- BBClist - maillist.psb.ugent.be

[Molecular-evolution] GCG/SeqLab petition
by Steve Thompson 21 Mar '08

21 Mar '08

Hi all - I apologize for my multiple cross-group postings but I feel the importance and urgency of this message warrant it. As many of you are aware, last summer Accelrys announced that they would be discontinuing support for GCG and SeqLab this upcoming June. That situation dismayed me and others and I wanted to do something about it. I contacted Steven Smith, one of the original authors of SeqLab, and discussed the situation with him. He volunteered to contact Accelrys in an attempt to minimally get SeqLab's license and code released to him. I gave Steve several months to try to persuade the company. Accelrys was not very cooperative. Therefore, I set about creating a petition in an attempt to add some leverage. I've contacted a few of you earlier regarding this initiative and appreciate your support. Anyway, I have created and posted that petition. It's at: http://www.petitiononline.com/gcg/petition.html And a nicely formatted PDF version is available in my own Web space: http://bio.fsu.edu/~stevet/Accelrys_petition.pdf I would very much appreciate you adding your name to this petition, if you agree with our sentiment. Thank you for your time! Cheers - Steve Steven M. Thompson A C T G stevet(a)bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 _______________________________________________ Mol-evol mailing list Mol-evol(a)net.bio.net http://www.bio.net/biomail/listinfo/mol-evol

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Summer School: Computational and Mathematical Modeling for Plant Systems Biology
by Roeland Merks 20 Mar '08

20 Mar '08

Summer school: Computational and Mathematical Modeling for Plant Systems Biology September 1-5, 2008, VIB Department of Plant Systems Biology and Ghent University, Ghent, Belgium Plant science is evolving from a reductionistic view on gene function to an integrated systems biology approach, in which gene functions are studied in the context of the dynamic behavior of physiological, cellular, or developmental processes. Mathematical and computational modeling play a central role in this multiscale systems biology approach. This summer school will bring together a wide range of computational systems biologists, working on problems at different organizational levels, relevant to plant biologists. The course will start with phenomena occurring at the subcellular and cellular scale, including photosynthesis, cell cycle regulation and the organization of the cytoskeleton. Then it will gradually "scale up" to the tissue, organ, and whole plant levels. It will conclude with pattern formation in tissues, the mechanics of growth, and whole plant development and evolution. Program The course will include a series of general lectures aimed at a general audience of plant biologists, and in-depth afternoon computer lab sessions introducing participants to the underlying mathematical and computational techniques. A PDF poster is in the attachment. For more information and registration, please go to http://www.psb.ugent.be/plantmodels. Organizers: - Roeland Merks (roeland.merks(a)psb.ugent.be) - Gerrit Beemster - Dirk Inzé - Xavier Draye Speakers: Genetic and metabolic networks - Xin-Guang Zhu (Urbana, IL, USA). Photosynthesis - Joe Pomerening (Bloomington, IN, USA). Cell cycle Single cell shape and mechanics - François Nédélec (Heidelberg, Germany). Cytoskeleton and mitosis - Bela Mulder (Amsterdam/Wageningen, Netherlands). Cell wall architecture and cytoskeleton Multicellular pattern formation - Hans Meinhardt (Tübingen, Germany). Reaction-diffusion models. - Verônica Grieneisen (Utrecht, Netherlands). Auxin fluxes in the developing root. - Richard Smith (Bern, Switzerland). Auxin fluxes during phyllotactic patterning. Plant growth mechanics - Alain Goriely (University of Arizona, Tucson, AZ, USA). Tip growth and vine twining - Roeland Merks (VIB Department of Plant Systems Biology, Ghent, Belgium). Cell-based modeling of plant tissues Whole plant development and evolution. - Xavier Draye (Louvain-la-Neuve, Belgium). Whole plant modeling, model integration - Przemyslaw Prusinkiewicz (Calgary, Canada). Whole plant modeling and evo-devo of plants -- ================================================================== Roeland Merks Group Leader "Plant Systems Modeling" Tel:32 (0)9 3313823 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM roeland.merks(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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GMOD Summer School, 11-13 July 2008, Durham, NC, USA
by Dave Clements 20 Mar '08

