- BBClist - maillist.psb.ugent.be

Research Informatics Scientist at VIB BITS
by Alexander Botzki | VIB | 18 Dec '14

18 Dec '14

VIB is looking to expand its Institute-wide bio- and research informatics and training platform, BITS, with a research informatics scientist. You will be employed in the Bioinformatics Training and Service (BITS) facility of VIB whose mission is to provide research informatics resources and services to VIB and to promote education in bioinformatics. You will be responsible for the technical support for end users of VIB’s electronic lab notebook system and the delivery of on-site training sessions. You will also provide support to individual scientists to solve bio- and research informatics bottlenecks and problems. You will play a key role in setting up bioinformatics tools and infrastructure to enable processing, analysis, visualization and dissemination of integrated OMICS datasets. Profile You have a PhD Degree in Biology, Biomedical Sciences, Bioinformatics or a related degree. Strong experience of electronic lab notebook systems, preferably E-Notebook, and Information management systems (document management, data repositories,…) is required. Strong experience with bioinformatics methods, databases, and managing larger 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. Working knowledge of basic principles of laboratory experiments using standard biological techniques (bioassays, instrumentation, animal experimentation,…) is desirable. Experience with training/teaching of students/end-users is beneficial. Working knowledge of computer technology (databases, client-server architectures, Windows, Mac, Linux operating systems, Citrix) is beneficial. Excellent knowledge of English, communication and teaching skills and the ability to interact proactively with research scientists and IT-personnel are essential requirements. How to apply? See http://www.vib.be/en/jobs/Pages/Research-Informatics-Scientist.aspx

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2 PhD student positions in computational biology at University of Antwerp
by Kris Laukens 18 Dec '14

18 Dec '14

Dear all, we are currently looking for two new PhD students to strengthen our team: 1. PhD student in bioinformatics of immune-response More info: http://www.biomina.be/careers/immunobioinformatics-2015 <http://www.biomina.be/careers/immunobioinformatics-2015> 2. PhD student position in computational drug discovery & metabolomics More info: http://www.biomina.be/careers/computational-drug-discovery-2015 <http://www.biomina.be/careers/computational-drug-discovery-2015> Feel free to spread the news to any potentially interested candidates. Kind regards Kris Laukens -- Advanced Database Research and Modelling (ADReM) University of Antwerp Middelheimlaan 1, G.219, B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)uantwerpen.be W www.uantwerpen.be/en/staff/kris-laukens/ Biomedical Informatics research center Antwerpen (biomina) Wilrijkstraat 10, B-2650 Edegem, Belgium W www.biomina.be

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Fwd: Vacancy for a web-developer at PDBe
by Wim Vranken 17 Dec '14

17 Dec '14

Dear all, For those with an interest in web development, a position is available at the EBI, see below. Best, Wim Begin forwarded message: > Hi all, > > We are looking to recruit an experienced Web Front-End Developer with an interest in biological data to work within the Protein Data Bank in Europe team (PDBe; pdbe.org) at the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK). > > For more information, please surf to: > > http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=53259&aid=15470 > > Feel free to pass the information on to any potentially interested and qualified people you may know. > > Thanks! > > --Gerard > > --- > Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK > gerard(a)ebi.ac.uk ..................... pdbe.org > Secretary: Pauline Haslam pdbe_admin(a)ebi.ac.uk > _______________________________________________ > bmrblist mailing list > bmrblist(a)lists.bmrb.wisc.edu > http://lists.bmrb.wisc.edu/mailman/listinfo/bmrblist

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FW: Next generation supercomputing in Flanders: value creation for your business !
by Katrijn Vannerum 16 Dec '14

