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[Biochemistry] Open letter to minister Sabine Laruelle about BEN
by fred opperdoes 07 Jul '09

07 Jul '09

Dear Colleagues, Many of you may be familiar with te functionalities of BEN, the Belgian EMBnet Node, our Belgian Bioinformatics server. Many of you have followed one or more of its courses as an introduction to sequence analyses and bioinformatics or have used or are still using its databases and search facilities. This national service, jointly operated by the VUB and the ULB and financially supported by the Belgian Science Policy, is about to be dismantled because of discontinuing government funding. In an effort to reverse this unfortunate decision I have written an open letter (see below) to Minister Laruelle of Belgian Science Policy. I would like to ask everybody who agrees with my views about this decision to send a similar letter to the responsible minister and the other responsible persons mentioned below with a copy to Guy Bottu (gbottu(a)vub.ac.be) and to the secretary of the BMB (info(a)biochemistry.be) Prof. Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf Bruxelles, le 6 juillet 2009 Mme Sabine Laruelle Ministre des PME, des Indépendants, de l'Agriculture et de la Politique Scientifique Avenue de la Toison d’Or 87 1060 Bruxelles Mr. Philippe Mettens Président du Comité de Direction de la Politique Scientifique fédérale Rue de la Science 8 1000 Bruxelles Mr. Christophe Hardy Directeur de cabinet Avenue de la Toison d’Or 87 1060 Bruxelles Lettre ouverte Madame, Messieurs, Le contrat passé entre Belspo et "Belgian EMB Net Node" (BEN) a pris fin le 30 avril 2009. Le seul scientifique encore responsable des ordinateurs et de l’ensemble de l’infrastructure est sans emploi depuis le 1er mai 2009. Il a cependant – et bénévolement - maintenu un contact par internet à partir de son domicile. On s’attend donc à ce que le réseau BEN disparaisse sous peu. La Belgique se trouvera alors revenue à l’âge de la pierre en ce qui concerne la bioinformatique. Pendant de nombreuses années, l’infrastructure matérielle et logicielle de même que les membres de l’équipe BEN ont rendu des services inestimables à la communauté scientifique et à l’industrie. Plus de mille jeunes chercheurs ont fait leurs premières armes en bio- informatique grâce aux instructeurs du réseau BEN. Personnellement j’ai envoyé au cours des quinze dernières années une centaine de mes étudiants suivre les cours organisés par BEN. Des milliers de scientifiques ont non seulement utilisé les ordinateurs et les programmes spécialisés développés par BEN, mais ils ont également profité de l’expertise et du savoir-faire des membres de l’équipe. A l’heure actuelle, BEN a créé et rendu opérationnelles 75 banques de données. Elles sont consultées quotidiennement par des chercheurs belges et étrangers grâce aux interfaces développées par l’équipe BEN. BEN fait partie d’un réseau européen de bioinformatique dans lequel chaque pays possède son propre centre. L’abandon du centre belge signifierait une perte considérable non seulement pour la Belgique mais pour l’Europe entière. Cette décision des pouvoirs publics belges d’abandonner BEN pourrait bien apparaître comme scandaleuse aux yeux de la communauté scientifique internationale. J’ose espérer que les responsables belges reconsidèrent la situation et annulent cette décision plus que malheureuse avant que ne s’installent des dommages irréparables. En espérant une réponse favorable, je vous prie d’agréer l’expression de ma haute considération. Prof. F. Opperdoes Professeur de Biochimie, Parasitologie et Bioinformatique Secrétaire de la Société Belge de Biochimie et de Biologie Moléculaire Brussel, 6 juli 2009 Mevrouw Sabine Laruelle Minister van KMO's, Zelfstandigen, Landbouw en Wetenschapsbeleid Guldenvlieslaan 87 1060 Brussel De Heer Christophe Hardy Kabinetsdirecteur Guldenvlieslaan 87 1060 Brussel De Heer Philippe Mettens Voorzitter van het Direktiecomité van het Federaal Wetenschapsbeleid Wetenschapsstraat 8 B-1000 Brussel Open brief Mevrouw, Mijne heren, Op 30 april 2009 werd het contract van Belspo met de "Belgian EMB Net Node" (BEN) beëindigd. De enige wetenschapper die tot dan nog verantwoordelijk was voor de computers en de gehele infrastructuur is sinds 1 mei werkloos. Hij bedient de computers nog van huis uit via het internet. Het is te verwachten dat binnenkort het netwerk in elkaar stort en dan bevindt België zich op het gebied van de bioinformatica weer in de steentijd. De BEN computers en de leden van het BEN team hebben gedurende vele jaren onschatbare diensten bewezen aan de wetenschappelijk gemeenschap en aan de industrie. Meer dan duizend meestal jonge onderzoekers hebben hun eerste schreden op het gebied van de bioinformatica gezet aan de hand van de BEN instructeurs. Persoonlijk heb ik in de afgelopen vijftien jaar een honderdtal van mijn studenten naar de BEN cursussen gestuurd. Duizenden wetenschappers hebben niet alleen gebruik gemaakt van de gespecialiseerde BEN computers en hun geavanceerde programmas, maar hebben ook kunnen profiteren van de gespecialiseerde kennis van de leden van het BEN team. Op het ogenblik zijn er op BEN 72 databanken operationeel en deze worden dagelijks geconsulteerd via de door het BEN team ontwikkelde web interfaces, niet alleen door Belgische onderzoekers, maar door onderzoekers uit de gehele wereld. BEN maakt onderdeel uit van een Europees netwerk voor bioinformatica met voor ieder land zijn eigen knooppunt. Het wegvallen van het Belgische knooppunt zou niet alleen voor België maar voor heel Europa een groot verlies betekenen. Bovendien zou de internationale wetenschappelijke gemeenschap dit als een schandaal kunnen ervaren. Ik hoop van ganser harte dat de Belgische verantwoordelijken deze ongelukkige beslissing ongedaan kunnen maken voordat er onherstelbare schade is aangericht. Hoogachtend, Prof. Fred Opperdoes Hoogleraar biochemie, parasitologie en bioinformatica UCL Secretaris Belgische Vereniging voor Biochemie en Moleculaire Biologie -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Biochemistry mailing list Biochemistry(a)icp.ucl.ac.be http://www.icp.ucl.ac.be/mailman/listinfo/biochemistry

