- BBClist - maillist.psb.ugent.be

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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Speed dating at the Bioinformatics Event in Maastricht
by Andra Waagmeester 04 Dec '08

04 Dec '08

On behalf of Miranda stobbe of the RSG the netherlands: Dear PhD student, Have you already registered for the special bioinformatics event on Sunday 14th of December? Registration is still possible. The RSG Netherlands is organizing a social event specially for PhD Students who have registered for this program. Please see the flyer attached for more details. See you there, Jayne Hehir Chair of RSG Netherlands, the network of PhD-students in bioinformatics

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Position for a Scientific Programmer at NMC
by marijana radonjic 01 Dec '08

01 Dec '08

Vacancy ** *Scientific Programmer* * **Description * The scientific programmer will be part of a team of five programmers located at various institutes in the Netherlands, constructing a metabolomics data warehouse infrastructure and related applications, within the Netherlands Metabolomics Centre (NMC, http://www.metabolomicscentre.nl/) Within this team, the specific tasks of the scientific programmer are to adapt and expand bioinformatics tools for biological interpretation of nutritional and biomedical metabolomics data. These tools allow to link the metabolomics data, directly from the data warehouse, to intracellular and intra-organ activities, pathways and processes. This will provide a generic bioinformatics evaluation and visualization tool to be used in the area of life style associated diseases such as obesity, atherosclerosis and diabetes type II. It will help in the early diagnosis of disease and developing disease prevention strategies. All data warehouse and applications will be made exportable to controlled vocabularies and ontologies, to make easy exchange of data possible. The programmer will assist in providing web interfaces for the metabolomics database and web-enabling of applications. The data warehouse should be constructed in such a way that overview over the study design, the type of analysis used and the toolbox used for biological interpretation can be queried at once. *Background* The Netherlands Metabolomics Centre is a multicenter research program in which biologists, analytical chemists, database builders and statisticians work together. Therefore excellent networking capacities will be essential for this project. Metabolomics technologies measure a multitude of small chemical molecules in a sample, to get an accurate picture of the physiology of a cell, organ or system (such as human). The research projects within the NMC are mainly focused on human health care, nutrition and plant sciences. The scientific programmer will be appointed at the University of Leiden but work in the Physiological Genomics team of the Biosciences Busniness Unit of TNO, located in Zeist. Physiological Genomics is responsible for the biological and physiological interpretation of "omics" data in (human) health research. At the moment our team exists of 12 (young) researchers. *Requirements* - Experience with HTML, PHP, MySQL, Java and Javascript. - Master in (bio)informatics, ICT / automation or related background with a strong affinity for life sciences, - Knowledge of ontologies and pathway visualization will be of advantage. - Team worker, self-reliant, flexible, and innovative. * *Additional Information: Dr. B. van Ommen, tel : 030 6944438, e-mail: ben.vanommen(a)tno.nl

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Position for a Bioinformatician at GSK
by Jacques van Helden 25 Nov '08

25 Nov '08

Begin forwarded message: From: jean-louis.ruelle(a)gskbio.com Date: 25 novembre 2008 16:16:27 GMT+01:00 Subject: Recrutement bioinfo Job Purpose ========== Within the Bioinformatics group in R&D, the bioinformaticians provide support and creative output in the DNA and protein sequence/structure aspects of vaccine design in all research projects. Bioinformatics has also taken the responsibility of statistical analysis of huge data sets coming from microarray experiments performed in various vaccine projects, in particular a novel class of oncology compounds, the therapeutic cancer vaccines. Activities in the latter field have substantially increased recently, and we are looking for an additional skilled person. You will join the vaccine headquarters located in Rixensart, Belgium, where 5 bioinformaticians are devoted to the bioinformatics support to the discovery and development of vaccines. Responsibilities ============ The job involves performing statistical data analysis of microarray experiments, in collaboration with molecular biology. This includes: - Development of prognostic and predictive classifiers in cancer using gene expression microarray data - Use of external datasets to validate and evaluate classifier performance - Collaborate with molecular biology group to facilitate the migration of diagnostic, prognostic and predictive marker-basedprojects from discovery to development and manufacturing, as regulatory approved commercial products - Interact with molecular biology group to establish and apply quality control pipeline to gene expression microarray data - Technology watch and development of new bioinformatic tools for cancer tumor classification and data processing - Share expertise and know-how - Support molecular biology and CIP with sequence analysis and annotation of biomarkers using genome databases - Maintaining and promoting contacts with external colleaguesand academic research. - Reporting on progress and results to the research project teams. Profile ===== - You have a Ph-D in Life Sciences or Computer Sciences or equivalent. - Proficiency in bioinformatics and statistics with good knowledge of sample classification methods using high dimensional data (background in machine learning is desirable) - Familiarity with pre-processing of gene expression microarray data (QC, normalization, etc ) - Knowledge in R programming is highly desirable - Knowledge of sequence analysis and annotation retrieval from genome databases will be advantageous - You are willing to learn everyday, you are open, creative, you can work autonomously. - You have excellent communication and organizational skills. - You have an good knowledge of English (oral and written). Contact and information: =================== Jean-Louis Ruelle <jean-louis.ruelle(a)gskbio.com>

