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2009 GMOD Summer Schools - Americas & Europe
by Dave Clements 16 Mar '09

16 Mar '09

We are now accepting applications for the 2009 GMOD Summer Schools: Americas, 16-19 July - National Evolutionary Synthesis Center (NESCent), Durham, NC, USA - Student tuition is free, thanks to NIH grant 1R01HG004483-01. - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas Europe, 3-6 August - University of Oxford, Oxford, United Kingdom - Part of GMOD Europe 2009, which includes the next GMOD Meeting - Student tuition is £95 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological, mostly genomic, data. GMOD is also a community of developers and users dealing with similar challenges. GMOD is used in diverse contexts, with both emerging and established model organisms. GMOD Summer Schools (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to the GMOD project and feature several days of hands-on training on how to install, configure and administer GMOD tools. The courses includes training on several GMOD components: * GBrowse - the widely used Generic Genome Browser * Chado - a modular and extensible database schema for biological data * Apollo - genome annotation editor * BioMart - biological data warehouse system * GBrowse_syn - a GBrowse based synteny viewer * JBrowse - a brand new Web 2.0 genome browser * Artemis-Chado Integration (Europe only) * MAKER - Genome annotation pipeline (Americas only) * Tripal - Web front end for Chado (Americas only) ***Please submit an application by the end of 6 April 2009, if you are interested in attending. *** Enrollment is limited to 25 students in each course. If applications exceed capacity (and we expect they will) then applicants will be picked based on the strength of their application. Applicants will be notified of their admission status in mid-April. Thanks, Dave Clements GMOD Help Desk help(a)gmod.org http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe http://gmod.org/wiki/GMOD_Europe_2009

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Position: Postdoctoral Scientist Bioinformatics VIB MicroArray Facility (Leuven - Belgium)
by Rudy van Eijsden 11 Mar '09

11 Mar '09

Vacancy Postdoctoral Scientist Bioinformatics MicroArray Facility VIB VIB is a non-profit research institute in the life sciences. Some 1100 technicians and scientists conduct strategic basis research on molecular mechanisms that control the functioning of the human body, plants, and micro-organisms. Through a close partnership with four Flemish universities – Ghent University, the Katholieke Universiteit Leuven, the University of Antwerp, and the Vrije Universiteit Brussel - and a solid investment program, VIB unites the forces of 65 research groups in a single institute. Their research aims at fundamentally extending the frontiers of our knowledge. Through its technology transfer activities, VIB strives to convert the research results into products for the benefit of consumers and patients. VIB also develops and distributes a broad range of scientifically substantiated information about all aspects of biotechnology. More info on: www.vib.be VIB MicroArray Facility The VIB MicroArray Facility (MAF- based at K.U.Leuven) provides an assortment of fee-based services for biological questions in the transcriptomics and genomics fields to VIB and non-VIB scientists throughout Flanders. Besides being an institutional service provider and core-lab for both Affymetrix® and Agilent® microarray platforms, the MAF team offers full service for transcriptomics data analyses and in house made custom cDNA arrays. In addition to arrays, the nCounter® Analysis system is available to perform non-enzymatic medium throughput expression quantification studies. Also, bioinformatics services (i.e. assistance with storage, analysis and interpretation of data) are part of the MAF service package. More info on: www.microarrays.be Job description/responsibilities ▪ Contribute to microarray data analysis procedures to process, analyze, interprete, track and archive data ▪ Design and write workflows for microarray data analysis ▪ Develop tools and workflows for data generated by new technologies ▪ Use of existing LIMS data bases ▪ Write and submit grant applications to expand the microarray data analysis efforts ▪ Ensure the smooth running of projects on a day-to-day basis ▪ Participate in discussions with customers regarding experimental set-up and assist them with the publication of their analysed results (i.e. data submission to public data bases) ▪ Participation at project meetings and attendance of relevant courses/trainings and conferences Profile ▪ PhD in bioinformatics/statistics/biology/biochemistry/genomics or relevant ▪ Strong knowledge of bioinformatics tools in genomic research ▪ Strong knowledge of sequence databases, pathway databases, DNA databases (e.g. ensemble, NCBI, Swissprot) ▪ Knowledge of relational databases (Oracle, SQL server) ▪ Experience with common script languages (Windows/Linux environment) ▪ Excellent communication skills Contact? The position is open for 6 months initially (replacement for maternity leave). Extension of the contract will be decided upon at a later point of time. If you are interested please send your CV, motivation letter and reference of at least 2 people to geert.vanminnebruggen(a)vib.be as soon as possible. ================================================= Rudy van Eijsden, Ph.D. VIB MicroArray Facility Herestraat 49 O&N 1, Post Box 816 3000 Leuven Belgium Tel: +32 (0)16 34 79 33 Fax: +32 (0)16 34 79 40 e-mail: <mailto:Rudy.vanEijsden@vib.be> Rudy.vanEijsden(a)vib.be web: <http://www.microarrays.be/> http://www.microarrays.be <blocked::http://www.vib.be/> http://www.vib.be =================================================

