- BBClist - maillist.psb.ugent.be

two-year post-doctoral position in computer sciences at INRA
by Karoline Faust 09 Nov '17

09 Nov '17

A two-year post-doctoral position in computer sciences is now opened at INRA-Dijon (France). The post-doctoral scientist will develop logic-based machine-learning algorithms for the reconstruction of microbial networks from metabarcoding datasets. We envision that these algorithms will be very useful to the biocontrol of plant pathogens in the near future, by allowing us to automatically identify candidate biocontrol agents. Plants are associated with a huge diversity of microorganisms that interact. Deciphering these microbial interactions is crucial since they underpin the regulation of plant diseases. These microbial interactions are usually identified using co-culture experiments. This is a tedious and time-consuming process that cannot easily be extended to the whole microbial community with which a pathogen interacts. A current challenge is to reconstruct microbial interaction networks directly from environmental DNA. The purpose of the project will be (1) to develop generic methods for learning microbial interaction networks from metabarcoding data and (2) to demonstrate that these new methods inform biological control of pathogens because they reveal antagonistic interactions between pathogen species and other microorganisms. This proof-of-concept study will be performed using both simulated datasets and real metabarcoding datasets on some major foliar pathogens of grapevine and wheat. The post-doctoral position is part of the BCMicrobiome project funded by the public-private Biocontrol Consortium*. Regular reporting to the Consortium will be requested and there will be an exclusivity period on the results obtained on the real metabarcoding datasets. The post-doctoral researcher will be based in Dave Bohan's lab at INRA-Dijon. He will work in close collaboration with the project's PI (Corinne Vacher, INRA-Bordeaux) and with other ecologists and plant pathologists involved in the project. A three-month stay in the Department of Computing at the University of Surrey will allow the post-doctoral researcher to gain new skills in machine-learning by working in collaboration with Alireza Tamaddoni-Nezhad. Close collaboration with the group of Stéphane Robin (AgroParisTech, Paris), who develops statistical methods of network inference, is also expected. The candidate should ideally have a background in machine-learning and/or statistics, good communication skills, and some interest in ecology and agriculture. Candidates having some experience in the analysis of ecological networks are also welcome to apply. Starting date: between January 2018 and April 2018 Gross salary: 3892 euros per month Contact: David Bohan (david.bohan(a)inra.fr) and Corinne Vacher (corinne.vacher(a)inra.fr<mailto:corinne.vacher@inra.fr>) * http://institut.inra.fr/Partenaires/Entreprises-et-filieres/Tous-les-magazi…

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Job opening: ELIXIR-EXCELERATE Training Impact Coordinator
by Celia van Gelder 06 Nov '17

06 Nov '17

FYI and please spread this vacancy as you see fit. We are looking for a Training Impact Coordinator for ELIXIR-EXCELERATE Training. Location: University of Cambridge, UK. Full description: http://www.jobs.cam.ac.uk/job/15618/ Best Celia Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder NEW Visiting address (as of 1 July 2017): DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht NEW Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht

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Scienitific day of the Bilille platform : Working with networks and pathways in molecular biology
by Eva-Maria Krammer 26 Oct '17

26 Oct '17

Hello, Bilille, the bioinformatics plateform of Lille, organises an scientific afternoon on le *20 novembre 2017* with the topic "*Working with networks and pathways in molecular biology*". The location of the meeting is *the campus of the Pasteur Institute of Lille* (Amphi IBL, 1 rue du professeur Calmette, Métro line 2 station "Lille Grand Palais"). Invited speakers: * Marie Beurton Aimar (LaBRI - Equipe Image et Son - Université de Bordeaux). /Visual Exploration of Feasible Pathways through Metabolic Network/ * Guillaume Brysbaert (UGSF - UMR 8576 CNRS - Université de Lille). /An overview of Cytoscape for network biology with a focus on residue interaction networks/ * Martina Summer-Kutmon (BiGCaT, Maastricht University). Title to be announced * Florence Pinet (Unité d'Epidémiologie et de Santé Publique - Inserm-U1167 - Institut Pasteur Lille). /Integrative network analysis with Cytoscape reveals time-dependent molecular events underlying left ventricular remodeling in post-myocardial infarction patients/ * Aura Ileana Moreno-Vega (Institut Curie - UMR Compartimentation et Dynamique Cellulaire). Title to be announced The program and the inscription are available on the internet site of the BILILLE Platform: https://wikis.univ-lille1.fr/bilille/networks_2017 Inscription deadline: 14 novembre 2017 (the inscription is free but obligatory). Cellule Animation Scientifique de Bilille -- -------------------------------------------- Eva-Maria Krammer Structure et Fonction des Membranes Biologiques CP 206/02 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: ekrammer(a)ulb.ac.be --------------------------------------------

