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NBIC Conference 2011: April 19 & 20, 2011, Lunteren, the Netherlands
by Femke Francissen 08 Feb '11

08 Feb '11

6th NBIC Conference, April 19 & 20 2011, Lunteren, the Netherlands We are proud to announce the 6th edition of the annual NBIC Conference organized by the Netherlands Bioinformatics Centre (http://www.nbic.nl) - Conference website: http://conference.nbic.nl - Abstract submission deadline: February 18, 2011 - Registration is open! Conference programme: - 4 keynote speakers: o Bas van Steensel - NKI; o Phil Bourne - University of California; o Dorus Gadella - SILS/UvA; o Ewan Birney - EBI, UK. - Parallel sessions with contributed lectures (by abstract selection) - Poster presentations and an application showcase, parallel workshops - Social activities: conference diner and drinks/event on the evening of April 19 - Awards for: best poster, best lecture, best application showcase The day before the conference (Monday, April 18) other meetings are planned, such as a PhD retreat organized by RSG Netherlands: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2011/rsg-ret… For more information visit the conference website: http://conference.nbic.nl Contact person at the NBIC Office: Femke Francissen, femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>, tel. 024-3619500

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2011 Galaxy Community Conference, May 25-26, Lunteren, the Netherlands
by Femke Francissen 07 Feb '11

07 Feb '11

2011 Galaxy Community Conference, May 25-26, Lunteren, the Netherlands We are pleased to announce the 2011 Galaxy Community Conference, being held May 25-26 in Lunteren, The Netherlands. This year the conference is co-organized by the Netherlands Bioinformatics Centre (NBIC). The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. Links: http://galaxy.psu.edu/gcc2011/Home.html and http://www.nbic.nl/about-nbic/events/all-events/detail/article/2011-galaxy-… Overview: This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: - Talks submitted by the Galaxy community - Integration of tools (including NGS analysis tools) and distributed job management - Deployment of Galaxy instances on local resources and on the Cloud - Management of large datasets with the Galaxy Library System - Using the Galaxy LIMS functionality at NGS sequencing facilities - Visualizing Data without leaving Galaxy - Performing reproducible research - Performing and sharing complex analyses with Workflows - An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers Registration: The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. Link: http://galaxy.psu.edu/gcc2011/Register.html Abstract submission: Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. Link: http://galaxy.psu.edu/gcc2011/Abstracts.html Sponsors: The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). Links: http://www.nbic.nl/ and http://www.nsf.gov/ About Galaxy: Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. - Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. - Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. - Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service (http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. We are looking forward to a great conference and hope to see you in Lunteren! The Galaxy and NBIC Teams

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Bioinformatics postdoc in Brussels
by Vincent Detours 01 Feb '11

01 Feb '11

A postdoc position in bioinformatics is immediately available at IRIBHM, Université Libre de Bruxelles, Belgium, for 2 years. IRIBHM is a leading European molecular biology lab with 130 researchers. The successful applicant will join an interdisciplinary team of molecular biologists and bioinformaticians passionate about cancer research. He/she will tackle the thyroid cancer transcriptome data sets generated using cutting edge microarray and next generation sequencing platforms. The project addresses fundamental problems related to thyroid 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-w-2011' in the subject line.

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Integrative Bioinformatics 2011: call for posters and software demonstrations
by Jack Leunissen 28 Jan '11

28 Jan '11

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). There still are opportunities for presenting posters and software demonstrations at the Symposium. You are invited cordially to send in an abstract for presenting a poster or a software demonstration. The conference website for registration and abstract submission can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. Please use the templates as provided on the Journal's website (http://journal.imbio.de/instructions.php) The deadline for abstracts for posters or a software demo is February 15th. Hope to see you in Wageningen. On behalf of the organising committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University and Research Centre, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V.