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PhD position at the Center for Human Genetics, KULeuven
by Stein Aerts 02 Jul '09

02 Jul '09

PhD position in bioinformatics, next-generation sequencing, and cancer genomics at the Center for Human Genetics, KULeuven The Laboratory of Computational Biology together with the Laboratory for Molecular Pathogenesis of Leukemia have a joint position for a motivated PhD student interested in genomics and systems biology of cancer. Research project The PhD research will focus on high-throughput approaches to further decipher the leukemia genome and to identify novel oncogenic mutations or structural variations that may underlie tumorigenesis. Secondary interest goes out to variations in transcriptional networks and the characterization of the underlying cis-regulatory variations. Available data include gene expression microarray data, GS FLX sequence data of candidate gene sets, and may even include full genome sequence data of multiple cancer patients. The challenge of this project is to handle large amounts of public and in-house genomic data and to use, benchmark, and develop state-of-the- art bioinformatics approaches, while maintaining a clear focus on important biological questions. Profile Master in Engineering, Bioinformatics, Computer Science, Bio- engineering, or equivalent. The candidate we are seeking should have basic programming or bioinformatics skills, with a strong interest in high-throughput technologies and genomics. Having any of the following skills is a plus: linux, R/Bioconductor, Matlab, Perl, Java, MySQL, data mining, clustering, classification, modeling, (bio)statistics, genome browsers. Environment The successful applicant will be hosted by the Laboratory of Computational Biology, headed by Prof. Stein Aerts, and will be in close collaboration with The Laboratory for Molecular Pathogenesis of Leukemia, headed by Prof. Jan Cools. Both labs are part of the Center for Human Genetics at the KULeuven. Contact Interested? Send your CV and motivation letter to stein.aerts(a)med.kuleuven.be Stein Aerts, PhD Laboratory of Computational Biology Center for Human Genetics, KULeuven http://med.kuleuven.be/lcb

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Bioinformatics research position at DSM
by Roubos, Hans 26 Jun '09

26 Jun '09

[cid:752194113@23062009-37CB] ________________________________ 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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Tenure track: Knowledge Discovery for Predictive Personalized Medicine at K.U.Leuven, Belgium
by Kurt Driessens 24 Jun '09

