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vacancy postdoc computational systems biology Amsterdam
by Hans van Beek 20 Jan '09

20 Jan '09

*Postdoc Position Computational Systems Biology 'Systems Bioinformatics: Computational Modelling Methods' f/m * * VU University Amsterdam, the Netherlands * *Research project * The goal of the project is to develop and implement computer methods for computational modelling of biological systems. This encompasses methods for computational model assembly, execution, analysis and parameter estimation. This means collaboration with several experimental groups which work among others on metabolism in micro-organisms, animals and humans, on plant biology, nutrition and disease processes such as cancer. We also interact with the mathematical modelling group of the Netherlands Institute for Systems Biology. In this way this project is part of the core activity in Dutch systems biology. The project focuses on developing and implementing computational methods generically useful for computational modelling of biological systems. This encompasses computational model assembly, modification, maintenance, execution, simulation, optimisation, parameter estimation etc. Parameter sensitivity spectrum analysis, ensemble simulation, model-based data analysis techniques, multiscale modelling, 'e-BioScience' approaches and data assimilation methods may be part of the project. Demonstration of the effectiveness of developed methods by application to modelling of some of the example biological systems is desirable. This Systems Bioinformatics project is funded by The Netherlands Consortium for Systems Biology (NCSB) and in total involves six Dutch bioinformatics centres. In addition, the Systems Bioinformatics group is part of the BioAssist programme of the Netherlands Bioinformatics Centre. The VU group coordinates the six centres involved in the Systems Bioinformatics project. The Postdoc plays an active role in coordination of the project with the bioinformatic and experimental partners. Further information: see website : http://www.vu.nl/nl/werken-bij-de-vu/vacatures/1-2008-00278.asp -- Hans van Beek ADDRESS : Section Medical Genomics Department of Clinical Genetics VU University Medical Centre Phone: +31 20 5987460 Contact details: Dr JHGM van Beek Mail address: van der Boechorststraat 7 1081 BT Amsterdam The Netherlands Visiting address: Faculty of Earth and Life Sciences (W&N building) De Boelelaan 1085 Amsterdam Room B-423 http://vumc.nl; http://ibivu.nl; http://home.hccnet.nl/jhgm.van.beek e-mail: hans.van.beek(a)falw.vu.nl secondary e-mail: hans.vanbeek(a)vumc.nl (checked infrequently) FOR YOUR INTEREST freely downloable scientific article on dynamics of energy conversion in the heart : Click http://home.hccnet.nl/jhgm.van.beek/prod02.htm#download and click on "Freely downloable article in American Journal of Physiology"

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The BBC mailing list
by BEN 08 Jan '09

08 Jan '09

Dear colleagues, Some of you will have received a wellcome message for the BBC mailing list. This is because each year we add the E-mail addresses of the attendants of the Benelux Bioinformatics Conference. The BBC list is hosted on the Mailman server of the Belgian Biodiversity Facility (http://www.biodiversity.be) and is moderated by the staff of the Belgian EMBnet Node (http://www.be.embnet.org) You can send a mail to this this list (BBClist(a)biodiversity.be) if you want to announce a public lecture or a job opening, if you have a question or if you want to start a discussion about bioinformatics in the Benelux. Note that only members of the list are allowed to post and that, because of the moderation, the messages are delivered with some delay (usually te next day in the morning). You can unsubscribe or customize the way you receive messages at http://mailman.biodiversity.be/mailman/listinfo/bbclist (do use the password mentioned in the wellcome message). On the same site you can consult archived messages and interested friends of yours can subscribe. In case of problems you can send an Email to the moderator at ben(a)vub.ac.be. Enjoy biocomputing, Guy Bottu, Belgian EMBnet Node ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre Marc Colet - Guy Bottu 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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Januray 12: CINBIOS program
by Marianne Rooman 08 Jan '09

