July 2009 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/ L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

1 1

progress report
by fred opperdoes 18 Jul '09

18 Jul '09

Dear All, We got almost at 350 signatures in 4 days for our petition "Keep BEN Alive" http://bit.ly/fJ5Ep . Not bad at all:-). We got also strong support from users of many EMBNet Nodes in the other European countries . Don't stop now!. Maybe we will get 400 signatures this WE? Thank you all! Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf

1 0

GMOD Community Meeting, 6-7 August, 2009, Oxford UK
by Dave Clements 18 Jul '09

18 Jul '09

There will be a GMOD Community Meeting, 6-7 August, 2009 at the University of Oxford, in Oxford, UK. GMOD (http://gmod.org) is a collection of interoperable, open-source software components for managing, visualizing, annotating, and sharing biological data. GMOD is also a community of users and developers addressing common challenges with their biological data. The popularity of next generation sequencing and other high-throughput methods has made this GMOD meeting particularly timely. GMOD meetings are an excellent opportunity to learn best practices from other researchers, to meet GMOD users and developers, and to learn and affect what is coming in the project. As with previous meetings, there will be a mixture of project talks, component-focused talks, and user talks. Registration for the meeting is now open and space is available on a first come, first served basis. Attendance is limited to the first 55 people to register. The meeting cost is £50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more. Please join us in Oxford this August. Cheers, Dave Clements GMOD Help Desk -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting

1 0

Benelux Bioinformatics Conference 2009 in Liège, first announcement
by Pierre Geurts 17 Jul '09

17 Jul '09

Dear Colleagues, This email to announce you that the next Benelux Bioinformatics Conference (BBC'09) will be organised in Liège, Belgium. The key dates are as follows: - Conference: December 14-15, 2009 - Deadline for abstract submission: October 11, 2009 Please mark these dates in your agenda! Further information will be sent in August. Best regards, Pierre Geurts

1 0

Two open positions at BITS, VIB's Bioinformatics Training and Service Facility
by Mark Veugelers 14 Jul '09

14 Jul '09

[cid:image001.jpg@01CA0473.359D93B0] VIB (http://www.vib.be) is looking to expand its Institute-wide bioinformatics platform, BITS (Bioinformatics Training and Services; http://www.bits.vib.be) with two positions: 1. Next-Generation Sequencing Bioinformatics Analyst 2. Bioinformatics Trainer Job descriptions: 1. Next-Generation Sequencing Bioinformatics Analyst You will play a key role in the processing, analysis, visualization and dissemination of genomics datasets to support research groups with the analysis of genome-wide next-generation sequencing experiments. Responsibilities include the analysis of next-generation DNA sequence data from multiple platforms, including alignment, genome assembly and annotation, genome re-sequencing, microRNA deep-sequencing, Chip-seq, gene expression analysis, SNP-analysis etc....for multiple species, including human. In this position, you will also meet with researchers and group leaders to discuss study design and sequence analysis strategies. You will assist in the analysis of the generated data and disseminate information through comprehensive research reports and presentations. Additionally, you will evaluate new and existing algorithms, software (commercial and open source) and computer infrastructure requirements to efficiently set up data analysis pipelines. You will have close interactions with other VIB facilities such as the VIB Microarray Facility and the VIB Genetic Service Facility. Profile We are seeking an experienced bioinformatics scientist for this position. Ideally, you will have a Master's or PhD Degree in Biology, Biomedical Sciences, Bioinformatics or a related degree. Strong experience with bioinformatics methods, databases, software (especially sequence analysis tools), statistics and managing large data sets is required. A good working knowledge of Linux/Unix and programming languages such as Perl, SQL, R, Java, Python or C would be desirable. Excellent collaboration, communication and reporting skills are also a requisite. Familiarity with next generation DNA sequencing technologies is a plus. Contact Marijke Lein (HR Director VIB) - Marijke.Lein(a)vib.be<mailto:Marijke.Lein@vib.be> 2. Bioinformatics Trainer As Bioinformatics Trainer, you will be responsible for training/teaching of VIB-scientists in the efficient use of the latest bioinformatics software and database tools. This will include organizing, hosting and teaching workshops/tutorials/seminars on how to efficiently access and use life sciences data and how to use bioinformatics software and databases, both at the beginner and advanced level. You will provide bioinformatics user support, including updating the BITS website, troubleshooting and helping in the analysis of genome, transcriptome, proteome, imaging data etc... You will also provide support to individual scientists to solve bioinformatics bottlenecks and problems. You will review and decide on the acquisition of new software tools/databases at the institutional level. We offer: Access to a broad platform of science and technology in a stimulating environment. Interactions and collaborations with top level scientists and bioinformaticians. A unique opportunity to expand your experience and knowledge of science and bioinformatics and to build a network of scientists and bioinformaticians. Profile * You have a university degree in Sciences (Biology/Biochemistry/Biotechnology/Bioinformatics) with several years of Bioinformatics experience * You are familiar with the latest bioinformatics tools and databases (Ensembl, TAIR, ...), sequence analysis, and have at least basic knowledge of computational programming in common scripting languages, such as (Bio)-perl or (Bio)-python. * You have demonstrated capabilities in data analysis using commercial and freeware software. Excellent knowledge of data/literature mining is a plus. * Knowledge of microarray data analysis and statistics is a plus. * Excellent knowledge of English, communication and teaching skills and the ability to interact proactively with research scientists are essential requirements. * Organizational talent. Contact Marijke Lein (HR Director VIB) - Marijke.Lein(a)vib.be<mailto:Marijke.Lein@vib.be>

