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Post-doc in Computational Biology at Orsay, France
by BEN 01 Aug '07

01 Aug '07

We were asked to forward the following announcement ------------------ Post-doc in Computational Biology at Orsay, France Pr. Joël Janin Yeast Structural Genomics, IBBMC Bd. 430 Université Paris-Sud, 91405-Orsay joel.janin(a)u-psud.fr http://genomics.eu.org/spip/,http://www.ibbmc.u-psud.fr/ The research program is a general analysis of the protein environment of ligand molecules in the Protein Data Bank aiming to (a) compare and classify binding sites and (b) develop applications to molecules of pharmacological interest in the frame of the SuMo software package (http://www.medit.fr/products-page2-sumo.html) The physical chemical properties of the sites and the conformation changes related to ligand binding will be considered. In parallel, the person will participate in setting up a Web server for these applications. The program is a collaboration with MEDIT (http://www.medit.fr/) a French start-up specializing in molecular modeling and drug discovery. It is part of POPS, a project aiming to develop high-performance computing systems up to 1 PetaFlops (1015 operations per second) and supported by the competitiveness cluster SYSTEM@TIC PARIS-REGION (http://www.systematic-paris-region.org/) Time schedule: 18 months starting no later than Dec. 1, 2007 Expertise required: Computational biology, computational chemistry, computer science ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre Marc Colet - Guy Bottu - David Coornaert - Valerie Ledent Tel. +32/2/6505146 | Address BEN ULB CP 257 Fax +32/2/6505124 | Boulevard du Triomphe email ben(a)vub.ac.be | B-1050 Bruxelles ----------------------------------------------------------------------------

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BE Live IT, October 16th 2007: Update on Confirmed Speakers
by Bert Coessens 27 Jul '07

27 Jul '07

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4th Integrative Bioinformatics Workshop - Call for Participation.
by Bert Coessens 26 Jul '07

