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Call for papers: Machine Learning in Systems Biology, Slovenia, 5-6 September
by Pierre Geurts 24 Apr '09

24 Apr '09

[apologies for multiple postings] ************************** Call for Papers ********************************* MLSB 09 Third International Workshop on Machine Learning in Systems Biology 5-6 September 2009, Ljubljana, Slovenia ****************************************************************************** http://mlsb09.ijs.si/ MOTIVATION Molecular biology and 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, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a 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 in the biomedical sciences in general. 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 systems biology (i.e., 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. LOCATION AND CO-LOCATION The workshop will take place 5-6 September 2009 at the Jozef Stefan Institute, Ljubljana, Slovenia. It will immediately precede ECML PKDD 2009, taking place 7-11 September 2009 in Bled, Slovenia (Bled is 30 miles from Ljubljana, transport will be organized). SUBMISSIONS INSTRUCTIONS For an oral presentation, please submit an extended abstract of maximum eight pages. Formatting instructions are available on the website of the workshop. Extended abstracts should be submitted online by 1 June 2009 via the Easychair submission system at http://www.easychair.org/conferences/?conf=mlsb09. The accepted submissions will be collected in the proceedings of the workshop. KEY DATES 01 June: deadline for submission of extended abstracts for oral presentation 03 July: notification for oral presentations 03 August: deadline for submission of abstracts for poster presentations 10 August: notification for posters & camera ready versions due 5-6 September: workshop TOPICS A non-exhaustive list of topics suitable for this workshop is given below: 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 Semi-supervised learning 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 function and structure prediction Protein-protein interaction networks Synthetic biology CONFIRMED INVITED SPEAKERS Ross D. King, Aberystwyth University, UK William Stafford Noble, University of Washington, USA MLSB09 PROGRAM CHAIRS Sašo Džeroski, Jozef Stefan Institute, Ljubljana, Slovenia Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium Juho Rousu, Department of Computer Science, University of Helsinki, Finland SCIENTIFIC PROGRAM COMMITTEE Florence d'Alché-Buc, University of Evry, France Saso Dzeroski, Jozef Stefan Institute, Slovenia Paolo Frasconi, Università degli Studi di Firenze, Italy Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy Pierre Geurts, University of Liège, Belgium Mark Girolami, University of Glasgow, UK Dirk Husmeier, Biomathematics & Statistics Scotland, UK Samuel Kaski, Helsinki University of Technology, Finland Ross D. King, Aberystwyth University, UK Neil Lawrence, University of Manchester, UK Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands Yves Moreau, Katholieke Universiteit Leuven, Belgium William Stafford Noble, University of Washington, USA Gunnar Rätsch, FML, Max Planck Society, Tübingen Juho Rousu, University of Helsinki, Finland Céline Rouveirol, University of Paris XIII, France Yvan Saeys, University of Gent, Belgium Guido Sanguinetti, University of Sheffield, UK Ljupco Todorovski, University of Ljubljana, Slovenia Koji Tsuda, Max Planck Institute, Tuebingen Jean-Philippe Vert, Ecole des Mines, France Louis Wehenkel, University of Liège, Belgium Jean-Daniel Zucker, University of Paris XIII, France Blaz Zupan, University of Ljubljana, Slovenia LOCAL ORGANIZATION Ivica Slavkov, Dragi Kocev, Tina Anžič, Jozef Stefan Institute, Ljubljana, Slovenia

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Call for participation: Workshop on Feature Selection in Bioinformatics
by Pierre Geurts 22 Apr '09

22 Apr '09

[apologies for multiple postings] ************** Call for Participation ******************** FSBIO 09 Feature Selection in Bioinformatics Workshop May 25th, 2009 Ghent, Belgium http://www.psb.ugent.be/~yvsae/fsbio09/ ********************************************************* MOTIVATION Feature or variable selection is an important topic in Bioinformatics, Systems Biology, and related fields. Important advantages of feature selection in these fields include the ability to create better and more compact models, as well as gaining a better insight into the processes described by the data. This workshop focuses on recent challenges for feature selection in Bioinformatics, such as the design of feature selection algorithms that scale well to high-dimensional spaces, can deal with small sample sizes, design robust feature sets and are able to support interactions or dependencies between variables. PROGRAM 09.50h Welcome 10.00h Badih Ghattas, Institut de Mathématiques de Luminy, Marseille, France Comparing different strategies for variable selection in large dimensions 11.00h Carolin Strobl, Institut für Statistik, Ludwig-Maximilians- Universität München, Germany Unbiased measures of variable importance for random forests 12.00h Alexandros Kalousis, Department of Computer Science, University of Geneva, Switzerland Stability of Feature Selection Algorithms LOCATION Department of Plant Systems Biology Ghent University Technologiepark 927 B-9052 Gent (Zwijnaarde) Belgium REGISTRATION Registration to the workshop is free of charge. In order to register, send a mail with your name and contact details to yvan.saeys(a)psb.ugent.be ORGANIZATION Yvan Saeys, Bioinformatics and Evolutionary Genomics group, Ghent University, Belgium Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium