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Royal Society conference: Modelling networks from sequence to consequence in eukaryotes (March 28-29, 2011)
by Frank Johannes 24 Jan '11

24 Jan '11

Dear list, The Royal Society (London) will host the following upcoming conference: Modelling networks from sequence to consequence in eukaryotes Date: March 28-29, 2011. Summary: The projected benefits of systems biology for understanding variation in human disease susceptibility or sustainable agriculture requires a bottom-up integration of research in genetics, statistics, mathematical modelling, bioinformatics and physiology. The meeting will bring together keynote speakers from the intersection of these disciplines who apply 'systems' approaches to study complex variation in plants, animals or humans. Link to the conference website: http://royalsociety.org/events/modelling-networks/ Keynote speakers: Dr Dirk Husmeier, Dr Arnis Druka, Professor John Whittaker, Professor Chris Rawlings, Professor Tim Aitman, Dr Enrico Petretto, Professor Stig Omholt, Professor Rebecca Doerge, Professor Ernst Wit, Professor Barbara Stranger, Dr Matthew Rockman, Dr Lauren McIntyre and Professor Robbie Waugh.

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Conference: Enabling Systems Biology
by Anton Feenstra 19 Jan '11

19 Jan '11

Dear all, I can strongly recommend the following conference, which boasts an impressive lineup on the cutting edge between Bioinformatics and Systems Biology. Please find more details below and on the website www.enfin.org/esb. Enabling Systems Biology April 11-14th, 2011, University College, London, UK. The conference "Enabling Systems Biology" is a one-off conference focusing on the interface between computational approaches in systems biology with experimental techniques. A world-leading set of invited speakers will be talking, and there will be a number of talks drawn from the set of submitted abstracts. Registration deadline is March 1st 2011. More information can be found at: http://www.enfin.org/page.php?page=esb Confirmed Speakers are: Ewan Birney (EBI, Cambridge, UK) Christine Orengo (UCL, London) James Adjaye (MPI, Berlin) Giulio Superti-Furga (CMM, Vienna) Geoff Barton (U. Dundee, Dundee) Michael Boutros (DKFZ, Heidelberg) Martha Bulyk (Harvard Medical School, Cambridge, US) Gianni Cesareni (U. Tor Vergata, Rome) Bertie Goettgens (CIMR, Cambridge, UK) John Hancock (MRC Harwell, UK) Jean-Karim Heriche (EMBL, Heidelberg) Jaap Heringa (VU, Netherlands) Henning Hermjakob (EBI, Cambridge, UK) Edda Klipp (Humboldt University, Berlin) Xuedong Liu (U Colorado, Boulder) Tomi Makela (U Helsinki, Finland) Aristidis Moustakas (Ludwig Institute, Uppsala) Stuart Newfeld (Tempe, Arizon) Erich Nigg (BioZentrum, Zurich) Christos Ouzounis (Institute of Agrobiotechnology, Thessaloniki) Bernhard Palsson (UCSD, San Diego) Dietmar Schomburg (Technical University Braunschweig) Eran Segal (Weizmann Institute, Jerusalem) Peter Sorger (Harvard, Cambridge, US) Alfonso Valencia (CNIO, Madrid) Jaak Vilo (Quretec, Tartu) Hans Westerhoff (University of Manchester, Manchester) Ioannis Xenarios (SIB, Geneva) -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "Just Give Me a Blip" (F. Black) | |_____________|_______________________________________________________|

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Workshop Comparative and Regulatory Genomics in Plants , 13-15 April 2011
by Klaas Vandepoele 05 Jan '11

05 Jan '11

Dear all, the first international *Workshop *on *Comparative and Regulatory Genomics in Plants* will be held at VIB - Ghent University, Belgium from April 13 to 15, 2011. This 3-day workshop will cover the application of different bioinformatics tools to study plant biology. Lectures will introduce the basic concepts of integrative sequence analysis and will be combined with practical sessions. The workshop is in English and open to undergraduate students and PhDs interested in gene and genome evolution, gene regulation & large-scale biology in plants. A series of step-by-step exercises will be used to guide applicants through the different tools and data sources (incl. gene family analysis and pathway evolution, detection of orthologous genes, reading phylogenetic trees, gene colinearity and genome organization, GO enrichment analysis, coexpression analysis and transcriptional regulation). More information including a detailed program is available here: http://bioinformatics.psb.ugent.be/crg_event/workshop/about Best regards, the scientific committee, Klaas Vandepoele /apologies for double postings/ -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail:Klaas.Vandepoele@psb.vib-ugent.be Website:http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

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Conference Comparative and Regulatory Genomics in Plants , 11-12 April 2011
by Klaas Vandepoele 04 Jan '11