16 Dec '14

Invitation to The Hercules VSC Industry day 27/01/15 Kind regards, Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01D01927.7F1D7400] From: Alexander Botzki | VIB | <Alexander.Botzki(a)vib.be<mailto:Alexander.Botzki@vib.be>> Subject: FW: Next generation supercomputing in Flanders: value creation for your business ! Date: 16 Dec 2014 11:04:50 GMT+2 To: Lennart Martens <lennart.martens(a)vib-ugent.be<mailto:lennart.martens@vib-ugent.be>>, Wim Vranken <wim.vranken(a)vib-vub.be<mailto:wim.vranken@vib-vub.be>>, Mark Fiers <mark.fiers(a)cme.vib-kuleuven.be<mailto:mark.fiers@cme.vib-kuleuven.be>>, Yvan Saeys <yvan.saeys(a)irc.vib-ugent.be<mailto:yvan.saeys@irc.vib-ugent.be>>, Wouter Van Delm <Wouter.VanDelm(a)vib.be<mailto:Wouter.VanDelm@vib.be>>, Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be<mailto:frederik.coppens@psb.vib-ugent.be>>, Ligia Mateiu <ligia.mateiu(a)molgen.vib-ua.be<mailto:ligia.mateiu@molgen.vib-ua.be>>, Bart Smets <bart.smets(a)molgen.vib-ua.be<mailto:bart.smets@molgen.vib-ua.be>>, Els Herregods | VIB | <els.herregods(a)vib.be<mailto:els.herregods@vib.be>> Cc: Diether Lambrechts <Diether.Lambrechts(a)med.kuleuven.be<mailto:Diether.Lambrechts@med.kuleuven.be>>, Stuart Maudsley <stuart.maudsley(a)molgen.vib-ua.be<mailto:stuart.maudsley@molgen.vib-ua.be>>, Steven Maere <steven.maere(a)psb.vib-ugent.be<mailto:steven.maere@psb.vib-ugent.be>>, Peter Tompa <peter.tompa(a)vib-vub.be<mailto:peter.tompa@vib-vub.be>>, Jurgen Del-Favero <jurgen.delfavero(a)molgen.vib-ua.be<mailto:jurgen.delfavero@molgen.vib-ua.be>>, Jeroen Raes <jeroen.raes(a)vib-kuleuven.be<mailto:jeroen.raes@vib-kuleuven.be>>, Frederic Rousseau <frederic.rousseau(a)switch.vib-kuleuven.be<mailto:frederic.rousseau@switch.vib-kuleuven.be>>, Joost Schymkowitz <joost.schymkowitz(a)switch.vib-kuleuven.be<mailto:joost.schymkowitz@switch.vib-kuleuven.be>>, Joost Schymkowitz <joost.schymkowitz(a)switch.vib-kuleuven.be<mailto:joost.schymkowitz@switch.vib-kuleuven.be>>, Yves Van de Peer <yves.vandepeer(a)psb.vib-ugent.be<mailto:yves.vandepeer@psb.vib-ugent.be>>, Kevin Verstrepen <Kevin.Verstrepen(a)biw.vib-kuleuven.be<mailto:Kevin.Verstrepen@biw.vib-kuleuven.be>> Dear colleagues, Please find below an invitation from the Hercules foundation on the Next generation supercomputing in Flanders. Please feel free to distribute in your network. Best regards, Alex From: Caroline Volckaert [mailto:Caroline.Volckaert@herculesstichting.be] Sent: maandag 15 december 2014 15:43 To: Jo Bury | VIB | Cc: Katrina Wright | VIB |; Sooike Stoops | VIB | Subject: Next generation supercomputing in Flanders: value creation for your business ! Geachte heer, Met de “Industry Day” organiseert het VSC (Vlaams Supercomputercentrum) voor het eerst een evenement waar bedrijven informatie krijgen over het potentieel van het gebruik van supercomputing voor hun bedrijf, aangevuld met hoe de VSC supercomputing infrastructuur te gebruiken. We zijn erin geslaagd een boeiend programma samen te stellen met sprekers uit enerzijds buitenlandse supercomputercentra die getuigen over hun ervaring met industriële partners en anderzijds enkele Vlaamse bedrijven die reeds de opportuniteiten van supercomputing ontdekten! Deelname is gratis mits registratie vóór 16 januari 2015 op www.vscentrum.be<http://www.vscentrum.be/> U bent van harte welkom ! Graag hadden wij op u een beroep gedaan om dit event zo breed mogelijk aan te kondigen. Mogen wij daarom vragen deze uitnodiging binnen uw organisatie te verspreiden? Mocht u meer informatie wensen, aarzel niet ons te contacteren hierover. Alvast hartelijk dank voor uw medewerking. Met vriendelijke groeten Caroline Volckaert stafmedewerker Tel ++ 32 (0)2 212 94 05 caroline.volckaert(a)herculesstichting.be<mailto:caroline.volckaert@herculesstichting.be> www.herculesstichting.be<http://www.herculesstichting.be/>