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Edinburgh Genomics Bioinformatics workshops for the remainder of 2017: Intro Linux, Intro ChIP-seq, Intro RNA-seq, Intro Linux and Workflows
by Bert Overduin 24 Oct '17

24 Oct '17

Dear all, For the remainder of 2017 we have the following workshops planned, on all of which there are still places left. With kind regards, Bert ********** 1-day LINUX FOR GENOMICS Date: Wednesday 8 November 2017 Registration deadline: Wednesday 25 October 2017 noon Places: 20 (first come, first served) Registration fee: £175 (includes coffee/tea and lunch) Details and registration: http://genomics.ed.ac.uk/services/linux-genomics 2-day INTRODUCTION TO ChIP-SEQ DATA ANALYSIS AND VISUALISATION USING ENSEMBL Date: Thursday 23 & Friday 24 November 2017 Application deadline: Thursday 26 October 2017 noon Places: 12 (selection of applicants) Registration fee: £350 (includes refreshments and lunch) Details and application: http://genomics.ed.ac.uk/services/introduction- chip-seq-data-analysis-and-visualisation-using-ensembl 2-day INTRODUCTION TO RNA-SEQ DATA ANALYSIS Date: Thursday 30 November & Friday 1 Decemberr 2017 Application deadline: Thursday 2 November 2017 noon Places: 12 (selection of applicants) Registration fee: £350 (includes refreshments and lunch) Details and application: http://genomics.ed.ac.uk/services/introduction- rna-seq-data-analysis Note: - if you have applied for this workshop before but were unsuccessful, please mention this in your application 5-day INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS Date: Monday 11 - Friday 15 December 2017 Registration deadline: Monday 27 November 2017 noon Places: 20 (first come, first served) Registration fee: £525 (includes coffee/tea, but no lunch) Details and registration: http://genomics.ed.ac.uk/services/introduction -linux-and-workflows-biologists -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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reminder NSBM Fall Meeting November 29th 2017
by Barbara.vanKampen＠radboudumc.nl 20 Oct '17

20 Oct '17

[logo.png]NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Fall meeting November 29th 2017 Venue: Boothzaal, University Library De Uithof, Utrecht The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands that work on three dimensional structures of biomolecules and biomolecular simulations. The NSBM cordially invites you to participate in its 2017 fall meeting in Utrecht. During the meeting, the floor will be given to PhD students and post-docs who study protein structure and/or structural bioinformatics or related topics. Location and dates · Date: November 29th, 2017, 10:00-17:00 · Venue: Boothzaal, University Library De Uithof, Heidelberglaan 3, 3584 CS Utrecht · http://www.uu.nl/universiteitsbibliotheek/locaties<http://www.uu.nl/universiteitsbibliotheek/locaties%20> Deadlines · Registration deadline to be considered for a short talk: November 17th · Registration deadline (including lunch): November 22nd Application procedure · Participants should send an email to register (required but free registration) to: g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> · Submission of an abstract is required if you want to present a poster. · Indicate in your email if you want be selected for a short oral presentation. Note: The maximum number of participants is limited to 75! So please register on time. Lead contact · Dr. Gerry Nicolaes - g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> http://www.3dstructure-function.nl/nsbm-fall-meeting/<http://www.3dstructure-function.nl/?page_id=912&preview=true> Preliminary Programme · 09:30-10:00 Arrival and coffee · 10:00-10:10 Welcome word · 10:10-11:00 Keynote I o Prof. Jürgen Pleiss, Institut für Technische Biochemie (ITB), Stuttgart University (D) o Data-integrated simulation of enzymes § 11:00-11:20 Short talk selected from abstracts § 11:20-11:40 Short talk selected from abstracts § 11:40-12:10 Lecture o Tom van den Bergh, Bio-Prodict, Nijmegen (NL) 12:10-12:30 Lecture § o Short talk selected from abstracts · 12:30-14:00 Lunch and poster session · 14:00-14:50 Keynote II: o Prof. Chris Ulens, KU Leuven (B). o Allosteric modulation of ligand-gated ion channels · 14:50-15:10 Short talk selected from abstracts · 15:10-15:30 Short talk selected from abstracts · 15:30-16:00 Coffee break · 16:00-16:50 Keynote III: o Dr. Chris de Graaf, VU Computational Medicinal Chemistry group, Amsterdam (NL) o 3D-e-Chem: Structural cheminformatics tools for navigating protein-ligand interaction space 16:50 Closure Costs Attendance is free of charge but registration is required. Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics. A flyer is enclosed. With kind regards, Barbara van Kampen --- Barbara van Kampen Operational manager CMBI [Radboudumckleine.png] CMBI 260 Radboud university medical center / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. 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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BioSB course: Protein Structures (4th edition) - 31 Oct-3 Nov 2017, Nijmegen, the Netherlands
by Celia van Gelder 20 Oct '17