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Vacancy project member at Netherlands Institute for Systems Biology and Centrum Wiskunde & Informatica
by Roeland Merks 24 Nov '08

24 Nov '08

The Netherlands Institute for Systems Biology (NISB) and Centrum voor Wiskunde & Informatica (CWI) invite applications for the position of a Project member (four years) Job description The project member will join a team of motivated postdocs and PhD students who study biological systems using quantitative and predictive models and multiscale computer simulations. Topics include blood vessel growth, plant development, genetic regulatory networks and metabolic networks in a multicellular context. He/she will develop innovative research codes in collaboration with the postdocs and PhD students, and turn new and existing research codes into more widely applicable, well-documented, and user-friendly modeling tools Hours on a weekly basis: 38 Location The work will be embedded in the Biomodeling and Biosystems Analysis group of the Netherlands Institute for Systems Biology (NISB; www.sysbio.nl ) and within the Life Sciences group of the Center for Mathematics and Computer Science (CWI) in Amsterdam. As the “core modeling group” of the Netherlands Consortium for Systems Biology, the Biomodeling and Biosystems Analysis group develops quantitative and predictive models and multiscale computer simulations in collaboration with systems biology groups at participating institutes. Competences Candidates ideally fulfill the following criteria: - A strong scientific background, e.g. an M.Sc. or Ph.D in computer science, mathematics, theoretical biology or physics, or equivalent experience - Able to communicate with scientists in biology and mathematics - Excellent programming skills in C++ or equivalent; experience with object-oriented design - Experience with scientific simulation and GUI-design is a pre Offer The vacancy concerns a temporary position for four years. Salary and terms of employment are in accordance with the "CAO- onderzoekinstellingen" and based on qualifications. Besides the salary and excellent working conditions, CWI offers attractive and flexible terms of employment, like a collective health insurance, pension-fund, and initial help with housing for foreigners. The position is for 38 hrs/week. Information Direct requests for information or applications before 15 December 2008 to: Dr. Roeland Merks, Roeland.Merks(a)sysbio.nl phone +31 20 592 4117 Center for Mathematics and Computer Science (CWI) and Netherlands Institute for Systems Biology (NISB) Kruislaan 413, 1098SJ Amsterdam, The Netherlands Also see: http://www.sysbio.nl and http://www.cwi.nl.

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Announcement Bioinformatics Event in Maastricht (14-12-2008)
by Andra Waagmeester 18 Nov '08

18 Nov '08

*The relevance of human genomics and bioinformatics for health sciences and the economical development of the BeNeLux and Euregio. * Genomics and bioinformatics event in the Bonnefanten museum in Maastricht on December 14. As a prelude to the annual Benelux Bioinformatics Conference which will be held in Maastricht on December 15 and 16, the Department of Bioinformatics from Maastricht University will organize an open genomics and bioinformatics event in the Bonnefanten Museum on December 14. During this evening the role of genomics and bioinformatics in health research and in the economic developments within the Benelux and the Euregio will be addressed. Bioinformatics is an emerging research field which forms the link between computer science, biomedical sciences and modern genomics research technology. We expect that this evening will not only lead to vivid discussions but will also serve as a meeting moment between conference participants, health scientist from the region and people involved in local economic developments. *Program December 14th* 17:00 Coffee/tea with cake at the aula of the Bonnefanten museum. 17:30 Opening by Dr. Chris Evelo, head of the department of Bioinformatics, Maastricht University, the Netherlands. 17:35 Welcome and introduction on behalf of Maastricht University, speaker to be announced. 17:45 Welcome by Marc Croijmans, delegate of the Maastricht municipal discussing the position of Life-Sciences in Maastricht and the Euregio. 18:00 Presentation given by Dr. Colja Laane, head of the Netherlands Genomics Initiative (NGI) and science director at DSM. 19:00 Discussion related to the theme of the presentation 19:45-22:00 Drinks and tapas at the conference location For more information about the program and venue location see http://www.nbic.nl/bbc2008/SundayEveningEvent/. To register please send an email to bbc2008(a)bigcat.unimaas.nl. I hope to welcome you at the Bonnefanten Museum in Maastricht on December 14th. Dr. Chris Evelo (Head of the department of Bioinformatics) Bioinformatics-BiGCaT The event is sponsored by:. Maastricht University the Maastricht municipality P.O. Box 616 6200 MD Maastricht Main Sponsors for the Benelux Bioinformatics the Netherlands. Conference as a whole are: T: +31(0)43-3881231 Universiteits fonds Limburg (SWOL), Netherlands E: chris.evelo(a)bigcat.unimaas.nl Bioinformatics Center (NBIC), KNAW, NWOW: www.bigcat.unimaas.nl

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