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vacature Centrum vor Medische Genetica Gent: junior software developer
by Björn Menten 12 Dec '14

12 Dec '14

Junior Software Developer: analyse van Next Generation Sequencing data binnen de genetische diagnostiek Werkomgeving Het Centrum voor Medische Genetica Gent (CMGG) is verantwoordelijk voor het opsporen en diagnosticeren van genetische afwijkingen bij kinderen, volwassenen alsook in prenatale context. Wij zijn op zoek naar een software developer die ons bioinformatica-team kan versterken. U zal instaan voor de ontwikkeling van webinterfaces voor de analyse van genetische data en het beheer van genetische data gegenereerd door onze sequencing faciliteit. Werkzaamheden Als (bio-)informaticus zijn je voornaamste taken: • Ontwikkelen en beheren van webapplicaties voor de analyse van genetische data • Ontwikkeling en implementatie van (bestaande) algoritmes voor data analyse van next generation sequencing data • Het runnen van verschillende diagnostische pipelines/flows • Managen (backuppen, activeren) van de data die door de sequencing faciliteit gegenereerd wordt Jouw profiel Wij zoeken een informaticus die de volgende kennis en ervaring met zich meebrengt: • Bachelor in de (toegepaste) informatica of bioinformatica of equivalent door ervaring • Programmeer ervaring met Python, Perl of andere scripting taal • Vertrouwt zijn met een linux/unix ontwikkelingsomgeving • Ervaring met JavaScript, HTML en CSS • Kennis, ervaring en/of interesse in user interface design • Werkervaring in web application development • Ervaring in de genetica is niet nodig, interesse hierin is echter wenselijk • Je neemt initiatief, bent analytisch, stressbestendig en inventief • Je werkt goed in groep • Goede kennis van Nederlands en Engels Interesse? Wil je meer informatie over de functie dan kun je contact opnemen met Björn Menten, via telefoonnummer: +32 (0)9 3325284 of email: bjorn.menten(a)ugent.be<mailto:bjorn.menten@ugent.be> www.cmgg.be<http://www.cmgg.be>

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Invitation to the 2015 GIGA Day
by Marilou Ramos Pamplona 11 Dec '14

11 Dec '14

Dear BBC colleagues, We cordially invite you to the 2015 GIGA Day symposium entitled "Current Advances in Medical Genetics and Genomics," which will take place on 27 January 2015, Tuesday, 09h00-17h00 at the Amphis Europe of the University of Liège. Invited speakers: Peter Fraser (Babraham Institute, Cambridge), Bart de Strooper (VIB, KU Leuven), Miikka Vikkula (de Duve Institute, UC Louvain), Jeroen Raes (VIB, KU Leuven), Nicola Pirastu (University of Trieste, Italy) and Matthew Robinson (University of Queensland, Australia) Information on the PROGRAM, REGISTRATION, ABSTRACT SUBMISSION (Deadline: 31 December) : www.giga.ulg.ac.be/jcms/c_2068318/fr/giga-day-2015 We look forward to meeting you in Liège in January! Sincerely, The 2015 GIGA Day Organizing Committee Prof Michel GEORGES, Coordinating scientist

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N2N RNA-sequencing mini-symposium on Jan 14, 2015 in Ghent.
by Katrijn Vannerum 10 Dec '14

10 Dec '14

Dear, The N2N Vandesompele lab organises a RNA-sequencing mini-symposium on Jan 14, 2015 in Ghent. Registration open. Abstracts will be added soon. vandesompelelab.ugent.be/rna_seq/<http://vandesompelelab.ugent.be/rna_seq/> You're kindly invited. Katrijn Vannerum Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01D0146B.B92C0370]

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[Stage] Internships call - Java Programming
by Johann Pellet 09 Dec '14

