April 2018 - BBClist - maillist.psb.ugent.be

Open position bioinformatician at Maastricht University
by Jennen, Danyel (TGX) 17 Apr '18

17 Apr '18

Dear all, The Department of Toxicogenomics, Maastricht University, The Netherlands is looking for a bioinformatician. For details please follow the following link: https://www.academictransfer.com/en/46020/bioinformatician-mv-10-fte/ Kind regards Danyel Jennen [cid:image001.jpg@01D3D62B.3EF619D0] Danyel Jennen Associate Professor Toxicoinformatics Department of Toxicogenomics danyel.jennen(a)maastrichtuniversity.nl www.toxicogenomics-um.nl<http://www.toxicogenomics-um.nl> Universiteitssingel 40, 6229ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3883983 Disclaimer<http://www.maastrichtuniversity.nl/web/show/id=6568779/langid=42> [cid:image002.jpg@01D3D62B.3EF619D0]Please consider your environmental responsibility before printing this e-mail.

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open position in functional genomics/Systems Biology Genoscope Evry France
by Marco Antonio MENDOZA PARRA 16 Apr '18

16 Apr '18

Dear BBC members; This time I'm contacting you because I wanted to let you know that this comming summer Im lauching my team "SysFate<https://marcomendozabpn.wixsite.com/sysfate>" as part of of the ISSB laboratory (formerly the Institute of Systems and Synthetic Biology) in the unit "metabolic genomics" UMR-8030, which is part of the Genoscope, the French National Sequencing Centre<http://jacob.cea.fr/drf/ifrancoisjacob/english/Pages/Departments/Genoscope.…>. (south of Paris). In this context Im currently looking for recruting postdocs as well as a bioinformatics engineer, thus if possible I would be glad if you could share the attached pdf document among your colleagues, in case any of them would be willing to join us. Notably, I have a particular postdoctoral fellowship for scientists that performed their PhD in France, and after a postdoc training out of the country they are willing to come back, thus in case you know french postdocs that are looking for possibilities to come-back, please do not hesitate to share this with them. Best regards ? Marco A. Mendoza; PhD CRCN - CNRS Institut de Génétique et de Biologie Moléculaire et Cellulaire 1 rue Laurent Fries 67404 Illkirch France Tel: +33 3 88 65 34 19 www.ngs-qc.org

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job opening: Data Steward at VIB
by Alexander Botzki 16 Apr '18

16 Apr '18

Dear all, We are currently looking for a Data Steward to coordinate the efforts of harmonizing data formatting and the data life cycle as well as to assure reusability and access to VIB's research data. Job ad see https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/12473/… Kind 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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NETTAB 2018: Call for Abstracts for oral communications
by Alexander Botzki 14 Apr '18

14 Apr '18

NETTAB 2018 Building a FAIR Bioinformatics environment October 22-24, 2018, Genoa, Italy http://www.nettab.org/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 . See full instructions at: 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 • Michael CRUSOE, Common Workflow Language, Lithuania • 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 • 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 • 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 - paolo.dm.romano(a)gmail.com

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Job opening for bioinformatician on precision oncology
by Katleen De Preter 12 Apr '18

12 Apr '18

Dear all, We are currently looking for a bioinformatician to enforce our team and implement genomics based precision oncology pipelines into the clinic (see attached document). Kind regards, Katleen De Preter Frank Speleman Bram De Wilde

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Last few spaces remaining on introductory bioinformatics courses at Edinburgh Genomics
by MEDD Nathan 10 Apr '18

10 Apr '18

Dear All There are still a handful of spaces remaining on this summer's introductory bioinformatics workshops here at Edinburgh Genomics. These excellent courses, taught by Dr Martin Jones (Founder, Python for Biologists, https://pythonforbiologists.com) are the perfect introduction to the world of coding for budding bioinformaticians. MONDAY 14th - FRIDAY 18th MAY - Introduction to Linux and Workflows for Biologists. Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. For more information and to sign up see: https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-biologi… MONDAY 11th - FRIDAY 15th JUNE - Introduction to Python for Biologists "Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackle problems in their own research and (2) continue their Python education in a self-directed way." For more information and to sign up see: https://genomics.ed.ac.uk/about-us/introduction-python-biologists-june-2018 The above courses are both held at the Kings Buildings Campus, University of Edinburgh. Check out the Edinburgh Genomics training page, https://genomics.ed.ac.uk/services/training, for more upcoming courses. Kind Regards Nathan Medd Edinburgh Genomics - Training Assistant -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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PhD position at the Maastricht Centre for Systems Biology
by Adriaens, Michiel (MACSBIO) 09 Apr '18

