhD and experience in molecular evolution, comparative genomics and/or bioinformatics. The candidates will apply for their own funds to the “Junta de ampliación de estudios” CSIC program. Conditions: PhD obtained in the last ten years To apply, please send the following: 1. Curriculum vitae 2. Names of 2 referees willing to provide a letter of recommendation upon request 3. A brief statement of your research goals and interests for future grant applications E-mail applications can be sent to Ignacio Marin: imarin@ibv.csic.es From wcom from worldcomp.cviog.uga.edu Mon Nov 24 11:53:35 2008 From: wcom from worldcomp.cviog.uga.edu (WORLDCOMP'09 Congress Conferences) Date: Mon Nov 24 18:22:22 2008 Subject: [Computational-biology] Call For Papers: Computer Science & Computer Engineering Conferences - July 13-16 2009, USA, WORLDCOMP'09 Message-ID: <20081124165335.6438151B4B@worldcomp.cviog.uga.edu> CALL FOR PAPERS and Call For Workshop/Session Proposals WORLDCOMP'09 The 2009 World Congress in Computer Science, Computer Engineering, and Applied Computing July 13-16, 2009, Las Vegas, USA (composed of 22 Joint Conferences) You are invited to submit a paper (and/or a proposal to organize a session/workshop). All accepted papers will be published in the respective conference proceedings. The 2009 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'09) is composed of the following 22 conferences (all will be held simultaneously, same location and dates: July 13-16, 2009, USA): o BIOCOMP'09: The 2009 International Conference on Bioinformatics and Computational Biology o CDES'09: The 2009 International Conference on Computer Design o CGVR'09: The 2009 International Conference on Computer Graphics and Virtual Reality o CSC'09: The 2009 International Conference on Scientific Computing o DMIN'09: The 2009 International Conference on Data Mining o EEE'09: The 2009 International Conference on e-Learning, e-Business, Enterprise Information Systems, and e-Government o ERSA'09: The 2009 International Conference on Engineering of Reconfigurable Systems and Algorithms o ESA'09: The 2009 International Conference on Embedded Systems and Applications o FCS'09: The 2009 International Conference on Foundations of Computer Science o FECS'09: The 2009 International Conference on Frontiers in Education: Computer Science and Computer Engineering o GCA'09: The 2009 International Conference on Grid Computing and Applications o GEM'09: The 2009 International Conference on Genetic and Evolutionary Methods o ICAI'09: The 2009 International Conference on Artificial Intelligence o ICOMP'09: The 2009 International Conference on Internet Computing o ICWN'09: The 2009 International Conference on Wireless Networks o IKE'09: The 2009 International Conference on Information and Knowledge Engineering o IPCV'09: The 2009 International Conference on Image Processing, Computer Vision, and Pattern Recognition o MSV'09: The 2009 International Conference on Modeling, Simulation and Visualization Methods o PDPTA'09: The 2009 International Conference on Parallel and Distributed Processing Techniques and Applications o SAM'09: The 2009 International Conference on Security and Management o SERP'09: The 2009 International Conference on Software Engineering Research and Practice o SWWS'09: The 2009 International Conference on Semantic Web and Web Services (a link to each conference's URL can be found at http://www.world-academy-of-science.org ) ACADEMIC CO-SPONSORS: Currently being prepared - it will include a number of active research laboratories and centers that have helped to shape our field. The Academic Co-Sponsors of the last offering of WORLDCOMP included research labs at Harvard University, UCLA, University of Minnesota, University of Illinois at Urbana- Champaign, Georgia Institute of Technology, Emory University, University of Texas at Austin, MIT, George Mason University, University of Iowa, Russian Academy of Sciences, NEMO/European Union, and others. Corporate Co-Sponsors included, Google, Salford Systems, Synplicity, Supermicro, NIIT, and others. General Co-Chair and Coordinator: H. R. Arabnia, PhD Professor, Computer Science Editor-in-Chief, The Journal of Supercomputing (Springer) Advisory Board, IEEE Technical Committee on TCSC Vice President, Int'l Society of Intelligent Biological Medicine The University of Georgia Department of Computer Science 415 Boyd Building Athens, Georgia 30602-7404, USA Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra@cs.uga.edu PURPOSE / HISTORY: This set of joint conferences is the largest annual gathering of researchers in computer science, computer engineering and applied computing. Many of the joint conferences in WORLDCOMP are the premier conferences for presentation