26 Jul '07

*** CALL FOR PARTICIPATION *** 4th Integrative Bioinformatics Workshop September 10-12, 2007 University of Gent, Belgium *** REGISTER ONLINE *** workshop web: http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib07/ IMPORTANT DATES August 13: Registration for participation deadline August 27: Poster submission deadline KEYNOTE TALKS Prof Carole Goble, School of Computer Science, University of Manchester, UK "myExperiment: A MySpace for the Self-serving Bioinformatician" Prof Søren Brunak, BioCentrum-DTU, Technical University of Denmark "Integrating data for interactome analysis across organisms" Dr David Searls, Senior Vice President, Informatics, GlaxoSmithKline Pharmaceuticals, USA "Integrative Drug Discovery" Dr Luis Serrano, EMBL, Heidelberg, Germany "Structure-based prediction of protein-protein and protein-DNA interactions" Sponsored by the European Science Foundation PROGRAMME Monday 10th September 2007 11:30 Registration desk opens 12:30 Lunch (buffet style) 13:10 Welcome followed by some administrivia Jacob Koehler and Martin Kuiper 13:20 keynote Understanding interactomes by data integration Søren Brunak (Technical University of Denmark) Session 1 Database Integration and Integrative Databases 14:00 A Methodology for Comparative Functional Genomics Alam, I; Cornell, M; Soanes, D M; Hedeler, C; Wong, H M; Rattray, M; Hubbard, S J; Talbot, N J; Oliver, S J; Paton, N W 14:25 Community-based Linking of Biological Network Resources: Databases, Formats and Tools Telgkamp, M.; Koschützki, D.; Schwöbbermeyer, H.; Schreiber, F. 14:50 Defining Mapping Mashups with BioXMash Hunt, E; Boesinger, C; Jakubowska, J; Norrie, M 15:15 Data Linkage Graph: computation, querying and knowledge discovery of life science database networks Lange, M.; Himmelbach, A.; Schweizer, P.; Scholz, U. 15:40 Coffee break 16:00 Exploring PSI-MI XML Collections Using DescribeX Samavi, R.; Consens, M.P.; Khatchadourian, C.; Topaloglou, T. 16:25 VINEdb: a data warehouse for integration and interactive exploration of life science data Hariharaputran, S; Töpel, T; Brockschmidt, B; Hofestädt, R 16:50 Integration of Heterogeneous Cis-Antisense Gene Pair Data Sets Mapping onto the Human Genome Orlov, YL; Zhou, J; Kuznetzov, VA 17:15 Exchange of integrated datasets - the OXL format Taubert, J; Sieren, KP; Hindle, M; Hoekman, B; Winnenburg, R; Philippi, S; Rawlings, C; Köhler, J. 17:40 Poster Session 19:30 BeerFest Tuesday 11th September 2007 10:00 keynote myExperiment: A MySpace for the Self-serving Bioinformatician? Carole Goble (University of manchester, UK) Session 2 Integrative Systems Biology I 10:40 Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models Lister, AL; Pocock, M; Wipat, A 11:05 Coffee break 11:20 Stochastic effects in a compartmental model for mitotic checkpoint regulation Ibrahim, B; Dittrich, P; Diekmann, S; Schmitt, E 11:45 Reactome: An integrated expert model of human molecular processes and access toolkit de Bono, B 12:10 A High-Level Petri Net Framework for Genetic Regulatory Networks Banks, R; Steggles, LJ 12:35 Lunch (buffet style) 13:30 keynote Structures in systems biology Pedro Beltrao1, Christina Kiel and Luis Serrano (CRG-EMBL Systems Biology Unit, Spain) Session 3 Integrative Systems Biology II 14:10 From MIN meta-model to ordinary differential equations Yartseva, A; Devillers, R; Klaudel, H; Kepes, F 14:35 GeneBrowser: a novel approach for integration and functional classification of microarray data Arrais, J.P.; Santos, B.; Fernandes, J.; Carreto, L.; Santos, M.A.S.; Oliveira, J.L. 14:50 Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network Futschik, ME; Chaurasia, G; Russ, J; Herzel, H 15:15 Coffee break Session 4 Data Analysis and Interpretation 15:45 Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags Souche, E.L.; Hellemans, B.; Van Houdt, J.K.J.; Canario, A.; Klages, S.; Reinhardt, R.; Volckaert, F.A.M. 16:10 Mapping protein information to disease terminologies Mottaz, A.; Yip, Y.L.; Ruch, P.; Veuthey, A.-L. 16:35 Developmental Anatomy Ontology of Zebrafish -an Integrative semantic framework Belmamoune, M.; Verbeek, F.J. 17:00 CIDA: An integrated software for the design, characterisation and global comparison of microarrays Khalid, S; Khan, M; Symonds, A; Wang, P; Liu, X; Li, S 17:25 IMS2 -- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath Baumbach, J; Bunkowski, A; Lange, S; Oberwahrenbrock, T; Kleinboelting, N; Rahmann, S; Baumbach, JI 17:50 Poster session 19:30 Conference dinner Wednesday 12th September 2007 10:00 keynote Integrative Drug Discovery David Searls (GlaxoSmithKline Pharmaceuticals, USA) Session 5 Data Classification 10:40 Supervised classification of combined copy number and gene expression data Riccadonna, S; Jurman, G; Merler, S; Paoli, S; Quattrone, A; Furlanello, C 11:05 Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data Reyes, J. A.; Gilbert, D. R. 11:30 Coffee break 11:50 Monophyletic clustering and characterization of protein families Zhang, J.; Zhao, Z.; Evershed, J.; Li, G. 12:15 A Tool for Evaluating Strategies for Grouping of Biological Data Jakoniene, V; Lambrix, P 12:40 Closing remarks 12:50 Lunch (buffet style) and Depart ORGANISING COMMITTEE Ralf Hofestädt, Bielefeld University, Germany Jacob Koehler, Rothamsted Research, UK Martin Kuiper, VIB, University of Gent, Belgium Paul Verrier, Rothamsted Research, UK CONTACT Karen Morris, BAB Division, Rothamsted Research, West Common, Harpenden, Herts. AL5 2JQ, UK email: karen.morris(at)bbsrc.ac.uk tel: +44 (0)1582 763133 extension 2813 fax: +44 (0)1582 467907

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First announcement: 5th Annual Cytoscape Public Symposium and Developers Retreat
by piet molenaar 18 Jul '07