20 Mar '08

GMOD Summer School 11-13 July, 2008 National Evolutionary Synthesis Center (NESCent) Durham, North Carolina, USA The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina, USA. GMOD is a collection of interoperable open source software components for managing genomic data. GMOD components are used in diverse contexts, with both emerging and established model organisms. The course will provide an overview of GMOD and cover these popular components in detail: * Chado - a modular and extensible database schema * Apollo - genome annotation editor * GBrowse - genome viewer * CMap - comparative map viewer * Community Annotation System - GMOD's most popular components in a single system This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to use GMOD. The National Evolutionary Synthesis Center (NESCent, http://nescent.org) has joined the GMOD project with the goal of lowering the barrier to entry for research communities focused on emerging model organisms. The GMOD Summer School is a part of this effort. NESCent is also extending GMOD components, particularly Chado, to better support comparative and evolutionary data. If you are interested in attending the GMOD Summer School please submit a Statement of Interest before April 15, 2008. The course is free but enrollment is limited. For application information and a tentative program see: http://gmod.org/GMOD_Summer_School Please let me know if you have any questions, comments, or requests. Thanks, Dave Clements GMOD Help Desk help(a)gmod.org ------------------------ NESCent offers various courses and workshops, as well as funding post-doctoral and sabbatical positions, working groups and other meetings. For more information about research and training opportunities at NESCent, visit our website at www.nescent.org. Sign up for our quarterly electronic newsletter at http://www.nescent.org/about/contact.php to automatically receive information about events at NESCent.

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4 months post-doc position in structural bioinformatics - Brussels
by Dimitri Gilis 19 Mar '08

19 Mar '08

4 months post-doc position in structural bioinformatics (June 1 - September 30, 2008) The post-doc researcher will be hired to perform a specific task in the framework of the TheraVIP project, funded by the Brussels Region. TheraVIP aims at developing a new therapeutic approach for the treatment of inflammatory diseases by the design of an artificial receptor/ligand pair combined to cell therapy. The researcher will be responsible for the modeling of the structure of a GPCR membrane receptor. The researcher will collaborate with the experimenter teams involved in the project. The candidate should have a PhD in bioinformatics, chemistry, physics or in a related area, with a strong experience in structural bioinformatics and in protein structure prediction. Application should include a cover letter and a curriculum vitae, and should be sent to Dimitri Gilis (dgilis(a)ulb.ac.be) or Marianne Rooman (mrooman(a)ulb.ac.be) before May 15, 2008. ------------------------------------------------------------------- Genomic and strucural bioinformatics Avenue F. D. Roosevelt, 50 CP 165/61 B-1050 Bruxelles (Belgium) Tél. +32 -2 2 650 36 15 / +32 -2 2 650 20 67 Fax 32-2 650 35.75 Email : dgilis(a)ulb.ac.be / mrooman(a)ulb.ac.be http://babylone.ulb.ac.be

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A BioSapiens workshop : From Genome to Proteome and Biological Function
by Olivier Sand 11 Mar '08

11 Mar '08

A BioSapiens workshop : From Genome to Proteome and Biological Function Wednesday April 2nd 2008 - Université Libre de Bruxelles Schedule 10.30 – 11.00 Registration and coffee 11.00 – 12.00 Introduction to the challenges of interpreting genome and proteome data Janet Thornton, EMBL Outstation - European Bioinformatics Institute, UK 12.00 – 12.45 Integrative themes: the human genome Søren Brunak, BioCentrum-Technical University of Denmark 12.45 – 14.00 Lunch and poster session 14.00 – 14.45 Gene annotations and regulation Ewan Birney, EMBL Outstation - European Bioinformatics Institute, UK 14.45 – 15.30 Protein annotations from sequence data Christine Orengo, University College London, UK 15.30 – 16.00 Coffee break 16.00 – 16.45 Protein annotations from structure data Anna Tramontano, University of Rome, Italy 16.45 – 17.30 Integrative themes: cancer and quantitative trait loci Alfonso Valencia, CNIO-Spanish National Cancer Centre 19:30 Conference dinner Program http://www.biosapiens.info/page.php?page=biosapiens_workshop Registration http://www.biosapiens.info/page.php?page=bs_work_reg Poster http://www.biosapiens.info/files/public/april_workshop/ Biosapiens_poster_FINAL.pdf Venue The meeting takes place in the Salle Dupréel, Université Libre de Bruxelles, Avenue Jeanne, Brussels. Map and directions: http://www.ulb.ac.be/docs/campus/sol_S.html http://www.ulb.ac.be/docs/campus/solaccp-uk.html Fee The registration fee is €80: this includes refreshments during the day, a light lunch, and dinner in the evening. Participants will be informed about the dinner venue later. Participants are invited to submit a poster on their own work in this field. The dimensions of the poster boards are 1.9m x 0.9m. A short (100 word max) abstract will be requested when registering. List of nearby hotels https://plus21.safe-order.net/resotel/sysres/hotels.php?id=10925

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Postdoc positions bioinformatics University of Konstanz, Germany
by Yves Van de Peer 01 Mar '08

