May 2019 - BBClist - maillist.psb.ugent.be

Job posting: Postdoc in Computational Biology
by Loh-Bode, Yen Lee 22 May '19

22 May '19

Dear person-in-charge, Please find attached our latest open position for the Department of Computational Biology for Infection Research. We would appreciate it if you could post this up in your job portals. Please do not hesitate to contact me if in need of further assistance. Thank you! Kind regards / Beste Grüße, Annie Loh-Bode Assistant to the Head of Department (Prof. Alice McHardy) Computational Biology for Infection ResearchDe Email: yenlee.loh-bode(a)helmholtz-hzi.de Tel.: +49 (0)531 391-55270 Braunschweig Integrated Centre of Systems Biology (BRICS) Rebenring 56, 38106 Braunschweig Helmholtz Centre for Infection Research GmbH (HZI) Inhoffenstrasse 7, 38124 Braunschweig ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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GCC2019 Early Registration ends this Friday
by Frederik Coppens 15 May '19

15 May '19

Hello All, An update on the 2019 Galaxy Community Conference: 1. A (final) reminder that *early registration* <https://galaxyproject.org/events/gcc2019/registration/> for the 2019 Galaxy Community Conference *ends this Friday night*, 17 May, at midnight Freiburg time (CEST / GMT +2). After that registration goes up by ~ 60%. So, register this week! 2. All accepted speakers have been notified and talks are being added to the schedule <https://gcc2019.sched.com/> as presenters confirm. There were far more talk submissions this year than in any previous year and that is reflected in the breadth and quality of the accepted talks. 3. *Poster and demo submission <https://galaxyproject.org/events/gcc2019/abstracts/> is still open!* However, space *will* fill up and when it's gone, it's gone. Got something to present? Submit it *soon*. We hope to see you in Freiburg! on behalf of the GCC2019 Organizers ------------------ *2019 Galaxy Community Conference (GCC2019) *1-8 July, Freiburg, Germany https://galaxyproject.org/gcc2019 ------------------ The 2019 Galaxy Community Conference (GCC2019) will be held 1-8 July in Freiburg, Germany. GCC brings together hundreds of faculty, clinicians, researchers, and students, all working in and supporting data intensive science that is accessible, sharable and reproducible. GCC2019 features oral presentations, lightning talks, posters, demos, birds-of-a-feather gatherings (BoFs), training, a CollaborationFest, and plenty of opportunities for networking. Presentations will cover the full spectrum of Galaxy applications, enhancements and deployments. If you are working in data intensive science then GCC2019 is an ideal conference for sharing your work, learning from others, and finding new collaborators. * Registration *Early registration starts at €49/day for students and postdocs, and €79 / day for other academics and non-profit researchers. Childcare is available and travel fellowships are available as well. Early registration ends 17 May, when rates go up by 60%. So, register early. *About Galaxy *Galaxy (https://galaxyproject.org/) is a platform for data integration and analysis in the life sciences. It enables researchers to build, run, share, and repeat their own complex computational analyses using only a web browser and without having to first learn system administration and command line interfaces. The Galaxy Project is driven by a vibrant community who publish workflows and analyses, wrap new tools, maintain and enhance the source code, provide support, and write documentation and training materials. Galaxy is open-source and freely available, and is deployed in hundreds of organizations, running on everything from laptops through supercomputers to public and private clouds. Over 150 of these platforms are publicly available and can be used with little or no setup. Thousands of tools have been ported to Galaxy ("wrapped") and are deployable from the Galaxy Tool Shed. Galaxy was developed to support life science research, but the software is domain agnostic and is now used in domains as diverse as natural language processing, constructive solid geometry, and social science. Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Job opportunity: computational scientist / bioinformatician at the Bernhard Nocht Institute for Tropical Medicine
by Guy Baele 15 May '19

15 May '19

The Department of Virology at the Bernhard Nocht Institute for Tropical Medicine in Hamburg invites applicants for a position starting as of 15 June 2019 or later for the role: Computational scientist/bioinformatician (m/f/d) You will explore, assess and implement bioinformatics algorithms, analysis pipelines, applications and tools from next generation sequencing (NGS) technologies to improve the bioinformatics analyses capacity of the Virology department of the BNITM. Activities occur with a moderate degree of supervision with latitude for independent judgement. More information concerning the position can be found here: https://www.bnitm.de/fileadmin/media/de/documents/ausschreibungen/Computati… Please send your application by 01.06.2019 with the usual documents (cover letter, high school and university certificates with grades, if applicable references) referring to "Computational scientist" preferably by e-mail in a PDF file to Ms. Jeannette Meurer (bewerbung(a)bnitm.de) or by mail to: Bernhard-Nocht-Institut für Tropenmedizin, Human Resources Department, BernhardNocht-Str. 74, 20359 Hamburg, Germany. For further questions please contact Dr. Sophie Duraffour (duraffour(a)bnitm.de, phone: +49 40 42818-932), Department of Virology -- Guy Baele, Assistant Professor Department of Microbiology and Immunology Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Bioinformatics service position in Cologne
by Andreas Beyer 15 May '19

