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Fwd: EMBO Practical Course on Computational Molecular Evolution
by Wouter Van Gool 09 Dec '09

09 Dec '09

Computational Molecular Evolution 3-12 May 2010 Iraklio (Heraklion), Crete http://cwp.embo.org/pc10-25/ Deadline for applications: 31 January 2010 Course summary This EMBO Practical Course aims to provide researchers with the theoretical knowledge and practical skills required to carry out molecular evolutionary analysis on their own data and on data drawn from sequence databases. The course will combine basic assumptions and ideas fundamental to the field with discussion of cutting-edge methodologies, and is therefore relevant to researchers with a range of different experience levels. This course is essentially the same as that which ran successfully as a Wellcome Trust Advanced Course at the European Bioinformatics Institute, Hinxton, UK, in Spring 2009. Programme * interpretation of molecular phylogenetic trees and sequence alignments * genomics resources and sequence alignments * phylogeny reconstruction models * hypothesis testing in phylogenetics * coalescent model and inference from population data Course organisers * Nick Goldman (European Bioinformatics Institute, Hinxton, UK) * Ziheng Yang (University College London) * Aidan Budd (European Molecular Biology Laboratory, Heidelberg) * Alexandros Stamatakis (Technical University of Munich) * Giorgos Kotoulas (Institute of Marine Biology and Genetics, Hellenic Center for Marine Research, Heraklion) Guest instructors * Michail Averof (Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion) * Martin Embley (University of Newcastle) * Olivier Gascuel (LIRMM, Montpellier) * Javier Herrero (European Bioinformatics Institute, Hinxton, UK) * John Huelsenbeck (University of California, Berkeley) * Carolin Kosiol (Veterinary Medical University, Vienna) * Aoife McLysaght (Trinity College Dublin) * Rasmus Nielsen (University of California, Berkeley) * Bill Pearson (University of Virginia) * Antonis Rokas (Vanderbilt University) * Mikkel Schierup (Aahrus University, Denmark) * Jeff Thorne (North Carolina State University) * Ken Wolfe (Trinity College Dublin) For full details, see http://cwp.embo.org/pc10-25/ or http://tinyurl.com/cme2010 ----------------------------------------------------------------------- Nick Goldman tel: +44-(0)1223-492530 EMBL - European Bioinformatics Institute fax: +44-(0)1223-494468 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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Fwd: Inserm workshop: Interactomics, spring 2010
by Jacques van Helden 07 Dec '09

