July 2015 - BBClist - maillist.psb.ugent.be

Vacature Hogeschool Leiden
by Stelling, Klaasje 11 Dec '15

11 Dec '15

Geachte heer/mevrouw, Het cluster Techniek van Hogeschool Leiden is op zoek naar inspirerende en onderzoekende "Docent(en)/onderzoeker(s) Bio-Informatica (1,2 fte - 2,0 fte)". Kijk voor meer informatie de bijlage of onze website, http://www.hsleiden.nl/over-hl/werken-bij/vacatures/vacatures Met vriendelijke groet, Klaasje Stelling Adviseur HRM Hogeschool Leiden Afdeling HRM Zernikedreef 11, kamer F2.006/F2.008/F2.013 Postbus 382, 2300 AJ Leiden Mobiel: 06-52781722 Website: www.hsleiden.nl<http://www.hsleiden.nl/> Is het écht nodig deze e-mail te printen? 'Hogeschool Leiden, jouw duurzame ruimte' Op deze e-mail zijn de voorwaarden van toepassing als vermeld op: The following conditions apply to this e-mail: http://www.hsleiden.nl/disclaimer-email

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Vacancy Scientist Bioinformatics at Galapagos Leiden
by Mate Ongenaert 30 Jul '15

30 Jul '15

We are looking for a Scientist Bioinformatics to strengthen the Galapagos Bioinformatics team. Please read all the details at http://www.glpg.com/index.php/careers/current-openings/ Galapagos is a mid-sized, clinical stage biotechnology company and is active in discovery and development of small molecule therapies, many of which are based on proprietary disease modifying drug targets in various disease areas. Galapagos funds its research through alliance payments from its pharma partners, licensing agreements, and its cash reserves. Our selective JAK1 inhibitor GLPG0634, is currently in Phase II trials for treatment of rheumatoid arthritis and Crohn's disease and is partnered with AbbVie for up to $1.4 billion in milestones and double-digit royalties. Together with its services company Fidelta, Galapagos' research activities across Europe are successful thanks to our highly motivated staff of 400 employees, a unique technology base, and a strong financial position. For our site in Leiden (The Netherlands), we are looking for a Scientist Bioinformatics (m/f) Full time - reference: LEI-053 Description This position gives you the opportunity to work in an exciting and dynamic environment of a well-known successful international biotech company. As a member of the bioinformatics team you will perform daily bioinformatics tasks supporting the different research projects of Galapagos. By making functional analyses and implementing novel analysis methodologies, end-user interfaces and data-integration efforts, you support the multidisciplinary disease biology and drug discovery teams in their decision making process. You will play a key role in implementing bioinformatics needs from research projects into proof-of-concept solutions that can be adapted for incorporation into Galapagos' software and data systems. This position offers an exciting opportunity to develop and provide data-based services to the science and business at Galapagos. Profile · You have a Master's degree or PhD in bioinformatics or Life Sciences with clear experience in bioinformatics. You have at least 2 years of working experience, preferably in a biotech or pharma company · You have broadly applicable general bioinformatics skills (expression-data analysis, pathway analysis, databases and repositories in the public domain) · You have a clear understanding of data structures and data-interchange formats (e.g. JSON), experience with document databases (such as MongoDB or Cassandra) and/or relational databases (Mysql/Oracle) · You have good working knowledge of Linux · Good knowledge of R (preferably with the BioConductor libraries), experience with reporting in R (sweave/knitr) and interactive web-interfaces (shiny) is a clear plus · Hands-on experience with modern web-frameworks (such as Django, Ruby on Rails or Perl Dancer) is a clear plus · Knowledge of disease related pathways and systems biology approaches, expression-data analysis, experience with developing analysis strategies in transcriptomics and/or genetics is a plus We are looking for candidates that have excellent communication and interpersonal skills and like to work in the environment of a biotech company where quality, speed, motivation, team spirit and results are of utmost importance to be successful. At Galapagos and Fidelta, we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos' leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment. Do you have the qualifications for this job opening, and are you up to the challenge of joining our entrepreneurial team? If so, please send your application (preferably by e-mail) to: Human resources Galapagos BV PO Box 127 2300 AC Leiden The Netherlands Tel: +31 71 7506700 Fax: +31 71 7506701 jobs_nl(a)glpg.com<mailto:jobs_nl@glpg.com> Please contact us only if you want to apply for this position. Other types of inquiries or business proposals will be ignored. The selection procedure will be monitored by Kelly Scientific Resources. Maté Ongenaert, PhD Senior Scientist Bioinformatics Computational Chemistry & Biology (CC&B) [http://guide/glpg/images/galapagoslogo_small.jpg] Galápagos Generaal De Wittelaan L11 A3 | 2800 Mechelen | Belgium T: +32 15 342 927 | F: +32 15 342 901 mate.ongenaert(a)glpg.com<mailto:mate.ongenaert@glpg.com> | http://www.glpg.com<http://www.glpg.com/> -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