15 May '19

Dear Colleagues: We are advertising a bioinformatics service position with a specialization in metabolomics/lipidomis data analysis. We greatly welcome your application! Andreas Beyer -- Prof. Dr. Andreas Beyer http://cellnet.cecad.uni-koeln.de/ Phone: +49 221-478 84429

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BaseClear is hiring: Bioinformatician (microbial genomics and NGS)
by Ali May 14 May '19

14 May '19

Hello, BaseClear <https://www.baseclear.com/>is hiring a Bionformatician, and if you are just starting, this is your chance to get involved in the microbial genomics revolution. Large-scale genome sequencing and analysis projects, microbiome research, bleeding-edge sequencing tech, advanced computing, and a team of highly-driven experts are waiting for you. Also an amazing salad bar. More info in the link below, don't hesitate to apply if you think there is a match! https://www.baseclear.com/career-jobs/bioinformatician/ Best regards, Ali May

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VIB: Vacancy Software Developer Bioinformatics Tools
by Alexander Botzki 11 May '19

11 May '19

Dear all, VIB is looking to expand its institute-wide VIB Bioinformatics Core with one bioinformatics tool developer to enhance and integrate VIB's flagship bioinformatics tools such as PhyD3, SCope, Contra, and SNPEffect. We are looking for a dedicated individual to join the team in Ghent who will jointly work on projects for several Bioinformatics groups at VIB (http://www.vib.be/en/research/scientists/Pages/default.aspx?category=Bioinf…) Our institute greatly values diverse standpoints and promotes an inclusive environment in which everyone is respected. The candidate needs to have outstanding communication skills to establish a close working relationship with the bioinformaticians and developers within the VIB Centers and the staff of the VIB Bioinformatics Core. The candidate will split his/her time between various VIB Bioinformatics groups and may be required to travel to all VIB sites (Ghent, Leuven, Brussels, Antwerp, and Hasselt). The close relationship within VIB's Bioinformatics community will allow the integration of cutting edge bioinformatics solutions aiming at higher visibility of VIB's bioinformatics achievements. You will participate actively in computational aspects of VIB's research projects which focus on the molecular mechanisms that are responsible for the functioning of the human body, plants, and microorganisms. The responsibilities include: continued development, maintenance, testing and evaluation of VIB's computational biology tools (often written in different programming environments enable relevant VIB software to be maintained long-term make "developed @ VIB" a mark of excellence and reliability provide an interface between VIB Bioinformatics Core and the bioinformatics community at VIB More information on the VIB Bioinformatics Core and the VIB Bioinformatics Community can be found at: https://corefacilities.vib.be/bits and https://www.bits.vib.be/bioit-at-vib Profile You have a Bachelor or Master's degree, preferably in informatics, science or engineering. You have an avid interest in software development and applied informatics. You are eager to acquire new skills under the guidance of experts. You can program in an object-oriented programming language, preferably Java or Python. You like front-end development and have worked with JavaScript frameworks like Node, Angular, React or Vue. You have experience with Linux server administration and with relational databases (e.g., MySQL). Experience in of DevOps product development and Cloud environments (e.g. GCE) are an asset. You are a team worker, who enjoys solving problems in close collaboration with others. We offer Start date: as soon as possible International environment in an academic context A challenging and stimulating work environment, at the edge of IT technologies and the latest research innovations How to apply? Motivated candidates are asked to apply online. https://vibvzw.jobsoid.com/apply/18621 Best 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/> [signatureFooter (002)]

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Systems Biology Modelling of Cancer Pathways, 21 June 2019
by Adriano Barbosa (London Academy of Life Data Science) 10 May '19