07 Dec '09

Begin forwarded message: Chers collègues, Vous trouverez ci-dessous l'annonce de notre atelier INSERM. N'hesitez pas à la diffuser autour de vous! Merci encore pour votre participation à l'atelier. Cordialement, Christine Brun - Jérôme Reboul - Nicolas Thierry-Mieg ------------------------------------------------------ Atelier de Formation Inserm 203 Interactomique: à l'intersection de la biologie et la bioinfomatique / Interactomics: at the crossroads of biology and bioinformatics Registration dealine: January 29, 2010 Info and registration forms: http://www.rh.inserm.fr/INSERM/IntraRH/RHPublication.nsf/mDisplayMotsClefsW… Phase I • Critical assessment March 30- April 1, 2010 • Saint-Raphaël • France Aims: Proteins rarely act alone: they often interact with other macromolecules in order to accomplish their functions. Protein-protein interactions are therefore critical to most biological processes. Systematic approaches for identifying them have been developped over the years, such as yeast two-hybrid or affinity purification-mass spectrometry. These methods have enabled the mapping of complex interaction networks in various model organisms, which are profoundly modifying our understanding of cellular mechanisms by providing us with an integrated view of biological processes. However, due to their complexity, such networks can be intimidating and difficult to take advantage of by hypothesis-driven experimental biologists. The main difficulties are typically methodological and technical (for example knowledge and application of bioinformatics tools), but also and more fundamentally they stem from the changes in reasoning required by the systems biology approach. Protein-protein interaction networks being a very rich but neglected source of information, the workshop will present the main strengths and challenges in producing and using this data. Indeed, a better understanding of the processes, questions and solutions proposed by labs that produce and analyze interactomics data should facilitate its general use. Audience: Researchers, physicians, post-docs, technicians, engineers and students interested in the interactome approach and the analysis of existing protein-protein interaction data, in order to benefit to their own research projects. The topics addressed will include 1) identifying protein-protein interactions: high-throughput methods, validation of results, quality assessment; 2) protein-protein interaction databases: contents, standards, direct submissions; 3) topological and functional analysis of protein-protein interaction networks: methods and tools; 4) application to biological questions: candidate genes, signaling, host-pathogen interactions, development, evolution. Confirmed speakers: Javier De Las Rivas (Salamanca, Spain), Etienne Formstecher (Paris, France), Anne-Claude Gavin (Heidelberg, Germany), Kristin Gunsalus (New York, USA), Henning Hermjakob (Hinxton, UK), Carl Herrmann (Marseille, France), Vincent Lotteau (Lyon, France), Fabio Piano (New York, USA), Evelyne Goillot (Lyon, France), Jolanta Polanowska (Marseille, France), Sylvie Ricard-Blum (Lyon, France), Benno Schwikowski (Paris, France), Jacques van Helden (Bruxelles, Belgium), Marc Vidal (Boston, USA). Phase II • Technical workshop May 2010 • Marseille Program: Participants will learn to use existing tools for extracting functional information from publicly available molecular interaction data. The course is aimed at two subgroups of participants, depending on their computer skills. The goal is to enable the participants to study their own results in the light of previously known biomolecular interactions. 15 participants will be selected among the phase I participants. Organizers: Christine Brun (TAGC, Marseille), Jérôme Reboul (CRCM, Marseille), Nicolas Thierry-Mieg (TIMC-IMAG, Grenoble)

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CfP: Special issue of Trans Comp Sys Biol on "Computational models for cell processes"
by Ion Petre 04 Dec '09

04 Dec '09

Call for papers: Transactions on Computational Systems Biology, special issue on Computational models for cell processes. Submission deadline: March 31, 2010 http://combio.abo.fi/special_issue_10.php Guest editors: - Ralph Johan Back (Åbo Akademi University, Finland) - Ion Petre (Åbo Akademi University, Finland) - Corrado Priami (Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Italy) - Erik de Vink (Eindhoven University of Technology, the Netherlands) LNBI Transactions on Computational Systems Biology calls for paper submissions for a special issue on Computational Models for Cell Processes. Original papers and surveys are sought in all areas that relate to the relevance and potential of formal methods and computational modeling and simulation in systems biology. Of special interest are contributions that present biological processes requiring special tools and techniques that have not been investigated so far in the context of formal methods, as well as extensions of already existing formalisms introduced to improve their applicability in the life sciences. Topics of interest include, but are not limited to: Formal models for cellular pathways Qualitative biological modeling Quantitative formal methods Theoretical comparison of formalisms for biological processes Biologically-inspired extensions to formal methods and concurrency theory Differential, discrete and/or stochastic modeling languages Reconstruction of biological networks based on empirical data Decomposition and modularization of large biological networks Applications of formal methods and computational modeling Membrane systems as a modeling platform The list of topics is suggestive rather than exhaustive. We are open to a wide range of approaches from theoretical methodological papers to case studies. Papers should be submitted to ipetre(a)abo.fi in the LNCS format (see link below). Manuscripts submitted to this special issue should have at most 25 pages, including figures, tables, and the list of references. For queries about this special issue, please feel free to contact the special issue guest editors, Ralph-Johan Back (backrj(a)abo.fi) Ion Petre (ipetre(a)abo.fi) Corrado Priami (priami(a)cosbi.eu) and Erik de Vink(evink(a)win.tue.nl). Important dates: - Paper submissions: March 31, 2010 - Acceptance notification: June 30, 2010 - Final papers: August 31, 2010 Submission guidelines: - http://www.springer.com/computer/lncs - http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0

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PhD Fellowships in Computational Biology and Scientific Computing
by Leonor Palmeira 03 Dec '09

