February 2012 - BBClist - maillist.psb.ugent.be

NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- 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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Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

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Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

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BBC11: Key information and updates
by Francisco Azuaje 14 Mar '12

14 Mar '12

Dear colleagues, submission of abstracts is well underway and approaching its deadline: Friday, 28 October. Also I remind you that updates on conference venue and travel are now available at: http://www.bbc11.lu/index.php?page=location We look forward to receiving your abstracts soon. All the best. Francisco Azuaje. (On behalf of the BBC11 Organisation).

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Postdoc in algorithmics for NextGen Sequencing data, Inria Rennes, France
by Leonor Palmeira 29 Feb '12

29 Feb '12

Inria project team SYMBIOSE is seeking highly qualified and motivated candidates for a 12 months postdoctoral position. Research Program : Next Generation Sequencing technologies generate data of a new type in huge volumes and crucial computational developments are needed to take full advantage of these data. The successful candidate will develop new algorithms to identify complex genomic variants, such as structural variants, in such data from multiple samples without the use of a reference genome. Our approach relies on a formal model based on the De-Bruijn graph data structure to handle huge amounts of data and extract biologically relevant information. For further details visit our website http://www.irisa.fr/symbiose/ and the project description http://www.irisa.fr/symbiose/index.php?option=com_docman&task=doc_download&… Profile : - PhD in computational biology or algorithmics with a strong interest for biology - good programming skills (C, C++, python, java, ...) - background in sequence and graph algorithmics - a prior experience with high throughput sequencing data will be appreciated Working environment : The position is located in France, in the city of Rennes at the INRIA Rennes - Bretagne Atlantique center. SYMBIOSE is a dynamic and multi-disciplinary research team working in computational biology and bioinformatics, and with a strong expertise in short reads assembly. The contract is for 12 months, starting as soon as January 2012. Salary is 2620 euros monthly before taxes deduction. Application : Please send a cover letter, a CV with publications and two references contacts to claire.lemaitre(a)inria.fr.

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PhD Student Positions in Machine Learning at Radboud University Nijmegen
by E.Marchiori＠cs.ru.nl 28 Feb '12

28 Feb '12

The Machine Learning group at Radboud University Nijmegen is looking for two PhD students. Both PhD students will be working on the development and application of machine learning algorithms for improved analysis of data related to neurological disorders. First, a PhD position is available within the NWO project MacBrain. The goal of MacBrain is to mine data from the Netherlands Brain Bank (NBB) describing clinical and pathological information collected from thousands of donors who are either healthy or affected by neuro-degenerative diseases (including Alzheimer's). Your task will be to develop machine learning methods for discovering computational disease profiles characterized by few features, which may be used by domain experts to perform targeted studies aimed at improving the prognosis, diagnosis and treatment of neuro-degenerative diseases. Second, a PhD position is available within the EU FP7 project TACTICS. The goal of TACTICS is to better understand the neural, genetic and molecular bases of compulsivity disorders such as autism spectrum disorder (ASD) and obsessive compulsive disorder (OCD). Your task will be to design machine learning methods that can integrate the different sources of data gathered by the various partners within the consortium. Requirements As a PhD student you should meet the following requirements: - a Master's degree (or equivalent) in Computer Science, Mathematics or a related field, with a strong interest in machine learning; - commitment and a cooperative attitude; - excellent proficiency in written and spoken English. You will be appointed for an initial period of 18 months, after which your performance will be evaluated. If the evaluation is positive, the contract will be extended by 2.5 years. The gross starting salary amounts to 2,042 per month based on full-time employment, and will increase to 2,612 per month in the fourth year. About Radboud University Nijmegen Radboud University Nijmegen is one of the leading academic communities in the Netherlands and is renowned for its leafy campus, modern buildings and state-of-the-art equipment. It has seven faculties and enrols over 17,500 students in approximately 90 study programmes. The university is situated in Nijmegen, the oldest city in the Netherlands, which has a rich history and one of the liveliest city centres in the Netherlands. The Intelligent Systems section of the Institute for Computing and Information Sciences (iCIS) at Radboud University Nijmegen conducts research on machine learning for applications in, for example, neuroscience and bioinformatics. iCIS in general and the Intelligent Systems section in particular received excellent scores in a recent national research assessment. Additional information Dr. Elena Marchiori (main contact for MacBrain) +31 24 3652467 elenam(a)cs.ru.nl Prof.dr. Tom Heskes (main contact for TACTICS) +31 24 3652696 tomh(a)cs.ru.nl How to apply http://www.ru.nl/vacatures/details/details_vacature_0?recid=507799