10 May '19

We would like to share with you this upcoming course of the London Academy of Life Data Science [1]. SYSTEMS BIOLOGY MODELLING OF CANCER PATHWAYS, 21 JUNE 2019 In this course you will learn how to represent the components of the MAPK pathway as a Systems Biology Gene Notation (SBGN) diagram, parametrize the reactions of the pathway and finally run the pathway simulation using the software COPASI. TUTOR: Adriano Barbosa da Silva, PhD. (LinkedIn [2]) _ Lecturer at Queen Mary University of London_ REGISTRATION FEE: * Undergrad students*: £60 (incl. VAT); * Ph.D/M.Sc students*: £80 (incl. VAT); * Professionals and Post-docs**: £100 (incl. VAT); *Students must present proof of school enrollment on the course day. **Post-docs are considered professionals and NOT eligible for student's rate. LOCATION: Carlton House Terrace, Lecture Room - LONDON - United Kingdom. For more information on this course and to book your place visit: https://lifedatascience.co.uk/systems-biology-course Kind Regards -- Adriano Barbosa da Silva [3], Ph.D. FOUNDER & DIRECTOR -- London Academy of Life Data Science 71-75 Shelton Street, Covent Garden, London, WC2H 9JQ. http://lifedatascience.co.uk/ [4] This email is sent on behalf of London Academy of Life Data Science and is strictly confidential and intended solely for the addressee(s). If you are not the intended recipient of this email you must: (i) not disclose, copy or distribute its contents to any other person nor use its contents in any way or you may be acting unlawfully; (ii) contact London Academy of Life Data Science immediately on info(a)lifedatascience.co.uk quoting the name of the sender and the addressee then delete it from your system. London Academy of Life Data Science has taken reasonable precautions to ensure that no viruses are contained in this email, but does not accept any responsibility once this email has been transmitted. You should scan attachments (if any) for viruses. London Academy of Life Data Science LTD. is a limited by shares company registered in England and Wales (Nr. 11891519). Registered office: 71-75 Shelton Street, Covent Garden, London, WC2H 9JQ. Links: ------ [1] https://lifedatascience.co.uk/missionhttps://lifedatascience.co.uk/ [2] https://www.linkedin.com/in/dr-adriano-barbosa-phd/ [3] https://lifedatascience.co.uk/director [4] http://lifedatascience.co.uk/

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Registration open: Data Steward Knowledge and Skills Workshops 11 and 12 June 2019, Utrecht
by Celia van Gelder 09 May '19

09 May '19

Dear colleagues, We are happy to announce that the registration is now open for our two one-day Data Steward Knowledge and Skills workshops on June 11 and 12, 2019 in Utrecht. Registration is free of charge and we hope to welcome many of you there for a working meeting with and for the Data Steward Community! Dates: Two one-day workshops. First one June 11 & the second one on June 12 June 2019. Maximum participants per day: 25. Location: Holland Heart House, Utrecht, <https://www.hollandhearthouse.nl/Routedescription_HHH.pdf> https://www.hollandhearthouse.nl/Routedescription_HHH.pdf Registration: https://docs.google.com/forms/d/e/1FAIpQLSccCFvNqcA-3fmBqelUXN2EMGHUq68W0Xfb BGt46tSOP7Govg/viewform Registration is free of charge. Lunch is included. Time: 10-16 hrs Programme: https://www.dtls.nl/events/data-steward-knowledge-and-skills-workshop/ and https://www.dtls.nl/events/data-steward-knowledge-and-skills-workshop-2/ Target audience Data stewards, data managers, policy makers, HR persons, funders and all other stakeholders that are interested to share their expertise in Data Stewardship, want to get updated about the work that is going on, and want to contribute to the next steps that will be taken. Although the main focus is for the Life Sciences domain, our work on the competencies and skills of the data stewards is rather generic and also useful for other disciplines. Therefore participants from other disciplines are very welcome to join. Goal of the meeting In a ZonMw- funded project where we are working on defining the profession, skills and training needs of Data Stewards in the life sciences. All the output of the project produced so far can be found on <https://zenodo.org/communities/nl-ds-pd-ls/> https://zenodo.org/communities/nl-ds-pd-ls/. It is our ambition to produce tangible outputs, that can be used and implemented in the organisations. To achieve these goals it is crucial to get input from the community. In this way we make further steps in defining community-endorsed outcomes and decide together which next steps are needed to improve data stewardship function descriptions, capacity, visibility, recognition and training. As a data steward, you will meet your peers, expand your network, and will be able to get insight in the current status of Data Stewardship in the Netherlands and beyond. Concept Programme for both June 11 and June 12 Please note that it will be an interactive day, with working sessions and we invite you to bring your own materials with you, for example your current job description, job advertisements from your organisation, the data management policy of your organisation, information about trainings that you have attended and found useful, etc. 9.30 Registration open 10.0 Welcome & Introduction (Celia van Gelder, DTL/ELIXIR-NL) * Introduction of the project * Who is in the audience? 10.30 Working session 1: Your job description & role (Salome Scholtens, UMCG) * Introduction of the Function Matrix and the Venn Diagram for the Data Steward roles * Interactive session to positioning yourself in the Data Stewardship landscape. Do you recognize your own role, what is your position in your organisation, does your job description match our derived function profile? What are you missing? 11.30 Coffee break 12.00 Working session 2: Your knowledge, skills and abilities (Mijke Jetten, Radboud University) * Introduction of the Knowledge, skills and learning objectives * Interactive session in groups to analyze specific parts of the KSA table * Report back from breakout groups. 13.00 Lunch 13.45 Working session 3: Your training * Introduction of the Training related plans * Working session 14.30 Coffee break 15.00 Working session 4: What's next * What are the next steps to be taken by the policy makers in organisations/institutes, funders, HR etc? 15.45 Wrap up * Conclusions of the meeting & next steps 16. 00 End of meeting Best regards on behalf of the project team, Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Fwd: Open position: Computational Scientist (m/f/d) - Monheim (Germany)
by Lieven Sterck 07 May '19