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BioSB course RNA-seq data analysis course (5th edition), 7-9 September 2015
by Celia.vanGelder＠radboudumc.nl 28 Jul '15

28 Jul '15

BioSB RNA- seq data analysis course (5th edition) Date: 7-9 September, 2015 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Celia van Gelder (BioSB, education(a)biosb.nl<mailto:education@biosb.nl> ) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: http://biosb.nl/education/enrollment-rna-seq/ More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description BioSB and partner LUMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis Programme The programme can be found here: http://biosb.nl/wp-content/uploads/2014/03/Prelimenary_RNAseq_program_v4.pdf Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded project RD-Connect and Marie Curie European Training Network TranCYST. BioSB Course Programme This course is part of the Course Portfolio<http://biosb.nl/education/course-portfolio-2/> of BioSB, the Netherlands Bioinformatics and Systems Biology research school, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Vacancy: scientist Biostatistics
by Jellema, Renger 27 Jul '15

27 Jul '15

Dear all, We are looking for a new colleague: a scientist Biostatistics. Interested in applying statistics in a business environment? The text and application procedure became available on our site today: http://www.dsm.com/corporate/careers/vacancies/dsmvacancies.html The Challenge Within the Genetics Department of the DBC there is a vacancy for the position of Scientist Biostatistics Located at Delft, The Netherlands The Position * As a Scientist Biostatistics, you will be located at the DSM Biotechnology Center in Delft, supporting business-driven R&D projects with design of experiments, data processing and statistically analysis for end-applications in food, pharma and/or bio-based chemicals and fuels. * Being part of the bioinformatics & modeling group, you will participate in multidisciplinary teams in which you will be the statistical expert across the different disciplines. * Projects may range from medium to high-throughput screenings for enzyme and strain development, applied biochemistry and analytical data, to QA/QC support for manufacturing, depending on your background and interest. * Your challenge will be to develop, implement and apply state-of-the-art statistical tools and workflows. The Ideal * Ph.D. in chemometrics, statistics, metabolic modeling, computational methods, bioinformatics, or a related discipline. Additional training or degree in biochemistry, molecular biology, food or biotechnology is considered to be an advantage. * Preferably 2-5 year experience, preferably in statistical data processing of biological data or fermentation data * Experience in setting up and applying statistical tools for quality control is an advantage. * Expert in R, Matlab, Spotfire, SAS, Minitab, Statgraphics or other statistical software packages * Experience using optimal experimental design techniques is a plus * Strong desire and proven ability to work collaboratively in multi-disciplinary project teams * Multidisciplinary team player, who takes initiative * Personal skills like problem analysis, creativity and being a strong communicator characterize your identity. 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 or 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/career. Level C40/C41 Terms of conditions LOCAL CONTRACT The Procedure and Contact The DSM Recruitment and Selection Process is in line with the general procedure outlined elsewhere on our Career World. Please apply on-line and send your CV & cover letter and include information on your current remuneration. Please submit your application before deadline:17th of August Reference check procedures are part of the DSM Recruitment & Selection Process. You will be contacted when these references checks are required. Kind regards, Renger Renger Jellema | Senior Scientist Statistics | Group Lead BioIT | DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | T +31 15 279 2886 | renger.jellema(a)dsm.com | DSM Biotechnology Center is part of DSM Food Specialties B.V., Trade Register Number 27235314 [http://static.dsm.com/content/dam/dsm/images/DSM_Email_EN.jpg] ________________________________ 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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Job listing for Stratified Medical UK
by John Overington 27 Jul '15

