- BBClist - maillist.psb.ugent.be

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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Bioinformatics - open positions at the VIB Center for Cancer Biology - KU Leuven
by Christel Vanslembrouck 12 Oct '17

12 Oct '17

Dear all, At the VIB Center for Cancer Biology KU Leuven we have actually the following open positions: - Bioinformatics Single-molecule sequencing Scientist The Laboratory of Translational Genetics of the VIB Center for Cancer Biology (CCB) at KU Leuven is looking for a Bioinformatics Single-molecule sequencing Scientist to support and contribute to projects and collaborations by performing downstream analysis of next-generation sequencing data, particularly those dealing with nanopore sequencing data. - Scientist in Bioinformatics The VIB Center for Cancer Biology (CCB) at KU Leuven is currently looking for a dynamic and highly motivated Scientist in Bioinformatics. The candidate will perform informatics to solve biological questions and will be involved in building and applying bioinformatics pipelines in order to analyze high-throughput sequencing data such as whole-genome, whole-exome, methylation and RNA data, guiding biologists in analyzing their own data and performing statistical tests and pathway analysis. Please have a look at http://www.vib.be/nl/over-vib/Pages/Jobs-bij-VIB.aspx - Leuven - for more detailed information. Met vriendelijke groeten, Best regards, Christel Vanslembrouck hr VIB-KU Leuven Center for Cancer Biology Department of Oncology, KU Leuven Campus Gasthuisberg ON 4 Herestraat 49 - B 912, 3000 Leuven Phone : +32 16 373 199 Christel.vanslembrouck(a)kuleuven.vib.be www.vibcancer.be<http://www.vibcancer.be/> I am not in the office on Wednesday afternoon. [signature_coBranded_Center-for-cancer-biology]

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Final Week for Early Bird Prices: Engaging Researchers in Good Data Management - 15th November, Cambridge
by Sergio Martinez Cuesta 12 Oct '17

12 Oct '17

Dear all, The following one-day conference may be of interest to some of you. Early bird registration closes in one week! All the best, Sergio Martinez Cuesta Postdoctoral research associate CRUK-CI and Department of Chemistry Cambridge, UK *----------------------------------------------------* *Engaging Researchers in Good Data Management* A one-day conference 15 November 2017, St Catharine’s College, Cambridge, UK *The University of Cambridge, together with SPARC Europe and JISC, will host a one-day conference sharing the latest thinking as well as good practices around creating and promoting effective practices in the management and sharing of research data. Via a combination of workshops and talks, focus groups and panel discussions, participants will discover how researchers across an array of disciplines, and librarians, are finding increasing success managing and providing greater access to research data.* *Who should attend?* Researchers and anyone working to support and engage with Open Research and Research Data Management; librarians and scholarly communications specialists included. We invite you to find out more and secure your place at: https://www.eventbrite.co.uk/e/engaging-researchers-in-good-data-management- registration-37769325068 *Register by 17th October for an early bird discount*

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Marie Curie Postdoctoral Fellowships in Delft
by Joana Gonçalves 11 Oct '17

11 Oct '17

Postdoctoral fellowships are available under the Marie Skłodowska-Curie Leading Fellows programme (http://leadingfellows.eu/ <http://www.google.com/url?q=http%3A%2F%2Fleadingfellows.eu%2F&sa=D&sntz=1&u…>). Applicants wanting to pursue a postdoc in computational biology at the TUDelft are most welcome to contact me at joana.goncalves(a)tudelft.nl. Our lab designs analytical approaches (algorithms, machine learning, statistics) to study regulatory mechanisms and predict novel targets for therapy in complex diseases. We have a special interest in cancer research and a synergistic collaboration with the Netherlands Cancer Institute. Please check our website for additional information ( http://homepage.tudelft.nl/c7g5f/) Deadline for next Leading Fellows call: 31 December 2017 Eligibility criteria: - PhD obtained between 1 July 2013 and 1 July 2018; - no more than 12 months spent in the Netherlands between 1 July 2015 and 1 July 2018. Kind regards, Joana *Joana Gonçalves* Assistant Professor @ TUDelft joanagoncalves.org *T**U *Delft, *Dept. Intelligent Systems* Pattern Recognition & Bioinformatics Office B36 13.290 T +31 15 27 83418 E joana.goncalves(a)tudelft.nl *NKI* *The Netherlands Cancer Institute* Guest Researcher, Computational Cancer Biology E j.goncalves(a)nki.nl <j.goncalves(a)tudelft.nl>