01 Mar '08

TWO POSTDOC POSITIONS - molecular evolution, genomics & bioinformatics At the University of Konstanz we expect to have two postdoc positions available starting on April 1, 2008 in the lab of Prof. Axel Meyer at the Department of Evolutionary Biology and Zoology at the University of Konstanz in Germany. Due to the funding of the University of Konstanz through the "excellence initiative" of the German government we are in the process of establishing a genomics/proteomics center at the university that will include microarray facilities and second generation sequencing technologies. Therefore, we are particularly interested in postdocs with expertise in molecular evolution, molecular phylogenetics and bioinformatics. We expect that a "junior professorship" in bioinformatics will be advertised shortly as well. These positions are affiliated with the new graduate school in chemical biology - for more information visit_ http://www.chembiol.uni-konstanz.de/_. For this new program we invite applications of qualified Masters students as well as Ph.D. candidates. The postdoc projects we are interested in have to do with fish genomics and in particular comparative genomics of cichlid fish. Other projects deal with the evolution of gene families the evolution of the genome in early chordates and vertebrates. Candidates should have a strong interest in bioinformatics, developmental and evolutionary biology and should be experienced in molecular techniques and/or computational biology. Appointments are for up to two years initially with a salary according to German TVL salary scale that includes extensive health and retirement benefits. The initial contract period would be for two years with the potential for additional years of funding. Informal inquiries should be addressed to Prof. Axel Meyer (_axel.meyer(a)uni-konstanz.de_) Further information on our research can be obtained from our web page: www.evolutionsbiologie.uni-konstanz.de Applications should include a CV, statement of research interests and email addresses of two references. Review of applications will commence on March 15th 2008. Starting dates are flexible. Applications should be sent as one pdf file to_ axel.meyer(a)uni-konstanz.de_ - or by mail to Prof. Axel Meyer, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. This search will remain open until the positions are filled.

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(geen onderwerp)
by Kris Gevaert 27 Feb '08

27 Feb '08

Dear all, Attached you will find a job opening for a junior postdoc in bioinformatics (proteomics). Could you please send this to anyone who might be interested? Kind regards, Kris Prof. Dr. Kris Gevaert VIB Department of Medical Protein Research, UGent Proteome Analysis and Bioinformatics Unit A. Baertsoenkaai 3 B9000 Gent Belgium Tel: +32-92649274 Fax: +32-92649496 http://www.proteomics.be http://www.vib.be/Research/EN/Service+Facilities/Proteomics+Expertise+Cente…

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Benelearn 2008 Call for Abstracts
by Pierre Geurts 21 Feb '08

21 Feb '08

[apologies for multiple postings] First Call for Abstracts 17th annual Belgian-Dutch Conference on Machine Learning BENELEARN 2008 Spa (Belgium) May 19-20 http://www.montefiore.ulg.ac.be/services/stochastic/benelearn08 Benelearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. Benelearn 2008 will be organised by the Systems and Modeling and Bioinformatics and Modeling research units of the Department of Electrical Engineering and Computer Science and GIGA-Research of the University of Liège. The conference will take place in the Solcress seminar center, at walking distance from the center of the city of Spa located in the Belgian Ardennes. Contributions are now being invited that are relevant to machine learning and related disciplines in a broad sense. Topics include, but are not limited to: Kernel Methods Web/Link Mining Bayesian Networks Case-based Learning Computational Learning Theory Data Mining Evolutionary Computation Hybrid Learning Systems Inductive Learning Learning and Ubiquitous Inductive Logic Programming Computing Knowledge Discovery in Databases Language Learning Learning in Bioinformatics Learning for Multi-Agent Learning in Dynamic Domains Systems Multi-strategy Learning Neural Networks Reinforcement Learning Robot Learning Scientific Discovery Meta-Learning Statistical Learning Learning for Language, Speech Computational models of Human Learning Applications FORMAT OF THE CONFERENCE The official language of the conference is English. The conference will include two days of technical sessions. Plenary talks will be given by internationally renowned invited speakers. Regular sessions will allow young and senior researchers from the Machine Learning community to present their work. A poster session will be organized during break and evening hours. A social dinner is planned on the first day evening. SUBMISSION Each submission consists of an abstract of the contribution and must be submitted online via the Easychair submission system: http://www.easychair.org/conferences/?conf=benelearn08 Formating instructions are available on the conference web site http://www.montefiore.ulg.ac.be/services/stochastic/benelearn08 Abstracts will be selected for oral or poster presentation according to their relevance and available slots. Electronic versions of 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 deadline for submission is April 4, 2008. Authors will be notified about the acceptance of their abstract on or before April 18, 2008. Final versions of the abstracts, if necessary, are due by April 25, 2008. LOCATION: SolCress seminar center located in the Belgian Ardennes, at walking distance from the center of Spa. http://www.solcress.be/incentives/EN/home.htm IMPORTANT DATES Abstract submission deadline: April 4, 2008 Notification of acceptance : April 18, 2008 Final version of abstracts: April 25, 2008 Conference: May 19-20, 2008 CONTACT For further information, please contact benelearn08(a)gmail.com or see the conference website: http://www.montefiore.ulg.ac.be/services/stochastic/benelearn08 ORGANIZING COMMITTEE Louis Wehenkel, Pierre Geurts, Raphaël Marée University of Liège, Belgium PROGRAMME COMMITTEE H. Blockeel, K.U. Leuven G. Bontempi, U.L. Bruxelles W. Daelemans, Universiteit Antwerpen P. Dupont, U.C. Louvain D. Ernst, Université de Liège A. Feelders, Universiteit Utrecht P. Geurts, Université de Liège B. Goethals, Univ. Antwerpen T. Heskes, Radboud Univ. Nijmegen B. Kappen, Radboud Univ. Nijmegen J. Kok, Universiteit Leiden B. Manderick, Vrije Universiteit Brussel R. Marée, Université de Liège B. de Moor, K.U. Leuven M. van Otterlo, Universiteit Twente J. Piater, Université de Liège L. de Raedt, K.U. Leuven J. Ramon, K.U. Leuven Y. Saeys, Universiteit Gent R. Sepulchre, Université de Liège M. van Someren, University of Amsterdam A. Siebes, Universiteit Utrecht Y. Smirnov, Universiteit Maastricht K. Van Steen, Université de Liège J. Suykens, K.U. Leuven A. van den Bosch, Universiteit Tilburg K. VanHoof, Universiteit Hasselt M. Verleysen, U.C. Louvain P. Vitanyi, Centrum voor Wiskunde en Informatica L. Wehenkel, Université de Liège

