- BBClist - maillist.psb.ugent.be

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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Bioinformatics position: genotyping and transcriptomics analysis
by Claesson, Marcus 01 Dec '14

01 Dec '14

Bioinformatics position for genotyping and transcriptomics from RNA-Seq data: http://www.ucc.ie/en/hr/vacancies/research/full-details-510713-en.html -- Marcus J. Claesson, PhD Lecturer, School of Microbiology & Alimentary Pharmabiotic Centre University College Cork Western Road, Cork, Ireland Tel: +353-(0)21-4901390 Email: m.claesson(a)ucc.ie<mailto:m.claesson@ucc.ie>

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Position in Computational Protein Design
by Marianne Rooman 01 Dec '14

01 Dec '14

Position in Computational Protein Design (Brussels/Belgium) At : Université Libre de Bruxelles with the possibility of integrating a start-up Function : Product developer Description : Development and application of software for protein optimization (C programming) ; Team work with a business developer Profile : Master in Bioinformatics, Informatics or Bioengineer; Autonomous and voluntary personality; No professional experience required Contract: Fixed-term contract starting in January 2015 Contact: Send your application with your CV and motivation letter to Marianne Rooman (mrooman(a)ulb.ac <mailto:mrooman@ulb.ac>.be)

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[Gtpb] GTPB Training course announcement IB14S - Reminder
by Pedro Fernandes 01 Dec '14

01 Dec '14

REMINDER Dear all The Applications for the Introductory Bioinformatics course, second edition in 2014, IB14S are open IMPORTANT DATES for this Course Deadline for applications: December 4th 2014 <============ Latest notification of acceptance: December 5th 2014 Course date: December 9th - December 12th 2014 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB14S/ this will be a 4 day long introduction that provides basic skills in biological sequence handling and analysis. The last day will be focusing on the analysis of Next Generation Sequencing data at a basic level. This is one of our most popular courses. Applications are approved and accepted in order of arrival and we only have 20 seats. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] IB14S GTPB Training course announcement
by Pedro Fernandes 24 Nov '14

24 Nov '14

Dear all The Applications for the Introductory Bioinformatics course, secode edition in 2014, IB14S are open IMPORTANT DATES for this Course Deadline for applications: December 4th 2014 Latest notification of acceptance: December 5th 2014 Course date: December 9th - December 12th 2014 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB14S/ this will be a 4 day long introduction that provides basic skills in biological sequence handling and analysis. The last day will be focusing on the analysis of Next Generation Sequencing data at a basic level. This is one of our most popular courses. Applications are approved and accepted in order of arrival and we only have 20 seats. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Get in before your time is out - register now for the SB@NL2014 symposium for a great time out in Maastricht
by Diman van Rossum | SB＠NL secretary 21 Nov '14