09 Dec '14

Dear all, We are pleased to announce 2 internships position at the European Institute for Systems Biology and Medicine (EISBM - Lyon, France): Internship 1: 6-month Java Programming Internship: France & Luxembourg Employer: CNRS Website: http://www.eisbm.org/ Location: CNRS-EISBM, Lyon, France & LCSB, Luxembourg Expires: 15/12/2014 Internship allowance: € 436.00 per month Qualifications: Undergraduate - Bachelor's degree Employment type: Temporary Job hours: Full-time Duration: 6 months Starting date: Beginning of 2015 Key words: Programming, Java, graphical languages, network representation, Systems Biology An internship position is available as part of the eTRIKS (European Translational Research Information and Knowledge Management Services) project, funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. For approximately 2 months the intern will be working in Luxembourg with our collaborators at the Luxembourg Center for Systems Biomedicine. The goal of this project is to develop a translator from Systems Biology Graphical Notation standard (file exported from CellDesigner software) into the LCSB MapViewer environment (Java). The translator will be developed in collaboration with LCSB Java programming experts. Prior knowledge in Systems Biology domain is not necessary. This is an excellent opportunity to get introduced into Systems Biology area and participate in a highly collaborative translational medicine project. Required Skills: Proficiency in Java programming and good communication skills in English. Recommended Skills: Knowledge of SQL and PostgreSQL would be helpful. Enthusiastic and motivated candidates are encouraged to contact Prof. Charles Auffray jobs(a)eisbm.org with a CV and a brief description of their programming skills. Internship 2: 6-month Java Programming Internship: Lyon, France Employer: CNRS Website: http://www.eisbm.org Location: CNRS-EISBM, Lyon, France Expires: 15/12/2014 Internship allowance: € 436.00 per month Qualifications: Undergraduate - Bachelor's degree Employment type: Temporary Job hours: Full-time Duration: 6 months Starting date: Beginning of 2015 Key words: Programming, Java, Graph Database, Neo4j, graphical representation, network representation, Systems Biology An internship position is available as part of the eTRIKS (European Translational Research Information and Knowledge Management Services) project, funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. The goal of the project is to develop a code in Java for translating a graphical model in Systems Biology Graphical Notation (SBGN, www.sbgn.org) into the Neo4j Graph Database representation. Systems Biology Graphical Notation standard (SBGN-ML file format) is used for unambiguous biological network representation. Transformation into the graph database environment will allow easier access to various data, graph database querying and network analysis. This position allows an intern to participate in a state-of-the-art EU systems biomedicine project. Required Skills: Proficiency in Java programming, good communication skills in English. Enthusiastic and motivated candidates are encouraged to contact Prof. Charles Auffray jobs(a)eisbm.org with a CV and a brief description of their programming skills.

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'Revolutionizing Next-Generation Sequencing: Tools and Technologies', the top NGS conference of 2015; Registration Deadline is 15 December
by Mark Veugelers | VIB | 08 Dec '14

