May 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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7th IAPR International Conference on Pattern Recognition in Bioinformatics in Tokyo
by benoit 30 May '12

30 May '12

PRIB2012 The 7th IAPR International Conference on Pattern Recognition in Bioinformatics ------------------------------------------------------------------------------ November 8-10 2012 Tokyo, Japan http://prib2012.org/ ------------------------------------------------------------------------------ =============== Call For Papers =============== In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc. The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners, and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology, and systems biology. Authors are invited to submit full papers in relevant research areas, which include but are not limited to: - Bio-sequence analysis - Gene and protein expression analysis - Biomarker discovery - Protein structure and interaction prediction - Motifs and signal detection - Metabolic modeling and analysis - Systems and synthetic biology - Pathway and network analysis - Immuno- and chemo-informatics - Evolution and phylogeny - Bio-imaging - Biological databases, integration, and visualization Pattern recognition techniques of interest include: - Statistical, syntactic, and structural pattern recognition - Data mining and machine learning - Evolutionary computation - Bayesian networks and graphical models - Neural networks and fuzzy systems =========== Publication =========== Papers should be submitted electronically through the conference website (http://prib2012.org/) Accepted papers will be published in Springer's Lecture Notes in Bioinformatics (LNBI). =============== Important dates =============== Full paper submission deadline: May 28, 2012 (Being extended by two weeks, please check the web site, which will be updated soon). Author notification of acceptance: July 31, 2012 Camera-ready paper deadline: August 23, 2012 Poster abstract submission : October 2, 2012

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PRIB2012 deadline extended to June 18
by Dick de Ridder - EWI 29 May '12

29 May '12

------------------------------------------------------------------------------ PRIB2012 The 7th IAPR International Conference on Pattern Recognition in Bioinformatics ------------------------------------------------------------------------------ November 8-10 2012 Tokyo, Japan http://prib2012.org/ ------------------------------------------------------------------------------ *** The deadline for full paper submission has been extended to June 18! *** =============== Call For Papers =============== In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc. The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners, and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology, and systems biology. Authors are invited to submit full papers in relevant research areas, which include but are not limited to: - Bio-sequence analysis - Gene and protein expression analysis - Biomarker discovery - Protein structure and interaction prediction - Motifs and signal detection - Metabolic modeling and analysis - Systems and synthetic biology - Pathway and network analysis - Immuno- and chemo-informatics - Evolution and phylogeny - Bio-imaging - Biological databases, integration, and visualization Pattern recognition techniques of interest include: - Statistical, syntactic, and structural pattern recognition - Data mining and machine learning - Evolutionary computation - Bayesian networks and graphical models - Neural networks and fuzzy systems =========== Publication =========== Papers should be submitted electronically through the conference website (http://prib2012.org/) Accepted papers will be published in Springer's Lecture Notes in Bioinformatics (LNBI). =============== Important dates =============== EXTENDED full paper submission deadline: June 18, 2012 Author notification of acceptance: July 31, 2012 Camera-ready paper deadline: August 23, 2012 Poster abstract submission : October 2, 2012 ------------------------------------------------------------------------------

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Final call for papers for Probabilistic Graphical Models (PGM2012) Workshop
by Manuel Gómez Olmedo 29 May '12