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(SCL: 999) [Fwd: Second announcement "Gene Golub Around the World"]
by Ida Tassens 18 Feb '08

18 Feb '08

Dear, As already announced, ESAT/SCD (EE Dept, K.U.Leuven) and CESAME (Universite Catholique de Louvain) organize an event in memory of Gene Golub in Leuven. The event is part of the Gene Golub Around the World Day (29th February, Gene Golub's birthday - see http://www.cs.nyu.edu/overton/genearoundtheworld/) On the website you can find the titles of the presentations, together with a short abstract: http://www.kuleuven.be/golub/ Preliminary program: 9:00: Opening: Bart De Moor, Paul Van Dooren, Sabine Van Huffel 9:30: G. Alistair Watson, Univ. Dundee, Div. Mathematics: Some extensions of Gene's work on total least squares 10:00: Claude Brezinski, Univ. des Sciences et Technologies de Lille: Errors in the solution of linear systems, with an application to regularization 10:30: Sabine Van Huffel, K.U.Leuven, EE Dept. (ESAT/SCD): Impact of numerical linear algebra in computational biomedical signal processing 11:00: Coffee 11:30: Paul Van Dooren, UCL, CESAME: How to improve your PR (in collaboration with C. de Kerchove and L. Ninove) 12:00: Martin H. Gutknecht, ETH Zurich, Applied Mathematics: Modified Moments for Indefinite Weight Functions 12:30: Raf Vandebril, K.U.Leuven, Dept. of Computer Science: On the A x equals Lambda B x problem 13:00: Lunch 14:00: Bo Kågström, Umea Univ., Dept. Computing Science: Illconditioned eigenvalue problems - a journey with Gene from Jordan to periodic Schur forms 14:30: Lieven de Lathauwer, EE Dept. (ESAT/SCD) 15:00: Annie Cuyt, Univ. Antwerpen, Dept. Mathematics and Computer Science: Gene's beloved "Shape from Moments" problem 15:30: Coffee 16:00: Gregory Boutry, Univ. Catholique de Lille, Faculte Libre des Sciences et Technologies: Gene from Marrakech to Stanford. 16:30: Bart De Moor, K.U.Leuven, EE Dept. (ESAT/SCD): Generalizations of the singular value and the QR decomposition for multiple matrices 17:00: End 18:00: Chinese Dinner The talks will have the right mix of technical contribution and fond memories of Gene Golub. The event will be followed by a dinner in a Chinese restaurant . Registration, coffee breaks and sandwich lunch are free of charge. The dinner will cost 40 euro. Please register on the website (http://www.kuleuven.be/golub/ ) before Feb. 20, and indicate if you will attend the dinner (please fill out the Dinner Registration Form). All practical details can be found on the website (payment details, hotel information, final program, ...): http://www.kuleuven.be/golub/ . We hope to welcome you at this event, Bart De Moor, Paul Van Dooren, Sabine Van Huffel -- Ida Tassens K.U.Leuven, ESAT/SCD (SISTA) Kasteelpark Arenberg 10 B-3001 Leuven, Belgium Tel. +32/16/32.17.09 Fax. +32/16/32.19.70 ida.tassens(a)esat.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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[Fwd: Royal Society and Académie des sciences Microsoft European Science Award - DEADLINE APPROACHING]
by BEN 08 Feb '08

08 Feb '08

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