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[Gtpb] Fwd: Bioinformatics training courses open for applications
by Pedro L. Fernandes 11 Oct '17

11 Oct '17

Dear member of the GTPB mailing list, This is a reminder about training courses currently open for applications. The GTPB training programme, running regularly at the IGC since 1999 has provided skills and usage independence to over 5000 international participants. 1) ELB17S Entry level Bioinformatics, is aimed at newcomers to Bioinformatics. We use an established method of centering in a single gene/problem to walk you through several aspects of using computer science to work with biological data, namely sequences and derived information. Then we focus on different techniques that are specific to Next Generation Sequencing (NGS) data on which a modern biologist needs to have developed analytical capabilities. The course is fully "hands-on". If you need to use sequencing data in your research and have not had a chance to acquire such skills, please consider applying. Feedback from previous editions clearly shows that, for most people, attending this course was well worth the time and effort, as it has significantly contributed the conduction of their research. http://gtpb.igc.gulbenkian.pt/bicourses/ELB17S/ 2) PM117 Precision Medicine is a hands-on training course on translational research applied to cancer diagnosis, therapy and follow-up. It will enable you to start from NGS data and analysis reports and achieve further interpretation that is then amenable to take informed decisions, confronting them with known clinical results. This understanding is absolutely fundamental to promote the practice of precision medicine, tailored to the individual patient while in agreement with known diagnostics, therapeutics and clinical outcomes. In this course we will focus on cancer genomics, but the methods could be ported to other complex diseases. http://gtpb.igc.gulbenkian.pt/bicourses/PM17/ Please feel free to point our courses to your colleagues. Best, Pedro -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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EuBIC 2018 developer’s meeting - Meeting registration & program
by EuBIC developer's meeting 10 Oct '17

10 Oct '17

*— EuBIC 2018 developer’s meeting —* Dear colleague, We are happy to announce that the registration for the EuBIC 2018 developer’s meeting has now been opened. We encourage everyone to register in a timely manner as the number of participants is limited and to be able to enjoy the reduced early bird rate. The meeting’s program has also been finalized, with various interesting hackathon projects and keynote speakers. Please find more information below and on the meeting website. We look forward to meeting you in Ghent! *Meeting registration* More information: http://uahost.uantwerpen.be/eubic18/registration.html Early registration fees: - General registration: €100 - PhD student at Ghent University: €50 The registration fees cover the following activities and items: - Meeting attendance - On-site catering including coffee breaks and lunches - Opening reception - Closing lunch Additionally you can join the social event on Wednesday 10th January for €10. *Hackathon projects* More information: http://uahost.uantwerpen.be/eubic18/hackathon.html Topics for the hackathon sessions are divided into the (i) quality control, (ii) workflows, protocols, and guidelines, and (iii) quantification tracks. You can find more information on the specific topics included in these three tracks on the meeting’s website. You can indicate the project to which you want to contribute during the registration. *Keynote speakers* More information: http://uahost.uantwerpen.be/eubic18/keynote.html The meeting is honored to welcome the following keynote speakers: - dr. Laurent Gatto, Cambridge University, United Kingdom - prof. dr. Lukas Käll, KTH Royal Institute of Technology, Sweden - dr. Frédérique Lisacek, SIB Swiss Institute of Bioinformatics, Switzerland - prof. dr. Lennart Martens, Ghent University, Belgium *Other useful information* Date: January 9-12, 2018 Location: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium Venue: http://uahost.uantwerpen.be/eubic18/venue.html Transport: http://uahost.uantwerpen.be/eubic18/transport.html Accommodation: http://uahost.uantwerpen.be/eubic18/accommodation.html *Key dates* November 10, 2017: Early bird meeting registration deadline December 22, 2017: Late meeting registration deadline January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *More information* - website: http://uahost.uantwerpen.be/eubic18/ - social media hashtag: #EuBIC18 - conference email: eubic18(a)gmail.com *Sponsorship *inquiries are still welcome at eubic18(a)gmail.com. Supported by FWO Scientific Research Network ‘Novel Knowledge from Public Life Sciences Data'.

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