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2009 GMOD Summer School - Europe
by Dave Clements 30 Mar '09

30 Mar '09

Hello, This is a reminder that the application deadline for the 2009 GMOD Summer School - Europe is 6 April, one week from now. The 2009 GMOD Summer School - Europe (http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe) will be held 3-6 August, 2009 at the University of Oxford, as a part of GMOD Europe 2009 (http://gmod.org/wiki/GMOD_Europe_2009) Tuition is £95. GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological data. It is also a community of developers and users dealing with similar challenges. The course offers hands-on training on how to deploy and administer: * Genome / Comparative Genomics Viewers - GBrowse, JBrowse, GBrowse_syn, Apollo * Genome Annotation - Apollo, Artemis-Chado Integration * Databases - Chado, BioMart Please contact the GMOD Help Desk (help(a)gmod.org) if you have questions. Thanks, Dave Clements GMOD Help Desk On Mon, Mar 16, 2009 at 1:48 PM, Dave Clements <clements(a)nescent.org> wrote: > 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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Bioinformatics postdoc position
by AHC van Kampen 29 Mar '09

29 Mar '09

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Vacancy: (Associate) Scientist Bioinformatics at DSM
by Roubos, Hans 27 Mar '09

27 Mar '09

DSM00680 DSM Biotechnology Centre (Associate) Scientist Bioinformatics Delft, the Netherlands DSM - the Life Sciences and Materials Sciences Company DSM creates innovative products and services in Life Sciences and Materials Sciences that contribute to the quality of life. DSM's products and services are used globally in a wide range of markets and applications, supporting a healthier, more sustainable and more enjoyable way of life. End markets include human and animal nutrition and health, personal care, pharmaceuticals, automotive, coatings and paint, electrics and electronics, life protection and housing. DSM has annual sales of almost EUR 8.8 billion and employs some 23,000 people worldwide. The company is headquartered in the Netherlands, with locations on five continents. DSM is listed on Euronext Amsterdam. To learn more about DSM, please visit our website at www.dsm.com<http://www.dsm.com/>. The Challenge DSM Food Specialties develops, produces and markets ingredients and processing aids for the Dairy, Savoury, Beverage and nutritional markets. The Business Group consists of the Business Units Savoury Ingredients, Enzymes & Dairy Ingredients, a Global Sales department, a DSM Biotechnology Center, an Operations organisation and also a number of staff departments. There is a strong cooperation within the with DSM Nutritional Products to develop new ingredients to the market of Functional Food. DSM Biotechnology Center (DBC) is the main center for biotechnological Research & Development and is located in Delft. DBC is focused on the creation of new and improved products for DSM business units such as DSM Food Specialties (DFS), DSM Anti-Infectives (DAI), DSM Nutritional Products (DNP) and DSM Fiber Intermediates (DFI), along with Emerging Business Areas for DSM such as White Biotechnology or Specialty Packaging (EBA-WB, EBA-SP). The DBC Genetics Department serves the different businesses by delivering new and improved strains for the production of biocatalysts and bioproducts by means of classical and GMO strain development and (HT) screening technology. Within the DSM Biotechnology Center, a vacancy occurred within the Genetics department for an (Associate) Scientist Bioinformatics. You will work and represent the bioinformatics discipline within multi-disciplinary project innovation teams. Your challenge will be to apply and improve bioinformatics workflows for the development of new products, microbial production strains and improved processes. The Bioinformatics group is part of the Department of Genetics. Projects will be associated with DSM Bioinformatics platform development and maintenance, (re)sequence data exploration, integrative omics data analysis and/or protein engineering, depending on your expertise. Terms of conditions LOCAL CONTRACT The Ideal We are looking for a Ph.D. in Bioinformatics, Metabolic Engineering or Molecular Biology with a track-record of applying bioinformatics to biotechnological applications. Preferably you have experience with protein engineering, genomics approaches to microbial strain development or fermentation process improvement. You are a multidisciplinary team player, who takes initiative. Personal skills like problem analysis, judgment, creativity, leadership, adaptability characterize your identity. You are a good communicator, preferably fluent in the Dutch and/or the English language. The Reward DSM's wide diversity of disciplines makes it possible to offer employees a great variety of roles throughout their career. For instance, you may start your career in an area related to your education/qualifications, but your future is what you make of it. At DSM we stimulate people to determine their own career path and we encourage international careers. We strive to be an Employer of Choice and ensure that our employees are nurtured and given the opportunity to develop their talents. To learn more about DSM's HR vision and policy, please visit our website at www.dsm.com/careers<http://www.dsm.com/careers> The Procedure The DSM Recruitment and Selection Process is in line with the general procedure outlined elsewhere on our Career World. Please apply on-line (www.dsm.com/careers<http://www.dsm.com/careers>) ref DSM00680 and send your CV & cover letter in English and include information on your current remuneration. Reference check procedures are part of the DSM Recruitment & Selection Process. You will be contacted when these references checks are required. ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Bioinformatics postdoc in Brussels
by Vincent Detours 24 Mar '09

24 Mar '09

Bioinformatics postdoc in Brussels A postdoc position in bioinformatics is available starting in July 2009 at the Université Libre de Bruxelles, Belgium, for 2 years. The successful applicant will join a interdisciplinary team of clinical oncologists, geneticists, molecular biologists and bioinformaticians passionate about basic cancer research and its applications in the clinic. He/she will tackle the integrative analysis of massive breast cancer genome, methylome and transcriptome data sets generated using cutting edge microarray and next generation sequencing platforms. The project addresses both clinical and fundamental problems related to breast 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 pcn2009' in the subject line. Principal investigators in this project are • Marc Abramovicz, IRIBHM – ULB • Vincent Detours, IRIBHM – ULB • François Fuks, Laboratory of Cancer Epigenetics – ULB • Christos Sotiriou, Institut Bordet – ULB Please post the ad (see attached PDF) in your institution and forward it without restriction.

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Call for abstracts Student Council Symposium, Stockholm, June 27th
by Jeroen de Ridder 20 Mar '09

20 Mar '09

CALL FOR ABSTRACTS Submit your abstract today to participate in the 5th Symposium of the International Society for Computational Biology Student Council on June 27th 2009 in Stockholm! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 8 student presentations will be selected from the submitted abstracts. This is your chance to present your work! Awards will be given to best poster and best presentation as well as the runner-ups in both categories. Travel Fellowships are available (see website)! *Submission website:* http://symposium.iscbsc.org/content/submissions *General information:* http://symposium.iscbsc.org/ Important dates: *April 9th:* 5th Student Council Symposium Abstract and Travel Fellowship submission closes *May 2nd:* Travel Fellowship winners notification *May 10th:* Abstract acceptance notification *Registration Fee:* 75 euro (incl. lunch, coffee breaks and abstract booklet) – full ISMB/ECCB registration not required! We look forward to receiving your abstract, Lucia Peixoto Conference Chair, 5th ISCB Student Council Symposium Jeroen de Ridder Conference Co-Chair, 5th ISCB Student Council Symposium

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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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