27 Jul '15

Hi, Can this be posted to your list. Many thanks, John Overington ====== We are looking for an innovative data scientist to make a significant contribution in our drug discovery process by applying your expertise in bioinformatics data analysis, algorithm and workflow development and use of machine learning approaches applied to biological/chemical data. Working alongside a team of other highly skilled data scientists applying the very latest approaches to data science (e.g. deep learning, SVM, machine learning, CNN’s, Deep Belief Networks, NLP, to name a few), and supported by industry-leading figures and mentors you will be well positioned to innovate and perform world-leading research. Responsibilities * Develop very large-scale bioinformatics components of our proprietary technology platform. * Research deep-learning and other AI-based approaches to target validation and lead discovery and drug optimization. * Maintain cutting edge awareness of the bio/cheminformatics fields. * Play a key role in hands-on contribution to our drug discovery programs. Essential Qualifications and Experience * Programming in e.g. Python, JavaScript, java, web-services, and workflow tools (e.g. Pipeline Pilot/KNIME). * Database experience – SQL, ideally also experience of MapReduce and NoSQL. * Proven track record of applying informatics-based techniques to solve drug discovery problems. * PhD and five-plus years of postdoctoral experience in a drug discovery environment. * Expert knowledge of gene and protein sequence analysis, structural biology, pathway analysis, impact of genetic variation, and protein modelling; combined with experience of a wide range of bioinformatics resources – e.g. Ensembl, UniProt, Pfam, PDB, ModBase, Human Protein Atlas, KEGG. This position will report to the Director of Bioinformatics. If you are interested in this role, please send a cv to john.overington(a)stratifiedmedical.com<mailto:john.overington@stratifiedmedical.com> -- John P. Overington PhD MBCS FRSB FRSC CChem Director of Bioinformatics Stratified Medical 3rd floor, 91-93 Farringdon Road London EC1M 3LN United Kingdom Email: john.overington(a)stratifiedmedical.com<mailto:john.overington@stratifiedmedical.com> Telephone: +44-20-7400-7714 Twitter: @johnpoverington Admin: Laura.Hayes(a)stratifiedmedical.com<mailto:Laura.Hayes@stratifiedmedical.com>

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FW: [Training-coordinators] Structural Bioinformatics course at EMBL-EBI, 12-16th October, 2015.
by Barbara.vanKampen＠radboudumc.nl 27 Jul '15

27 Jul '15

Structural Bioinformatics course, 12-16th October 2015 Venue: EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge UK Course organisers: Gerard Kleywegt (EMBL-EBI), Christine Orengo (UCL) and Tom Hancocks (EMBL-EBI) Full programme and registration details can be found at: http://www.ebi.ac.uk/training/course/structural-bioinformatics Course overview This course will explore bioinformatics data resources and tools that are available for the interpretation and exploitation of biomacromolecular structures, focusing on how best to use structural information to gain the most from it in specific research contexts. This will include investigating the impact of genetics variation on structure, predicting protein structure and function and exploring interactions with other macromolecules as well as with low-MW compounds. Course Audience This course is aimed at researchers who want to learn more about the application of structural information in their work and how to use the bioinformatics resources that are available. No previous experience of structural bioinformatics is required. Syllabus During this course you will learn about: * Public repositories of structural data: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), and tools to search and analyse information in these repositories from PDBe (Protein Data Bank in Europe) * Computational approaches to structure prediction: ModBase, Rosetta, PHYRE, Interactome 3D * Impact of genetic variation on protein structure: Ensembl VEP, DBSeq, SAAPdb * Protein analysis and classification: Pfam, CATH, SCOP, InterPro, PDBeFold, PDBePISA, ProFunc * Tools and resources for drug discovery: ChEMBL This message sent to you as member of the NSBM mailinglist Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Reminder; Bioinformatics Symposium, Utrecht September 14th
by Breukelen, B. van (Bas) 27 Jul '15