24 Jun '09

Tenure track Academic Position Knowledge Discovery for Predictive Personalized Medicine The Science, Engineering and Technology Group of K.U.Leuven invites applications for a full-time academic position in the domain of Knowledge discovery for predictive personalized medicine at the Department of Computer Science. 1. DUTIES 1.1. Research The tenure track positions are intended to foster high quality research in strategically selected domains. The successful candidate will be expected to develop a research program that delivers excellent, international level research results and to support and enhance national and international research collaboration. More specifically, this research will concentrate on ‘Knowledge discovery for predictive personalized medicine’. This research is motivated by the fast development of science and technology for medicine. The use of ‘Patient Data Management Systems’ in intensive care units, combined with extensive lab tests and genetic screening, generates massive amounts of personal data on patients. The study of data from different sources and time periods provides unprecedented possibilities to discover new knowledge. One of the outcomes could be a personalized medicine that orients the therapy according to the genetic profile of the patient. The sheer amount of data, their heterogeneity and complexity, necessitates the use of knowledge discovery and data mining techniques. Knowledge discovery is a novel branch in computational sciences, which integrates techniques from databases, machine learning, knowledge technology and artificial intelligence with statistics. It is concerned with the development of new algorithms, the formalization and introduction of background knowledge and ultimately the discovery of new knowledge that can be added to the knowledge base of a given discipline. The research program should develop in close contact with the bio banking initiative for translational medicine, and lead to a fruitful collaboration with applied research in the area of patient care. Research will be conducted within the framework of the Leuven ICT Centre (LICT) and the Department of Computer Science. The successful candidate will collaborate intensively with biomedical research groups (e.g. Intensive Care Medicine). 1.2. Teaching The successful candidate will take on teaching responsibilities allocated to the Department of Computer Science in study programs of the Faculty of Engineering, Faculty of Science or other faculties. They are expected to meet the reigning K.U.Leuven standards regarding academic program level and orientation and to adhere to the K.U.Leuven’s concept of education. Commitment to quality of education as a whole is a matter of course. 2. QUALIFICATIONS Candidates should hold a PhD or doctoral degree in Engineering or in Science, with specific expertise in the domain of computer sciences or informatics. They are expected to be excellent researchers who show independence and originality. More specifically we are looking for candidates with a strong background and experience in data mining and knowledge discovery for complex data (relational data mining, graph and network mining, heterogeneous data,…), in knowledge technology and artificial intelligence for medical applications (e.g. intensive care), in interdisciplinary collaborations and fund raising. They are dedicated to high-quality teaching and will contribute to the quality of both research and teaching at the Faculty and the Department. The candidate’s research ability should be evidenced by publications in international peer-reviewed journals. International research experience is most important. In their application, candidates should include a description of objectives they wish to realise/methods they plan to use during the five-year period of the position. At K.U.Leuven the main language of instruction is Dutch. Successful applicants who are not proficient in Dutch, will be provided language training in order to be able to also instruct in the Dutch language within three years time. Near-native proficiency in the English language is expected of all applicants. The full-time position will be offered for a period of five years starting on March 15, 2010 at the level of assistant professor (docent). A positive evaluation at the end of the five-year appointment will result in a tenured appointment as associate professor (hoofddocent). The K.U.Leuven pursues a policy of equal opportunity and diversity. More information: Pierre.Verbaeten(a)cs.kuleuven.be (chair Dept. of Computer Science), Luc.DeRaedt(a)cs.kuleuven.be (Machine Learning Research Group) Maurice.Bruynooghe(a)cs.kuleuven.be (Lab for Declarative Languages and Artificial Intelligence); Should you encounter any problems with the electronic registration, please contact Katoe Buyle e-mail: katoe.buyle(a)pers.kuleuven.be tel.: +32 (0)16 328 324. See also Website: http://www.kuleuven.be/personeel/jobsite/vacatures/engineering.html Deadline for Applications 30 September 2009 -- Kurt Driessens Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Last CfP and deadline extension: Computational Models for Cell Processes 2009
by Ion Petre 21 Jun '09

