- BBClist - maillist.psb.ugent.be

post-doc position KULeuven - CGH arrays analysis
by Enrico Carlon 07 Oct '09

07 Oct '09

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CfPart: Tutorial on Comp. SysBio, Workshop on Computational Models for Cell Processes
by Ion Petre 06 Oct '09

06 Oct '09

Call for participation for two events connecting computer science and biology, in conjunction with Formal Methods 2009: 1. Tutorial on Computational Systems Biology Eindhoven, the Netherlands, November 2, 2009 http://combio.abo.fi/tcsb09/ Registration deadline: October 16, 2009 2. Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ Registration deadline: October 19, 2009 1. Tutorial on Computational Systems Biology (November 2, 2009, full day event) -------------------------------------------- - Lecturers: Ion Petre and Ralph-Johan Back, Abo Akademi University, Finland - Content: This one-day tutorial provides an introduction to computational systems biology, starting with a crash course on molecular biology for computer scientist and continuing with discrete, continuous and stochastic modeling techniques, as well as formal methods-based approaches. A demonstration is included on Copasi (Complex Pathway Simulator), a useful tool for modeling and simulating sysbio projects. The well-known heat shock response, that the lecturers and their research groups have been working on already for some years, will serve as a running example connecting the various topics. - Registration deadline: October 16, 2009 2. Workshop on Computational Models for Cell Processes (November 3, 2009) ------------------------------------------------------ FOCUS ----- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) ACCEPTED PAPERS --------------- - Bogdan Aman and Gabriel Ciobanu. Mobile Membranes with Timers - Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo Schettini and Paolo Milazzo. On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems - Jiri Barnat, Lubos Brim, Ivana Cerna, Sven Drazan, Jana Fabriková and David Safranek. BioDiVinE: A Framework for Parallel Analysis of Biological Models - Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini and Giancarlo Mauri. A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis - Luca Bortolussi and Alberto Policriti. Hybrid Semantics of Stochastic Programs with Dynamic Reconfiguration. - Mario Coppo, Ferruccio Damiani, Elena Grassi, Mike Guether and Angelo Troina. Modelling an Ammonium Transporter with SCLS - Laurence Loewe, Stuart Moodie and Jane Hillston. Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA - Heike Siebert. Dynamical and Structural Modularity of Discrete Regulatory Networks REGISTRATION AND IMPORTANT DATES --------------------------------- - Registration: http://www.win.tue.nl/fm2009/ - Registration deadline: October 19, 2009 - Late registration: after October 19, including on-site registration - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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Invitation_"Schrödinger_seminar"
by Prevost Martine 30 Sep '09

30 Sep '09

INVITATION "Schrödinger seminar" The Application of Recent Advances in Biomolecular Modeling to Drug Discovery Problems *** Dear Colleague, We are pleased to invite you to attend a Schrödinger seminar to take place on Wednesday October 21st, 2009 at the Université Libre de Bruxelles, http://www.ulb.ac.be/ Language: English Organizers: The seminar is jointly organized by Dr. Martine Prevost, Structure and Function of Membrane Biology Laboratory at the Université Libre de Bruxelles (http://sfmb.ulb.ac.be/index_uk.html) , and Schrödinger Inc. (http://www.schrodinger.com/) Schedule The seminar is divided up into two sessions: - A morning session with presentation of case studies highlighting the use of key techniques such as loop refinement, protein flexibility in ligand docking via «Induced Fit Docking », detection of multiple binding modes in ligand-based design, QM/MM methods and the exposure of the XP scoring function to identify key protein/ligand interactions for lead optimization. - The afternoon session will provide an opportunity for introductory demo on the use of Schrödinger software and for direct interaction with Schrödinger Application Scientist. Registration Participation is free of charge, but we kindly ask you to register by contacting me (katia.dekimeche(a)schrodinger.de) at your earliest convenience as seats are limited. Who Should Attend? The Seminar is suitable for attendees with varying backgrounds, from those with little experience of the use of computational techniques wanting to learn more about their potential impact on drug discovery, through to practicing computational chemists wanting to learn more about the use of recent advances in the Schrödinger suite and take advantage of the introductory training and direct contact with Schrödinger scientists. Agenda 9:00 Welcome & Coffee 9:30 General presentation of the Schrödinger suite with a focus on the application of key computational techniques to real world problems · Modeling and Simulation o The use of active site characterization tools to exploit regions of the binding site and optimize ligand interactions o The use of improved loop refinement to build missing information · Structure Based Design o Use of Docking methods with a focus on the Induced Fit Docking procedure to explore protein flexibility involved in the P38 DFG in/out loop movements o The use of fragment docking and exposure of the Glide XP scoring function to elucidate key interactions in 1kv2 structure · Ligand Based Design o Use of ligand based pharmacophores methods with a focus on multiple binding mode detection techniques to identify the two binding modes in P38 DFG in/out in the absence of protein data 12:30 Lunch 13:30 Demo · Short introduction on QM and QM/MM methods · How to get started with Maestro o Importing, exporting o Concept of the Project (Project Table) o Tools bar and Short-cut o Protein and Ligand Preparation o Recap of Interface for Morning Applications o Job submission, job monitoring o Analysis tools o Help and Documentation Videos Webinars · How to automate Schrödinger workflows using KNIME or Python 15:30 Questions/Answers 16:30 END Thank you and we look forward to welcome you there! Kind Regards, Katia Dekimeche Senior Account Manager, Academia and Government Schrödinger T: +33 1 46 55 85 17 M: +33 6 74 50 63 55 F: +33 1 70 24 86 78 katia.dekimeche(a)schrodinger.de http://www.schrodinger.com <http://www.schrodinger.com/> __________________________________________________________ Siège de la société /Registered Office: Schrödinger GmbH, Dynamostr 13, D-68165 Mannheim Directeur Général/Managing Director: Dr. Jörg Weiser Numéro dimmatriculation/Commercial Register: HRB 9583 , Tribunal d'instance: Mannheim -------------------------------------------- Martine Prévost Structure et Fonction des Membranes Biologiques CP 206/2 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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Last CFP AICCSA'2010
by talbi 30 Sep '09