1 0

1st Symposium on Systems Genetics; October 1-2, 2009 in Groningen
by Morris Swertz 14 Jul '09

14 Jul '09

FYI: ------------------------------------------------------------------------ Appologies for multiple postings.

1 0

Keep BEN alive
by fred opperdoes 13 Jul '09

13 Jul '09

Dear colleagues, I have now created an on-line petition "Keep BEN alive" where you can support our initiative to try and reverse the unfortunate decision of the Belgian Science Policy makers to stop the funding of BEN, the Belgian bioinformatics server. Please visit http://www.petitionspot.com/petitions/belgianben/ to sign this petition. Thank you for your support, Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf

1 0

Ghent university is looking for a tech transfer manager and a PhD student in bioinformatics ...
by Yves Van de Peer 08 Jul '09

08 Jul '09

--------------------------------------------- The computational systems biology team in the Bioinformatics & Evolutionary Genomics group (http://bioinformatics.psb.ugent.be/) at the VIB Department of Plant Systems Biology studies the structure, function and evolution of biological networks in multiple organisms. As part of its research, the team continuously develops, in collaboration with other Flemish universities, novel software tools for the integration of large-scale data sets and the inference of regulatory networks. To strengthen the technology transfer mission of the department, we are currently looking for a Systems biology technology transfer manager As a member of VIB's technology transfer team, you will be responsible for the commercialization of our software tools and, in close collaboration with the research scientists, for the development of software usability improvements. Responsibilities include: * Developing and implementing software improvements and extensions, especially with regards to usability improvement (user interface, output visualization, etc.) and integration of multiple tools (often written in different programming environments). * Setting up collaborations and providing consultancy services for software testing and validation: definition of suitable test data sets, NDA, running software and analyzing output together with the company's bioinformatics team. * Writing project applications (e.g. IWT) for proof-of-concept studies. * Participating in meetings with bio, pharmaceutical, agbio and food companies to present our in-house systems biology software tools. Profile: * PhD in computational or biological sciences, with experience or strong interest in computational systems biology. * Fluent in English. * Excellent communication skills. * Strong interest in technology transfer and research commercialization. * Fluent in multiple programming languages (Java, Matlab, Perl, etc.). * Work experience in industry is a plus. Contact: If you have the necessary skills and would like to be considered, please send your resume by email to Yves Van de Peer ( yves.vandepeer(a)psb.ugent.be <mailto:yves.vandepeer@psb.ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). Applications will be accepted until the position is filled. --------------------------------------------- The Laboratory of Protistology and Aquatic Ecology and the Bioinformatics Group of the VIB Department of Plant Systems Biology, University of Ghent, Belgium are seeking a PhD student in Bioinformatics Analysis of Diatom Life Cycle Regulation Job description: We are looking for a motivated and enthusiastic PhD student for the Laboratory of Protistology and Aquatic Ecology working on diatom biology and physiology. You will be involved in a project where transcriptomics and genomic investigations are used to understand key aspects of diatom life cycle regulation. Your work will be highly complementary to ongoing research in the group, where cDNA-AFLP, microarray, and interaction data related to diatom cell division, growth and sexual reproduction are generated. You will be responsible for the application and development of computational methods to analyze and integrate these data, to be performed in the Bioinformatics group of PSB/VIB, which has strong experience in genomics data analysis and large computer facilities (http://bioinformatics.psb.ugent.be/) You will collaborate with both experimental and computational biologists to obtain an understanding of diatom life cycle control. Profile: * You have a degree in Bioinformatics, Informatics, Biology, Biotechnology, Biochemistry or Bioengineering * You are motivated by Biology and the new opportunities given to enlarge knowledge through the analysis of Genome data * You read, write and speak English fluently * You have good communication skills. * You are a team player. You are independent and like to take initiative. You are flexible. We offer: Contract of 1 year, within Ghent University, with the possibility of prolongation. Start date: As soon as possible, the position remains vacant until a suitable candidate is found. Further information can be obtained by contacting Prof. Wim Vyverman ( Wim.Vyverman(a)ugent.be <mailto:Wim.Vyverman@ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) or Prof. Yves Van de Peer ( yves.vandepeer(a)psb.vib-ugent.be <mailto:yves.vandepeer@psb.vib-ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Application: Send your letter of motivation, your CV and references to Prof. Wim Vyverman ( Wim.Vyverman(a)ugent.be <mailto:Wim.Vyverman@ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Biochemistry] Open letter to minister Sabine Laruelle about BEN
by fred opperdoes 07 Jul '09