18 Jul '07

*5th Annual Cytoscape Public Symposium and Developers Retreat * Amsterdam - Netherlands *November 8, 2007: Public Symposium:* *Integrative Bioinformatics: At the cutting edge of network analysis and biological data integration* *Leroy Hood* –Institute of Systems Biology *Ewan Birney* – European Bioinformatics Institute *Peter Sorger* – Harvard University *Trey Ideker* – University of California, San Diego *Chris Sander* – Memorial-Sloan-Kettering Cancer Center *Benno Schwikowski* – Institute Pasteur *Andrew Hopkins*—Pfizer Global Research & Development* * *November 6,7 and 9, 2007: Developers retreat * *Department of Human Genetics, **Academic** **Medical** **Center* *University of Amsterdam**, **Netherlands* We are pleased to announce the forthcoming 2007 Cytoscape Symposium and Retreat to be held at the Academic Medical Center, University of Amsterdam , Netherlands on 6-9 Nov 2007. More information, updates and registration will be available at: http://www.cytoscape.org/retreat2007 This years meeting is particularly exciting since it is the first time it will be held in Europe, specifically in the vibrant historic city of Amsterdam. 'Floating' on a web of canals, with its unique combination of old-world charm and cosmopolitan culture, Amsterdam is one of the most popular European cities for international visitors. To reach Cytoscape's large European user base a Public Symposium will be held on November 8th for which there is a formidable list of confirmed speakers. Apart from the Symposium the retreat consists of hands-on demo's, user-training sessions and informal, technically focused developer meetings: - *Tues 6th Nov:* Cytoscape Developer's Discussions - *Wed 7th Nov:* *Application showcase, hands-on sessions, tutorials * - *Thur 8th Nov:* *Public Symposium* - *Fri 9th Nov:* Development of Cytoscape Roadmap for 2007, 2008 The Symposium on the 8th is of general interest to both biologists and informaticians. Current and future users of Cytoscape are invited to visit the Application showcase on the 7th also. The developers days are targeted at the core developers of Cytoscape and plugins. We hope that you can join us! The Organizing Committee, 5th Cytoscape Retreat 2007 Annette Adler - Agilent Technologies Piet Molenaar - Human Genetics Department AMC Guy Warner - Unilever *Contact*: cytoretreat(a)cytoscape.org* * *The retreat is supported by*: Unilever (www.unilever.com) Netherlands Bioinformatics Center (NBIC) ( www.nbic.nl) Agilent ( www.agilent.com) *About Cytoscape:* Cytoscape (www.cytoscape.org) is an open source bioinformatics software platform for *visualizing* molecular interaction networks and *integrating *these interactions with gene expression profiles and other state data. The software architecture enables adaptation of Cytoscape functionality to the specific needs of biologists and bioinformaticians. It is jointly developed by the groups of Benno Schwikowski (Pasteur Institute, Paris), Trey Ideker (University of California San Diego), Chris Sander (Memorial Sloan-Kettering Cancer Center), Lee Hood (Institute of Systems Biology, Seattle), Annette Adler (Agilent Technologies, Santa Clara, CA) and Bruce Conklin (Gladstone/UCSF, GenMAPP). PS: Excuse us for cross-posting; we're trying to avoid this as much as possible. However, to reach a large audience we decided to include several relevant maillists also thereby increasing the risk that users get this mail several times.

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FW: bioinformatician position
by Bruno Dombrecht 10 Jul '07

10 Jul '07

Dear bbclist administrator, Could you post the following bioinformatics position on your list? Cheers, Bruno Bioinformatician, Molecular Biology Job Description The position requires an experienced bioinformatician with a strong affinity for the development of tools for protein sequence analysis. The candidate will report to the director Informatics and work in close collaboration with the Molecular Biology team and other departments within the company. More info at: http://www.cvwarehouse.com/ablynx/jobsite_new/jobdetail.aspx?id=3759 Bruno Dombrecht PhD Scientist Molecular Biology ABLYNX NV Technologiepark 4 B- 9052 Zwijnaarde Phone +32 (0)9 262 01 07 www.ablynx.com <http://www.ablynx.com> ----------------------------------------------------------------------- THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. -----------------------------------------------------------------------

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Alma-grid/ GIGA training in bioinformatics - Liège, October 1, 2 and 3 2007
by Raphael.Maree. 03 Jul '07

03 Jul '07

Dear all, GIGA Formation and alma-grid organize a training in bioinformatics on October 1, 2 and 3 2007, in Liège, Belgium. This training session is dedicated to biologists, doctors in medicine, engineers, computer scientists, researchers involved in the process of life science data analysis, or researchers willing to be initiated to this field. Some computer practise is needed. The training will be held in English. Deadline for registration is September 9 2007. Would you need more information about the training content and the registration terms and conditions, go and visit the alma-grid website http://www.alma-grid.com/Pages/p_news.html and/or the GIGA website http://www.giga.ulg.ac.be/extranet/training.htm Please find the training programme and registration form in attachments too. Interested? Dont hesitate to contact us: Rachel Navet : phone : 0032 4 366 43 94, @ : rachel.navet(a)ulg.ac.be Annick Pierrard : phone : 0032 4 366 44 97, @ : a.pierrard(a)ulg.ac.be We are looking forward to meeting you on October 1, 2 and 3 2007. Kind regards, Rachel Navet (GIGA Training) and Annick Pierrard (alma-grid coordination office)

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2nd CFP Machine Learning for Systems Biology (Extended deadline)
by Pierre Geurts 28 Jun '07

