- BBClist - maillist.psb.ugent.be

Job opening
by L.M. Kamminga 07 Oct '16

07 Oct '16

Dear all, I am looking for a computational biologist to study genetics and epigenetics of developmental biology to join my team. You can find the details about the job opening in the attachment. To apply go to: https://www.radboudumc.nl/werkenbij/Pages/Vacatures.aspx?vacid=39541&naam=Co mputational%20Biologist%20Genetics%20and%20Epigenetics%20of%20Developmental% 20Biology&afdeling=Department%20of%20Physiology&plaats=nijmegen Kind regards, Leonie Kamminga -- Leonie Kamminga, PhD Assistant Professor Molecular Biology RadboudUMC/RIMLS T +31(0)24 361 6850/3988 F +31(0)24 361 0520 http://rimls.aride.nl/people/k/kamminga/ MAIL RIMLS/RadboudUMC | 274 Dept. Molecular Biology | PO BOX 9101| 6500HB Nijmegen | The Netherlands VISITOR Molecular Biology 274 | Geert Grooteplein 26-28 | 6525GA Nijmegen | The Netherlands SHIPMENT RIMLS M850/3.079 Dept of Mol. Biol. 274 | Geert Grooteplein 30 | 6525GA Nijmegen | The Netherlands

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Schedule BIG N2N seminars 2016 - 2017
by Sophie Maebe 06 Oct '16

06 Oct '16

Dear All, Please find attached an overview of the BIG N2N seminars in 2016-2017. With kind regards, Sophie Sophie Maebe Administrative assistant Tel:+32 (0)9 331 38 08 Department of Plant Systems Biology VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be

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BioSB Course Matlab (2nd edition), 28 October 2016, Wageningen
by Celia.vanGelder＠radboudumc.nl 04 Oct '16

04 Oct '16

BioSB Course Matlab, 28 October 2016, Wageningen Website: http://biosb.nl/education/course-portfolio-2/course-matlab/ . Coordinators: Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder(a)biosb.nl<mailto:celia.van.gelder@biosb.nl>) Registration: http://biosb.nl/education/course-portfolio-2/course-matlab/enrollment-cours… Please note that if you are (or become) a member of BioSB this course is free of charge for PhD students and with reduced fee for other researchers! Goal The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are: 1. To learn the philosophy behind Matlab and its syntax 2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab Target audience Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations. Course Description This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of "vectorized thinking" while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical. Programme 09:45 Coffee/Tea 10:00 Welcome 10:05 Introduction Matlab Basics (functions, variables, matrices, etc) 10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models) 12:00 Afternoon: Solving basic and advanced problems in Matlab - hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research. 12:30 Lunch 15:00 Coffee/tea 16:30 End BioSB Education Programme This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl/> or via education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl<http://www.dtls.nl/>, www.biosb.nl<http://www.biosb.nl/> skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht 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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Registration open: BioSB course Comparative Genomics (3rd edition), 21-25 November 2016, Nijmegen
by Celia.vanGelder＠radboudumc.nl 04 Oct '16

04 Oct '16

BioSB Course Comparative Genomics: from evolution to function (3rd edition) - Registration open Date: November 21-25, 2016 Location: CMBI, Radboudumc, Nijmegen, the Netherlands Course coordinators: Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (BioSB) Course website: http://biosb.nl/education/course-portfolio/course-comparative-genomics/ Registration: http://biosb.nl/education/course-portfolio/enrollment-comparative-genomics-… More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying biological processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why these methods sometimes fail (or misdetect) as a consequence of a variety of biological /evolutionary causes, and in which situations which method is most appropriate. The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of the most sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology). This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements and of RNA structures Target audience The course is intended for PhD students and master students in bioinformatics or geneticists and experimental biologists with a strong interest in evolution of the eukaryotes. It is especially relevant to students who want to compare various types of genomics data between species. Participants are expected to have some hands on experience with tools like blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. Programme Monday November 21: Distant homology and protein domains (lecturer Jaap Heringa) Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, jackhmmer, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction Tuesday Nov 22: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam) Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization Wednesday nov 23: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel) Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission Thursday nov 24 : Genome duplications (lecturer Berend Snel) Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart Friday nov 25: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen) Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. BioSB Education Programme This course is part of the Education Programme 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 Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl<mailto:celia.van.gelder@dtls.nl> websites: www.dtls.nl<http://www.dtls.nl/>, www.biosb.nl<http://www.biosb.nl/> skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht 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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Online Galaxy training material hackathon
by Frederik Coppens 04 Oct '16

