April 2016 - BBClist - maillist.psb.ugent.be

Network Inference workshop at ECCB2016: abstract submission deadline on May 1st
by bonnet 12 Apr '16

12 Apr '16

We are glad to announce the ECCB 2016 workshop: Network Inference : New Methods and Data ABSTRACT SUBMISSION DEADLINE: May 1st http://www.eccb2016.org/programme/workshops/w2/ Scope This one day session (SIG) will bring together experts from computational biology and machine learning to present recent advances in the development and application of gene regulatory network inference methods, as well as novel emerging data types (such as single-cell, epigenomics ...) suitable for network inference. The SIG will be split into two half day sessions. The first half will focus entirely on novel network inference methods, while the second half will focus on opportunities and challenges arising from new data types. Each session will feature an invited speaker and three short talks. Registration https://easychair.org/conferences/?conf=ninf2016 Venue The workshop will take place in the World Forum Convention Centre of Hague, The Netherlands on September 4th 2016 as part of the 15th European Conference on Computational Biology (ECCB 2016). Topics Network Inference Machine learning Biological networks Biological data types NGS Applications of biological network inference Audience The workshop is suitable for wide audience as computational biologists interested in networks inference, computational and experimental biologists, clinicians, plant biologists and anyone who is interested to be exposed to the latest trends and applications of network biology inference from various types of biological data. Organizing Committee: Dr. Anagha Joshi, Roslin Institute, University of Edinburgh, UK. Dr. Tom Michoel, Roslin Institute, University of Edinburgh, UK. Dr. Eric Bonnet, Centre National de Génotypage, CEA, Paris, France.

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[Gtpb] IB16F - Introductory Bioinformatics - with a soft introduction to NGS Data Analysis - Announcement
by Pedro Fernandes 11 Apr '16

11 Apr '16

*REMINDER* Dear all, The Applications for the bioinformatics training course IB16F - Introductory Bioinformatics - which is our ENTRY LEVEL training course, with a soft introduction to NGS Data Analysis - are still *OPEN* New deadline IMPORTANT DATES for this Course Deadline for applications: April 14th 2016 <======= NEW !!! Course date: April 18th - April 22nd 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. *WARNING* this is one of our most popular training courses. It usually gets fully booked quite rapidly. Details, including application instructions, are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB16F This is an ENTRY LEVEL course, not because it is too simple, but because the level of the pre-requisites is very low. It is designed for participants with no a-priori knowledge about Bioinformatics. A variety of reasons, technical and economical, have led to a situation where affordable nucleotide sequencing data comes exclusively from Next Generation Sequencing machinery. This creates extra needs in knowing how to handle such data. Our course will cover this subject in a soft way. As usual in our courses we have two aims: to transfer a lot of skills by hands-on experience, and to maximise usage independence. All of this is achieved in highly interactive sessions, using teamwork and feedback techniques quite extensively. Best wishes, Pedro Fernandes -- Pedro Fernandes GTPB Coordinator 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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CFP META'2016 Marrakech
by El-ghazali Talbi 10 Apr '16

10 Apr '16

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2016 International Conference on Metaheuristics and Nature Inspired Computing 27-31 Oct 2016 Marrakech, Morocco http://meta2016.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2016 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. META'2016 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2016 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META’2016 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, scatter search, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Parallel algorithms * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S1 and S2 will be published in a Springer book and international journals (ISI journals). - Predefined styles are available on the website http://meta2016.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline 15th April 2016. contact el-ghazali.talbi(a)univ-lille1.fr Important dates _______________ - Submission deadline: May 6, 2016 - Notification of acceptance: June 3, 2016 E-G. Talbi (Conference Chair) -- ********************************** META'2016 Marrakech, 27-31 Oct 2016 http://meta2016.sciencesconf.org ********************************** Prof. E-G. Talbi Univ. Lille, CNRS, INRIA

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Computational cancer biology position in Amsterdam
by Lodewyk Wessels 08 Apr '16

