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NETTAB 2018: Building a FAIR Bioinformatics environment - Call for Abstracts for oral communications - Submit within May 20, 2018
by Frederik Coppens 14 May '18

14 May '18

Submission deadline end of this week ! NETTAB 2018 Building a FAIR Bioinformatics environment October 22-24, 2018, Genoa, Italy http://www.nettab.org/2018/ <http://www.nettab.org/2018/> Submission deadline for abstracts for oral communications: Sunday May 20, 2018. CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS NETTAB 2018 is organised in collaboration with ELIXIR Nodes of the UK and Italy as well as the Italian Society of Bioinformatics, BITS. The main focus will be on FAIR principles in bioinformatics, a challenging topic that we hope will attract many researchers from all over the world, including but not limited to, Bioinformaticians, Biologists, Computer Scientists, and others working or interested in the above research scope. The FAIR Guiding Principles for scientific data management and stewardship, published in 2016, has sparked worldwide interest across the biology community: from grassroots to policymakers, and from data providers to publishers. In order to make the FAIR concept a reality, we need to answer many questions, like: What is FAIRness? How to make FAIR data a reality? How to facilitate the translation to FAIR data? How to measure it? On these topics, there are many ongoing projects, such as EOSCpilot, FAIRmetrics, FAIRsharing, and GO-FAIR. Now is the perfect time to discuss on these topics and related actions, and to move on from FAIR principles to FAIR practice. The workshop will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics. TOPICS Methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics including, but not limited to: FAIR concept • Specification and revision of components, conceptual issues. • Criticisms and review of FAIR principles Development tools • FAIR Web Services, metadata for FAIR tools, revision of standard formats. FAIRification methodologies • FAIRification best practices and training • Experiences of FAIR methods • Best practices and lessons learned from domains outside bioinformatics. • FAIRness evaluation • FAIRness validation and correction tools. • FAIR metrics: Levels of FAIRness, FAIRness scores, FAIRness minimal levels. FAIR environment • Integration and interoperation of FAIR data and systems. • FAIR and its demonstrated contribution to open science and reproducible results • FAIR principles and practices of research outputs other than data: workflows, scripts, tools, models, training materials, SOPs etc • Surveys of FAIR resources and methods FAIR value • Examples of FAIR in practice and the benefits of FAIR resources • Related initiatives to FAIR: for example Data Commons and EOSC • The economics of FAIR • Incentives for FAIR stewardship throughout the data lifecycle The topics of NETTAB 2018 also include the usual topics of NETTAB workshops. INSTRUCTIONS AND DEADLINES Submission of abstracts for oral communications: Sunday May 20, 2018 Notification: Monday June 18, 2018 Abstracts of maximum four A4 pages must be submitted through EasyChair at: https://easychair.org/conferences/?conf=nettab2018 <https://easychair.org/conferences/?conf=nettab2018> . See full instructions at: http://www.igst.it/nettab/2018/submissions/instructions-for-authors/ <http://www.igst.it/nettab/2018/submissions/instructions-for-authors/> . KEYNOTE SPEAKERS Michel DUMONTIER, MaastrichtUniversity, The Netherlands Frederik COPPENS, Gent University , Belgium Patricia PALAGI, SIB, Switzerland Christine DURINX, ELIXIR, Switzerland GUEST SPEAKERS Rob HOOFT, DTLS, The Netherlands Rafael JIMENEZ, ELIXIR, UK Marco ROOS, LUMC, The Netherlands Amnon SHABO, Siemens, Germany Tutorial/Hackathon programme under definition. WORKSHOPS ORGANIZORS Carole Goble, University of Manchester Paolo Romano, Ospedale Policlinico San Martino, Genoa Mauro Giacomini, University of Genoa SCIENTIFIC COMMITTEE The Scientific Committee is being defined. Many invitations are still pending. Oya Deniz BEYAN, Fraunhofer FIT, Germany Jan Willem BOITEN, Lygature, The Netherlands Robin CHAMPIEUX, Oregon Health & Science University, USA Michael CRUSOE, Common Workflow Language, Lithuania Peter DOORN, DANS-KNAW, The Netherlands Michel DUMONTIER, Maastricht University, The Netherlands Leyla Jael GARCIA CASTRO, EMBL-EBI, United Kingdom Mauro GIACOMINI, University of Genoa, Italy Carole GOBLE, University of Manchester, United Kingdom Alasdair GRAY, Heriot-Watt University, United Kingdom Paul GROTH, Elsevier Labs Paolo MANGHI, CNR/ISTI & OpenAIRE, Italy Patricia PALAGI, Swiss Institute of Bioinformatics, Switzerland Helen PARKINSON, EMBL-EBI, United Kingdom Paolo ROMANO, Ospedale Policlinico San Martino, Italy Susanna Assunta SANSONE, Oxford eResearch Center, United Kingdom Kees VAN BOCHOVE, The Hyve, The Netherlands Mark WILKINSON, UPM, Spain Katherine WOLSTENCROFT, Leiden University, The Netherlands Paolo Romano on behalf of Workshop Organizors Paolo Romano Ospedale Policlinico San Martino Genova, Italy Skype: p.romano Email: paolo.romano(a)hsanmartino.it <mailto:paolo.romano@hsanmartino.it> - paolo.dm.romano(a)gmail.com <mailto:paolo.dm.romano@gmail.com> CON TE LA NOSTRA RICERCA PUO' DIVENTARE CURA DEVOLVI IL TUO 5 X 1000 AL SAN MARTINO! FINANZIAMENTO DELLA RICERCA SANITARIA CODICE FISCALE 02060250996 5xmille.ospedalesanmartino.it <http://www.ospedalesanmartino.it/sostienici.html> Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Exciting postdoc opportunity in Copenhagen
by Magali Michaut 14 May '18