of advances in their respective fields. We anticipate to have 2,400 or more attendees from over 85 countries participating in the 2009 joint conferences. The motivation is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. The model used to form these annual conferences facilitates communication among researchers from all over the world in different fields of computer science, computer engineering and applied computing. Both inward research (core areas of computer science and engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications) will be covered during the conferences. WORLCOMP'09 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. In recent past, keynote and/or tutorial speakers included: Prof. David A. Patterson (U. of California, Berkeley); Prof. Michael J. Flynn (Stanford U.); Prof. John H. Holland (U. of Michigan, Ann Arbor); Prof. Brian D. Athey (U. of Michigan, Ann Arbor), Prof. H. J. Siegel (Colorado State U.); Prof. Barry Vercoe (MIT); Prof. Ruzena Bajcsy (U. of California, Berkeley); Prof. Jun Liu (Harvard U.); Dr. Jim Gettys (OLPC + developer of X Window); Dr. Chris Rowen (President and CEO, Tensilica, Inc.); and many other distinguished speakers. SUBMISSION OF PAPERS: Prospective authors are invited to submit their draft papers by uploading them to http://worldcomp.cviog.uga.edu/ . Submissions must be received by Feb. 25, 2009 and they must be in either MS doc or pdf formats (about 5 to 7 pages - single space, font size of 10 to 12). All reasonable typesetting formats are acceptable (later, the authors of accepted papers will be asked to follow a particular typesetting format to prepare their papers for publication.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, and email address for each author. The first page should also identify the name of the Contact Author and a maximum of 5 topical keywords that would best represent the content of the paper. Finally, the name of the conference that the paper is being submitted to must be stated on the first page. Papers will be evaluated for originality, significance, clarity, impact, and soundness. Each paper will be refereed by two experts in the field who are independent of the conference program committee. The referees' evaluations will then be reviewed by two members of the program committee who will recommend a decision to the chair of the track that the paper has been submitted to. The chair will make the final decision. Lastly, the Camera-Ready papers will be reviewed by one member of the program committee. PROPOSAL FOR ORGANIZING SESSIONS/WORKSHOPS: Each session will have at least 6 paper presentations from different authors (12 papers in the case of workshops). The session chairs will be responsible for all aspects of their sessions; including, soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings and on the cover of the books. Proposals to organize sessions should include the following information: name and address (+ email) of proposer, title of session, a 100-word description of the topic of the session, the name of the conference the session is submitted for consideration, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). email your session proposal to H. R. Arabnia (address is given above). We would like to receive the proposals by January 16, 2009. IMPORTANT DATES: Jan. 16, 2009: Proposals for organizing/chairing sessions/workshops Feb. 25, 2009: Submission of papers (about 5 to 7 pages) March 25, 2009: Notification of acceptance April 25, 2009: Camera-Ready papers and Registration due July 13-16, 2009: The 2009 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'09 - 22 joint conferences) MEMBERS OF PROGRAM AND ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; AI; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra@cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, a short biography together with research interests and the name of the conference offering to help with. Many who have already joined the committees of individual tracks are renowned leaders, scholars, researchers, scientists and practitioners of the highest ranks; many are directors of research laboratories, fellows of various societies, heads/chairs of departments, deans and provosts. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, health spa, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (recreational destinations, Golf courses, ...) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= This email was sent to: comp-bio@net.bio.net To opt out of this email list: http://worldcomp.cviog.uga.edu/cgi-bin/rm/full.cgi?1B77F664-BA23-11DD-860B-BBF22591F2FB From masulli from disi.unige.it Wed Nov 26 04:15:54 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Wed Nov 26 11:16:48 2008 Subject: [Computational-biology] Call for Papers - IJCNN 2009 - Special Session on Soft Computing tools for Bioinformatics (Dec 15 2008 deadline) Message-ID: <200811261015.54920.masulli@disi.unige.it> [apologies for multiple posts] ----------------------------------------------------------------------------------------------------------------- CALL FOR PAPERS - Special Session on Soft Computing tools for Bioinformatics at International Joint Conference on Neural Networks (IJCNN 2009) sponsored by SIG on Bioinformatics of the International Neural Network Society (INNS) Location: Westin PeachTree Hotel, Atlanta, Georgia, USA, June 14-19 2009 Conference Web Site: http://cnd.memphis.edu/ijcnn2009/ Special Session Web Site: http://www.disi.unige.it/person/MasulliF/conferences/IJCNN2009-SS.html Description and Scope: The body of information surrounding molecular and genomic experiments and clinical investigations is rapidly growing as the magnitude and rate of applications involving large-scale high-throughput technologies are ever-increasing. Bioinformatic data mining efforts now range from more recent methods including miRNA target identification and protein structure prediction to classical methods such as ANN and RBFN classification of DNA microarray gene expression data. Data fusion and integration are also gaining considerable attention for merging signals, features, images, and text data from multiple sensors together in order to understand influences of data components on early detection and diagnosis of disease. Altogether, bioinformatics has become a very promising multidisciplinary research area in the life sciences because results provide new insights for interpretation and establish new leads for deeper understanding. Each year there are numerous Soft Computing and Machine Learning algorithms introduced providing new examples of application in related fields (clustering, feature selection, text mining, signal and image processing, data visualization, etc.). This session will take stock in new soft computing methods for bioinformatic data mining in general, and Neural Network methods in particular. Topics: We welcome papers which present novel algorithms or refined classical methods for the analysis of high dimensional bioinformatic data sets. The target problems include but are not limited to: * Data integration and fusion * Ensemble techniques * Biological sequence identification * DNA/CGH/SNP/miRNA arrays * Gene regulatory and ontology networks * Protein-protein, protein-small molecule interactions * Protein structure prediction * Cellular metabolism and signaling * Pharmacogenomics and pharmacodynamics * Metabolic pathways * Signal processing * Unsupervised and supervised classification * Imaging/data visualization * Text mining methods * Biomarker selection Organizers: Alexandru Floares (1), Francesco Masulli (2,3), (1) Department of Artificial Intelligence Oncological Institute Cluj-Napoca 400015 Str. Republicii, Nr. 34-36, Cluj-Napoca Romania E-mail: alexandru.floares iocn.ro (2) DISI Dept. Computer and Information Sciences University of Genova Via Dodecaneso 35 16146 Genoa, Italy E-mail: masulli disi.unige.it (3) Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, 1900 N 12th Street Philadelphia, PA 19122, USA. Important dates: As soon as possibile: Inform by email the Special Session organizers of your willness to submit a paper Paper submission deadline: December 15, 2008 (&) Author notification of acceptance or rejection: Gennuary 30, 2009 Deadline for final paper re-submission: March 10, 2009 (&&) (&) Paper submission (deadline Dec 15, 2008): At http://cnd.memphis.edu/ijcnn2009/submission.html you'll find the Instruction for Authors and the link to the IJCNN 2009 submission site. After uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your paper. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09". (&&) Final Paper re-submission (deadline March 10, 2009): After re-uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your revised paper and a letter indicating in detail all changes made. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09 (revised)". ------------------------------------------------------- -- <--------------------------------------------------------------------> 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 jeedward from yahoo.com Wed Nov 26 09:13:07 2008 From: jeedward from yahoo.com (John Edward) Date: Wed Nov 26 17:21:29 2008 Subject: [Computational-biology] BCBGC-09 call for papers Message-ID: <990832.94513.qm@web45911.mail.sp1.yahoo.com> BCBGC-09 call for papers ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. 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 John Edward Publicity committee ? ?