29 May '12

Probabilistic Graphical Models (PGM2012) Workshop Granada, Spain, 19-21 September 2012 (http://leo.ugr.es/pgm2012) *Final call for papers:* The aim of the workshop is to bring together people interested in probabilistic graphical models and provide a forum for discussion of the latest research developments in this field. The workshop is organized so as to facilitate discussions and collaboration among the participants also outside the workshop sessions. To facilitate the spreading of research results and promote interactions among the participants, parallel sessions will be avoided and the workshop will be organized around a single thread of plenary and posters sessions. We welcome theoretical and applied contributions related to the following topics: - Principles of Bayesian (belief) networks, chain graphs, decision networks, influence diagrams, and other probabilistic graphical models (PGMs). - Information processing in PGMs (exact and approximate inference). - Learning and data mining in the context of PGMs: machine learning approaches, statistical testing and search methods, MCMC simulation. - Exploitation of results from related disciplines for the construction of PGMs, e.g., statistics, information theory, optimization, decision making under uncertainty, multivariate statistical analysis. - Software systems based on PGMs. - Application of PGMs to real-world problems. We invite submissions that concern oneCHANGED or more of the above topics, or any other aspects related to probabilistic graphical models. Papers submitted for review should report on original, previously unpublished work. Each submitted paper will be reviewed by at least two reviewers. Submission procedure PGM 2012 requires electronic submission of papers according to the instructions found on the web page http://leo.ugr.es/pgm2012/author-instructions.php. The authors must prepare their papers according to the PGM proceedings format, and submit the full version of the papers by the deadline found below. The page limit is 8 pages, including figures and bibliography. The page for author instructions contains format information and provides access to style files and templates. Paper presentation Papers will be accepted for plenary or poster presentation. All accepted papers will be included in the proceedings (with ISBN), which will be made available at the workshop reception. At least one author of accepted papers is expected to attend the workshop. After the workshop, authors of selected papers will be invited to submit an extended version of their paper to appear in a special issue of a high quality journal. All of the submitted papers will undergo a full reviewing process. Important Dates Call for papers opened November 2011 Deadline for abstract submissions June 4, 23:59 GMT, 2012 Paper submissions June 8, 23:59 GMT, 2012 Notification of acceptance July 20, 2012 Final versions due August 24, 23:59 GMT, 2012 Welcoming reception September 18, 2012 Workshop dates September 19-21, 2012 -- Manuel Gomez Olmedo e-mail:mgomez@decsai.ugr.es Dpto. de Ciencias de la Computacion e Inteligencia Artificial E.T.S. Ingenierias Informatica y de Telecomunicacion Universidad de Granada Tel.: +34 958 246143 18071 - GRANADA (Spain) Fax: +34 958 243317

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[Gtpb] BFG12-Bioinformatics and Functional Genomics using R and Bioconductor
by Pedro Fernandes 27 May '12

27 May '12

Please excuse us for cross or duplicated messages ANNOUNCEMENT / REMINDER BFG12 Bioinformatics and Functional Genomics using R and Bioconductor with Javier de las Rivas and Celia Fontanillo from Universidad de Salamanca (USAL), Salamanca, ES and Consejo Superior de Investigaciones Científicas (CSIC) IMPORTANT DATES for this Course Deadline for applications: June 11th 2012 Notification of acceptance dates: EARLY: June 8th 2012 (on special request, see Application) NORMAL: June 14th 2012 Course date: June 18th to June 20th 2012 Course description: This is a practical course on Bioinformatics applied to analysis of Gene expression and Genomic data using mainly R and Bioconductor tools and algorithms. The course will focus in the use of robust methods to analyse microarray datasets, mainly from Affymetrix platform and from clinical-biomedical studies, integrating several strategies to achieve an optimum construction and analyses of gene expression profiles. The Course will be mostly practical using computers and prepared protocols. It will be divided in three major sessions: 1. Gene Expression Profiling. Microarrays genome-wide expression data integration, normalization, gene-based signal calculation, differential expression (using different algorithms: SAM, Bayesian and Limma) and clustering. Databases that integrate gene signatures. 2. Classification and Prediction using genomic data. Application of machine learning techniques to the analysis of gene expression data to allow classification of different states or different diseases subtypes. Error calculations. Class-prediction using de novo samples. 3. Gene Functional Enrichment. Gene list functional annotation using tools for statistical enrichment based on multiple concurrent annotation. Application of algorithms that measure outcome and response to assign specific functions to gene expression datasets. Target Audience Researchers in Biology and Biomedical areas (PhD students, PostDocs or Senior) working with genomic and gene expression data or with gene lists in general, that what to learn useful and powerful tools and methods for bioinformatic analysis. Course Pre-requisites Basic familiarity with genomic data and bioinformatics data resources. Minimum familiarity with R (although most scripts and command lines will be provided with written tutorials). Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/BFG12/ thank you for your interest Pedro Fernandes GTPB Coordinator _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] BFG12-Bioinformatics and Functional Genomics using R and Bioconductor
by Pedro Fernandes 24 May '12

