- BBClist - maillist.psb.ugent.be

GMOD Summer School, Application Deadline 15 April
by Dave Clements 09 Apr '08

09 Apr '08

Hello all, This is a reminder that we will start reviewing applications for the GMOD Summer School one week from today, on Wednesday, 15 April. See http://gmod.org/GMOD_Summer_School and http://gmod.org/GMOD_Summer_School_Statement_of_Interest for more information. I've also attached a PDF with an overview of the course. Please let me know if you have any questions. Thanks, Dave Clements GMOD Help Desk On Thu, Mar 20, 2008 at 10:00 AM, Dave Clements <clements(a)nescent.org> wrote: > 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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Job opening at Vrije Universiteit Brussel: Computing/X-ray facility manager
by Joke Reumers 04 Apr '08

04 Apr '08

The VIB Department of Molecular and Cellular Interactions at the Vrije Universiteit Brussel is looking for a highly motivated X-ray facility/computing manager. The successful candidate will provide expert support to our in house structural biology community and will conduct research in the area of structural biology through internal and/or external collaborations. The department currently contains four groups involved in structural biology totalling around 40 people. A Bio-NMR group is to be established beginning next year. Details on the research conducted in the department can be found on our websites (http://www.vib.be/ and http://ultr.vub.ac.be/) Experience with UNIX/LINUX system administration is a must and experience with the computational side of protein crystallography is desirable, although we will also consider candidates with a (structural) bioinformatics background interested in moving towards X-ray crystallography. The main service duties will include: - Maintaining and upgrading the crystallographic and NMR computing facilities and reassuring of data back-up - Maintenance of the in-house X-ray data collection facilities - Organizing and streamlining synchrotron trips Interested candidates should send their cv to Remy Loris (reloris(a)vub.ac.be) together with the names and contact details of at least two reference persons. Salary will be discussed and will depend on the level of experience and qualifications of the successful candidate. Remy Loris Vrije Universiteit Brussel Plkeinlaan 2 B-1050 Brussel Belgium

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BioScope-IT seminar on High Performance Computing for Life Sciences Research, April 24, 2008, IBM Forum Brussels
by Bert Coessens 03 Apr '08

03 Apr '08

Dear Madam / Sir, You are cordially invited to the BioScope-IT seminar on high performance computing for life sciences research that will take place on *April 24, 2008 at the IBM Forum in Brussels*. The purpose of this seminar is to give the participants an overview of high performance computing solutions currently used or useful in a life sciences context, both from a hardware and software point of view. To complete the programme, we invited several researchers from the life sciences industry to talk about their experiences with HPC. The presented case studies will exemplify the practical use of HPC in life sciences research. We conclude the programme with a quick look into the near future of both HPC and life sciences research. Who should attend?This seminar is directed towards scientists confronted with data analysis task that typically surpass the capacity of their desktop computer or to anyone wondering how HPC might be of use to them and what types of biological questions could be answered in this context. Detailed programme 10.00h-10.30hRegistration with coffeeHall 10.30h-11.15hGeneral introduction to HPC<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>- *Gerd Van Mechelen* (IBM) Ensor & Magritte 11.15h-12.00hHPC programming: parallel computing and software optimization<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Francois Thomas* (IBM France) Ensor & Magritte 12.00h-13.00hLunchHall 13.00h-14.00hPenguins in Parallel - Getting your feet wet<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Luc Ducazu* (Fit-IT) Ensor & Magritte 14.00h-15.00hDivide et Impera – Message from the Field<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Wouter Van Delm* (ESAT-SCD, K.U.Leuven) Ensor & Magritte 15.00h-15.30hCoffee breakHall 15.30h-16.30hMolecular docking in drug design<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Marc De Jonge* (Molmo) Ensor & Magritte 16.30h-17.00hTBC: Visionary talk<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– Ensor & Magritte 17.00h-…Closing & drinkHall Pricing and Registration Academia & FlandersBio members: *€80* (VAT excl.) Other: *€100* (VAT excl.) The fee includes coffee, drinks, lunch, and seminar documentation. You can register at the BioScope-IT website.<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…> Registration deadline: April 21, 2008 Registration binds you or your institution to pay the registration fee. All fees are VAT excluded. There is no refund in case of cancellation after the registration deadline. Replacement by a colleague is allowed. Venue details The seminar will take place at IBM Forum Brussels, Bourgetlaan 42, 1130 Brussel. You can find directions here: http://www-05.ibm.com/be/ibm/en/access/location_brussels.html Participants can park their car in the IBM customer parking at level -1 of the IBM Forum building (entrance at the back of the building). Organizing Partners IBM Belgium, BioScope-IT, and FlandersBio