08 Jan '09

Dear all, Here is the final program (attached) of the CINBIOS meeting (centre de BioInformatique et BioModélisation, ULB), which will take place on Monday January 12 at the ULB. Everybody is wellcome ! All the best, Marianne Rooman -- --------------------------------------------------------- Marianne Rooman Unité de Bioinformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés Université Libre de Bruxelles 50 avenue Roosevelt, CP 165/61, 1050 Bruxelles, Belgium Tel : 32-2-650 2067 Email: mrooman(a)ulb.ac.be ---------------------------------------------------------

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BioSapiens European School of Bioinformatics in Brussels
by Jacques van Helden 07 Jan '09

07 Jan '09

The Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) from the Université Libre de Bruxelles is organizing the 9th Biosapiens European School of Bioinformatics The course will run from January 26th to 30th 2009, at ULB (Brussels , Belgium). The goal of the school is to initiate biologists to the utilization of bioinformatics software tools. The course will cover the following topics: Mon Jan 26 Analysis tools and databases for protein sequences Teacher: Jennifer McDowall (InterPro team, EBI, UK). Tools: UniProt, InterPro, InterProScan. Tue Jan 27 Browsing and comparing genomes with EnsEMBL Teacher: Giulietta Spudich (EnsEMBL team, EBI, UK). Topics: browsing genomes, comparing multiple genomes, variation, functional elements, ... Tools: EnsEMBL genome browser, BLASTZ, PECAN, ENREDO, ORTHEUS, tBLAT, BLAST, ... Wed Jan 28 Analysis of regulatory sequences Teachers: Morgane Thomas-Chollier, Jean-Valéry Turatsinze, Olivier Sand, Matthieu Defrance (BiGRe team, ULB, Belgium) Topics: Detection of cis-acting elements in genomic sequences. Discovering motifs from promoters of co-regulated genes. Tools: Regulatory Sequence Analysis Tools Thu Jan 29 Protein structures Teacher: Oliver Redfern (CATH group, University College London, UK) Topics: accessing and handling protein structures from databases. Modelling protein structures. Tools: CATH Biomolecular networks and pathways Teacher: Sylvain Brohée (BiGRe team, ULB, Belgium) Topics: bioinformatics approaches to analyze biomolecular networks (protein interactions, regulatory networks, metabolic pathways). Tools: Network Analysis Tools, CytoScape, STRING. Fri Jan 30 Systems biology Teachers: Florian Reisinger (EBI, UK), Hedi Peterson (Quretec, Estonia) Topics: the ENFIN data integration, workflow management. Network reconstruction using gene expression, network visualisation with expression data, network combining and mining. Tools: EnCORE, KEGGAnim, GraphWeb. More information and registration form are available from the Web site: http://www.bigre.ulb.ac.be/9esb/ Registrations are restricted to a maximum of 40 participants. The deadline for applications is January 15th 2009. Contact: Olivier Sand <oly(a)bigre.ulb.ac.be> Myriam Loubriat <mloubria(a)ulb.ac.be> Please spread this information around.

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Protein folds in infectious and neurodegenerative diseases
by Marianne Rooman 06 Jan '09

06 Jan '09

Here attached is the announcement of the conference: Protein folds in infectious and neurodegenerative diseases which will take place in Aussois (Savoie), France, from 25-29 April 2009 ------------------------------------------------------------------------- Marianne Rooman Unité de BioInformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés (3BIO) Université Libre de Bruxelles avenue Roosevelt 50, CP 165/61, 1050 Bruxelles, Belgium Tél: +32-2-650 2067 Email: mrooman(a)ulb.ac.be -------------------------------------------------------------------------

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January 12: CINBIOS
by Marianne Rooman 29 Dec '08

29 Dec '08

Dear all, Please have a look at the program (attached) of the CINBIOS meeting (centre de BioInformatique et BioModélisation, ULB), which will take place on Monday January 12 at the ULB. Everybody is wellcome ! All the best, Marianne Rooman ------------------------------------------------------------------------- Marianne Rooman Unité de BioInformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés (3BIO) Université Libre de Bruxelles avenue Roosevelt 50, CP 165/61, 1050 Bruxelles, Belgium Tél: +32-2-650 2067 Email: <mailto:mrooman@ulb.ac.be> mrooman(a)ulb.ac.be -------------------------------------------------------------------------

