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Second announcement: Alma-grid/ GIGA training in bioinformatics - Li ège, October 1, 2 and 3 2007
by Raphael.Maree. 28 Aug '07

28 Aug '07

Dear all, GIGA Formation and alma-grid organize a training in bioinformatics on October 1, 2 and 3 2007. 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? Don't 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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Postdoc vacancy - Checked by AntiVir DEMO version -
by Marc De Maeyer 21 Aug '07

21 Aug '07

Postdoc position available at K.U.Leuven Task description: In the laboratory for bio-molecular modelling at K.U.Leuven a vacancy for a postdoc is available. A research project (Interdisciplinary Research program IDO) involving chemists, molecular biologists and modellers has been granted and a vacancy for a highly motivated postdoc in the field of molecular modelling and drug design is available. The subject of the program entitles: Design of chemical compounds for the inhibition of protein-protein interactions. The candidate will conduct research designing in silico protein-protein inhibitors. The candidate will work closely with chemist guiding the synthesis of the proposed modelled compounds. Active knowledge of computerprograms related to drug design is a plus. Besides research the candidate has to spent part of his time in teaching or giving exercises to 3rd bachelor and master biochemistry students. Starting from October 2007 for 17 months. Contact: Prof. Dr. Marc De Maeyer K. Universiteit Leuven Biochemie moleculaire en structurele biologie Laboratorium biomoleculaire modelling Celestijnenlaan 200 G bus 2403 (room 1.56) B-3001 Heverlee Belgium e-mail: marc.demaeyer(a)fys.kuleuven.be tel: +32-16-32 75 21 fax: +32-16-32 79 74 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Benelux Bioinformatics Conference 2007 - First announcement and call for abstracts
by Yves Moreau 21 Aug '07

21 Aug '07

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[Fwd: [cinbios] Fwd: PhD at the EBI]
by BEN 21 Aug '07

21 Aug '07

-------- Original Message -------- Subject: [cinbios] Fwd: PhD at the EBI Date: Mon, 20 Aug 2007 23:27:58 +0200 From: Jacques van Helden <Jacques.van.Helden(a)ulb.ac.be> To: Guillaume Desmottes <gdesmott(a)ulb.ac.be>, Gilles VANDERSTOCKEN <Gilles.Vanderstocken(a)ulb.ac.be>, Grégory GATHY <ggathy(a)ulb.ac.be>, Alexandre LUTUMBA <alexandre.lutumba(a)belgacom.net>, Julien Heck <heck.julien(a)gmail.com>, Khatib MASSAAOUDI <massaaoudi(a)hotmail.com>, Eric Bareke <ericbareke(a)gmail.com>, John Crousse <jcrousse(a)ulb.ac.be>, Patrick Broen <patrick_broen(a)hotmail.com>, Hicham HACHEM BAYDOUN <hmahmoud(a)ulb.ac.be>, Fatima Chicker <fchiker(a)yahoo.fr>, cinbios(a)listserv.ulb.ac.be References: <46C9A963.1030207(a)ebi.ac.uk> Begin forwarded message: From: Alison Barker <alison(a)ebi.ac.uk> Date: August 20, 2007 4:46:59 PM GMT+02:00 To: Alison Barker <alison(a)ebi.ac.uk> Subject: PhD at the EBI Dear Colleagues The chance to join EBI for a PhD studentship has arrived! Can you please forward this information to anyone for whom it may be of interest. The winter PhD has just opened. The deadline for applications is 17th December 2007. Successful applicants are expected to start in October 2008 (although this may be varied). Please proceed to the EMBL Studentship pages for further information on the International PhD program and an application form. http://www.embl.org/training/phdprogramme/applications.html Good luck The Outreach and Training Team -- Alison Barker Outreach Administrative Assistant EBI EMBL Outstation European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44-(0)1223-494-604 Fax: +44-(0)1223-494-468 email: alison(a)ebi.ac.uk -- ---------------------------------------------------------------------------- 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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Opening registration: "Integrative Bioinformatics": 5th Annual Cytoscape Public Symposium
by piet molenaar 17 Aug '07

17 Aug '07

*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 Ruedi Aebersold – Swiss Federal Institute of Technology *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 opening of registration for the forthcoming 2007 Cytoscape Symposium and Retreat to be held at the Academic Medical Center, University of Amsterdam, Netherlands on 6-9 Nov 2007. Registration is now possible 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. In addition to the Public 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 Thursday 8th November 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 to people with an interest in the development of the Cytoscape software and associated 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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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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