14 May '18

You want to be happy and do some cool work? ;-) Here is your chance: cancer stem cell research with exciting single cell data in the capital of happy people! Check it out and/or spread the word: http://jobportal.ku.dk/alle-opslag/?show=147220 <http://jobportal.ku.dk/alle-opslag/?show=147220> If you have questions about our group, please contact me. Looking forward to hearing from you, Magali

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2 positions for Computational Systems Biology Postdoc at Institut Curie
by Alexander Botzki 12 May '18

12 May '18

Dear colleagues, We are looking for brilliant postdocs to join our Cancer Computational Systems Biology group. Please could you spread the word about this opportunity and forward the attached announcements to whoever might be interested? Many thanks in advance. Best wishes Emmanuel Emmanuel.Barillot(a)curie.fr

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FW: Data Carpentry workshop June (Brussels) & ELIXIR Train the Trainer August (Antwerp)
by Alexander Botzki 08 May '18

08 May '18

Dear all, ELIXIR-BE<https://www.elixir-belgium.org/> is hosting two events that might be of your interest or that you might be able to recommend to people around you. The first one is a Data Carpentry workshop in Brussels, next month (June 12-13) https://inbo.github.io/2018-06-12-bru-datacarpentry-inbo-elixir/ The second is an ELIXIR Train the Trainer workshop in Antwerp, last week of (August 20-21) https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-tickets-45… Please don't hesitate to contact me if you have any questions. Kind regards, Paula Andrea Martinez Data science and bioinformatics trainer TeSS<https://tess.elixir-europe.org/events> - find our events [Image removed by sender.]

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[Gtpb] PDA18 - Course announcement / Reminder
by GTPB Administration 07 May '18

07 May '18

Course Announcement / Reminder PDA18 Proteomics Data Analysis with Lennart Martens, Harald Barsnes and Lieven Clement Key terms: Proteomics data, identfication, quantification, statistics IMPORTANT DATES for this Course Deadline for applications: May 20th 2018 Course date: May 28th - June 1st 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The core focus will be on shotgun proteomics data. Quantification through isobaric labels (iTRAQ, TMT) and label-free precursor peptide (MS1) ion intensities will also be introduced. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: this is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PDA18/ Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Systems Biology job opening in BASF in Nevele
by Koen Bruynseels 07 May '18