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BioSapiens School of Bioinformatics in Brussels
by Jacques van Helden 16 Dec '08

16 Dec '08

The Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) from the Université Libre de Bruxelles is organizing the 9th Biosapiens European School of Bioinformatics The course will run from January 26th to 30th 2009, at ULB (Brussels , Belgium). The goal of the school is to initiate biologists to the utilization of bioinformatics software tools. The course will cover the following topics: Biological databases Sequence analysis Protein structures Analysis of regulatory sequences Biomolecular networks and pathways Systems biology More information and registration form are available from the Web site: http://www.bigre.ulb.ac.be/9esb/ Registrations are restricted to a maximum of 40 participants. The deadline for applications is January 15th 2009. Contact: Olivier Sand <oly(a)bigre.ulb.ac.be> Myriam Loubriat <mloubria(a)ulb.ac.be> Please spread this information around.

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JOBIM 2009
by Jacques van Helden 10 Dec '08

10 Dec '08

--------------------------------------------------------------------------------------------- JOBIM - Journées Ouvertes en Biologie Informatique Mathématiques Nantes, du 9 juin au 11 juin 2009 --------------------------------------------------------------------------------------------- [english version below] La dixième édition de JOBIM se tiendra du 9 juin au 11 juin 2009 à Nantes, au Palais des Congrès. Toutes les informations sont disponibles à l'adresse http://www.jobim2009.fr Vous pouvez également contacter le comité d'organisation jobim09(a)univ-nantes.fr ---------------------------------------------------------------------------------------------- Appel à communication ---------------------------------------------------------------------------------------------- Les thèmes abordés par JOBIM couvrent le spectre de la bio-informatique dans ses multiples composantes. Cela comprend à la fois des aspects méthodologiques en amont (modélisation mathématique, informatique, statistique, physique) et des contributions applicatives allant jusqu'à l'établissement de nouveaux résultats en biologie. Sans être exhaustif, on peut citer les domaines suivants : * génomique, génomique comparative et métagénomique * réseaux biologiques * modélisation des systèmes dynamiques et biologie des systèmes * analyse de séquences, comparaison de génomes, et recherche de motifs * structures des macromolécules * protéomique et interactions * ARN non-codants * évolution et phylogénie * expression des gènes * haplotypes et polymorphismes (SNP) * ontologies, bases de données, intégration de données * algorithmique et statistiques appliquées à la bio-informatique * épigénétique, épigénomique * algorithmique pour le traitement de données de séquençage haut-débit * inférence de motifs, domaines, prédiction fonctionnelle Deux types de contribution sont possibles: résumé étendu (4 à 6 pages) ou poster (1 à 2 pages), en français ou en anglais. Les instructions sont disponibles sur le site de la conférence. Dates importantes : -------------------------------------- - date limite de soumission : 29 janvier 2009 - notification aux auteurs : 20 mars 2009 - conférence : 9-11 juin 2009 Journées Satellites ----------------------------------- Si vous souhaitez proposer une journée satellite, veuillez prendre contact avec les coordinateurs : - Dominique Tessier <tessier(a)nantes.inra.fr> - Jin Kao Hao <hao(a)info.univ-angers.fr> --------------------------------------------------------------------------------------------------- JOBIM - Open days in biology, computer sciences and mathematics --------------------------------------------------------------------------------------------------- The tenth JOBIM conference will be held in Nantes, from June 9th to 11th, 2009. JOBIM is the major annual event in bioinformatics in France. It brings together researchers working in this multidisciplinary field in an informal setting that encourages fruitful exchanges. More information is available at the website: http://www.jobim2009.fr For information, please contact jobim09(a)univ-nantes.fr ---------------------------------------------------------------------- Call for communication ---------------------------------------------------------------------- Topics of interest include, but are not limited to * Genomics, comparative genomics and metagenomics * Biological networks * Dynamic system modelling and systems biology * Sequence analysis, genome comparison, pattern matching * Molecular structures * Proteomics and macromolecular interactions * Non coding RNAs * Evolution, phylogeny * Gene expression * Haplotypes, polymorphisms * Ontology, knowledge representation, data bases * Algorithmics and statistics for bioinformatics * Epigenetics, epigenomics * Algorithmics for the processing of high throughput sequencing data * Motif inference, domains, function prediction You are invited to submit an extended abstract (from 4 to 6 pages) or a poster (1 or 2 pages). Formatting instructions are available at the conference website. The official languages of the conference are English and French. key dates ------------------------------ - submission deadline: January 29, 2009 - acceptance notification: March 20, 2009 - conference : June 9-11, 2009 Satellite meetings ----------------------------- If you wish to propose a satellite meeting, please contact the organizers : - Dominique Tessier <tessier(a)nantes.inra.fr> - Jin Kao Hao <hao(a)info.univ-angers.fr

