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[Gtpb] ARANGS16 - ARANGS16 Automated and reproducible analysis of NGS data
by Pedro Fernandes 13 Apr '16

13 Apr '16

ANNOUNCEMENT / REMINDER Applications for ARANGS16 - ARANGS16 Automated and reproducible analysis of NGS data with Darin London and Rutger Vos are OPEN IMPORTANT DATES for this Course Deadline for applications: May 2nd 2016 Course dates: May 9th - May 13th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Description Next generation sequencing (NGS) technologies for DNA have resulted in a yet bigger deluge of data. Researchers are learning that analyzing the data efficiently requires the creation of sophisticated pipelines, typically using command line tools in a Linux or other Open source Unix variant compute environment. Many researchers have created these pipelines to successfully analyse their data. Now they are faced with the challenge of making these pipelines available to their colleagues. The issue of reproducibility has emerged as a major issue, as researchers, peer reviewers, and even pharmaceutical companies discover that the software and data used to produce a particular research finding are either not available, poorly documented, or targeted to specific compute infrastructures that are not available to the wider research community. To remedy this, funding agencies and journals are creating policies to promote software reproducibility. In this brief workshop we will establish several best practices of reproducibility in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use cases that illustrate the underlying principles. Building on the basis of an existing pipeline of command line utilities, we will illustrate how the entire compute environment used to run the pipeline can be packaged into a unit that can be shared with other researchers such that they can make full use of the environment on their own machines, or on standard cloud compute environments such as Amazon or Google. Best practices Command line scripting of analysis steps Provisioning systems to standardise software environment requirements Packaging of compute environment into static, portable units Sharing of compute environment packages Technologies Next generation sequencing platforms Command-line executables, command line scripting and batching Provisioning Systems: Puppet, Dockerfile Virtualization with Virtualbox and Vagrant Containerization with Docker More details at the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS16/ 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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Vacancy for a tenure track lecturer in structural bioinformatics at Vrije Universiteit Brussel
by Stefan Weckx 13 Apr '16

13 Apr '16

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TransMed 2016 (ISMB - Florida, July 8) - Call for abstracts
by Johann Pellet 12 Apr '16

12 Apr '16

We are happy to announce the TransMed 2016: Translational Medicine Informatics & Applications meeting, to be held during the ISMB 2016, (Orlando, USA), on July 8, 2016. Knowledge-based translational medicine is a rapidly growing discipline in biomedical research and aims to expedite the discovery of new diagnostic tools and treatments by using a multi-disciplinary, highly collaborative, "bench-to-bedside" approach. Large amounts of multi-omics, imaging (medical and molecular) and clinical data can now be captured for given patient populations. In addition to the challenges of data curation and harmonisation, new computational methods are required to identify molecular signatures that suggest disease subtype. These signatures may be predictive of outcome or progression, and impact on disease management by suggesting personalised therapeutic strategies for patients. Such approaches will further the development of a new taxonomy of disease. In the TransMed SIG meeting, we will explore the current status of computational biology approaches within the field of translational medicine. Authors are invited to submit abstracts (1 page) for presentations and posters by April 15, 2016. Details of submission process are available on the TransMed2016 SIG website: http://transmedit.org/Main_Page. Keynote Speakers Confirmed: Prof. Russ Altman, Professor of Bioengineering, Genetics, Medicine and Computer Science; Director, Biomedical Informatics Training Program, School of Medicine, Stanford University Prof. Sean Mooney, Professor of Biomedical Informatics and Medical Education, University of Washington; Chief Research Information Officer (CRIO) of UW Medicine Prof. John Overington, Director of Bioinformatics at Stratified Medical, Visiting Professor at the Institute of Cardiovascular Science, University College London and the Farr Institute Key dates: Abstract submissions deadline: April 15, 2016 Poster and Presentation acceptance notifications: May 6, 2016 Final program available: May 27, 2016 TransMed 2016 SIG: July 8, 2016 If you have any further questions regarding the submission of abstracts, do not hesitate to contact our committee at the following email address: transmed-coord(a)googlegroups.com.

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Open Positions at Coimbra Genomics
by Pedro Lopes 12 Apr '16

12 Apr '16

Hi! Coimbra Genomics S.A. is a young company working in Digital Health and Precision Medicine, which has recently sealed six partnerships for the global expansion of its first product ELSIE - a software platform developed by the company and designed to allow any doctor, anywhere, to use genomic information from patients to make better decisions on prescriptions and diagnosis, all in the setting of a regular medical appointment. More info at: www.coimbra-genomics.com Coimbra Genomics is looking for skilled candidates for 3 positions: - Bioinformatics Expert ( http://www.coimbra-genomics.com/news-posts/bioinformatics-expert-job-opening ) hands-on bioinformatics experience in genetic/genomics applications, preferably in the design and maintenance of NGS pipelines. Proficiency in Python and/or other languages is required. - Human Genetics Expert ( http://www.coimbra-genomics.com/news-posts/genetics-expert-job-opening) in-depth knowledge of human genetics; ability to work with small groups of specialists; be familiar with recent trends in genetics/genomics (e.g. WGS, WES, gene panels, gene mutation databases, etc). - Head of Marketing and Communication ( http://www.coimbra-genomics.com/news-posts/head-of-marketing-and-communicat… ) strong background in healthcare industry; previous experience in marketing genetics-related products or services would be a plus. The successful candidate will lead the creation and implementation of a global marketing strategy for the commercial deployment of ELSIE. The first two positions require frequent presence at the Biocant Park, in Cantanhede, but candidates wishing to remain based in other regions are encouraged to apply. The position for the Head of Marketing and Communication will be based in Portugal, Germany or UK, and will require frequent international travelling. Applicants should send a brief letter of motivation and a CV, in English, until 15th April to Sandra Tomé at sandra.tome(a)biocant.pt You can find the full job's description in the files attached to this email. Best, Pedro http://www.coimbra-genomics.com/

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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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