03 Dec '09

>> from Hannes Luz @ Max Planck, Berlin: Dear colleague, the International Max Planck Research School for Computational Biology and Scientific Computing, a joint graduate program of the Freie Universitaet Berlin and the Max Planck Institute for Molecular Genetics, Berlin, invites applications for a PhD program. The PhD program is open for international students holding a Master (or equivalent) degree in bioinformatics, computer science, physics, mathematics, or biology. The closing date for applications is February 21, 2010. We would be grateful if you could communicate the announcement to interested students. A poster can be downloaded from http://www.imprs-cbsc.mpg.de/download/poster2010.pdf For further details and the application procedure, please visit http://www.imprs-cbsc.mpg.de Thanks for your efforts, the IMPRS-CBSC team ----------------------------------------------------------------------- International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) Contact: Hannes Luz Max Planck Institute for Molecular Genetics | Tel: +49 30 8413-1154 Computational Molecular Biology | Fax: +49 30 8413-1152 Ihnestrasse 73 | Email:luz@molgen.mpg.de D-14195 Berlin, Germany | www.imprs-cbsc.mpg.de -----------------------------------------------------------------------

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EMBL Practical Bioinformatics Course Protein Sequence Analysis
by Wouter Van Gool 30 Nov '09

30 Nov '09

Hi All, I'd like to draw your attention to some nice bioinformatics course about protein sequence analysis organized at the EMBL, this next January. You can find more information and register online at: http://www.embl.de/training/courses_conferences/course/2010/EMP10-01/ Or read below for a short course summary. Best Regards, Wouter Van Gool EMPA2010 - Protein Sequence Analysis Practical Bioinformatics Course EMBL-Heidelberg Tuesday 19th - Friday 22nd January 2010 This 3.5 day practical bioinformatics course, aimed at wet-lab biologists with only limited experience, will focus on protein sequence analysis, and analysis/prediction of protein modular architecture. www.embl.de/courses/empa2010 The deadline for applications is Friday 4 December 2009, and there is an application fee of 250 euros (which also covers meals and accommodation). The course is aimed at wet-lab biologists who are looking to exploit bioinformatic tools in their work - setting the scene by introducing the biological concepts behind protein architecture modules and providing extensive hands-on application of the relevant bioinformatics tools with appropriate example proteins. The power - but also the limitations, which remain substantial - of the currently available software will be examined. People should feel free to get in touch with Aidan (budd(a)embl.de) if they've any questions about the course.

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(no subject)
by Bogaert, D. 27 Nov '09

27 Nov '09

Dear Madam/Dear Sir, Would you please be so kind to inform all your list members about this vacancy (see text below) at the University Medical Centre (UMC) Utrecht Kind regards, Debby Bogaert Vacancy: Postdoc Bio-informatics We are a microbiology and infectious diseases group in The Netherlands, investigating microbial flora in health and disease in relation to prevention of bacterial infections. We are looking for a postdoctoral fellow bioinformatics/-statistics who will help us to analyze complex metagenomic data in relation to epidemiological parameters. Besides the complex problem of interpreting phylogenetic data of microbiota, we find there are currently no generally accepted statistical methods available to analyze complex communities in relation to epidemiological determinants, especially not in multivariate ways. Our final goal is to model complex microbiota with the help of environmental and individual characteristics, with the ultimate goal to predict when disease will develop and to design preventive strategies. We are looking for someone with experience in the field of metagenomics, bio-informatics, or adjacent fields, who does not dislike statistics and epidemiology, is not afraid of developing new tools, is creative, efficient, independent, and likes to work in a multi-disciplinary team. The position is guaranteed for at least 3 years. The salary is depending on previous experience and according to the CAO for university medical centres (CAO-UMC: salary scale 10). If you are interested, please contact: Debby Bogaert d.bogaert(a)umcutrecht.nl <mailto:d.bogaert@umcutrecht.nl> . Tel. +31-88-7551754 D. Bogaert, MD, PhD UMC Utrecht-WKZ Department of Pediatric Immunology Lundlaan 6 (room KC.03.068.0) 3584 EA Utrecht, The Netherlands Phone: +31-88-7551754 E-mail: dbogaert(a)umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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NBIC PhD Course Algorithms for Biological Networks open for registration
by Celia van Gelder 23 Nov '09