04 Jan '11

Dear, the first international Conference on *Comparative and Regulatory Genomics in Plants* will be held at VIB - Ghent University, Belgium April 11-12, 2011. This conference will give an overview of the most recent developments in plant genomics and will discuss the integration of experimental high-throughput data with computational approaches to study gene functions, genome organization and transcriptional regulation. A panel of international invited speakers includes experts in the field of plant next-gen genome sequencing, genome evolution, comparative transcriptomics, ChIP profiling and plant regulatory networks. More information including invited speakers is available here: http://bioinformatics.psb.ugent.be/crg_event/conference/about Best regards, the scientific committee, Klaas Vandepoele /apologies for double postings/ -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

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postdoctoral position in structural bioinformatics
by Tom Lenaerts 22 Dec '10

22 Dec '10

The Machine Learning group at the Computer Science Department of the Université Libre de Bruxelles (Brussels, BELGIUM) invites motivated and enthusiastic young scientists to apply for a postdoctoral position, offering a tenure of 36 months. Research context and tasks This position is part of a new interdisciplinary FRFC project called “Unraveling the information processing patterns of SH2 domains participating in the JAK/STAT pathway”. In this project the applicant is expected to research algorithms that 1. Identify residue patterns responsible for the information exchange within the 3D structure of proteins and their domains. 2. Determine the evolutionary relevance of such patterns within the domain or protein family. 3. Produce chimeras of particular domains with specific functionality. This work will be performed in close collaboration with the new VIB BioNMR lab located at the Vrije Universiteit Brussel and the Signal transduction & molecular hematology group located in the Ludwig Institute for Cancer Research and de Duve Institute of the Université Catholique de Louvain. The project provides an excellent opportunity to improve skills in fields of structural bioinformatics, complex networks, data analysis and machine learning. Location The Machine Learning Group is a research group that carries out theoretical and applied research in predictive modeling, simulation and computational biology, and takes part in several applied research projects in domains as diverse as data mining, (structural) bioinformatics to learning dynamics and biomedical engineering. Located in heart of Brussels, the Université Libre de Bruxelles is known for quality research through its prestigious affiliate research centers and world-renowned faculty. Brussels, the capital of Belgium and the European Union, is a cosmopolitan city famous for its picturesque squares and buildings, serene parks and gardens and a very vibrant cultural life spiced up by many international languages. Candidate profile The ideal candidate should have a recent PhD on a subject related to computational biology, (structural) bioinformatics, machine learning or pattern detection. Since a large part of the research involves the development of algorithms to either generate/extract data or to detect particular patterns, the applicants are expected to have strong programming skills (knowledge of C++ is a strong plus). In addition the ideal candidate knows how to work independently, has strong interpersonal skills, has good English writing and oral communication skills. Knowledge of French or Dutch is an asset. Upon offer of a position in MLG-ULB, the candidates who are non-EU citizens are required to obtain an appropriate long-term Schengen visa; further information is available from their nearest Belgian embassy. More information for international applicants can be found in this web-document: http://www.ulb.ac.be/international/docs/ResearcherattheULB2010.pdf Deadline Applicants are encouraged to apply as soon as possible as positions will remain open until filled by a suitable candidate. Contact Candidates are invited to send their CV with the detailed list of publications, a research statement, a copy of the thesis and the names of at least two references in .pdf format by email to Tom.Lenaerts(a)ulb.ac.be. The subject field of your email must be MLG-JOB: postdoc. Equal Opportunity Employer ULB is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. ULB wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply.

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NBIC PhD Course Pattern Recognition, Jan 17-21 2011, Delft
by Celia van Gelder 19 Dec '10

19 Dec '10

*PhD Course: Pattern Recognition* On Jan 17-21, 2011 the NBIC PhD School organises the second edition of the PhD Course 'Pattern Recognition' in Delft. Course Coordinator: Dick de Ridder (Delft University) The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. More information about the course, including information about the course programme, can be found on <http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t…>http://www.nbic.nl/education/nbic-phd-school/course-schedule/pattern-recogn…. Please note: the course is free for PhD students working in a BioRange (including matching) or BioAssist project and for PhD students from SIB. Others can participate as well when paying a course fee (see http://www.nbic.nl/education/nbic-phd-school/enrolment/) This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl><http://www.nbic.nl>-> Education -> NBIC PhD School). -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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