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Postdoc Plant Genome Assembly, Reference number: DPW 09-10
by Ham, Roeland van 25 Feb '09

25 Feb '09

Postdoc Plant Genome Assembly Laboratory of Bioinformatics of Wageningen University and Researchcentre Wageningen (The Netherlands), 38 hours per week Reference number: DPW 09-10 Background: Wageningen University and Research Centre (WUR) is involved in the international efforts to sequence the genomes of the Solanceous crops tomato and potato. To support these efforts, WUR has recently extended its sequencing capacity with the acquisition of a next generation sequencing platform. Our activities in plant genome sequencing are supported by a strong team of bioinformaticians involved in (comparative) genome analysis and responsible for the development and application of genome assembly and annotation strategies. The tomato genome is being sequenced by the SOL Consortium, a collaboration of 10 countries and in which the dutch effort is financed through the Centre of BioSystems Genomics and the EU-SOL project. Recently, the consortium has begun whole genome shotgun sequencing using novel technologies as a complementary approach to the ongoing BAC-by-BAC sequencing strategy. This initiative is led by the CBSG and EU-SOL from the Netherlands and covers coordination of the whole genome shotgun assembly effort. Job description: A postdoc position is immediately available in the Laboratory of Bioinformatics of WUR to work on the whole genome shotgun assembly of the tomato genome. This will involve very intensive (inter)national collaboration. Datasets will include sequence data from the Roche/454, SOLiD, Solexa and Sanger-ABI platforms. The candidate will participate in a team involved in the development of a bioinformatics platform for next generation sequencing technologies, which will be based on an advanced ICT infrastructure (Grid computing), webservices and workflow management technology. This development is linked to the BioAssist <http://www.nbic.nl/support/bioassist/> initiative of the Netherlands Bioinformatics Centre (NBIC). Profile: We are looking for a communicative team player with: * A PhD in bioinformatics or related area and a strong publication record * Strong background in sequence analysis and genome assembly * Advanced programming and database development skills (Java, SQL, Python, C++ or Perl) * Knowledge of next generation sequencing technologies and the data produced by these platforms * Experience with Grid computing, workflow management technology and creating and implementing webservices * The drive, ambition and skills to make a frontier sequencing project to a success; for this a cooperative spirit and good communication skills are a must. Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 4374,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> . Application: Send your letter with CV, list of publications and the names of two references before March 16th, 2009 to Mrs. Dorien Wissink, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number DPW 09-10

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Vacancy: scientific programmer, Delft
by Dick de Ridder 06 Feb '09