30 Sep '09

========================================================================== The Eight ACS/IEEE International Conference on Computer Systems and Applications AICCSA 2010 May 16-19, Hammamet, Tunisia http://www.lifl.fr/AICCSA2010 =========================================================================== The eight ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-2010) will be held in Hammamet, Tunisia May 2010. This is an ideal time to be in Tunisia. AICCSA is the premier Computer Science and Engineering Conference in the Middle East and North Africa. Authors are invited to submit papers describing new advances in computer systems and their applications. We welcome papers that are theoretical, conceptual, descriptive in nature, or a survey of the state of the art. Topics of interest include, but are not limited to: Algorithms and Bioinformatics Computer Architecture and Real time Systems Database and Data Mining DSP/Image Processing/Pattern Recognition/Multimedia· Modeling and Simulation Networking and Telecommunications Parallel and Distributed Systems Security and Information Assurance Soft Computing (AI, Neural Networks, Fuzzy Systems, Evolutionary algorithms, etc.) Software engineering -------------------------------------------------------------------------- Important Due Dates: Paper and Poster Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Workshop, Tutorial and Panel Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Notification of acceptance: December 19, 2009 Camera ready copy due: February 5, 2010 Author Registration: February 5, 2010 -------------------------------------------------------------------------- Proceedings Papers selected for presentation will appear in the Conference Proceedings, which will be published by the IEEE Computer Society and be available at IEEE XploreTM. Extended versions of selected papers will be considered for possible publication in scholarly international journals. Submission Guidelines To submit a paper, visit http://www2.lifl.fr/AICCSA2010/index.php?n=Main.AuthorsInstructions Regular Papers Papers must be submitted electronically by October 13, 2009. Each paper will be evaluated by at least three reviewers, and will be accepted based on its originality, significance and clarity. Submissions should not exceed 8 two-column, 8.5x11 inch pages (including figures, tables, and references) in 10 point fonts. Please include 5-10 keywords, complete postal and e-mail address, and fax and phone numbers of the corresponding author. If you have difficulties with electronic submission, please contact Technical Program Co-Chairs. Papers must not be published or under consideration to be published elsewhere. Short Papers Submitted papers that are deemed of good quality but could not be accepted as regular papers will be accepted as short papers. Workshops, Tutorials and Panels Submissions Proposals for workshops, tutorials and panels should be submitted directly to the appropriate chair. Posters and Doctoral Symposium Research still in early stages and doctoral research proposals may be submitted as extended abstracts that must not exceed 750 words. Accepted abstracts will be included in a special poster session dedicated to doctoral research proposals and related research. Extended abstracts should be submitted directly to the Posters Chair. -- Prof. El-Ghazali TALBI University of Lille - INRIA - CNRS http: www.lifl.fr/~talbi ------------------New book -------------------- "Metaheuristics: from design to implementation" E-G. Talbi Wiley 2009 (624pp) ISBN: 978-0-470-27858-1 -----------------------------------------------

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Benelux Bioinformatics Conference 2009: first call for abstracts
by Pierre Geurts 25 Sep '09