21 Jun '09

Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ In conjunction with Formal Methods 2009 -------------------------------------------------------------------- === Deadline extended: July 15, 2009 === === Proceedings will be published in the new EPTCS series === -------------------------------------------------------------------- THE MEETING ----------- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. SUBMISSIONS ----------- We seek papers and extended abstracts in all areas that relate to the relevance and potential of formal methods and computational modeling/simulation in systems biology. In particular, we welcome contributions that present biological processes requiring special computational and formal techniques that have not been investigated so far in the context of formal methods, as well as extensions of formal methods formalisms introduced to improve their applicability to biology. 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, concurrency theory, or logical methods - 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 Authors are invited to submit extended abstracts or full papers of up to 15 pages formatted according to EPTCS guidelines. Electronic submissions should be formatted in PDF. Simultaneous submission to other conferences or workshops with published proceedings is not allowed. A special issue of a high-level international journal, based on the workshop, is planned after the workshop. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) IMPORTANT DATES --------------- - Deadline extended: July 15, 2009 - Notification: September 10, 2009 - Final version: October 1, 2009 - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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Position for postdoc and PhD student
by AHC van Kampen 19 Jun '09

19 Jun '09

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PhD position in Gent
by Stefanie De Bodt 18 Jun '09

18 Jun '09

-- PhD student Systems Biology of Yield -- Job description: For our group, we are looking for enthusiastic PhD students in bioinformatics/systems biology. You will be involved in a project which is highly complementary to ongoing research in the group, where microarray, proteomics and interaction data related to growth control is generated. You will be responsible for the application and development of computational methods to analyze and integrate these data. You will collaborate with both experimental and computational biologists to obtain a systems-level understanding of leaf growth (http://www.psb.ugent.be/groups/systems-biology-of-yield-group) . Profile: • You have a degree in Bioinformatics, Informatics or in Biotechnology/ Biochemistry/Bioengineering. • You have a good knowledge/experience in programming (Perl, R, Java and/or C++). • You have knowledge or experience with databases (mySQL). • You have an interest in web design (PHP). • You speak English fluently. • You have good communication skills. You are a team player. You are independent and like to take initiative. You are flexible. We offer a contract of 2 years, within University Gent, with the possibility of prolongation. We offer a diverse job in a young team, an open and informal work atmosphere and in modern facilities. The Department of Plant Systems Biology, VIB, University Gent (www.psb.ugent.be) is an internationally renowned and dynamic research institute that employs molecular genetics, genomics and bioinformatics to unravel developmental processes in plants and is led by Prof. Dirk Inzé. Start date: as soon as possible, the position remains vacant until a suitable candidate is found. Information: Further information can be obtained by contacting Stefanie De Bodt (stefanie.debodt(a)psb.ugent.be) Application: Send your letter of motivation, your CV and if possible references to: Hilde Diegenant Department of Plant Systems Biology Technologiepark 927 9052 Gent Tel: +32 93313806 or through email to hilde.diegenant(a)psb.ugent.be -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

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Final CFP Machine Learning in Systems Biology (deadline extended)
by Pierre Geurts 02 Jun '09

02 Jun '09

[apologies for multiple postings] Deadline for submission has been extended to ** FRIDAY, JUNE 12 ** ************************** 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. The Workshop is organized as "core - event" of Pattern Analysis, Statistical Modelling and Computational Learning - Network of Excellence 2 (PASCAL 2, http://www.pascal-network.org/) 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 We invite you to submit an extended abstract of maximum 8 pages, formatted according to the Springer Lecture Notes in Computer Science style. Each extended abstract must be submitted online via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb09 The extended abstracts will be reviewed by the scientific programme committee. The papers will be selected for oral or poster presentation according to their originality and relevance to the workshop topics. Electronic versions of the extended abstracts will be accessible to the participants prior to the conference and will be made publicly available on the conference web site after the conference. The accepted papers will be published in Journal of Machine Learning Research (JMLR) Workshop and Conference Proceedings (http://jmlr.csail.mit.edu/) KEY DATES ** 12 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 Diego di Bernardo, University of Naples "Federico II", Italy 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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Marie Curie PhD position Systems Biology on Flowering Network, Wageningen, The Netherlands
by Ham, Roeland van 02 Jun '09