07 May '18

Dear Sir/ Miss, Can you post the following on the BBC mailing list? We have a job opening in the R&D Digitalization Unit / Systems Biology in BASF in Nevele. The job posting is added as attachment. As Systems Biologist you will integrate and analyze molecular and phenotypic data derived from plants, fungi and/or microorganisms. You will drive the innovation of novel systems biology analysis, visualization and interpretation methodologies, and the constant improvement of existing methodologies. You will actively interact with peers and stakeholders to develop the content of work packages, execute the analyses, and communicate about the results. The position is based in Nevele, Belgium, and is part of an international and interdisciplinary team of scientists in the BASF R&D Digitalization department. The BASF R&D Digitalization Department is responsible for the digitalization of R&D across BASF. BASF has about ten thousand employees working in research and development worldwide. As Systems Biologist you will engage in the following: * Proactively identify and drive the development of Systems Biology methods and analyses, in close interaction with internal customers across BASF. * Integration and mining of molecular and phenotypic data from experiments. * Design of -omics experiments together with bench scientists and analysis of the results. * Interpretation of results, in interaction with specialists in agronomy, white biotech or toxicology. * Communication about the work packages and the analysis results to various stakeholders. * Interact with customers and potential customers in BASF, and with external companies and academic partners Further information can be found in the attachment. Best regards, Koen Dr. Koen Bruynseels Head of BASF Systems Biology (Digitalization in R&D, ROM/BB) Phone: +32 92423-456 Mobile: +32 474 296 225 Fax: +32 9 242 33 81 E-Mail: koen.bruynseels(a)cropdesign.com Postal Address: CropDesign N.V., Kerrebroek 66B, 9850 Nevele, Belgium CropDesign N.V. - A BASF Plant Science Company Registered address: CropDesign N.V. - Technologiepark 21 - 9052 Gent (Zwijnaarde) - Belgium - rpr gent: 0463 222 213 - General Telephone: 32-9-242 34 00 - Fax: 32-9-242 34 89 Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)cropdesign.com.

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Bioimage analysis Training Courses in Edinburgh, 16-19 October 2018
by Alexander Botzki 04 May '18

04 May '18

Van: bioinfo-request(a)sfbi.fr <bioinfo-request(a)sfbi.fr> namens Perrine Paul-Gilloteaux <perrine.paul(a)gmail.com> ? Onderwerp: [bioinfo] Bioimage analysis Training Courses in Edinburgh, 16-19 October 2018 Dear colleagues, NEUBIAS, the Network of European BioImage Analysts (www.neubias.org<http://www.neubias.org>), is delighted to announce two new Training Schools on BioImage Analysis: for Early Career Investigators (life scientists) for Facility staff (imaging & analysis staff from core-facilities) The focus of training will be on construction and automation of BioImage Analysis workflows, using as examples more than one toolbox and different exercises. The schools will be held in Edinburgh 16-19th of October 2018, hosted by the MRC Center for Regenerative Medicine/Imaging facility and co-organized by the University of Edinburgh and University of Dundee. NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >30 specialists at the event) and "....a great mix of intensive learning and community networking" (former trainee testimonial!). The schools will include practical sessions and seminars on ImageJ for analysis and publication, scripting/macros in ImageJ and Matlab, Omero, CellProfiler, QuPath, Ilastik, Ethics in Image Analysis and work on own data. - Applications are now open (each school has 20 available seats and ~7 trainers) - Applicants are highly encouraged to bring their own laptops and data. - Within the COST framework (funders of NEUBIAS), 7 travel grants per school are offered to applicants who qualify. - Registration requires a "letter of motivation" (filled in application form) and later a confirmation of status. - Application deadline: May 11th 2018 - Selection notification: 1st week of June 2018. More information about schools (programme & trainers) and venue, travel & lodge available at our website: www.neubias.org<http://www.neubias.org> -> "Training Schools" http://eubias.org/NEUBIAS/training-schools/eci/ts8-edinburgh-2018/ http://eubias.org/NEUBIAS/training-schools/staff/ts9-edinburgh-2018/ We kindly ask that you help us reach all potential interested applicants. on behalf of all NEUBIAS members, of local organizers (Bertrand Vernay & Graeme Ball) and programme organizers (Anna Klemm, Laura Murphy, Graeme Ball and Sebastien Herbert) --------------------------------------------------------------- NEUBIAS is an European network of >220 members and 41 countries, which aims to promote the communication between Life Scientists, Instrumentalists, Developers and BioImage Analysts and to establish and promote the role of Bioimage Analysts in Life Science. Our mission includes: - A training programme for 3 different target audiences:"Early Career" researchers, (core) Facility Staff and Bioimage Analysts (running until 2020 - expected 400 trainees and 15 training schools). - Promote different yearly events (NEUBIAS Conference, workshops [training schools], Taggathons) - Online Resources: Repository of tools and workflows e.g. biii.eu<http://biii.eu>, Benchmarking and Sample datasets, Training material and Open Textbook. - A Short Term Scientific Mission mobility programme for Scientists to visit Host Labs and get in depth insights into cutting edge Image Analysis technology. - A "ITC conference grants" programme to support travel for Early career Investigators from Inclusiveness Target Countries to present their work at conferences. - Outreach material. ... more at www.neubias.org<http://www.neubias.org>