25 Sep '09

******************** First Call for Abstracts ************************* Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium *********************************************************************** http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 SCOPE The Benelux Bioinformatics Conference is a two-day international conference on bioinformatics. It is the primary community event for bioinformatics researchers in the Netherlands, Belgium, and Luxemburg with excellent networking opportunities. The conference is aimed at both academic and industry researchers. This year's edition, BBC 2009, will take place in Liège, Belgium on December 14-15, 2009. Check out the conference web site at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/. CALL FOR ABSTRACTS The BBC 2009 program will feature four invited talks together with oral presentations and poster sessions. Participants are cordially invited to submit an abstract (max. 500 words) for their conference contribution. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. VENUE The conference will take place at the Academic Room of the University of Liège, place du 20-Août, 9, 4000 Liège, Belgium. The venue is located in the heart of Liège, near Christmas markets and other tourist interests. Liège is a thousand-year-old city with a historical centre and numerous monuments, churches, and museums. Liège is located one hundred kilometers east of Brussels. KEY DATES * Deadline for abstract submission October 19, 2009 * Notification of selection of oral contributions November 9, 2009 * Deadline for early registration November 20, 2009 * Conference December 14-15, 2009 LOCAL ORGANIZING COMMITEE Louis Wehenkel, Pierre Geurts, Kristel Van Steen, Eric Bullinger Department of EE and CS and GIGA-R, University of Liège, Belgium

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2 Positions (1 Post Doc, 1 Research Assistant) in Cambridge, UK
by Rekin's Janky 23 Sep '09

23 Sep '09

2 Bioinformatician Positions (1 Post Doc, 1 Research Assistant) at University of Cambridge, Department of Haematology Transcriptional Networks in Blood Stem Cells and Leukaemia The molecular control of blood stem cell development and differentiation is underpinned by regulatory networks that define the gene regulatory state of blood stem/progenitor cells, and in response to external stimuli control cell fate decisions. Work in the Gottgens group employs both experimental and bioinformatic approaches to identify and characterise blood stem cell regulatory networks. We are now looking for enthusiastic bioinformaticians to join our multidisciplinary team. The postholders will apply and further develop bioinformatic tools to analyse ChIP‐Seq and gene expression datasets as well as perform comparative genomic analysis of gene regulatory elements. The Gottgens group is based in the Cambridge Institute for Medical Research, the flagship Institute of the Medical School of Cambridge University with excellent infrastructure and a vibrant research environment. The group enjoys productive collaborations with research groups both within Cambridge and beyond. The group has been highly productive with over 40 papers in the last 4 years as well as a paper in Developmental Cell and a paper in Nature currently in press. Please contact Bertie Gottgens at bg200(a)cam.ac.uk for more information. For more details on the group, please see: http://www.cimr.cam.ac.uk/investigators/gottgens/index.html http://hscl.cimr.cam.ac.uk/index.html

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Call for participation: CompMod 2009, Nov 3, 2009, Eindhoven, the Netherlands
by Ion Petre 22 Sep '09

22 Sep '09

Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ In conjunction with Formal Methods 2009 ---------------------------------------------------------------------------- --- === Date: November 3, 2009 === === Webpage: http://combio.abo.fi/compmod09/ === === Related event: Tutorial on Computational Systems Biology, Nov 2, 2009 === === http://combio.abo.fi/tcsb09/ === ---------------------------------------------------------------------------- --- THE MEETING ----------- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) ACCEPTED PAPERS --------------- - Bogdan Aman and Gabriel Ciobanu. Mobile Membranes with Timers - Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo Schettini and Paolo Milazzo. On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems - Jiri Barnat, Lubos Brim, Ivana Cerna, Sven Drazan, Jana Fabriková and David Safranek. BioDiVinE: A Framework for Parallel Analysis of Biological Models - Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini and Giancarlo Mauri. A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis - Luca Bortolussi and Alberto Policriti. Hybrid Semantics of Stochastic Programs with Dynamic Reconfiguration. - Mario Coppo, Ferruccio Damiani, Elena Grassi, Mike Guether and Angelo Troina. Modelling an Ammonium Transporter with SCLS - Laurence Loewe, Stuart Moodie and Jane Hillston. Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA - Heike Siebert. Dynamical and Structural Modularity of Discrete Regulatory Networks REGISTRATION AND IMPORTANT DATES --------------------------------- - Registration: http://www.win.tue.nl/fm2009/ - Registration deadline: October 19, 2009 - Late registration: after October 19, including on-site registration - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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position for scientific programmer
by AHC van Kampen 21 Sep '09