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post-doc position: Bioinformatics for the melon project (Melonomics)
by Stephane Rombauts 05 Dec '08

05 Dec '08

---------- Forwarded message ---------- From: *Roderic Guigo Serra* <roderic.guigo(a)crg.cat> Date: Thu, Dec 4, 2008 at 5:46 PM Subject: melon /*Post Doctoral position BGG-1*/: Bioinformatics for the melon project (Melonomics) The BGG is part of the Melonomics project, a project sponsored by Genoma España to sequence the melon genome. Sequencing will be performed using a combination of the traditional BAC based approach, and the new sequencing technologies (454 and solexa). The main task of the candidate will be to use available tools, as well as to develop appropriate tools for genome assembly and gene annotation. The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for genome assembly and gene finding and annotation. The candidate should also be very skilled with scripting languages. A background in Plant Genomics is a plus. -- ******************************************************************************* 10 La Caixa-CRG fellowships available to carry our PhD studies in the CRG International PhD program Deadline for applications: January 18, 2009 Information and application forms available at http://pasteur.crg.es ******************************************************************************* (1) Centre de Regulacio Genomica (2) Grup de Recerca en Informatica Biomedica (IMIM and UPF) Dr. Aiguader, 88 +34 93 3160168 ph +34 93 3160110 ph secretary E-08003 Barcelona +34 93 3969983 fax email: roderic.guigo(a)crg.cat http://genome.imim.es -- ================================================================== Stephane Rombauts scientific staff Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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post-doc position: Bioinformatics for the melon project (Melonomics)
by Stephane Rombauts 05 Dec '08

05 Dec '08

---------- Forwarded message ---------- From: *Roderic Guigo Serra* <roderic.guigo(a)crg.cat> Date: Thu, Dec 4, 2008 at 5:46 PM Subject: melon /*Post Doctoral position BGG-1*/: Bioinformatics for the melon project (Melonomics) The BGG is part of the Melonomics project, a project sponsored by Genoma España to sequence the melon genome. Sequencing will be performed using a combination of the traditional BAC based approach, and the new sequencing technologies (454 and solexa). The main task of the candidate will be to use available tools, as well as to develop appropriate tools for genome assembly and gene annotation. The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for genome assembly and gene finding and annotation. The candidate should also be very skilled with scripting languages. A background in Plant Genomics is a plus. -- ******************************************************************************* 10 La Caixa-CRG fellowships available to carry our PhD studies in the CRG International PhD program Deadline for applications: January 18, 2009 Information and application forms available at http://pasteur.crg.es ******************************************************************************* (1) Centre de Regulacio Genomica (2) Grup de Recerca en Informatica Biomedica (IMIM and UPF) Dr. Aiguader, 88 +34 93 3160168 ph +34 93 3160110 ph secretary E-08003 Barcelona +34 93 3969983 fax email: roderic.guigo(a)crg.cat http://genome.imim.es -- ================================================================== Stephane Rombauts scientific staff Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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