27 Jul '15

The Utrecht Bioinformatics Center (UBC) proudly announces the: Annual UBC Bioinformatics (Mini) Symposium, September 14th 2015 (Location: Utrecht, Zaalverhuur 7 @ Boothstraat 7, Netherlands). Everyone who is interested in bioinformatics and would like to hear a few great talks is welcome to attend. There is no fee at all, we only ask you to register yourself to make sure that there are enough chairs to sit on, coffee at the start and drinks afterwards. You can register by clicking on the link below or via http://ubc.uu.nl : http://www.eventbrite.nl/e/ubc-annual-mini-symposium-registration-149561201… Programme: 13:00 Welcome with coffee and tea 13:15 Introduction • Berend Snel: Welcome and Utrecht Bioinformatics Center progress report 13:30 Wouter de Laat: Gene regulation in the 3D genome 14:00 Alexandre Bonvin: Structure, affinity and specificity riddles in biomolecular interactions 14:30 Coffee and tea break 15:00 Frank Holstege: Understanding regulatory circuitry through large-scale genetic perturbation analyses 15:30 Keynote: Søren Brunak: Creating Disease Trajectories from Big Biomedical Data covering Millions of Patients 16:15 Reception (till 18:00) The UBC symposium is an ideal way to meet and talk to other bioinformaticians in the field and perhaps start some interesting collaborations. Everyone is welcome, See you soon, Berend Snel, Patrick Kemmeren and Bas van Breukelen p.s. Please spread the word: You are welcome to forward this mail to anyone you think might be interested in this symposium. Bas. van Breukelen, PhD Assistant Professor, Biomolecular Mass Spectrometry and Proteomics | http://www.hecklab.com | Utrecht University Coordinator Bioinformatics | Utrecht Bioinformatics Center (UBC) | http://ubc.uu.nl | Utrecht University Hugo R. Kruytbuilding | Room O605 | Padualaan 8 | 3584 CH Utrecht | T +31(0)30253 9761 | M +31(0)6 42222520 | b.vanbreukelen(a)uu.nl<mailto:b.vanbreukelen@uu.nl> [cid:2CDF3FE1-6FA1-40F3-A816-1D933B578100@science.uu.nl]

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Fwd: Structural Bioinformatics course at EMBL-EBI, 12-16th October, 2015.
by Frederik Coppens 23 Jul '15

23 Jul '15

> Structural Bioinformatics course, 12-16th October 2015 > Venue: EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge UK > Course organisers: Gerard Kleywegt (EMBL-EBI), Christine Orengo (UCL) and Tom Hancocks (EMBL-EBI) > > Full programme and registration details can be found at: http://www.ebi.ac.uk/training/course/structural-bioinformatics <http://www.ebi.ac.uk/training/course/structural-bioinformatics> > > Course overview > > This course will explore bioinformatics data resources and tools that are available for the interpretation and exploitation of biomacromolecular structures, focusing on how best to use structural information to gain the most from it in specific research contexts. This will include investigating the impact of genetics variation on structure, predicting protein structure and function and exploring interactions with other macromolecules as well as with low-MW compounds. > > Course Audience > > This course is aimed at researchers who want to learn more about the application of structural information in their work and how to use the bioinformatics resources that are available. No previous experience of structural bioinformatics is required. > > Syllabus > > During this course you will learn about: > > Public repositories of structural data: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), and tools to search and analyse information in these repositories from PDBe (Protein Data Bank in Europe) > Computational approaches to structure prediction: ModBase, Rosetta, PHYRE, Interactome 3D > Impact of genetic variation on protein structure: Ensembl VEP, DBSeq, SAAPdb > Protein analysis and classification: Pfam, CATH, SCOP, InterPro, PDBeFold, PDBePISA, ProFunc > Tools and resources for drug discovery: ChEMBL > > > > --------------------------------------------- > Dr Sarah Morgan > Training Programme Manager > > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton > Cambridge > CB10 1SD > UK > ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313692 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

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vacancies for bioinformaticians @CMGG-UGent
by Katleen De Preter 17 Jul '15

17 Jul '15

Dear All, The Speleman Research Team at the Center for Medical Genetics (Ghent) is seeking for 2 bio-informaticians: 1 post-doc and 1 PhD position are available. Please find further information in attachments. Kind regards, Frank and Katleen

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Just two weeks left until ICBO 2015 in Lisbon
by Francisco Couto 15 Jul '15

15 Jul '15

There are still places available to join your fellow ontologists in Lisbon for the International Conference on Biomedical Ontology. Lisbon is a historical and cultural city by the sea, with a mixed panorama of modern and medieval architecture. ICBO will be held at the Faculdade de Ciencias Campo Grande Campus, just a short metro ride from the city centre. Don’t miss out on the great weather, great discussions and great food! The schedule of the full event, including two days of workshops and two days of main conference sessions, is now available online at http://icbo2015.fc.ul.pt/program.html#schedule. Registration is open at http://icbo2015.fc.ul.pt/registration.html.

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