02 Jun '09

PhD Systems Biology on Flowering Network Wageningen Universiteit & Research Centre, Plant Research International, Bioinformatics Wageningen (The Netherlands), 38 hours per week Reference number: 09.Biosc.08. Background: Wageningen University and Research Centre (WUR) is an internationally renowned knowledge institute in the fields of life sciences and sustainability. It makes an essential contribution to the quality of life through pioneering research and education. One of its research focal points is Systems Biology, and the Bioinformatics group has a strategic position within several of these systems biology approaches, with extensive collaborations both with experimental biology and mathematical groups within Wageningen UR. Recently, we obtained funding for an EU-funded Marie Curie PhD project, which applies systems biology to plant reproductive development. This project is highly complementary to ongoing projects in our group, which include bioinformatics analyses of protein-protein interactions of key players in this biological process, analysis of protein-DNA interactions, and application of modelling techniques to related systems such as floral organ development and the flowering transition. Job description: A position for a PhD is available in the Bioinformatics group at Plant Research International (WUR) to work on the Marie Curie project "SYSFLO" (Training in Systems Biology Applied to Flowering). This project involves collaboration with various European partners (9 PhDs in total, both experimental and computational), linking the capture of large-scale datasets to advanced computational analysis and modelling. The aim of the project is to apply systems biology to reproductive development in Arabidopsis. Laboratory-based groups will generate datasets covering e.g. spatial and temporal gene expression, network relations and chromatin accessibility. Together with other computational groups, the PhD will apply statistics, data mining and modelling in order to generate a network model. This will specifically involve 1) prediction and analysis of network interactions; and 2) computational modelling of network dynamics. Both tasks will be tightly linked to experimental data collection and will suggest validation experiments for the laboratory teams. Profile: We are looking for a communicative team player with: * A background (MsC) in computational biology, bioinformatics or related area (either biologically oriented with knowledge of mathematics or mathematics oriented with interest in biology) * Some knowledge of programming (e.g. Perl, Python or R) * The drive and skills to collaborate with both experimental and computational biologists to obtain a systems-level understanding of plant reproductive development * Good written and spoken command of English According to Marie Curie ITN rules, this position is open to all nationalities except Dutch nationals (for detailed eligibility criteria for recruitment see: ftp://ftp.cordis.europa.eu/pub/fp7/docs/fp7-mga-annex3intramulti_en.pdf <ftp://ftp.cordis.europa.eu/pub/fp7/docs/fp7-mga-annex3intramulti_en.pdf> ). Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of genomics and systems biology related topics; a state-of-the art computational infrastructure; close collaboration with laboratory biologists who have expert knowledge of the biological system, and with computational and mathematical experts, embedded in an international project. The position is available for 4 years, full time; this period should be finished with a PhD examination. After 12 months, the performance of the candidate will be evaluated to decide whether there is sufficient progress to expect a successful completion of the PhD thesis within the remaining period. Preferred starting date: 1 October 2009. Estimated maximum salary per month: EUR 2000 in the first year rising to EUR 2558 in the fourth year Information: dr. Aalt-Jan van Dijk, +31-317-480994, aaltjan.vandijk(a)wur.nl <mailto:aaltjan.vandijk@wur.nl> or dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> . Application: Send your letter with CV and the names of two references before July 1st, 2009 to Mrs. Lydia Bikker, Plant Research International, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number 09.Biosc.08.

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2nd CfP: Computational Models for Cell Processes 2009
by Ion Petre 27 May '09

27 May '09

Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ In conjunction with Formal Methods 2009 -------------------------------------------------------------------- === Deadline for submissions: June 29, 2009 === === Proceedings will be published in the new EPTCS series === -------------------------------------------------------------------- THE MEETING ----------- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. SUBMISSIONS ----------- We seek papers and extended abstracts in all areas that relate to the relevance and potential of formal methods and computational modeling/simulation in systems biology. In particular, we welcome contributions that present biological processes requiring special computational and formal techniques that have not been investigated so far in the context of formal methods, as well as extensions of formal methods formalisms introduced to improve their applicability to biology. 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, concurrency theory, or logical methods - 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 Authors are invited to submit extended abstracts or full papers of up to 15 pages formatted according to EPTCS guidelines. Electronic submissions should be formatted in PDF. Simultaneous submission to other conferences or workshops with published proceedings is not allowed. A special issue of a high-level international journal, based on the workshop, is planned after the workshop. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) IMPORTANT DATES --------------- - Submission: June 29, 2009 - Notification: September 10, 2009 - Final version: October 1, 2009 - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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