23 Nov '09

Dear researcher, The third course of the NBIC PhD School is now open for registration: PhD-Course: Algorithms for Biological Networks Date: 11-15 January 2010 Location: Delft, the Netherlands Course Credits: 3 EC Course Coordinator: Dick de Ridder, TUD, Delft *Short course description* In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behavior will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed. Finally, we will give some examples of applications of graph mining algorithms (dense subgraph extraction, small recurring subgraph enumeration, graph alignment) to learn about biology. More information about the course can be found on the course website: http://inpc55.et.tudelft.nl/nbic/abn/ *Registration* You can register via the registration form on http://www.nbic.nl/education/nbic-phd-school/enrolment/. Please note: the course is free for PhD students working in a BioRange (including matching) or BioAssist project. Others can participate as well when paying a course fee (see Enrolment page). This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl> -> Education -> NBIC PhD School). Best regards, Celia van Gelder Netherlands Bioinformatics Centre (NBIC) Dr. Celia van Gelder Projectleader Education NBIC +31 (0)24 3666120 (direct) +31 (0)24 36 19500 (office) -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Fwd: CNIO International PhD and Postdoctoral Programmes_2010 call
by Jacques van Helden 16 Nov '09

16 Nov '09

Begin forwarded message: From: "Training Cnio" <training(a)cnio.es> Date: 16 November 2009 16:42:09 CET To: <Jacques.Van.Helden(a)ulb.ac.be> Subject: CNIO International PhD and Postdoctoral Programmes_2010 call Dear Dr. VAN HELDEN , I would like to draw your attention to the 2010 calls for the International PhD and Postdoctoral Programmes at the Spanish National Cancer Research Centre (CNIO). We would greatly appreciate if you could forward the information about these exciting programmes to potential candidates. The CNIO offers excellent training and research opportunities in cutting edge basic and applied cancer research. The programmes are open to outstanding young graduates from all over the world who want to pursue ambitious research projects. The CNIO International Postdoctoral Programme offers up to 6 very competitively funded two-year postdoc positions to outstanding junior scientists. Applications are considered at regular intervals, this call closes on December 31st, 2009. The CNIO International PhD Programme each year supports 10 candidates for a 4-year PhD. We have one selection per year. The deadline for applications is March 15th, 2010. Our webpage provides further information on both programmes and the application procedure: - Postdoc Programme: www.cnio.es/postdoc To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/postdoctorado/Poster_postdoc_2009.pdf - PhD Programme: www.cnio.es/phd To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/doctorado/Poster_PhD_2010.pdf Please feel free to distribute this message on your local institute network and thank you very much in advance for advertising our programmes in your institution. Best regards, Mar Pérez, PhD Training Manager Fax: +34 912246980 E-mail: phd(a)cnio.es or postdoc(a)cnio.es Website: www.cnio.es/phd and www.cnio.es/postdoc In compliance with the Spanish Law on Personal Data Protection (“Ley Organica” 15/1999 of December 13), we inform you that your data, collected from databases and sources of public access, has been incorporated into an automated confidential file, duly registered with the Spanish Agency for Data Protection and owned by the Spanish National Cancer Research Centre (CNIO), for the communication of professional training activities, future events and of publications. You may exert your rights to oppose such treatment, as well as your rights to access, cancel or amend as acknowledged by the mentioned law on matters of protection of data of a personal nature by sending a request to the following address: unsubscribe(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Dataflows in het Labo - Studiedag KVCV Sectie Analytische Chemie 08/12/2009
by Tony Houthaeve 13 Nov '09