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workshop metabolomics data analysis
by R.Breitling 24 Feb '12

24 Feb '12

Dear colleague, On March 29/30, 2012 we will be holding the Fourth Workshop on Metabolomics Data Analysis at Glasgow University. Attendance is limited to 25 participants, but there are still a few places available. The workshop is divided into two sections, an introduction to metabolomics data analysis on Day 1, and an advanced session focusing on mzMatch analyses on Day 2. Both days can be booked together or individually. Details on the program and how to register are available at: http://mzmatch.sourceforge.net/workshop.php Best regards, Rainer Breitling Prof. Dr. Rainer Breitling SULSA Professor of Systems Biology, University of Glasgow Honorary Professor of Computational Systems Biology, University of Groningen Mailing address: Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences Joseph Black Building, B3.10 University of Glasgow Glasgow G12 8QQ Scotland, United Kingdom tel: (+44) (0)141-330-7374 e-mail: rainer.breitling(a)glasgow.ac.uk http://tinyurl.com/rbreitling http://gbic.biol.rug.nl/~rbreitling

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7th Netherlands Bioinformatics Conference (NBIC2012), April 24 & 25, Lunteren, the Netherlands
by Femke Francissen 14 Feb '12

14 Feb '12

We are proud to announce the 7th edition of the annual Netherlands Bioinformatics Conference (NBIC2012) organized by the Netherlands Bioinformatics Centre (http://www.nbic.nl) - Conference website: http://conference.nbic.nl - Abstract submission deadline: March 12th, 2012 - Registration is open! ** Conference programme ** - 3 confirmed keynote speakers: o Gerard Kleywegt - Protein Data Bank in Europe (PDBe), EMBL-EBI o Dorus Gadella - the Centre for Advanced Microscopy (CAM), University of Amsterdam o Harmen Bussemakers - Columbia University, Biological Sciences - Parallel sessions with contributed lectures (by abstract selection) - Poster presentations and an application showcase, parallel workshops - Social activities: conference diner and drinks on the evening of April 24th - Awards for: best poster, best lecture, best application showcase The day before the conference (Monday, April 23rd) a PhD retreat is organized by the RSG Netherlands: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/program… For more information about abstract submission, registration and programme, 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>

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CALL FOR ABSTRACTS - 8th ISCB Student Council Symposium 2012
by Francescatto, M. 13 Feb '12

13 Feb '12

8th ISCB Student Council Symposium 2012 Submit your abstract now for the 8th Symposium of the International Society for Computational Biology Student Council, to be held on the 13th of July, 2012 in Long Beach, California, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB)! The ISCB Student Council Symposium 2012 will bring together young computational biologists from several research areas and regions of the world. As the central part of our symposium, 10 students will be selected for an oral presentation from the submitted abstracts. This is your chance to present your work to an international audience of young scientists. We welcome abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. All abstracts accepted for oral presentation will be published in a special issue of BMC Bioinformatics journal. As in previous editions, awards will be given to outstanding posters and presentations. Travel Fellowships will also be available: all candidates with accepted abstracts are encouraged to apply! Travel Fellowship submission will be open for one entire week after acceptance notification. Submission information: http://symposium.iscbsc.org/content/submissions Travel Fellowship information: http://symposium.iscbsc.org/content/travel-fellowships General information: http://symposium.iscbsc.org/ Important dates January 30, 2012: Abstract and Travel Fellowship submission open April 2, 2012: Abstract submission closes April 16, 2012: Abstract acceptance notifications April 23, 2012: Travel Fellowships submission closes April 30, 2012: Travel Fellowships acceptance notification We look forward to receiving your abstract, Alexander Goncearenco Chair, 8th ISCB Student Council Symposium 2012 Olga Botvinnik Co-Chair, 8th ISCB Student Council Symposium 2012

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Fwd: Trans.: opening for project leader in computational genomics
by Marc Lensink 13 Feb '12

13 Feb '12

-- Marc F. Lensink, CR1, PhD Interdisciplinary Research Institute (IRI) - USR3078 CNRS Computational Biology marc.lensink(a)iri.univ-lille1.fr Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

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