07 May '19

FYI > From: "erick antezana" <erick.antezana(a)gmail.com> > To: "erick antezana" <erick.antezana(a)gmail.com> > Sent: Tuesday, 7 May, 2019 15:11:54 > Subject: Open position: Computational Scientist (m/f/d) - Monheim (Germany) > (apologies for cross-posting) > Dear colleague, > We are looking for a 'computational scientist' with the following profile: > * Scientific master degree in bioinformatics or similar > * Experience in building and maintaining (bio-)ontologies as well as in > automatizing ontology maintenance tasks (e.g. using scripts) > * Experience/exposure with master data management (data stewardship and > governance) and with biological data integration as well as algorithms design > and implementation > * Experience in semantic web technologies and standards, e.g. with OBO, RDF, > OWL, SHACL, SPARQL, SKOS > * Familiar with graph-based systems (e.g. triple stores) > * Good understanding of ontology reasoning services and ontology editing tools > as well as of public resources as gene ontology, plant ontology, traits > ontology > * High ability to solve problems and to structure and simplify complex tasks and > ability to contribute in an international and dynamic research and development > team > * Fluent in English, both written and spoken > More details: > [ > https://jobs.bayer.com/job/Monheim-Computational-Scientist-%28mfd%29-Nort/5… > | > https://jobs.bayer.com/job/Monheim-Computational-Scientist-%28mfd%29-Nort/5… > ] > If you have any questions, don't hesitate in contacting me. > Best regards, > Erick Antezana

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HELIS Academy: Omics data analysis 11-14 June
by Tuur Muyldermans 07 May '19

07 May '19

?Dear, HELIS Academy presents the workshop "Omics data analysis through data integration - using biological pathways, networks, and linear models" What: The first HELIS Academy<https://helisacademy.com/en> Omics Data Analysis course will teach you about transcriptomics data analysis and multi-omics data integration. Topics that will be discussed: * Addressing how you obtain published data from data repositories and cover basic pre-processing steps, * Introducing you to molecular pathways, from what they are, to how to make your own, to how to use them in advanced omics data analysis (transcriptomics, proteomics, metabolomics) and how this compares Gene Ontology analysis, * Zooming out to utilize your pathway analysis in a broader network analysis so you can see the bigger picture, * How to integrate Omics data sets in an unsupervised statistical way using linear models. When: Tuesday 11 - Friday 14 June 2019. Following separate days/topics is possible. Full program details can be found here<https://training.vib.be/helis-academy-course-omics-data-analysis-through-da…>. For who: Scientists from industry and academia who wish to improve their hands-on knowledge on data integration techniques. Some basic experience with programming and scripting languages like Java and R is appreciated. This course is part of the Data Analysis and Stewardship theme of Helis Academy<https://www.helisacademy.com/en> and is organised by Maastricht University and VIB. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website<https://www.helisacademy.com/en/data-analysis-stewardship> and also on the Helis Academy page on the DTL website<https://www.dtls.nl/training-and-education/helis-academy/>. Please spread this announcement in your organisation as you see fit. Kind regards, Tuur Muyldermans On behalf of the HELIS-DAS Academy team Tuur Muyldermans - ELIXIR Bioinformatics Trainer ELIXIR Belgium | VIB Bioinformatics Core Rijvisschestraat 126, 9052 Ghent | +32 9 248 16 15 www.elixir-belgium.org<https://www.elixir-belgium.org/> | https://corefacilities.vib.be<https://corefacilities.vib.be/> [ELIXIR logo]

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