06 Feb '09

Delft University of Technology has a vacancy for a scientific programmer (m/f) in the Delft Bioinformatics group. Please feel free to bring this vacancy to the attention of any suitable candidate. The organisation: The faculty of Electrical Engineering, Mathematics and Computer Science of Delft University of Technology is known world wide for its high academic quality and social relevance of its research programs. The faculty’s excellent facilities accentuate its international position in teaching and research. The faculty offers an interdisciplinary setting for its 500 employees, 350 PhD students and 1700 undergraduates. Together they work on a broad range of technical innovations in the fields of sustainable energy, telecommunications, microelectronics, embedded systems, computer and software engineering, interactive multimedia and applied mathematics. Within the faculty, the Computer Science Department of Mediamatics focuses on media and knowledge processing. Four important application domains are telecommunications, consumer electronics, industrial automation, and life/health sciences. The department consists of three groups: Computer Graphics, Human Computer Interaction and Information and Communication Theory. The latter group focuses on processing, analysis, and interpretation of multimedia, biological and biomedical data with knowledge-based signal processing techniques, and is home to the Delft Bioinformatics group. The Delft Bioinformatics group has a strong background in pattern recognition/machine learning, and we apply this expertise to design (predictive) models that contribute to novel biological insights. Recent examples of our contributions include the discovery of 250 novel cancer genes by analyzing and modelling insertional mutagenesis data; proposing (combinatorial) cultivation dependent transcription factor activities based on a decomposition of transcriptomics data; assessing gene therapy protocols by integrating viral insertions with gene expression data; and modelling the mechanisms that underlie chromosomal arrangement in the nucleus. This is accomplished by closely co-operating with (among others) biotechnologists at Delft University of Technology and molecular biologists at the Netherlands Cancer Institute in Amsterdam, university medical centres in Rotterdam and Leiden, and companies such as DSM and Organon. Job description: The Delft Bioinformatics group is part of the Netherlands Bioinformatics Center (NBIC, www.nbic.nl) which coordinates bioinformatics research, tool development, service and education in the Netherlands. For the NBIC tool development and service program, we are looking for a scientific programmer that can take up a wide a variety of short-term bioinformatics problems arising within the different Genomic Centers in the Netherlands (www.ngi.nl) and in particular within the Kluyver Center for Genomics of Industrial Fermentation (www.kluyvercentre.nl) The candidate should be able to independently perform routine data analyses using existing tools, and to assist researchers in the different Genomic Centers in practical issues in the application of bioinformatics, e.g. through setting up databases, developing (web-based) applications, etc. Furthermore, (s)he should aid in the implementation, delivery and support of novel data analysis algorithms developed by researchers in the Netherlands Bioinformatics Centre. Finally, the candidate should act as an interpreter between the biologists and bioinformaticians, by signalling opportunities for the development and application of novel data analysis tools and setting up collaborations to this end. Job requirements: The candidate should have a well-founded basis in statistics, computer science and molecular biology, have excellent programming skills and should hold a BSc or higher in Bioinformatics or Computational Biology (or Computer Science, with a strong affinity to molecular biology and genomics). The candidate should have experience with working in multidisciplinary teams. (S)he should have good communication and organization skills, have a service-oriented attitude and be an enthusiastic team player. Conditions of employment: This is a full-time, fixed-term position for a period of four years. The starting salary, depending on age and experience, varies from scale 8 to 9 (€ 2.267-3.422 gross per month). TU Delft offers an attractive benefits package, including a flexible work week, free high-speed Internet access from home, and the option of assembling a customized compensation and benefits package (the 'IKA'). Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities. Application and information: For more information about this position, please contact Marcel Reinders, phone: +31 (0)15-2786424, e-mail: M.J.T.Reinders(a)tudelft.nl; or Dick de Ridder, phone: +31 (0)15-2785114, e-mail: D.deRidder(a)tudelft.nl. To apply, please send a CV together with a letter of application and two references, before March 1, 2009 to: Dick de Ridder, Information & Communication Theory Group, Faculty of EEMCS, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands; or by e-mail to D.deRidder(a)tudelft.nl.