08 Dec '14

REVOLUTIONIZING NEXT-GENERATION SEQUENCING: Tools and Technologies 15-16 JANUARY 2015 // LEUVEN, BELGIUM We would like to invite you to 'Revolutionizing Next-Generation Sequencing: Tools and Technologies', a VIB conference taking place in the heart of Europe (Leuven, Belgium) from 15-16 January, 2015. The meeting features several top scientists in the field, as well as many speakers from top management scientists of companies advancing the state of the art in NGS. The meeting will include sessions on Population Sequencing, Sample Prep, Next-Gen Platforms, Single-Cell Genomics, Epigenomics, Next-Gen Transcriptomics, Ultra-long reads and Assembly, and Bioinformatics. Join us for great talks and networking with colleagues in the field; our meeting has already attracted more than 250 participants ! SPEAKERS Academic Jan Korbel (EMBL), Xu Xun (BGI), Eske Willerslev (Centre for GeoGenetics), David Jaffe (Broad Institute), Mark Akeson (UCSC), Evan Eichler (University of Washington), Fuchou Tang (Peking University), Mats Nilsson (SciLifeLab), Ido Amit (Weizmann Institute), Ryan Lister (University of Western Australia), Jin Billy Li (Stanford University), James Eberwine (University of Pennsylvania), Patrick Stahl (SciLifeLab and Karolinska Institute), Nick Loman (University of Birmingham), James Taylor (Johns Hopkins University), Peter Van Loo (Cancer Research UK) Industry Alex Dickinson (Illumina), Radoje Drmanac (Complete Genomics), Mike Lelivelt (Thermo Fisher/Life Technologies), Marie Mikkelsen (Samplix), Jeremy Gillespie (Enzymatics), Max Van Min (Cergentis), Gordon Hamilton (Picoseq), Johnsee Lee (Personal Genomics), Paul Schaffer (Roche), David Johnson (Gigagen), Jay West (Fluidigm), Tobias Ost (Cambridge Epigenetix), Sharon Squazzo (Diagenode), Annabelle Gerard (HiFiBio), Alexander Seitz (Lexogen), Gary Schroth (Illumina), Mikael Samuelsson (Spatial Transcriptomics), Ralph Vogelsang (Pacific Biosciences), Han Cao (BioNano Genomics), John Oliver (Nabsys), Mike Furness (DNAnexus), Hans Karten (Genalice), Roald Forsberg (CLC Bio-Qiagen), Pieter van Rooyen (Edico Genome) MEMBERS OF THE ORGANIZING COMMITTEE Mark Veugelers, VIB Headquarters, Gent Peter Verhasselt, VIB Nucleomics Core Facility, Leuven Albena Jordanova, VIB Department of Molecular Genetics, University of Antwerp Halina Novak, VIB Headquarters, Gent Evy Vierstraete, VIB Headquarters, Gent [cid:image001.jpg@01D012FA.CF964480] [cid:image002.jpg@01D012FA.CF964480]<http://vib.createsend1.com/t/r-l-mhlkdll-l-d/>

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postdoc position in evolutionary systems biology
by Katrijn Vannerum 03 Dec '14

03 Dec '14

POSTDOC IN EVOLUTIONARY SYSTEMS BIOLOGY The VIB/UGent Department of Plant Systems Biology (PSB, www.psb.vib-ugent.be<http://www.psb.vib-ugent.be>) is a world-leading plant science institute with the mission to integrate genetics, genomics and computational biology to unravel the biology of plants and to further explore the potential of plants to build a sustainable world. The Evolutionary Systems Biology lab at PSB (http://www.psb.vib-ugent.be/esb) is looking for a talented and highly motivated postdoc to work on modeling the evolution of transcriptional systems from a mechanistic perspective (3 year position, extendable to 4 years, available immediately). Project description The goal of the Evolutionary Systems Biology lab is to understand how biological systems work and how they evolve. In this project, we will use fine-grained, sequence-based genotype-phenotype mapping models in combination with population-based evolutionary algorithms to study the evolution of molecular systems through gen(om)e duplication under stabilizing, directional and fluctuating selection. We will in particular study the mechanisms by which duplicates in gene regulatory networks may diverge, and the impact of duplications on the origin of emergent system properties such as robustness and evolvability. The framework to be developed will also be instrumental in investigating the impact of neutral versus adaptive evolutionary mechanisms on the origin of complexity in gene regulatory networks, an issue that has thus far remained understudied from a mechanistic modeling perspective. Profile - You have a PhD in Computational Biology, Mathematics, Physics, Engineering, Biological Engineering or Computer Science. - You have a strong interest in molecular evolution; experience in the use of mathematical techniques to model the evolution of biological systems is a major plus. - You have a passionate interest in pursuing fundamental research in a stimulating and competitive field of science. - You have an outstanding publication record in peer-reviewed international journals. - You found a good balance between working in a team and working independently. - Experience in guiding MSc or PhD students is a plus. - You are fluent in English (spoken and written) and at least one programming language. - You are meticulous, well organized, responsible and self-critical. - You take pride in delivering high-quality work. - You can think outside the box. We offer: - An exciting work environment in a top research institute. - The opportunity to be part of a young, dynamic, interdisciplinary and international team. - An attractive salary that will be based on previous experience and skills. Please e-mail your CV, a letter of motivation and the contact details of three referees to Prof. Dr. Ir. Steven Maere (steven.maere(a)psb.vib-ugent.be<mailto:steven.maere@psb.vib-ugent.be>). More info about the lab can be found at http://www.psb.ugent.be/esb/. The position is available immediately. Applications are accepted until the position is filled.

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