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Research Assistant (one year; M.Sc.-level) on the subject of multiscale modelling of the gut microbiota in infants
by Roeland Merks 03 May '18

03 May '18

Centrum Wiskunde & Informatica (CWI) has a vacancy in the Scientific Computing research group for a talented * Research Assistant (one year; M.Sc.-level) on the subject of multiscale modelling of the gut microbiota in infants The opening is a research position within the field of applied mathematics or computational science. The position may be prolonged to a period of maximum four years, in which case the candidate is expected to work towards an academic promotion. The one-year position will be financed by, and will be carried out in part at a large international Food Company. * Research group The work will be embedded in the Biomodeling and Biosystems Analysis team at the CWI in Amsterdam. The group carries out biomodeling research with experimental collaborators, and focuses on modelling pattern formation and morphogenesis in multicellular organisms and bacterial ecosystems. * Job description The central hypothesis of the project is that the intestinal microbiota of the infant contributes to the physiological performance. The microbial composition and metabolic product blend, due to digestion, are linked with each other. The microbial products can be produced with various physiological effects. The aim of this project is to identify control strategies for steering the microbial composition and the production of selected metabolic products by the gut microbiota. The objective of the project is to further develop our existing, spatial, multiscale simulation platform of the gut microbiota (Van Hoek and Merks, BMC Systems Biology 2017) towards a platform that can be as a hypothesis generator for how nutritional composition and structure of dairy products is linked to digestive performance in the infants. The model includes detailed metabolism of bacterial populations based on flux-balance analysis, partial-differential equations to model the exchange of nutrients, and agent-based models of bacterial population dynamics.. * Requirements Candidates are required to have a Master’s degree in applied mathematics, computational physics, theoretical biology, computer science or a related discipline, and able to communicate with scientists in biology and mathematics. Preferable qualifications for candidates include proven research talent, excellent programming skills in C++, an excellent command of English, and good academic writing and presentation skills. * Terms and conditions The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The gross monthly salary, for a Research Assistant on a full time basis, is €2672,- during the first year. Employees are also entitled to a holiday allowance of 8% of the gross annual salary and a year-end bonus of 8,33%. CWI offers attractive working conditions, including flexible scheduling and help with housing for expat employees. * Application Applications can be sent before 25th May 2018 to apply(a)cwi.nl <mailto:apply@cwi.nl>. All applications should include a detailed resume, motivation letter, list of your MSc courses and grades, copy of your Master’s thesis and preferably a list of publications. * For more information about the vacancy, please contact prof. dr. Roeland Merks, email Roeland.Merks(a)cwi.nl <mailto:Roeland.Merks@cwi.nl>, telephone +31(0)20 592 4117. For more information about CWI, please visit www.cwi.nl <http://www.cwi.nl/>. More information about the group can be found on http://biomodel.project.cwi.nl <http://biomodel.project.cwi.nl/>. Or watch our video “A Fundamental Difference” about working at CWI. * About Centrum Wiskunde & Informatica Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and is part of the Institutes Organisation of NWO. The mission of CWI is to conduct pioneering research in mathematics and computer science, generating new knowledge in these fields and conveying it to trade, industry, and society at large. -------------------------------- Roeland M. H. Merks, Ph.D Professor of Multiscale Mathematical Biology Centrum Wiskunde & Informatica (CWI) - office L125 Science Park 123, 1098 XG Amsterdam, The Netherlands Mathematical Institute (MI) - office 206a2 Leiden University, Leiden, The Netherlands Cell phone +31 6 4523 1485 http://biomodel.project.cwi.nl

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Post-doc Computational Biology
by Andreas Beyer 02 May '18

02 May '18

The research group Cellular Networks and Systems Biology of Andreas Beyer invites applications for a Postdoc in computational biology. The offered position is part of a collaborative project with Martin Leeb (Max F. Perutz Laboratories, Vienna). The application deadline is May 22nd. Please, see here for more details: https://www.stellenwerk-koeln.de/sites/default/files/pdf/university/wiss180…

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Job Opening: Front-end Developer at Applied Maths / bioMérieux
by CLAEYS Filip 02 May '18

02 May '18

Applied Maths is an innovative, world leading bioinformatics software development company, part of bioMérieux, the global leader in microbial diagnostics. To expand and strengthen our development team answering to the ever-changing challenges of microbiology, we are looking for a motivated and creative Front-end Developer. See below for more information: http://www.applied-maths.com/careers-applied-maths AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments.

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