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NBIC PhD-Course: Managing life science information
by Celia van Gelder 17 Apr '09

17 Apr '09

*NBIC PhD-Course: Managing life science information* Date: 25-29 May 2009 Location: Science Park, Amsterdam, the Netherlands Course Coordinator: Marco Roos, UvA. This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. Students will gain insight into Semantic Web languages and tools, XML and XQuery, data integration, data warehouses, federated databases, (Taverna) workflows, and Web2.0. More information about the course can be found on the NBIC-website: http://www.nbic.nl/biowise/school/EduProg/InfoMan09/ . Please note: the course is free for PhD students working in a BioRange project. Others can participate as well when paying a course fee (see course information on website). 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: http://www.nbic.nl/biowise/school/ . Best regards, Celia van Gelder Projectleader Education NBIC ------------ 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, celia.van.gelder(a)nbic.nl websites: www.cmbi.ru.nl, www.nbic.nl NBIC Office Phone: +31 (0)24 36 19500 E-mail: office(a)nbic.nl Netherlands Bioinformatics Centre 260 NBIC P.O. Box 9101 6500 HB Nijmegen Fax: +31 (0)24 36 19395

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Business Personality of the Year 2009 !
by benjdami＠bioxpr.be 09 Apr '09

09 Apr '09

Good day, Here is an unusual request on this mailing-list. My name in Benjamin Damien, manager of BioXpr (bioinformatics service company in Belgium) and one of the 10 finalists of the "business personality of the year" contest. This final step is the results of several rounds of selection and trials. For the last trial, I need to gather as much votes as possible on the website : http://www.bpy2009.be This kind of prize is usually given to more "casual" businesses (marketing, sales, fashion,...) and it would be great to see biotech (and bioinformatics) win that kind of contest for once. Moreover, the "winner" will be able to communicate in the media regularly in the next 12 months (tv and newspapers), and I plan to use this platform to promote entrepreneurship and the scientific/technical careers (biotech first of all, of course). So I need your help to win this trial (I'm in second position, and the votes are closing on sunday 12/04), and to vote on http://www.bpy2009.be Thanks for your help in advance, and best regards, Benjamin

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[Biomath-ned] Positions in biological modeling and simulation
by Roeland Merks 08 Apr '09

08 Apr '09

Positions in biological modeling and simulation in Amsterdam, The Netherlands Within the Netherlands Consortium for Systems Biology (NCSB), biologists, computer scientists, physicists and mathematicians of Dutch universities and research institutes have joint forces to develop innovative systems biology approaches for tackling challenging, multi-factorial biological problems related to human health, plant sciences, and white biotechnology. Computer modeling and simulation are central to this highly multidisciplinary effort. NCSB’s core modeling group Biomodeling and Biosystems Analysis at CWI, the Dutch national research institute for mathematics and computer science, develops innovative simulation approaches and coordinates modeling projects at the participating institutes. The Biomodeling and Biosystems Analysis group invites applications for the following positions: Postdoctoral researcher Modeling dynamics and evolution of hierarchically regulated, eukaryotic gene networks See: http://www.cwi.nl/en/node/1044 PhD student Cell-based modeling of blood vessel formation See http://www.cwi.nl/en/node/1045 Scientific programmer / PhD student Bringing modeling and simulation to the biologist’s lab bench See http://www.cwi.nl/en/node/1043 Requirements for all positions: - A scientific background in simulation and modeling: a degree in theoretical biology or computational physics, computational science, or equivalent experience - Able to communicate with scientists in biology and mathematics - Good programming skills in C++ or equivalent - Minimum academic degree: for postdoc, PhD; for PhD, M.Sc.; for programmer, B.Sc. Information For full description of these positions, see http://www.cwi.nl/en/ jobs. For more information about CWI, NISB, NCSB and the Biomodeling and Biosystems Analysis group, visit http://www.cwi.nl, http://www.sysbio.nl , and http://www.cwi.nl/~merks. Contact: Roeland Merks, CWI, Roeland.Merks(a)sysbio.nl, Tel. +31-20-5624117 Application deadline is May 1st, 2009. ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M136 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199 _______________________________________________ Biomath-ned mailing list Biomath-ned(a)few.vu.nl http://mailman.few.vu.nl/mailman/listinfo/biomath-ned

