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Fwd: CORBEL train-the-trainer and course development hackathon 4-5-6 July Amsterdam
by Celia van Gelder 26 Apr '18

26 Apr '18

Fyi Verstuurd vanaf mijn iPhone Begin doorgestuurd bericht: > Van: Vera Matser <matser(a)ebi.ac.uk> > Datum: 25 april 2018 om 17:37:46 CEST > Aan: Celia van Gelder <celia.van.gelder(a)dtls.nl> > Onderwerp: CORBEL train-the-trainer and course development hackathon > > Dear Celia, > > As part of the CORBEL project (http://www.corbel-project.eu) we are organising a train-the-trainer course (TtT) and course development hackathon event on the 4-6th July in Amsterdam. > > This workshop is for you if you work within a research infrastructure; you may be a trainer, educator, training coordinator or project manager with training falling under your remit. > > The aim of the workshop is to provide participants with new ideas and tools to make their training events or workshops even better and easier to run and prepare. The course development event allows you to put these new ideas into practice and work on your own training concepts with input from colleagues. > > Date: 4-5th July (TtT) 6th July (course hackathon) > Location: Lloyd Hotel & Cultural Embassy, Amsterdam, Netherlands > Registration deadline: 2nd May 2018 > Cost: Free > > This event combines two separate events, a 2-day train-the-trainer workshop and a 1-day course development hackathon. You can choose to attend one or both events. > > For registration and more details see the announcement pdf (attached) and the CORBEL webpage: > http://www.corbel-project.eu/news-events/event-articles/train-the-trainer-w… > > Any question please don't hesitate to get in touch! > > Kind regards > > Vera > > -- > Vera Matser PhD > Training Liaison Officer, EMBL-EBI > ORCID: 0000-0002-2010-6844 > > Tel: +44 (0)1223 49 4149 > Skype: vera_matser > e-mail: matser(a)ebi.ac.uk > Twitter: @VeraMatser > URL: www.ebi.ac.uk/training > Find us in on-course®: www.on-course.eu > > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Genome Campus > Hinxton > Cambridge > CB10 1SD > UK

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BioSB 2018 - detailed scientific programme online!
by Femke Francissen 25 Apr '18

25 Apr '18

4th Dutch Bioinformatics & Systems Biology Conference - BioSB 2018 May 15-16, 2018 Congrescentrum De Werelt, Lunteren Conference website: www.aanmelder.nl/biosb2018 The detailed scientific programme of our annual conference in Lunteren is now online. The quality of submitted abstracts and the profiles of the keynotes make us look forward to a very exciting meeting! Take a look at the conference programme <https://www.aanmelder.nl/biosb2018/part_program> The 2-day programme features: Four international keynote speakers: Chiarra Dalla Man (University of Padova), Martin Kircher (Berlin Institute of Health), Jason Locasale (Duke University) and Alexander van Oudenaarden (Hubrecht Institute). Two plenary HotTopics sessions: Single Molecule Sequencing & Single Cell Omics Topical parallel sessions on: Genomics, Personalized medicine, Metabolomics, Tools & resources, Network biology, Metabolic modelling, Microbiome & Ecosystems, Regulation & signalling, Integration of (omics) data sets, Genetic variants & population studies, RNA & protein diversity. Featuring both invited (senior) as selected presentations. An ELIXIR-NL parallel track with sessions focussing on FAIR Data and Agrifood Data concepts and applications. Poster & demo sessions Five breakout sessions on May 16. Conference dinner and social event in the evening of May 15. Join us now & register! More about the conference fees & registration can be found here <https://www.aanmelder.nl/biosb2018/wiki/267520/registration>. We look forward to meeting you all in Lunteren! On behalf of the organizing & programme committee Femke Francissen Community manager BioSB Research School Visiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl <mailto:femke.francissen@biosb.nl>

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Announcement: Conference Systems Epigenetics: Towards Precision Cancer Medicine, Amsterdam, 27-30 Nov 2018
by P.D. Moerland 20 Apr '18

20 Apr '18

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Advanced bachelor programme of bioinformatics via distance learning
by Howest 20 Apr '18