21 Sep '09

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Fwd: EXTENDED DEADLINE SEPT 28th: EMBNET-RIBio Oct25-29 2009 Internatl. Conference
by Jacques van Helden 18 Sep '09

18 Sep '09

From: Julio Collado Vides <collado(a)ccg.unam.mx> Date: 18 September 2009 00:14:36 GMT+02:00 To: collado(a)ccg.unam.mx Cc: BJ Morrison <bj(a)sdsc.edu> Subject: EXTENDED DEADLINE SEPT 28th: EMBNET-RIBio Oct25-29 2009 Internatl. Conference Dear colleagues: We would like to remind you of the SEPTEMBER 28th EXTENDED DEADLINE TO SUBMIT AN ABSTRACT FOR THE International EMBnet-RIBio Conference 2009, jointly organized by the European Molecular Biology network (EMBnet) and the Red Iberoamericana de Bioinformática (RIBio) at the Paradisus Riviera Cancun Resort, located at the Mayan Riviera, Quintana Roo, Mexico, from the 26th to the 29th of October, 2009. Visit the conference site: http://www.embnet.org/en/EMBnet-RIBio2009 Monday October 26th we will give official birth to the Iberoamerican Society for Bioinformatics, you are welcome to be a funding member ¡¡ We are pleased to announce RESOURCES FOR PARTIAL FUNDING for students, posdocs and researchers from Iberoamerica to attend the meeting PROVIDED THEY SUBMIT AN ABSTRACT to the conference. There is also funding for ISCB affliiated students to attend the meeting with similar requirements. Don't miss the deadline of this exciting conference in a wonderful setting in the Mexican Caribbean! The Organizing Committee ------------------------------------------------------------------ ------------------------------------------------------------------ More detailed information: This will be the first time the EMBnet's Annual General Meeting will take place outside of Europe, bringing together bioinformaticians from all over the world, together with the Iberoamerican Annual General Meeting, and representatives of other major Bioinformatics societies in the World. We will give official birth to the Iberoamerican Bioinformatics Society. Tri Institutional Professor Chris Sander (http://www.mskcc.org/mskcc/html/11655.cfm ), an authority in bioinformatics and founder of the field will give a keynote lecture at the conference. The conference is open to submissions. The main topics will be: High Throughput Technologies, the Interface of Bioinformatics and Systems Biology and Open Software for Bioinformatics, but we are accepting submissions in all areas of bioinformatics (such as genomics, proteomics, trancriptomics, metagenomics, data and text-mining, ontologies, education and e-learning tools available in Bioinformatics, among others) --See the Abstract guidelines--. Additionally, selected papers will be reviewed and published on the "EMBnet.news 15.4" (EMBnet.news is a quarterly publication with a peer reviewed research section indexed by PubMed (starting from 15.4), devoted to research, projects, events, news and announcements related with the bioinformatics, biomedical and in general to the "bio-" and "omics-" communities & industry all-over the world). All information dealing with submitting abstracts, registration and hotel booking can be found in the site of the conference at: http://www.embnet.org/EMBnet-RIBio2009 Don't miss the deadline of this exciting conference in a wonderful setting in the Mexican Caribbean! On behalf of The Organizing Committee -- Julio Collado-Vides, Ph.D. Head of the Program on Computational Genomics Center for Genomic Sciences, UNAM Av. Universidad s/n. Cuernavaca, Col. Chamilpa, Morelos 62210; Mexico phone: (52) 777-313-2063; 55-5622-7693 Fax: (52) 55 5622-7694 http://www.ccg.unam.mx/Computational_Genomics/

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IUAP BioMaGNet Annual meeting 2009
by Klaas Vandepoele 15 Sep '09

15 Sep '09

Dear colleagues, The Bioinformatics and Evolutionary Genomics division of the Department of Plant Systems Biology (VIB -- Ghent University) is organizing *BioMaGNet's Annual Meeting* on *October 22nd 2009*. We invite all scientists working on bioinformatics, modelling or related disciplines to participate in this one-day symposium which will focus on research topics covered by the different national and international partners of the Interuniversity Attraction Pole BioMaGNet. Apart from the keynote talks and contributed BioMaGNet presentations, abstracts can be submitted for the poster session. Invited speakers: -Mark Veugelers, Integration Manager VIB -Stein Aerts, Laboratory of Computational Biology -Florence d'Alché-Buc, Université d'Evry-Val d'Essonne The meeting will take place at the "Fiers-Schell-Van Montagu" FSVM research building at the Technologiepark 927 in Ghent, Belgium. For more information about registration, abstract submission and updates of the program, please visit http://bioinformatics.psb.ugent.be/biomagnet_2009 We are looking forward to see you at the conference! The organization committee -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/

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