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Call for Participation: 4th ISCB Student Council Symposium and Visual Reflections on Science Exhibition
by M.D. Stobbe 01 Apr '08

01 Apr '08

Dear colleagues, we would like to invite you to participate in the 4th ISCB Student Council Symposium and the Visual Reflections on Science Exhibition that will take place at ISMB 2008 in Toronto (Canada). Both events are organized by the ISCB Student Council. Please see the calls for participation below for details and forward this anyone who might be interested. Thank you very much! Best regards, Nils Gehlenborg Chair, ISCB Student Council Lucia Peixoto Chair, 4th ISCB Student Council Symposium Milana Frenkel-Morgenstern Chair, Visual Reflections on Science Exhibition ---------------------------------------------------------------------- CALL FOR PARTICIPATION: 4th ISCB Student Council Symposium * Website: http://symposium.iscbsc.org * Date & Location: Friday, 18 July 2008 in Toronto, Canada * Submission Deadline: 26 May 2008 * Registration Fee: 60 US Dollars (incl. lunch and coffee breaks). ISMB 2008 registration not required. We are accepting submissions for both posters and oral presentations and will award the best of each category. This year's panel discussion topic will be "Career Paths in Bioinformatics and Computational Biology", and will provide delegates with the opportunity to ask questions about their career future they always wanted to ask but never had a chance to. Furthermore, we will have keynotes by renowned scientists, student presentations and a poster session. ---------------------------------------------------------------------- CALL FOR PARTICIPATION: Visual Reflections on Science Exhibition * Website: http://www.iscb.org/ismb2008/vrs_instructions.php * Date & Location: Open for the duration of ISMB in Toronto, Canada * Submission Deadline: 11 April 2008 For the ISMB 2008 Visual Reflections on Science Exhibition we invite all interested conference attendees to submit artistic images and videos that have been generated as part of a research project. We are also soliciting images and videos resulting from creative efforts that involve scientific concepts or employ scientific tools and methods. Participate in this exciting new ISMB event to surprise and inspire us, to open our eyes and minds!

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Software validation and testing in the life sciences – April 17, 2008
by Bert Coessens 26 Mar '08

26 Mar '08

Dear Madam / Sir, You are cordially invited to the *BioScope-IT seminar on software validation and testing in the life sciences*. The seminar will take place on *April 17, 2008 in Leuven*, Huis Bethlehem, K.U.Leuven, Schapenstraat 34, 3000 Leuven. The purpose of this seminar is to give the participants an overview of the software systems validation and testing realm and its applicability and use in a life sciences context. During this seminar you will learn what software validation and testing means, how a validation environment can be set up, and what this means in practice for the projects you are running or services you are providing. Who should attend? This seminar is directed towards life sciences software developers and project managers seeking to learn more about how they can establish and assure the good quality of the software systems their projects and services rely on. Detailed programme 09.30h-10.00hRegistration with coffeeHall 10.00h-11.00hProject management in a validated environment<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Stefan Thys* (Quantum Consulting & Management) Wolfspoort auditorium 11.00h-12.00hAutomating testing and available software<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Wim Demey* (Sogeti) Wolfspoort auditorium 12.00h-13.00hLunchHall 13.00h-14.00hTBC: Result-driven testing / Maintaining the validated state<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…> Wolfspoort auditorium 14.00h-15.00hA practical approach to lean computer systems validation<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Yves Dene* (Sogeti) Wolfspoort auditorium 15.00h-15.30hCoffee breakHall 15.30h-16.30hSoftware provider view on testing<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…>– *Kurt Van Looveren* (MIPS) Wolfspoort auditorium 16.30h-17.30hTBC Pharma / Healthcare view<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…> Wolfspoort auditorium 17.30ClosingHall Pricing and Registration Academia & FlandersBio members: *€80* (VAT excl.) Other: *€100* (VAT excl.) The fee includes coffee, drinks, lunch, and seminar documentation. You can register through the BioScope-IT website at http://www.bioscope-it.be<http://www.bioscope-it.be/index.php?option=com_attend_events&task=view&id=1…> Registration deadline: April 14, 2007 Organizing Partners Sogeti, BioScope-IT, and FlandersBio Hope to see you at the meeting. Kind regards, The BioScope-IT team +32 484 995 775 info(a)bioscope-it.be

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[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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