09 Apr '18

Dear all, The Maastricht Centre for Systems Biology is currently looking for a PhD candidate to strengthen our research activities in mathematical modelling and machine learning approaches to gain a better understanding of blood glucose control and its relation to physical activity and wellbeing. For more information and to apply, please follow the link: https://www.academictransfer.com/employer/UM/vacancy/45921/lang/en/ Kind regards, Michiel Adriaens -- Michiel E. Adriaens, PhD Assistant Professor Maastricht Centre for Systems Biology - MaCSBio Universiteitssingel 60, 6229 ER Maastricht, The Netherlands

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Announcement Elixir-SE RaukR Advanced R Summer school 11-21 June
by Jessica Lindvall, PhD, Training coordinator 08 Apr '18

08 Apr '18

Elixir-SE (NBIS/SciLifeLab, www.nbis.se) is excited to announce a brand new international Summer School in R for Bioinformatics calked "RaukR Summer school: Advanced R for Bioinformatics"! The Summer School is beautifully located in the middle of the UNESCO World Heritage city of Visby, Sweden, and during 2 weeks you will get the opportunity to learn R from internationally renowned R wizzards and senior bioinformatics staff from NBIS/SciLifeLab. We believe that RaukR will take your bioinformatics R analysis and visualization skills to a new level, so don’t miss out on this unique opportunity! RaukR Summer School: Advanced R for Bioinformatics 11-21 June 2018. Visby, Gotland, Sweden Registration deadline: April 15, 2018 Register today at https://nbisweden.github.io/workshop-RaukR-1806/ Please help us spread the word! Best regards,Jessica Lindvall, PhD, Training coordinator Elixir-SE NBIS/SciLifeLab www.nbis.se, www.scilifelab.se Twitter: https://twitter.com/search?q=%23RaukR&src=typd Hashtag: #RaukR Note: A “Rauk” is a characteristically shaped stone formation, common on the Island of Gotland, Sweden. See for example https://sv.wikipedia.org/wiki/Rauk#/media/File:Gotland-F%C3%A5r%C3%B6_Rauka…

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Computational Biology/Bioinformatics PhD-position available at the Erasmus Medical Center.
by Harmen van de Werken 06 Apr '18

06 Apr '18

Could you please add the following text on the bbc mailing list: "Computational Biology/Bioinformatics PhD-position available at the Erasmus Medical Center. The PhD-student will work with a collaborative team from the Department of Medical Oncology and the Cancer Computational Biology Center (CCBC) in the emerging field of Computational Cancer Pharmacogenomics. For more information please visit the website: https://www.werkenbijerasmusmc.nl/en/vacancy/phd-student_120218tddh" Kind regards, Harmen van de Werken -- Harmen van de Werken, Ph.D. Assistant Professor in Computational Biology at the Department of Urology at Erasmus MC & Managing Director Cancer Computational Biology Center (CCBC) at Erasmus MC P.O. Box 2040, Be-355 3000 CA Rotterdam, the Netherlands Visiting address: Josephine Nefkens Building, office Be-330a Wytemaweg 80 3015 CN Rotterdam, the Netherlands Tel: +31-10-7044467 (office) Tel: +31-10-7044488 (department) Fax: +31-10-7044661 https://ccbc.erasmusmc.nl/ Email: h.vandewerken(a)erasmusmc.nl Skype: harmen.vandewerken

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Job opening for a Single-Cell Bioinformatics Specialist
by Stein Aerts 06 Apr '18

06 Apr '18

Dear all, We have a job opening for a Single-Cell Bioinformatics Specialist in the VIB Center for Brain and Disease Research: https://www.nature.com/naturejobs/science/jobs/638647-single-cell-bioinform… Best regards, Stein Aerts

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