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2009 GMOD Summer School - Europe
by Dave Clements 30 Mar '09

30 Mar '09

Hello, This is a reminder that the application deadline for the 2009 GMOD Summer School - Europe is 6 April, one week from now. The 2009 GMOD Summer School - Europe (http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe) will be held 3-6 August, 2009 at the University of Oxford, as a part of GMOD Europe 2009 (http://gmod.org/wiki/GMOD_Europe_2009) Tuition is £95. GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological data. It is also a community of developers and users dealing with similar challenges. The course offers hands-on training on how to deploy and administer: * Genome / Comparative Genomics Viewers - GBrowse, JBrowse, GBrowse_syn, Apollo * Genome Annotation - Apollo, Artemis-Chado Integration * Databases - Chado, BioMart Please contact the GMOD Help Desk (help(a)gmod.org) if you have questions. Thanks, Dave Clements GMOD Help Desk On Mon, Mar 16, 2009 at 1:48 PM, Dave Clements <clements(a)nescent.org> wrote: > We are now accepting applications for the 2009 GMOD Summer Schools: > > Americas, 16-19 July > - National Evolutionary Synthesis Center (NESCent), Durham, NC, USA > - Student tuition is free, thanks to NIH grant 1R01HG004483-01. > - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > > Europe, 3-6 August > - University of Oxford, Oxford, United Kingdom > - Part of GMOD Europe 2009, which includes the next GMOD Meeting > - Student tuition is £95 > - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > > GMOD (http://gmod.org/) is a collection of interoperable open source > software components for managing, visualizing, annotating and > integrating biological, mostly genomic, data. GMOD is also a > community of developers and users dealing with similar challenges. > GMOD is used in diverse contexts, with both emerging and established > model organisms. > > GMOD Summer Schools (http://gmod.org/wiki/GMOD_Summer_School) > introduce new GMOD users to the GMOD project and feature several days > of hands-on training on how to install, configure and administer GMOD > tools. > > The courses includes training on several GMOD components: > * GBrowse - the widely used Generic Genome Browser > * Chado - a modular and extensible database schema for biological data > * Apollo - genome annotation editor > * BioMart - biological data warehouse system > * GBrowse_syn - a GBrowse based synteny viewer > * JBrowse - a brand new Web 2.0 genome browser > * Artemis-Chado Integration (Europe only) > * MAKER - Genome annotation pipeline (Americas only) > * Tripal - Web front end for Chado (Americas only) > > ***Please submit an application by the end of 6 April 2009, if you are > interested in attending. *** > > Enrollment is limited to 25 students in each course. If applications > exceed capacity (and we expect they will) then applicants will be > picked based on the strength of their application. Applicants will be > notified of their admission status in mid-April. > > Thanks, > > Dave Clements > GMOD Help Desk > help(a)gmod.org > > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > http://gmod.org/wiki/GMOD_Europe_2009 >

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Bioinformatics postdoc position
by AHC van Kampen 29 Mar '09

29 Mar '09

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Vacancy: (Associate) Scientist Bioinformatics at DSM
by Roubos, Hans 27 Mar '09