20 Apr '18

If you are not able to see this mail, click http://mrbe.r.a.d.sendibm1.com/2d8puzbwqx0jf.html Please feel free to forward to anyone who might be interested Dear colleague, We would like to inform you about the start of our advanced bachelor programme of bioinformatics via distance learning (@home). The programme is intended for every technician (bachelor), master and PhD with a profound knowledge of molecular biology and an interest in (bio)informatics who is currently working in the biological or biomedical work field. During the two years programme (30 ECTS/year) we focus on new and emerging technologies within the work field and the application of computer science techniques for “wet lab” problems. We divide the course units in three categories: informatics, bioinformatics and programming. Within the field of informatics, you learn to work on a Unix system, to store biological data in databases and to analyse large datasets using data mining techniques. Second, you become familiar with comparative genomics, structural bioinformatics, systems biology and the analysis of high-throughput experimental data. In the last important topic, programming skills are introduced to create web applications (HTML, PHP, CSS), to script bioinformatics pipelines in Python and to perform statistical and exploratory analysis in R. The programme is organized at the request of the labour market and several courses are given by experts in the field. After two years the transformation from wet-lab to dry-lab scientist is complete, future proof to work within a constantly changing working field and a perfect blend between the ICT expert and the molecular biologist. Per module three contact moments of two hours are organized. The contact moments take place every two weeks on the campus in Bruges from 6 PM to 8 PM, but can also be followed via live stream on YouTube. The subject matter is mainly processed via self-study, in combination with coaching/exercises/questions or a crash course during the contact moments. During the first year, it is possible to apply for educational leave to follow the programme. If you are interested to follow the advanced bachelor programme of bioinformatics, please come and visit us at one of the [ information sessions on the campus ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxbh8qx0jd ). You can also have a look on the [ website ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxc9oqx0jd ) for more information or contact us at [ bit(a)howest.be ]( mailto:bit@howest.be ). Best regards, Advanced Bachelor of Bioinformatics Biomedical Laboratory Science Howest University of Applied Sciences Howest University of Applied Sciences Campus Rijselstraat Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 [ ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxd24qx0jd ) Please feel free to forward to anyone who might be interested [ Unsubscribe here ]( http://mrbe.r.a.d.sendibm1.com/2d8puzbwqx0jg.html ) © 2018 Howest

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Job openings at The Hyve: System Administrator and more
by Ward Weistra 18 Apr '18

18 Apr '18

Dear all, At our bioinformatics company The Hyve we are looking for multiple new colleagues to complement the team. The System Administrator job description is listed below, but please find all our open positions at https://thehyve.nl/the-hyve/working-at-the-hyve/. Thank you for sharing! Best regards, Ward Weistra System Administrator *Job description* The Hyve is a young, innovative and fast growing company employing software engineers, bioinformaticians and data scientists. We are dedicated to developing software and data management tools to support scientists in life sciences and healthcare R&D with open source software, open data and open standards. We maintain a growing farm of Cloud servers as part of our professional open source software hosting and service contracts. Our clients include top universities, hospitals, and a number of international pharma and food companies. If you are an experienced system administrator looking for a varied role, then this is an excellent opportunity to join The Hyve. As system administrator you are responsible for keeping the infrastructure operational. You are trustworthy and reliable. A service oriented problem solver. A team player and excellent communicator with developers, managers and clients. *Tasks:* - Set up and configure new servers - Maintain servers - Security, availability and vitals monitoring - Backup management - Application deployment automation - Application support: problem diagnosis, configuration changes, assist with code changes (i.e. bug fixes) - Network infrastructure configuration - Cloud infrastructure configuration / scripting - Performance monitoring and optimization *Required are:* - Linux System administration (Ubuntu, RedHat, main focus: command line tools) - Deployment automation / configuration management tools (Puppet, Ansible, Vagrant) - Networks (TCP/IP, VPN, SSH tunnels, etc.) - Website hosting (Apache, SSL certificates, etc.) - Database configuration (PostgreSQL, MySQL, Oracle) - Personality and ability to learn new technologies - Fluency in English (oral and written) - Based in the Netherlands (or willing to relocate) - Proven experience with system and/or application security *Desired are:* - Puppet configuration management - Experience in scaling applications (Java/Scala backends) and databases (PostgresDB, MySQL, MongoDB) - Hadoop stack experience (especially Spark, Parquet, HDFS) - Technical support for Mac and Windows computers - Remote access tooling (Citrix, RDP, etc.) - Git and Github (see https://github.com/thehyve) - Hypervisors (OpenStack APIs, especially Nova, VMware, etc.) - Knowledge of ISO27001 or similar information security management standards - Fluency in Dutch *We offer:* We offer a 32-40 hours workweek, a competitive salary and a pleasant working environment with young and bright colleagues. *More information?* Marinel Cavelaars, Manager Services Jojanneke Blaak, HR Officer +31 30 7009713 or hr(a)thehyve.nl -- Ward Weistra | Team Lead Data Warehousing *Out of office on Friday* E. ward(a)thehyve.nl T. +31 30 700 9713 W. www.thehyve.nl Skype. wardweistra | M. +1 347 979 2731 | Twitter <https://twitter.com/WardWeistra>. | LinkedIn <https://www.linkedin.com/in/wardweistra/>.

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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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