24 May '12

Please excuse us for cross or duplicated messages ANNOUNCEMENT / REMINDER BFG12 Bioinformatics and Functional Genomics using R and Bioconductor with Javier de las Rivas and Celia Fontanillo from Universidad de Salamanca (USAL), Salamanca, ES and Consejo Superior de Investigaciones Científicas (CSIC) IMPORTANT DATES for this Course Deadline for applications: June 11th 2012 Notification of acceptance dates: EARLY: June 8th 2012 (on special request, see Application) NORMAL: June 14th 2012 Course date: June 18th to June 20th 2012 Course description: This is a practical course on Bioinformatics applied to analysis of Gene expression and Genomic data using mainly R and Bioconductor tools and algorithms. The course will focus in the use of robust methods to analyse microarray datasets âmainly from Affymetrix platform and from clinical-biomedical studies, integrating several strategies to achieve an optimum construction and analyses of gene expression profiles. The Course will be mostly practical using computers and prepared protocols. It will be divided in three major sessions: 1. Gene Expression Profiling. Microarrays genome-wide expression data integration, normalization, gene-based signal calculation, differential expression (using different algorithms: SAM, Bayesian and Limma) and clustering. Databases that integrate gene signatures. 2. Classification and Prediction using genomic data. Application of machine learning techniques to the analysis of gene expression data to allow classification of different states or different diseases subtypes. Error calculations. Class-prediction using de novo samples. 3. Gene Functional Enrichment. Gene list functional annotation using tools for statistical enrichment based on multiple concurrent annotation. Application of algorithms that measure outcome and response to assign specific functions to gene expression datasets. Target Audience Researchers in Biology and Biomedical areas (PhD students, PostDocs or Senior) working with genomic and gene expression data or with gene lists in general, that what to learn useful and powerful tools and methods for bioinformatic analysis. Course Pre-requisites Basic familiarity with genomic data and bioinformatics data resources. Minimum familiarity with R (although most scripts and command lines will be provided with written tutorials). Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/BFG12/ thank you for your interest Pedro Fernandes GTPB Coordinator -- Upcoming GTPB Courses BIG12, RNA12, MPA12, ADNMO12, BFG12, BPB12 Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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PhD POSITION on BIOINFORMATICS METHODS FOR EPIGENOMICS (ULB, Brussels)
by Matthieu Defrance 22 May '12

22 May '12

PhD POSITION on BIOINFORMATICS METHODS FOR EPIGENOMICS (ULB, Brussels) Job description: PhD position is available in a joint project of the Laboratory of Cancer Epigenetics and the Machine Learning Group (Université Libre de Bruxelles) on bioinformatics approaches to transcriptomics and epigenomics in health and diseases. Given the strong interdisciplinary nature of the project the candidate is expected to share his/her time between the medical lab and the computer science unit. The research goal is to understand, study and develop a bioinformatics methodology to perform integrative analysis of high-throughput transcriptomics and epigenomics data sets generated using cutting edge next-generation sequencing platforms (available in the medical lab). Both fundamental and clinical aspects of human diseases will be addressed. The position is funded for 2 years, with a 2 years renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected. Profile: The candidate should have a master degree in Bioinformatics, Bio-engineering, Biomedical Sciences, Engineering or Computer Sciences and demonstrate proficiency in programming (e.g. perl, python), computational statistics (e.g. R) and/or machine learning. Experience with sequence data, genome-wide data sets (ChIP-Seq, RNA-Seq, ...) or massive datasets analysis will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. How to apply? Informal enquiries, CV (+ ranking and grades during studies) and names of two referees should be send to: Dr. Matthieu Defrance (defrance(a)bigre.ulb.ac.be) Dr. François Fuks (ffuks(a)ulb.ac.be) Pr. Gianluca Bontempi (gbonte(a)ulb.ac.be)

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Professor Jack Leunissen
by Nijveen, Harm 19 May '12

19 May '12

It is with deep sadness I inform you that Jack Leunissen, Professor of Bioinformatics at Wageningen University, passed away Monday May 14 after a long illness at the age of 57. As a pioneer in bioinformatics he has made a great contribution to the development of the bioinformatics discipline. His enthousiasm and views have inspired generations of young researchers and students in the world. He was involved with his staff and students until the very end. His passion and knowledge of bioinformatics will remain an inspiration to us all. We wish Jack's family strength to cope with this loss. Harm Nijveen Laboratory of Bioinformatics, Wageningen University, The Netherlands. Funeral announcement card, in Dutch: http://www.bioinformatics.nl/rouwkaart-jack.pdf Condolences: http://www.condoleance.nl/13691/

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