07 Jul '09

Dear Colleagues, Many of you may be familiar with te functionalities of BEN, the Belgian EMBnet Node, our Belgian Bioinformatics server. Many of you have followed one or more of its courses as an introduction to sequence analyses and bioinformatics or have used or are still using its databases and search facilities. This national service, jointly operated by the VUB and the ULB and financially supported by the Belgian Science Policy, is about to be dismantled because of discontinuing government funding. In an effort to reverse this unfortunate decision I have written an open letter (see below) to Minister Laruelle of Belgian Science Policy. I would like to ask everybody who agrees with my views about this decision to send a similar letter to the responsible minister and the other responsible persons mentioned below with a copy to Guy Bottu (gbottu(a)vub.ac.be) and to the secretary of the BMB (info(a)biochemistry.be) Prof. Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf Bruxelles, le 6 juillet 2009 Mme Sabine Laruelle Ministre des PME, des Indépendants, de l'Agriculture et de la Politique Scientifique Avenue de la Toison d’Or 87 1060 Bruxelles Mr. Philippe Mettens Président du Comité de Direction de la Politique Scientifique fédérale Rue de la Science 8 1000 Bruxelles Mr. Christophe Hardy Directeur de cabinet Avenue de la Toison d’Or 87 1060 Bruxelles Lettre ouverte Madame, Messieurs, Le contrat passé entre Belspo et "Belgian EMB Net Node" (BEN) a pris fin le 30 avril 2009. Le seul scientifique encore responsable des ordinateurs et de l’ensemble de l’infrastructure est sans emploi depuis le 1er mai 2009. Il a cependant – et bénévolement - maintenu un contact par internet à partir de son domicile. On s’attend donc à ce que le réseau BEN disparaisse sous peu. La Belgique se trouvera alors revenue à l’âge de la pierre en ce qui concerne la bioinformatique. Pendant de nombreuses années, l’infrastructure matérielle et logicielle de même que les membres de l’équipe BEN ont rendu des services inestimables à la communauté scientifique et à l’industrie. Plus de mille jeunes chercheurs ont fait leurs premières armes en bio- informatique grâce aux instructeurs du réseau BEN. Personnellement j’ai envoyé au cours des quinze dernières années une centaine de mes étudiants suivre les cours organisés par BEN. Des milliers de scientifiques ont non seulement utilisé les ordinateurs et les programmes spécialisés développés par BEN, mais ils ont également profité de l’expertise et du savoir-faire des membres de l’équipe. A l’heure actuelle, BEN a créé et rendu opérationnelles 75 banques de données. Elles sont consultées quotidiennement par des chercheurs belges et étrangers grâce aux interfaces développées par l’équipe BEN. BEN fait partie d’un réseau européen de bioinformatique dans lequel chaque pays possède son propre centre. L’abandon du centre belge signifierait une perte considérable non seulement pour la Belgique mais pour l’Europe entière. Cette décision des pouvoirs publics belges d’abandonner BEN pourrait bien apparaître comme scandaleuse aux yeux de la communauté scientifique internationale. J’ose espérer que les responsables belges reconsidèrent la situation et annulent cette décision plus que malheureuse avant que ne s’installent des dommages irréparables. En espérant une réponse favorable, je vous prie d’agréer l’expression de ma haute considération. Prof. F. Opperdoes Professeur de Biochimie, Parasitologie et Bioinformatique Secrétaire de la Société Belge de Biochimie et de Biologie Moléculaire Brussel, 6 juli 2009 Mevrouw Sabine Laruelle Minister van KMO's, Zelfstandigen, Landbouw en Wetenschapsbeleid Guldenvlieslaan 87 1060 Brussel De Heer Christophe Hardy Kabinetsdirecteur Guldenvlieslaan 87 1060 Brussel De Heer Philippe Mettens Voorzitter van het Direktiecomité van het Federaal Wetenschapsbeleid Wetenschapsstraat 8 B-1000 Brussel Open brief Mevrouw, Mijne heren, Op 30 april 2009 werd het contract van Belspo met de "Belgian EMB Net Node" (BEN) beëindigd. De enige wetenschapper die tot dan nog verantwoordelijk was voor de computers en de gehele infrastructuur is sinds 1 mei werkloos. Hij bedient de computers nog van huis uit via het internet. Het is te verwachten dat binnenkort het netwerk in elkaar stort en dan bevindt België zich op het gebied van de bioinformatica weer in de steentijd. De BEN computers en de leden van het BEN team hebben gedurende vele jaren onschatbare diensten bewezen aan de wetenschappelijk gemeenschap en aan de industrie. Meer dan duizend meestal jonge onderzoekers hebben hun eerste schreden op het gebied van de bioinformatica gezet aan de hand van de BEN instructeurs. Persoonlijk heb ik in de afgelopen vijftien jaar een honderdtal van mijn studenten naar de BEN cursussen gestuurd. Duizenden wetenschappers hebben niet alleen gebruik gemaakt van de gespecialiseerde BEN computers en hun geavanceerde programmas, maar hebben ook kunnen profiteren van de gespecialiseerde kennis van de leden van het BEN team. Op het ogenblik zijn er op BEN 72 databanken operationeel en deze worden dagelijks geconsulteerd via de door het BEN team ontwikkelde web interfaces, niet alleen door Belgische onderzoekers, maar door onderzoekers uit de gehele wereld. BEN maakt onderdeel uit van een Europees netwerk voor bioinformatica met voor ieder land zijn eigen knooppunt. Het wegvallen van het Belgische knooppunt zou niet alleen voor België maar voor heel Europa een groot verlies betekenen. Bovendien zou de internationale wetenschappelijke gemeenschap dit als een schandaal kunnen ervaren. Ik hoop van ganser harte dat de Belgische verantwoordelijken deze ongelukkige beslissing ongedaan kunnen maken voordat er onherstelbare schade is aangericht. Hoogachtend, Prof. Fred Opperdoes Hoogleraar biochemie, parasitologie en bioinformatica UCL Secretaris Belgische Vereniging voor Biochemie en Moleculaire Biologie -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ Biochemistry mailing list Biochemistry(a)icp.ucl.ac.be http://www.icp.ucl.ac.be/mailman/listinfo/biochemistry