08 Apr '16

Integrative Bayesian modelling to identify therapy resistance mechanisms Project description The purpose of this project is to identify the underlying resistance mechanisms in invasive lobular carcinoma (ILC). ILCs are known as ‘slow killers’ as they grow relatively slowly, but respond poorly to therapy, eventually killing the patient. To unravel the resistance mechanisms, we have generated comprehensive molecular profiles (gene expression, mutational, copy number and (phospho-)proteomics profiles) from matched pairs of sensitive and resistant mouse models of ILCs. We will employ integrative computational (Bayesian) modeling to integrate prior knowledge and the molecular datasets to identify candidate resistance factors. These will be validated in genetic and pharmacological perturbation studies in cultured ILC cell lines and mouse models. Knowledge of these mechanisms will enable us to design combination therapies able to block the development of resistance, leading to improved therapy response. The successful candidate will be responsible for carrying out all the computational analyses, including the complete analysis workflow starting at the basic analyses of the DNA and RNA sequencing and mass spectrometry data up to the more complicated integrative analyses and the Bayesian pathway modelling. He/She will also be expected to coordinate the project and to liaise with the molecular biologists, the animal facility, the genomics core facility and the proteomics facility. The project will be carries out in close collaboration with the groups of Jos Jonkers (mouse models of breast cancer) and Maarten Altelaar (proteomics). Candidate profile We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science or a related discipline. Applicants should be experienced in cancer biology and clinical applications and should be skilled in analysing high-throughput molecular data. Experience in analyses of (phospho)-proteomics data is a plus. The candidate needs to be proficient in common bioinformatics scripting and programming languages (e.g. R, Python). Interested? For further information please contact Lodewyk Wessels (telephone +31 20 5127987 or e-mail: l.wessels(a)nki.nl) Also see ccb.nki.nl for further information. You can mail your application to work(a)nki.nl. Include a CV, a list of publications and the names and contact information of at least two references. Deadline 1 June 2016

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Fwd: Users Meeting Flyer/Email
by Wouter Meuleman 07 Apr '16

07 Apr '16

[image: Image] <http://www.encode2016.org> Dear colleagues, Registration for the ENCODE 2016: Research Applications and Users Meeting is now open: www.encode2016.org This is a great opportunity for both novice and experienced users of genomic data to learn about ENCODE resources and how to leverage them for their own research. The meeting will take place *June 8th - June 10th, 2016*, at the Stanford Li Ka Shing Center, at 219 Campus Drive, Palo Alto CA, and will feature: ٭ Hands-on training workshops to learn to navigate, analyze, and integrate ENCODE and mouse ENCODE data into your research. No programming experience required. ٭ Leading-edge research applications from distinguished invited speakers. ٭ Tutorials on newly-available informatics pipelines that greatly facilitate working with ENCODE data. ٭ Short talks selected from abstracts. *Registration is only $100 for academic attendees and $250 for non-academic attendees. This does not include transportation or lodging, but does cover meals.* *KEYNOTE SPEAKER* ٭ Nancy Cox, Vanderbilt University *CONFIRMED SPEAKERS* ٭ Matthew Freedman, Dana Farber/Harvard Cancer Center ٭ Tom Gingeras, Cold Springs Harbor Laboratory ٭ Brenton Graveley, University of Connecticut Health Center ٭ Mathieu Lupien, Princess Margaret Cancer Centre ٭ Katherine Pollard, The Gladstone Institute at UCSF ٭ Tim Reddy, Duke University ٭ Bing Ren, University of California, San Diego ٭ Yijun Ruan, The Jackson Laboratory ٭ Michael Snyder, Stanford University ٭ Barbara Stranger, University of Chicago ٭ Zhiping Weng, University of Massachusetts Medical School ٭ Grace Xiao, University of California, Los Angeles *WORKSHOP TOPICS* ٭ Viewing, querying, and downloading ENCODE data ٭ Running ENCODE processing pipelines on your own data (including ChIP-seq, eCLIP-seq, RNA-seq, DNase-seq, DNA methylation) ٭ Integrating ENCODE data with those from your lab or other major projects ٭ Using ENCODE data to interpret human variation, personal genomes, and disease (including cancer) genomes ٭ Connecting regulatory elements to their target genes across the genome ٭ Integrative analysis ٭ See the website for more details about training workshops We look forward to seeing you at Stanford University! The ENCODE Outreach Working Group www.encode2016.org Information & Registration <http://www.encode2016.org>

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BioSB 2016: Full programme online: register now! Registration deadline: April 14
by Femke Francissen 05 Apr '16