13 Nov '09

Beste, Op dinsdag 8 december 2009 plant de Sectie Analytische Chemie van KVCV (www.kvcv.be) een studiedag met als thema ‘Dataflows in het labo’. Hoofddoel van de studiedag is problemen & oplossingen én de nieuwste trends rond alle mogelijke dataflows in het laboratorium aan te kaarten en te bespreken aan de hand van cases uit de praktijk en de recente producten van de leveranciers ter zake. Items als: upgraden LIMS & CDS, globale versus lokale oplossingen, interfacing van apparatuur, ELN & PDA & RFID, evolutie van de markt, kosten, auditeren van datasystemen, etc… wensen we tijdens deze dag aan bod te laten komen. De dag bestaat uit een combinatie van: - Plenaire voordrachten; waarin algemene thema’s worden gebracht alsook een aantal cases van gebruikers uit de praktijk. - Twee parallelle breakout-sessies; één specifiek rond LIMS en één rond de interfacing van alle apparatuur & datastromen. Daarnaast bieden wij leveranciers de mogelijkheid om hun producten voor te stellen (voordrachten, exhibitie, demo's). Alle info en het programma staat op http://analytische.kvcv.be/agenda.html Graag uw medewerking voor deelname en verspreiding aan de collega's binnen de labowereld, bv VIB voor wie dit een meerwaarde kan betekenen (bv BITS commitee, ...). Alvast bedankt & Met vriendelijke groeten, Mit freundliche Grüsse, Sincerely yours, Hi, On Tuesday 08 December 2009, the section Analytical Chemistry of the KVCV organizes, for the Benelux, a Symposium 'Dataflows in the lab' in Grobbendonk. Presentations feature: - Labsoftware (LIMS, ELN, CDS), PDA, RFID & barcode scanning, interfacing lab equipment, lab-KPI, evolutions & trends of dataflows in the labmarket, ... - cases & experiences brought by end-users & vendors With the collaboration of : Starlims, Thermo Fisher Scientific, LabVantage Solutions, Siemens, LabWare, Waters, Agilent Technologies, DatAction, LabFactor, Raak Lab Informatics, Dionex, Labwing, Atos Origin, IS-X, Agfa, VMW, FAVV, ... See for more information: http://analytische.kvcv.be/agenda.html for more information & http://events.linkedin.com/Dataflows-het-labo/pub/128457 We hope to meet you there. If not applicable, please do pass on this information to a colleague. Met vriendelijke groeten, Mit freundliche Grüsse, Sincerely yours, Dr. Ing. Tony Houthaeve BASF Antwerpen lid bestuur Sectie Analytische Chemie KVCV Ijsvogelstraat 80-82 B-2170 Merksem tel: (32)-3-290.82.44 Tony.Houthaeve(a)telenet.be http://www.linkedin.com/in/tonyhouthaeve

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BBC 2009 - Call for posters and participation
by Pierre Geurts 12 Nov '09

12 Nov '09

************** Call for Posters and Participation *************** Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium ******************************************************************* http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 CALL FOR POSTERS Abstract submission for oral presentation is now closed but participants are still cordially invited to submit an abstract for poster presentation before November 23. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. CONFIRMED INVITED SPEAKERS Thomas Sauter Life Sciences Research Unit, Université du Luxembourg "Modeling and Analysis of Metabolic and Signaling Networks using Bottom-Up Approaches" M. Madan Babu MRC Laboratory of Molecular Biology, University of Cambridge "Intrinsically Unstructured Proteins: Regulation and Disease" Pierre Rouzé BioInformatics & Systems Biology, VIB Department of Plant Systems Biology, Ghent, Belgium "From protists to plants, fungi and animals : eukaryote genomes are not born equal" REGISTRATION Registration is now open: http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/registration.php The deadline for early registration is November 23. SPONSORS The conference is sponsored by the Netherlands Bioinformatics Center (NBIC), the Alma in Silico project (Interreg IV Program), PEPITe, Sciforma and KeyGene. It is organized within the framework of the Belgian Network BIOMAGNET (Bioinformatics and Modeling: from Genomes to Networks), funded by the Interuniversity Attraction Poles Programme, initiated by the Belgian State, Science Policy Office.

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