27 Mar '09

DSM00680 DSM Biotechnology Centre (Associate) Scientist Bioinformatics Delft, the Netherlands DSM - the Life Sciences and Materials Sciences Company DSM creates innovative products and services in Life Sciences and Materials Sciences that contribute to the quality of life. DSM's products and services are used globally in a wide range of markets and applications, supporting a healthier, more sustainable and more enjoyable way of life. End markets include human and animal nutrition and health, personal care, pharmaceuticals, automotive, coatings and paint, electrics and electronics, life protection and housing. DSM has annual sales of almost EUR 8.8 billion and employs some 23,000 people worldwide. The company is headquartered in the Netherlands, with locations on five continents. DSM is listed on Euronext Amsterdam. To learn more about DSM, please visit our website at www.dsm.com<http://www.dsm.com/>. The Challenge DSM Food Specialties develops, produces and markets ingredients and processing aids for the Dairy, Savoury, Beverage and nutritional markets. The Business Group consists of the Business Units Savoury Ingredients, Enzymes & Dairy Ingredients, a Global Sales department, a DSM Biotechnology Center, an Operations organisation and also a number of staff departments. There is a strong cooperation within the with DSM Nutritional Products to develop new ingredients to the market of Functional Food. DSM Biotechnology Center (DBC) is the main center for biotechnological Research & Development and is located in Delft. DBC is focused on the creation of new and improved products for DSM business units such as DSM Food Specialties (DFS), DSM Anti-Infectives (DAI), DSM Nutritional Products (DNP) and DSM Fiber Intermediates (DFI), along with Emerging Business Areas for DSM such as White Biotechnology or Specialty Packaging (EBA-WB, EBA-SP). The DBC Genetics Department serves the different businesses by delivering new and improved strains for the production of biocatalysts and bioproducts by means of classical and GMO strain development and (HT) screening technology. Within the DSM Biotechnology Center, a vacancy occurred within the Genetics department for an (Associate) Scientist Bioinformatics. You will work and represent the bioinformatics discipline within multi-disciplinary project innovation teams. Your challenge will be to apply and improve bioinformatics workflows for the development of new products, microbial production strains and improved processes. The Bioinformatics group is part of the Department of Genetics. Projects will be associated with DSM Bioinformatics platform development and maintenance, (re)sequence data exploration, integrative omics data analysis and/or protein engineering, depending on your expertise. Terms of conditions LOCAL CONTRACT The Ideal We are looking for a Ph.D. in Bioinformatics, Metabolic Engineering or Molecular Biology with a track-record of applying bioinformatics to biotechnological applications. Preferably you have experience with protein engineering, genomics approaches to microbial strain development or fermentation process improvement. You are a multidisciplinary team player, who takes initiative. Personal skills like problem analysis, judgment, creativity, leadership, adaptability characterize your identity. You are a good communicator, preferably fluent in the Dutch and/or the English language. The Reward DSM's wide diversity of disciplines makes it possible to offer employees a great variety of roles throughout their career. For instance, you may start your career in an area related to your education/qualifications, but your future is what you make of it. At DSM we stimulate people to determine their own career path and we encourage international careers. We strive to be an Employer of Choice and ensure that our employees are nurtured and given the opportunity to develop their talents. To learn more about DSM's HR vision and policy, please visit our website at www.dsm.com/careers<http://www.dsm.com/careers> The Procedure The DSM Recruitment and Selection Process is in line with the general procedure outlined elsewhere on our Career World. Please apply on-line (www.dsm.com/careers<http://www.dsm.com/careers>) ref DSM00680 and send your CV & cover letter in English and include information on your current remuneration. Reference check procedures are part of the DSM Recruitment & Selection Process. You will be contacted when these references checks are required. ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Bioinformatics postdoc in Brussels
by Vincent Detours 24 Mar '09

24 Mar '09

Bioinformatics postdoc in Brussels A postdoc position in bioinformatics is available starting in July 2009 at the Université Libre de Bruxelles, Belgium, for 2 years. The successful applicant will join a interdisciplinary team of clinical oncologists, geneticists, molecular biologists and bioinformaticians passionate about basic cancer research and its applications in the clinic. He/she will tackle the integrative analysis of massive breast cancer genome, methylome and transcriptome data sets generated using cutting edge microarray and next generation sequencing platforms. The project addresses both clinical and fundamental problems related to breast cancer progression. Only applicants with demonstrated proficiency in programming, and statistics and/or machine learning will be considered. Experience with sequence data, genome-wide data sets and demonstrated interest in oncogenomics will be assets. We highly value creativity and autonomy. Please, e-mail PDFs of 1) a cover letter explaining why you are skilled and motivated for the job, 2) your CV with the contact of three qualified referees, and 3) a copy of your best (preferably first author) publication to Vincent Detours, vdetours(a)ulb.ac.be, with 'postdoc pcn2009' in the subject line. Principal investigators in this project are • Marc Abramovicz, IRIBHM – ULB • Vincent Detours, IRIBHM – ULB • François Fuks, Laboratory of Cancer Epigenetics – ULB • Christos Sotiriou, Institut Bordet – ULB Please post the ad (see attached PDF) in your institution and forward it without restriction.

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Call for abstracts Student Council Symposium, Stockholm, June 27th
by Jeroen de Ridder 20 Mar '09

20 Mar '09

CALL FOR ABSTRACTS Submit your abstract today to participate in the 5th Symposium of the International Society for Computational Biology Student Council on June 27th 2009 in Stockholm! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 8 student presentations will be selected from the submitted abstracts. This is your chance to present your work! Awards will be given to best poster and best presentation as well as the runner-ups in both categories. Travel Fellowships are available (see website)! *Submission website:* http://symposium.iscbsc.org/content/submissions *General information:* http://symposium.iscbsc.org/ Important dates: *April 9th:* 5th Student Council Symposium Abstract and Travel Fellowship submission closes *May 2nd:* Travel Fellowship winners notification *May 10th:* Abstract acceptance notification *Registration Fee:* 75 euro (incl. lunch, coffee breaks and abstract booklet) – full ISMB/ECCB registration not required! We look forward to receiving your abstract, Lucia Peixoto Conference Chair, 5th ISCB Student Council Symposium Jeroen de Ridder Conference Co-Chair, 5th ISCB Student Council Symposium

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