05 Apr '16

*------------------------------------------------------* *Dutch Bioinformatics & Systems Biology Conference 2016* Date: April 19 / 20, 2016 Venue: Congrescentrum De Werelt, Lunteren, NL <http://www.aanmelder.nl/biosb2016>Conference website <http://www.aanmelder.nl/biosb2016> Register here <https://www.aanmelder.nl/biosb2016/wiki/154973/registration> (deadline: April 14) ---------------------------------------------------------- *Detailed programme now online* The programme of the conference is now online. The conference features keynote speakers, thematical sessions, evening programme with dinner and after dinner keynote speaker, poster presentations and lots of opportunities for networking. View the full programme here <https://www.aanmelder.nl/biosb2016/part_program> Our keynote speakers: - Sander Tans, AMOLF - Daniel Huson, University of Tübingen - Adriano Henney, VHP Institute Leuven - Mick Watson, University of Edinburgh - Jonathan Karr, Icahn School of Medicine at Mount Sinai, NY You can still submit abstracts <https://www.aanmelder.nl/biosb2016/wiki/154972/abstract%20submission> for a poster presentation! Submission deadline: April 14, 2016. *BioSB research school meeting* The research school is organising a plenary session on April 19. The BioSB board invites everyone interested to join the meeting. Topics in the meeting will include a.o. BioSB activities and plans, the Education and Scientific Committees that have been installed, BioSB finances and the evaluation of the membership model that has been in place for one year now. Read more <https://www.aanmelder.nl/biosb2016/wiki/187792/biosb%20research%20school%20…> *Winner of the BioSB Young Investigator Award 2016 * The selection committee selected a winner for this year's BioSB Young Investigator Award: Sara Pulit of the UMC Utrecht. The award will be presented to her on April 19 after which she will give an honorary lecture with the title: 'Genome-wide significance, claims of association, and the big data era'. The award is sponsored by the BioSB research school. Read more <https://www.aanmelder.nl/biosb2016/wiki/164489/biosb%20young%20investigator…> *BioSB PhD retreat - April 18* The Young Computational Biologists are organising a PhD retreat <https://www.aanmelder.nl/biosb2016/wiki/154925/biosb%20phd%20retreat> on April 18, the day preceding the BioSB 2016. The retreat will feature: - Keynote: Fiona Nielsen, Repositive - Keynote: Jonathan Karr, Icahn School of Medicine at Mount Sinai, NY - Workshop organised by Fiona Nielsen: 'Genome sequencing projects around the world and how to find data for your research' - 5 minute flash talks - dinner in Lunteren followed by social activity *Our sponsors* - The Hyve - DSM - Utrecht Bioinformatics Center (UBC) - Keygene NV - Wageningen UR - ELIXIR-NL *Contact:* Femke Francissen, community manager BioSB <http://www.biosb.nl>, email: femke.francissen(a)biosb.nl The conference is organised by the BioSB research school together with Wageningen University & Research Centre. Use: #BioSB2016 on Twitter. Follow us on Twitter via @BioSB_NL <https://twitter.com/biosb_nl> and Facebook <https://www.facebook.com/BIOSB-122337454509903/>

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omics/epigenetics conference in Ghent, 12-15 September 2016: call for abstracts
by Katrijn Vannerum 05 Apr '16

05 Apr '16

Invitation to submit abstract to omics/epigenetics conference in Ghent, 12-15 September 2016 Dear all, We are very excited to announce that the joint SETAC/iEOS conference on environmental and (eco)toxicological omics and epigenetics will take place in Ghent, 12-15 September, 2016. Sessions will include fundamental and applied environmental, ecological, evolutionary, archaeological, microbial, and (eco)toxicological genomics, epigenetics and metagenomics. All details about program, venue, abstract submission and registration can be found here: http://epigenetics.setac.eu Abstracts for platform and poster presentations can be submitted until 15 June. Special registration fees apply for students. Confirmed session keynote speakers so far are: - Prof. Jeroen Raes, VIB, UGent, Belgium - Prof. Mark Blaxter, University of Edinburgh, UK - Prof. Eske Willerslev, University of Cambridge, UK - Prof. Mark Viant, University of Birmingham, UK - Prof. Juliette Legler, University of Amsterdam, NL - Prof. Ben Brown, University of California, USA - Prof. Joe Shaw, University of Indiana, USA - Prof. Joëlle Rüegg , Swedish Toxicology Science Research Center, Stockholm We look forward to welcoming you at our conference! Sincerely, Prof. Karel De Schamphelaere Dr. Jana Asselman (UGent members of the organizing committee) Karel De Schamphelaere, Ph D Associate Professor www.ecotox.ugent.be Follow us on Twitter @GhEnToxLab Ghent University (UGent) Laboratory of Environmental Toxicology and Aquatic Ecology Environmental Toxicology Unit (GhEnToxLab) Jozef Plateaustraat 22 B9000 Gent Belgium Tel. +32 9 264 3764 Fax +32 9 264 3766