1 0

PhD position at the Center for Human Genetics, KULeuven
by Stein Aerts 02 Jul '09

02 Jul '09

PhD position in bioinformatics, next-generation sequencing, and cancer genomics at the Center for Human Genetics, KULeuven The Laboratory of Computational Biology together with the Laboratory for Molecular Pathogenesis of Leukemia have a joint position for a motivated PhD student interested in genomics and systems biology of cancer. Research project The PhD research will focus on high-throughput approaches to further decipher the leukemia genome and to identify novel oncogenic mutations or structural variations that may underlie tumorigenesis. Secondary interest goes out to variations in transcriptional networks and the characterization of the underlying cis-regulatory variations. Available data include gene expression microarray data, GS FLX sequence data of candidate gene sets, and may even include full genome sequence data of multiple cancer patients. The challenge of this project is to handle large amounts of public and in-house genomic data and to use, benchmark, and develop state-of-the- art bioinformatics approaches, while maintaining a clear focus on important biological questions. Profile Master in Engineering, Bioinformatics, Computer Science, Bio- engineering, or equivalent. The candidate we are seeking should have basic programming or bioinformatics skills, with a strong interest in high-throughput technologies and genomics. Having any of the following skills is a plus: linux, R/Bioconductor, Matlab, Perl, Java, MySQL, data mining, clustering, classification, modeling, (bio)statistics, genome browsers. Environment The successful applicant will be hosted by the Laboratory of Computational Biology, headed by Prof. Stein Aerts, and will be in close collaboration with The Laboratory for Molecular Pathogenesis of Leukemia, headed by Prof. Jan Cools. Both labs are part of the Center for Human Genetics at the KULeuven. Contact Interested? Send your CV and motivation letter to stein.aerts(a)med.kuleuven.be Stein Aerts, PhD Laboratory of Computational Biology Center for Human Genetics, KULeuven http://med.kuleuven.be/lcb

1 0