20 Oct '17

BioSB course Protein Structures: production, prowess, power, promises, and problems (4th edition) Date: 31 October - 3 November 2017 Location: CMBI, Radboudumc, Nijmegen, the Netherlands Course coordinator: Gert Vriend (CMBI, Radboudumc) Lecturers: Daniel Hoffmann (University Duisburg/Essen (TBC)), Hanka Venselaar (CMBI), Wouter Touw (CMBI) Website: <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> course website Registration: registration form <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro’s and cons so a certain ‘prowess’ is needed to follow all ‘promises’ and start attacking bio-medical ‘problems’ using protein structures. The course will be split in three parts: * Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. * Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. * Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling seminar Day 2: Protein structure comparison seminars Day 3: Electrostatics and molecular dynamics seminars Day 4: Protein structure determination and validation seminars Day 5: Own project executed with help from CMBI staff Examples of questions you will be able to answer after follwing the course: * Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? * This enzyme converts mannose. Can I make is specificity broader? * This enzyme doesn’t function in my in vitro assay. Should I add some ions? * I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? * This receptor binds a ligand, but if I look at the structure, that ligand doesn’t fit at all. Can I predict motions that take place upon ligand binding? This course is part of the <http://biosb.nl/education/course-portfolio-2/> 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 <http://www.biosb.nl/> www.biosb.nl. Femke Francissen Community manager BioSB Research School NEW Visiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht NEW Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: <mailto:femke.francissen@biosb.nl> femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn <http://nl.linkedin.com/in/femkefrancissen> link <http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg>

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PhD position Epigenome-wide association studies
by Thomas Van Parys 16 Oct '17

16 Oct '17

Opening for a PhD position (bioinformatics) in an EU-funded training network on "Epigenome-wide association studies". More info: https://nioo.knaw.nl/en/vacancies-epidiverse Project RP05: https://nioo.knaw.nl/en/rp5-epigenome-wide-association-studies

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call for abstracts OLA'2018@spain
by El-ghazali Talbi 12 Oct '17

12 Oct '17

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2018 International Workshop on Optimization and Learning: Challenges and Applications 26-28 Feb 2018 Alicante Spain http://ola2018.sciencesconf.org/ **************************************************************************************** A special issue in the ISI journal ITOR (International Transactions in Operational Research) is planned. OLA is a workshop focusing on the future challenges of optimization and learning methods and their applications. The workshop OLA'2018 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2018 welcomes presentations that cover any aspects of optimization and learning research such as new high-impact applications, parameter tuning, 4th industrial revolution, new research challenges, hybridization issues, optimization-simulation, meta-modeling, high-performance and exascale computing, surrogate modeling, multi-objective optimization, optimization for machine learning, machine learning for optimization. Important dates - Submission deadline Nov 3, 2017 - Proposals of invited sessions Nov 3, 2017 - Notification of acceptance Nov 17, 2017 Paper submission - Abstracts of maximum 2 pages -- ****************************** OLA'2018 26-28 Feb 2018, Alicante, Spain http://ola2018.sciencesconf.org ****************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille 1 - INRIA - CNRS

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Job: lecturer bioinformatics at Hogeschool van Arnhem en Nijmegen (Dutch)
by Bruggen Martijn van der 12 Oct '17

12 Oct '17

Dear all, We have an opening for a lecturer bioinformatics/informatics. Please also forward to any potentially interested candidates you might know. https://www.han.nl/start/corporate/werken-bij-de-han/vacatures/_detail/inde… (Lecturer) Thanks, Martijn. Drs. M.H.H. van der Bruggen Docent bioinformatica / Opleidingscoördinator bioinformatica Hogeschool van Arnhem en Nijmegen (HAN) Instituut voor Toegepaste Biowetenschappen en Chemie Postadres: postbus 6960 | 6503 GL NIJMEGEN | Nederland Bezoekadres: Laan van Scheut 2 | Kamer 0.07 | 6525 EM NIJMEGEN | Nederland | +31-6-55206344 Aanwezig: maandag - dinsdag - woensdag - donderdag - vrijdag [untitled]

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Open slots for several VIB courses in November 2017
by Alexander Botzki 12 Oct '17

12 Oct '17

Dear all, Just to let you know that registrations to the following VIB courses are still open for international participants: * Fundamental data skills for data-driven research - http://www.vib.be/en/training/research-training/courses/Pages/Fundamental-d… * Protein structure analysis - http://www.vib.be/en/training/research-training/courses/Pages/Protein-Struc… Thanks a lot. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/>

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