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VIB BITS Upcoming Bioinformatics Training Sessions - FYI
by Alexander Botzki 04 Apr '16

04 Apr '16

[VIB] [VIB] VIB Bioinformatics Training May sessions IN THIS ISSUE * Basic statistics theory * Hands-on introduction to ChIP-Seq analysis Basic statistics theory This training is an introduction to a series of hands-on trainings on the statistical analysis of life sciences data: 'Basic statistics in R<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-t/>' and 'Basic statistics in Graphpad Prism<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-i/>'. If you want to follow one of these trainings, you are strongly advised to follow this introduction. Ít will give you all the theoretical background that you need.. Date: 2 May Location: Park Inn, Leuven Trainer: Janick Mathys (BITS) More information and registration: VIB website<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-d/> Hands-on introduction to ChIP-Seq analysis This training gives an introduction to ChIP-Seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. Requirements: * Basic knowledge of Illumina NGS read structure. People who lack this knowledge can follow the Introduction to NGS data analysis<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-o/> training. * Basic Linux command line understanding. If you have no experience with Linux command line, you should follow the Linux for bioinformatics<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-b/> training. Date: 20 May Location:Park Inn, Leuven Trainer:Morgane Thomas-Chollier (Ecole normale supérieure, Paris) More information and registration: VIB website<http://bits.cmail20.com/t/r-l-edrjuut-shyuuqkd-n/>

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CSC Summer School in HPC, Jun25-Jul3 2016, (deadline for registration April 10 2016)
by Celia.vanGelder＠radboudumc.nl 03 Apr '16

03 Apr '16

* CSC Summer School in High-Performance Computing 2016 (Jun 25 - Jul 3) * Seven days of coding, sport activities and good company right in the middle of beautiful Finnish nature just 30km from Helsinki. Join the fun and register now at: https://www.csc.fi/web/training/-/csc_summerschool_2016 The 7th CSC Summer School in HPC brings together undergraduate and graduate students as well as postdoctoral researchers from different disciplines of scientific computing. The school consists of lectures and hands-on training on parallel programming, code optimization and other essential skills in development of scientific software. During the school you can build up your HPC expertise from almost zero up to an intermediate / semi-advanced level. The aim of the school is to give you the skill set necessary to start writing high-performance scientific software! ... and to have a great time while doing it! A more detailed program together with further details about the school is available on-line: https://www.csc.fi/web/training/-/csc_summerschool_2016 -- * See the full list of events and courses at CSC: www.csc.fi/training * Follow us on Twitter: twitter.com/CoursesAtCSC * Feel free to pass this message along! * Unsubscribe: postit.csc.fi/sympa/sigrequest/compute-server-announcements _______________________________________________ Training mailing list Training(a)elixir-europe.org https://lists.elixir-europe.org/mailman/listinfo/training 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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RSG Belgium Symposium 2016: Bioinformatics/Computational Biology
by Cuypers Bart 01 Apr '16

01 Apr '16

Dear Colleague, I would like to invite you to the upcoming RSG Belgium Symposium 2016. The symposium will take place on June 3, 2016, 2PM at the University of Leuven. (Room 331-01 Landbouwinstituut Hoofdgebouw, Kasteelpark Arenberg 20, 3001 HEVERLEE) The event is focused around young bioinformaticians/computational biologists (master students, PhD students, young post-docs), who will get the opportunity to present their work in a broad research context and network with one another. I am very happy to announce our keynote speaker for this event, prof. dr. Yves Moreau. Prof. Moreau's research focuses on systems biology techniques to understand how variation in a genome leads to variation in risk and severity of genetic diseases. He also applies these techniques for diagnosis and disease gene discovery in congenital genetic disorders. Additionally, Prof. Moreau is an active member of the ISCB community. Not only is he currently a member of the ISCB board of directors, he also chaired ECCB in 2010 and in 2014. Registration is free but mandatory, and can be done by filling in the form at: http://goo.gl/forms/whU1ay8YLe After the symposium (incl. reception), for those interested, we will have a social event in Leuven (walk, dinner, drinks). You can submit an abstract for an oral presentation until April 30, 2016 by mail to rsg-belgium(a)iscbsc.org<mailto:rsg-belgium@iscbsc.org>. You are most welcome to send this invitation to anyone that might be interested! Hope to see you there, Bart Cuypers RSG Belgium President

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