21 Nov '14

SB@NL | BioSB <http://www.ncsb.nl/> SB@NL2014 symposium: get in before your time is out deadline this Monday, 2014-11-24 Mailing date: 2014 November 21 Message for: BBC mailing list Email address: bbclist(a)psb.ugent.be Dear Madam, Sir, This is your last chance to register and submit an abstract for the SB@NL2014 systems biology symposium, which will be held in Maastricht on 2014 December 15-16. The deadline is set at the end of the forthcoming Monday, 2014 November 24. You wont regret to participate in two exhilarating symposium days packed with numerous front-line presentations, all set against the background of the laid-back city of Maastricht. Come and enjoy by joining your colleagues! The fourth Musketeer, d'Artagnan, stands as a sentinel just outside our building to guard the site of our meeting. Also, film shots of the somewhat popular TV-series Flikken Maastricht were taken recently in the corridor just outside our meeting hall. ............................................................................ .............................. Key symposium information Symposium: SB@NL2014 symposium Theme: Tackling complexity through data integration Dates: 2014 December 15-16 (Monday-Tuesday) Venue: Auditorium, <http://www.maastrichtuniversity.nl/web/Faculties/SBE/Theme/AboutTheSchool.h tm> School of Business and Economics (SBE), University Maastricht, Tongersestraat 53, 6211LM Maastricht Hotel: Amrath Grand Hotel de lEmpereur, Stationsstraat 2, 6221BP Maastricht <http://www.hotel-empereur.nl> www.hotel-empereur.nl Website: <http://www.biosb.nl/sbnl2014> www.biosb.nl/sbnl2014 Programme: <http://www.biosb.nl/sbnl2014/programme> www.biosb.nl/sbnl2014/programme Registration: <http://www.biosb.nl/sbnl2014/registration/registrationform> www.biosb.nl/sbnl2014/registration/registrationform Deadline: 2014 November 24 Abstract: <http://www.biosb.nl/sbnl2014/registration/abstractform> www.biosb.nl/sbnl2014/registration/abstractform Deadline: 2014 November 24 Speakers: <http://www.biosb.nl/sbnl2014/speakers> www.biosb.nl/sbnl2014/speakers Organisers: <http://www.biosb.nl/sbnl2014/organisation> www.biosb.nl/sbnl2014/organisation ............................................................................ .............................. Line up of seventeen (17!) great speakers The theme of this 6th edition of the annual systems biology symposium is Tackling Complexity through Data Integration. The SB@NL2014 symposium will bring together systems biologists from the Netherlands and adjoining countries and even from further afield. The most recent version of the symposium programme can be downloaded from the website: <http://www.biosb.nl/sbnl2014/programme> www.biosb.nl/sbnl2014/programme. INVITED SPEAKERS The programme features the following high-level, senior invited speakers (in alphabetical order). <http://biosb.nl/wp-content/uploads/2014/07/Armitage_Portrait_100x136_201001 05.jpg> <http://biosb.nl/wp-content/uploads/2014/07/Bader_Portrait_100x141_20140903. jpg> <http://biosb.nl/wp-content/uploads/2014/07/Balling_Portrait_100x154_2014082 0.jpg> <http://biosb.nl/wp-content/uploads/2014/07/Evelo_Portrait_100x123_20111024. jpg> <http://biosb.nl/wp-content/uploads/2014/07/Franke_Portrait_100x140_20140825 .jpg> <http://biosb.nl/wp-content/uploads/2014/07/Greef_Portrait_100x152_20140822. jpg> <http://biosb.nl/wp-content/uploads/2014/07/Hoen_Portrait_100x137_20140724.j pg> <http://biosb.nl/wp-content/uploads/2014/07/Ommen_Portrait_100x143_201407241 .jpg> <http://biosb.nl/wp-content/uploads/2014/07/Peyrieras_Portrait_100x136_20140 820.jpg> <http://biosb.nl/wp-content/uploads/2014/07/Raes_Portrait_100x140_20140912.j pg> <http://biosb.nl/wp-content/uploads/2014/07/Weijers_Portrait_100x120_2014072 4.jpg> <http://biosb.nl/wp-content/uploads/2014/07/Wolstencroft_Portrait_100x127_20 140825.jpg> <http://biosb.nl/wp-content/uploads/2014/07/Xenarios_Portrait_100x146_201409 12.jpg> >From left to right 1st row: Judy Armitage (UK), Gary Bader (US), Rudy Balling (LU), Roel van Driel (NL), Chris Evelo (NL); 2nd row: Lude Franke (NL), Jan van der Greef (NL), Peter-Bram t Hoen (NL), Laurens Landeweerd (NL), Gert-Jan B. van Ommen (NL); 3rd row: Nadine Peyriéras (FR), Jeroen Raes (BE), Tsjalling Swierstra (NL), Dolf Weijers (NL), Hans Westerhoff (NL); 4th row: Katy Wolstencroft (NL), and Ioannes Xenarios (CH). For more information on these speakers, go to <http://www.biosb.nl/sbnl2014/speakers> www.biosb.nl/sbnl2014/speakers. SESSIONS TOPICS Session 1 Systems and personalised medicine Session 2 Network biology Session 3 Bioinformatics Session 4 Integrating data in the life sciences Session 5 Responsible research and innovation in systems biology (ERASysAPP) Session 6 Systems biology of microbial cells Session 7 Systems biology of multicellular organisms ............................................................................ ............................... Poster/Flyer A symposium poster has been distributed to systems biology research groups in the Netherlands and also abroad. The corresponding flyer can be downloaded from the symposium website ( <http://www.biosb.nl/sbnl2014/communication> www.biosb.nl/sbnl2014/communication) and printed in A4 format. ............................................................................ .............................. Sponsors This SB@NL2014 symposium is supported by the following organisations. MAIN SPONSORS ERASysAPP: <http://www.erasysapp.eu/> www.erasysapp.eu <http://biosb.nl/wp-content/uploads/2014/02/ERASysAPP.jpg> <http://www.erasysapp.eu/> Netherlands platform for systems biology (SB@NL): <http://www.biosb.nl/sbnl> www.biosb.nl/sbnl <http://www.maastrichtuniversity.nl/> <http://biosb.nl/wp-content/uploads/2013/07/SBNL_Logo_100x29_20140731.jpg> OTHER SPONSORS Maastricht Centre for Systems Biology (MaCSBio): <http://macsbio.maastrichtuniversity.nl/> macsbio.maastrichtuniversity.nl <http://biosb.nl/wp-content/uploads/2014/08/MaCSBio_Logo_155x24_20140720.jpg > Maastricht University (UM): <http://www.maastrichtuniversity.nl/> www.maastrichtuniversity.nl <http://biosb.nl/wp-content/uploads/2014/07/UM_Logo_256x198_20131014.jpg> Netherlands Consortium for Systems Biology (NCSB): <http://www.ncsb.nl/> www.ncsb.nl <http://biosb.nl/wp-content/uploads/2014/07/NCSB_Logo_250x53_20081127.jpg> Netherlands Institute for Systems Biology (NISB): <http://www.sysbio.nl/> www.sysbio.nl <http://biosb.nl/wp-content/uploads/2014/08/NISB_Logo_7304x1080_20081028.gif > BioSB Research School: <http://www.biosb.nl/> www.biosb.nl <http://biosb.nl/wp-content/uploads/2014/07/BioSB_Website_Image_400x67_20140 417.jpg> ............................................................................ ............................... On behalf of the SB@NL2014 chair Prof. Dr Ir Ilja Arts, Diman van Rossum, PhD SB@NL secretary Netherlands Systems Biology Platform (SB@NL) c/o Centrum Wiskunde & Informatica (CWI) PO Box 94079 | 1090GB Amsterdam | The Netherlands (visiting address: Science Park 123, 1098XG Amsterdam) <mailto:diman.vanrossum@ncsb.nl> diman.vanrossum(a)ncsb.nl <http://www.biosb.nl/sbnl> www.biosb.nl/sbnl

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JOB: Computational Biologist Postdoc position in the Laboratory of Developmental Signaling
by Mark Fiers 21 Nov '14

21 Nov '14

The Laboratory of Developmental Signaling, headed by An Zwijsen, is looking for a highly motivated and creative postdoctoral computational biologist/bioinformatician to join the team. The postdoctoral scientist will focus on the role of BMP signaling in endothelial plasticity. The project follows from the recent work on BMP signaling heterogeneity in different vascular endothelial phenotypes and cross-talk with Notch signaling (Moya et al., Dev Cell 2013; Beets et al., TIG, 2013). The project focuses on deciphering the dynamics and consequence of perturbation of BMP signaling cascades on effector oscillatory gene expression and cell competence/competition. The candidate will perform and analyze comparative transcriptome studies. The applicant is expected to model the oscillatory gene network. The computational analyses and models will be validated with independent perturbation experiments and will feed new experiments. more details are in the attachment with best regards Mark Fiers

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