28 Jun '07

** Our apologies if you receive multiple copies of this announcement ** SUBMISSION DEADLINE HAS BEEN EXTENDED TO JULY 6TH. **************************** Call for Papers *************************** International Workshop on Machine Learning in Systems Biology 24-25 September 2007, Evry (near Paris), France ************************************************************************ http://mlsb07.ibisc.fr Motivation Molecular biology and also all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the “-omics” suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First of all, the amount of available experimental data is not at all a limiting factor any more; on the contrary, there is a plethora of it. The challenge has shifted towards identifying the relevant pieces of information given the question, and how to make sense out of it (a “data mining” issue). Secondly, rather than to focus on components in isolation, we can now try to understand how biological systems behave as the result of the integration and interaction between the individual components that one can now monitor simultaneously (so called “systems biology”). Taking advantage of this wealth of “genomic” information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and more generally in biomedical sciences. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. Objective The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to complex biological and medical questions by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. A non-exhaustive list of topics suitable for this workshop: Methods Machine Learning Algorithms Bayesian Methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel Methods Probabilistic Inference Structured output prediction Systems identification Graph inference, completion, smoothing Applications Sequence Annotation Gene Expression and post-transcriptional regulation Inference of gene regulation networks Gene Prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic Reconstruction Protein Structure Prediction Protein Function Prediction Protein-protein interaction networks Submissions We invite to submit an extended abstract of maximum five pages, formatted according to the Springer Lecture Notes in Computer Science style. Papers should be submitted online via the Easychair submission system at http://www.easychair.org/MLSB07/. The deadline for submissions is *July 6* (Extended) The accepted submissions will be edited in the proceedings of the workshop. Further information concerning the workshop can be found on the workshop web site http://mlsb07.ibisc.fr Important dates - 6 July: deadline for submissions - 24 July: response to authors - 25 August: camera-ready papers (extended abstracts) - 24-25 September: workshop Location The workshop will take place at University of Evry,in the Genopole® campus, located in Evry, at the heart of the Ile-de-France region, 25 km south of Paris. Evry has many transportation infrastructures (A6 and Francilienne highways, two RER regional train lines making it possible to reach the center of Paris in 40 minutes) and the Orly and Charles-de-Gaulle airports (15 km and 70 km away respectively). Chairs : Florence d’Alché-Buc, IBISC CNRS FRE 2873 & Université d’Evry, France Louis Wehenkel, GIGA & Université de Liège, Belgique Programme Committee Florence d’Alché-Buc (University of Evry, France) Christophe Ambroise (University of Evry, France) Laurent Bréhelin (University of Montpellier, France) Vincent Frouin (CEA, France) Pierre Geurts (University of Liège, Belgium) Mark Girolami (University of Glasgow, UK) Samuel Kaski (University of Helsinki, Finland) Kathleen Marchal (Katholieke Universiteit Leuven, Belgium) Gunnar Raetsch (Max Planck Institute,Tuebingen) Juho Rousu (University of Helsinki, Finland) Céline Rouveirol (University of Paris XIII, France) Yvan Saeys (University of Gent, Belgium) Koji Tsuda (Max Planck Institute, Tuebingen) Jacques Van Helden (Université Libre de Bruxelles, Belgium) Jean-Philippe Vert (Ecole des Mines, France) Louis Wehenkel (University of Liège, Belgium) Jean-Daniel Zucker(University of Paris XIII, France)

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BE Live IT: Bridging Life Sciences and IT - First Announcement
by Bert Coessens 27 Jun '07

27 Jun '07

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Lecturer in Bioinformatics University College Cork
by Jos Boekhorst 11 Jun '07

11 Jun '07

Attached document: a vacancy for a 4-year position as Lecturer in Bioinformatics/Computational Biology, University College Cork, Ireland.

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vacaturetekst bio-informatica - Checked by AntiVir DEMO version - - Che
by Marja Krosenbrink-Gruijters 11 Jun '07

11 Jun '07

Geachte heer/mevrouw, Heel fijn dat onze vacaturetekst via de "bblist" verstuurd kan worden. Hierbij stuur ik u de vacaturetekst voor docent van de opleiding Bio-informatica. Hopelijk komt deze e-mail nu wel goed aan. Zo niet, dan hoor ik het graag. Met vriendelijke groet, Marja Krosenbrink dr. M.J.G. Krosenbrink-Gruijters Secretaris Examencommissie Bio-informatica Hogeschool Leiden Cluster Techniek, Opleiding Bio-informatica telefoon: 071-518 8561 fax: 071-518 8415 bezoekadres: Zernikedreef 11 2333 CK Leiden Postadres: Postbus 382 2300 AJ Leiden

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