04 Oct '16

Hi all I would like to bring this hackathon to your attention: https://www.elixir-europe.org/events/galaxy-training-material-hackathon <https://www.elixir-europe.org/events/galaxy-training-material-hackathon> It’s an online contribution fest organized by the Galaxy Training Network, October 6-7. This stems from an idea at GCC2016 to centralize Galaxy training material on github. Bjoern Gruening already collected a lot of material (checkout https://github.com/bgruening/training-material <https://github.com/bgruening/training-material>) and we’d like to further grow this resource and make it more uniform. You can (optionally) indicate your interest here: https://github.com/bgruening/training-material/issues/58 <https://github.com/bgruening/training-material/issues/58> You can find a list of topics here: https://github.com/bgruening/training-material/issues <https://github.com/bgruening/training-material/issues> Everybody’s welcome to join, you really don’t need programming skills to contribute. If the hackathon doesn’t fit your schedule (it’s a bit short notice, I realise), you can always contribute at a later point, as everything is available on github. cheers Frederik ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 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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Internship opportunities at EdgeLeap
by Thomas Kelder 03 Oct '16

03 Oct '16

Dear all, We at EdgeLeap http://www.edgeleap.com/ have multiple opportunities for internship projects for aspiring data scientists! Check out the attached description for details and please forward to your prospective bioinformatics students. Many thanks in advance! Best regards, The EdgeLeap team ------------ Thomas Kelder, PhD Chief Scientific Officer EdgeLeap B.V. Hooghiemstraplein 15 3514 AX Utrecht The Netherlands Phone: +31-6-41941301 Email: thomas(a)edgeleap.com www.edgeleap.com

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Bioinformatics scientist vacancy in HZPC
by Sanchez Perez, Gabino 30 Sep '16

30 Sep '16

Dear all, There is a job opening for bioinformatics at the breeding company HZPC. See attached file for more detailed information. Please, forward to any interested colleagues, Kind regards, Gabino

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GIGA Imaging Platform - Bioinformatician position available
by rh.giga＠ulg.ac.be 27 Sep '16

27 Sep '16

Dear all, The GIGA Imaging Platform is recruiting a bioinformatician. Please find attached the job description. Regards, Sandra Lopez and Sandrina Evrard GIGA Université de Liège Quartier Hôpital Avenue de l'Hôpital 11 - B34 B-4000 LIEGE Tél + 32 4 366 98 03 Fax + 32 4 366 41 98 www.giga.ulg.ac.be

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Internship – Bayesian methods for disease subtype discovery
by Johann Pellet 23 Sep '16

23 Sep '16

6-month Programming Internship: France (Lyon) Employer: CNRS Location: CNRS-EISBM, Lyon, France Qualifications: Undergraduate – Bachelor’s degree Salary: Depending on qualifications and experience, based on CNRS salary grid Duration: 6 months Starting date: Available immediately, expected to start by January/February 2017 Key words: Programming, GP-GPU, Python, R, C, Java, Bioconductor, disease sub-types, Systems Biology An internship position is available as a part of the European Translational Research Information and Knowledge Management Services project (eTRIKS), funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). 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. He will work closely with the team led by Prof Yi-Ke Guo at the Data Science Institute of Imperial College in London, UK. The aim of the internship is to evaluate the performance of recent algorithms for identification of disease sub-types using Bayesian methods; specifically, this will involve implementing existing programs, where possible exploiting GP-GPU and Apache spark architectures to address the computationally intensive aspect of the problem. It is anticipated that some of the approaches evaluated will be used for analysis of multi omics datasets from new systems medicine projects. This position allows an intern to participate in a state-of-the-art EU systems biomedicine project. Required skills: Good programming skills (eg. python, java, C, R); 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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Internship – Programmer / Software Developer
by Johann Pellet 23 Sep '16

23 Sep '16

Employer: CNRS Location: CNRS-EISBM, Lyon, France Expires: 15th December 2016 Qualifications: BSc, MSc Salary: Depending on qualifications and experience, based on CNRS salary grid Duration: 6 months Starting date: Available immediately, expected to start by February/March 2017 Key words: web development, open-source, data visualisation, layout algorithms, computational systems biology, systems medicine, graphical standard A software developer intenship position is available as a part of the European Translational Research Information and Knowledge Management Services project (eTRIKS), funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). The successful applicant will work on developing an application that enables automatic assembly and layout of biological networks. The goal of this project is to develop a plugin for an open-source web-based graph editor which functionality is based on Cytoscape.js. The work will be done in close interaction with a team of experiences software architects, software developers, experts in layout algorithms, systems biologists and bioinformaticians. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Dr. Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. Required qualification and skills: Candidates should have a BSc or MSc in Computer Science, in Bioinformatics or equivalent. Strong programming skills are required. Experience in Web programming (HTML, or/and JavaScript, or/and CSS) and in graph visualisation tools / libraries is an advantage. Background in pathway informatics / system biology / data visualization is a plus. The position requires good communication skills in English and involves working in collaboration with eTRIKS partners on translational medicine projects across Europe. Application: Please send your CV and motivation letter to Dr. Charles Auffray: jobs(a)eisbm.org.

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