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Vacancy PhD student
by Stefan Weckx 06 Feb '09

06 Feb '09

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Postdoc Plant Genome Assembly, Reference number: DPW 09-10
by Ham, Roeland van 05 Feb '09

05 Feb '09

Postdoc Plant Genome Assembly Laboratory of Bioinformatics of Wageningen University and Research Centre Wageningen (The Netherlands), 38 hours per week Reference number: DPW 09-10 Background: Wageningen University and Research Centre (WUR) is involved in the international efforts to sequence the genomes of the Solanceous crops tomato and potato. To support these efforts, WUR has recently extended its sequencing capacity with the acquisition of a next generation sequencing platform. Our activities in plant genome sequencing are supported by a strong team of bioinformaticians involved in (comparative) genome analysis and responsible for the development and application of genome assembly and annotation strategies. The tomato genome is being sequenced by the SOL Consortium, a collaboration of 10 countries and in which the dutch effort is financed through the Centre of BioSystems Genomics and the EU-SOL project. Recently, the consortium has begun whole genome shotgun sequencing using novel technologies as a complementary approach to the ongoing BAC-by-BAC sequencing strategy. This initiative is led by the CBSG and EU-SOL from the Netherlands and covers coordination of the whole genome shotgun assembly effort. Job description: A postdoc position is immediately available in the Laboratory of Bioinformatics of WUR to work on the whole genome shotgun assembly of the tomato genome. This will involve very intensive (inter)national collaboration. Datasets will include sequence data from the Roche/454, SOLiD, Solexa and Sanger-ABI platforms. The candidate will participate in a team involved in the development of a bioinformatics platform for next generation sequencing technologies, which will be based on an advanced ICT infrastructure (Grid computing), webservices and workflow management technology. This development is linked to the BioAssist <http://www.nbic.nl/support/bioassist/> initiative of the Netherlands Bioinformatics Centre (NBIC). Profile: We are looking for a communicative team player with: * A PhD in bioinformatics or related area and a strong publication record * Strong background in sequence analysis and genome assembly * Advanced programming and database development skills (Java, SQL, Python, C++ or Perl) * Knowledge of next generation sequencing technologies and the data produced by these platforms * Experience with Grid computing, workflow management technology and creating and implementing webservices * The drive, ambition and skills to make a frontier sequencing project to a success; for this a cooperative spirit and good communication skills are a must. Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 4374,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> . Application: Send your letter with CV, list of publications and the names of two references before February 23, 2008 to Mrs. Dorien Wissink, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number DPW 09-10

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Joint PhD position at CWI and NKI, Amsterdam
by Gunnar W. Klau 30 Jan '09

30 Jan '09

The National Centre for Mathematics and Computer Science (CWI) and the Netherlands Cancer Institute (NKI), both located in Amsterdam, The Netherlands, invite applications for a jointly advised PhD position on Subnetwork module construction for improved diagnostic classiﬁcation and subtyping CWI is the national research institute for mathematics and computer science in the Netherlands. CWI performs frontier research in mathematics and computer science and transfers new knowledge in these fields to society in general and trade and industry in particular. The newly established Life Sciences group develops algorithms, theory, and models, and performs simulations for a wide range of biological topics with a strong focus on systems biology. The Netherlands Cancer Institute is the only dedicated cancer center in the Netherlands and maintains an important role as a national and international center of scientific and clinical expertise, development and training. Research within the Netherlands Cancer Institute covers all major areas of cancer research, with a strong emphasis on translational research. The Bioinformatics and Statistics group closely collaborates with basic scientists and clinicians and conducts research on a wide range of topics, focusing on integrative bioinformatics. The opening is a research position within the field of bioinformatics/ computational biology and will be a joint appointment between the two institutes. The research will be carried out in close collaboration of the involved partners. The successful candidate will contribute to building better predictors of disease outcome based on functional interaction network modules, which are predictive of a speciﬁed phenotype, e.g., outcome in cancer. To this end, development of new algorithms to detect these modules given a complex interaction graph has to be combined with protocols for building predictive classiﬁers given the activation patterns of the retrieved modules. The ideal candidate has a background in bioinformatics, computer science, statistics, physics, or biology, strong algorithmic and/or machine learning skills, and experience with the analysis of high- throughput data. Applications consisting of motivation letter, Curriculum Vitae, a list of publications, and a list of references should be send by email before 15 March 2009 to Dr. G.W. Klau or Dr. L.F.A. Wessels, who can also supply further information about this position. Please see the website http://www.cwi.nl/en/node/961 for further details.

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Two postdoc vacancies for toxicogenomics bioinformatics at the National Institute for Public Health and the Environment (RIVM)
by Jeroen Pennings 23 Jan '09

23 Jan '09

Please feel free to forward this mail to suitable candidates or to bring them to our attention. Two postdoc vacancies for toxicogenomics bioinformatics at the National Institute for Public Health and the Environment (RIVM) Within the context of the Netherlands Toxicogenomics Centre (NTC), a multidisciplinary research effort will be executed. We aim to develop novel genomics-based methods for assessing human health risk associated with chemical exposures. The project is broken up in different work packages according to specific endpoints of toxicity (carcinogenesis, immune toxicity, reproductive toxicity, organ toxicity), and an overarching work package devoted to bioinformatics. The two postdocs will provide bioinformatics support for the analysis of transcriptomics data as well as emerging omics data (e.g. proteomics, metabolomics, SNPs, miRNA). Multi-platform experimental and literature data will be integrated to identify genes and pathways involved in toxicological mechanisms. This will be used to develop in silico systems biology models for toxicology prediction in research models appropriate for the other work packages. Systems toxicology models will be validated regarding translation to humans and applicability in regulatory decision making. We offer an exciting working environment in a fast developing scientific field. Experience with bioinformatics, and the ability to connect mathematical approaches with biology are prerequisites. The work place will be Bilthoven; affiliations will be with Maastricht University. The salary will be at the level 10 according to the Collective Employment Agreement of the Dutch Universities. For more general information, please visit http://www.toxicogenomics.nl. For more specific information contact: Dr. J. Pennings, 030-2742214, jeroen.pennings(a)rivm.nl Please send applications ultimately February 9, 2009, to: Prof. dr. H. van Loveren, RIVM PO Box 1 3720 BA Bilthoven the Netherlands ---------------------------------------------------------------------------------------------------- Jeroen Pennings National Institute for Public Health and the Environment (RIVM) Laboratory for Health Protection Research (GBO) P.O.Box 1, 3720 BA Bilthoven, The Netherlands T: +31 (0)30 - 274 2214 F: +31 (0)30 - 274 4446 E: Jeroen.Pennings(a)rivm.nl ---------------------------------------------------------------------------------------------------- Disclaimer RIVM

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L'Evolution aujourd'hui: à la croisée de la biologie et des sciences humaines
by Jacques van Helden 22 Jan '09

22 Jan '09

L'Académie Royale de Belgique organise un colloque de 3 jours sur le thème de l'Evolution. Attention, le nombre de places est restreint, si vous désirez y assister il vaudrait mieux ne pas traîner pour vous inscrire. Cordialement, Jacques van Helden Jacques van Helden <Jacques.van.Helden(a)ulb.ac.be> http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Laboratory of Genome and Network Bioinformatics Université Libre de Bruxelles.

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Vacancy Genomics Database Developer
by Roland Siezen 21 Jan '09

21 Jan '09

Dear all, We have a vacancy for a Genomics Database Developper which needs to be filled urgently. Interested candidates are invited to send in their CV, including names of referees. Please also kindly forward this email to your colleagues who are interested. many thanks Prof. Roland J. Siezen Bacterial Genomics Group CMBI 260, room 21 Radboud University NIjmegen Medical Centre / NCMLS PO Box 9101, 6500HB Nijmegen Tel: 31-24-3619559 Fax: 31-24-3619395 email: r.siezen(a)cmbi.ru.nl <mailto:r.siezen@ncmls.ru.nl> www.ncmls.ru.nl/cmbi <http://www.ncmls.ru.nl/cmbi>

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