- BBClist - maillist.psb.ugent.be

Helis Academy Course: FAIR Data Stewardship - digital data scholarship for wetlab scientists, 27-29 May, 2019, Niel (Antwerp), Belgium
by Celia van Gelder 03 May '19

03 May '19

Dear colleague, >From 27-29 May, 2019, we will organize the first course in Data Analysis and Stewardship theme of the Helis Academy: FAIR Data Stewardship - digital data scholarship for wet lab scientists The target audience is wet-lab scientists - from industry and academia - and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers. The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course will introduce the trainees to important concepts of data stewardship <https://www.dtls.nl/fair-data/research-data-management/research-data-manage ment/> . We start with a general introduction covering the data life cycle, the FAIR principles <https://doi.org/10.1038%2Fsdata.2016.18> and a definition of data stewardship and data stewards. We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course. * Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. * Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase. * Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by <http://www.dtls.nl/> DTL and delivered as a joint effort by DTL partners. You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course This course is part of the Data Analysis and Stewardship theme of Helis Academy <https://www.helisacademy.com/en> and is organised by DTL and DTL collaborators. 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 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. Best regards, Celia van Gelder 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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Course: Bioinformatics workflows with Snakemake
by TRAIN edgenomics-training 02 May '19

02 May '19

Are you running data analysis workflows? Want to step up to the next level of organisation and efficiency? Save yourself time, increase replicability, and master your analysis with Snakemake. The Snakemake workflow system provides effective solutions to organise your tasks, document and share your methods, make effective use of compute resources, and handle unexpected errors in processing. Edinburgh Genomics are offering a two-day course that will have you confident in using Snakemake to tackle complex workflow problems and in your day-to-day research. There are still places remaining for the first instance of this course: 30th - 31st May 2019. Sign up now here: http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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ELIXIR training course taking place 13, 14th of May and 15th of May in Ghent: Genomics and Best practises for Open Software - last days for registration
by Alexander Botzki 01 May '19

01 May '19

Dear all, I would like to send again the announcement of two ELIXIR training course taking place 13, 14th of May and 15th of May in Ghent. Introduction to Reproducible Genomics: Data Carpentry This is a Data Carpentry Workshop, with a special focus on sequence handling for variant calling using the cloud resources, the workshop will introduce you to Genomic concepts and scripting. Registration: https://training.vib.be/data-carpentry-genomics Best practises in Open Software In recent years, scientific research has become more data driven and data intensive and it is no longer possible to carry out the analysis without the use of computers and research software. Unfortunately, software is not always developed following best practices that ensure its quality and sustainability. Four simple recommendations to encourage best practices in open research software<https://f1000research.com/articles/6-876/v1> is a publication that addresses this issue by providing a simple, yet robust framework of recommendations that encourage the adoption of existing best practices in research software development. Registration: https://training.vib.be/4-oss-best-practises-open-software Trainers: Mateusz Kuzak, Toby Hodges Location: Ghent, training room in walking distance from Ghent Sint Pieters station Please feel free to spread further in your network if you see fit. 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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Positions available: 2 Research Engineers in Network Biology and Network Bioinformatics (TAGC; Marseille)
by Christine Brun 29 Apr '19

29 Apr '19

Dear all We have been funded for 2 Research Engineer positions in our labs (2 years each), working on systems genetics and network biology of cardiac aging in flies. Details are in the adds bellow. Please spread the information around you, Best Regards, Christine Brun, PhD, DR CNRS TAGC Deputy Director TAGC Inserm U1090, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, Case 928, 13288 Marseille cedex 9, France +33 4 91 82 87 12 christine-g.brun(a)inserm.fr <mailto:christine-g.brun@inserm.fr> https://tagc.univ-amu.fr/en/users/brun-christine <https://tagc.univ-amu.fr/en/users/brun-christine> and Laurent Perrin, CNRS Theories and Approaches of Genomic Complexity (TAGC) INSERM/AMU UMR_1090 Parc Scientifique de Luminy case 928 163, avenue de Luminy 13288 Marseille France Phone: 33491828727 laurent.perrin(a)univ-amu.fr <mailto:laurent.perrin@univ-amu.fr> Websites: https://tagc.univ-amu.fr/ <https://tagc.univ-amu.fr/> https://tagc.univ-amu.fr/en/users/perrin-laurent

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Postdoc positions in London
by Peter Van Loo 28 Apr '19

28 Apr '19

Hi all, For those interested in cancer genomics, we’ve got two postdoc positions in sarcoma genomics in London (one at Crick, one at UCL, in collaboration with Adrienne Flanagan): https://www.crick.ac.uk/research/labs/peter-van-loo/vacancies Best wishes, Peter -- Peter Van Loo, PhD Winton Group Leader – Cancer Genomics The Francis Crick Institute 1 Midland Road London NW1 1AT http://www.crick.ac.uk/peter-van-loo The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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Register now for our BioSB course Algorithms for Genomics - 1-5 July 2019 in Delft
by Femke Francissen 23 Apr '19

23 Apr '19

BioSB course: Algorithms for Genomics (1st edition) Date: 1-5 July 2019 Location: Delft, the Netherlands Course information: website Registration: link Comparative genomics aims to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how comparative genomics is developing is important to shape your own research. In this course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field. Participants are expected to have experience in command-line usage (Unix shell) and programming (Python), and have basic knowledge of genomics. Learning outcomes After having followed this course, the student has a good understanding of algorithms and data structures in comparative genomics, is able to read and understand method papers in bioinformatics in detail, and is able to work with state-of-the-art command-line tools for genomics. Course coordinators: • dr. Thomas Abeel (TU Delft), • prof. dr. Alexander Schönhuth (CWI) • dr. Sandra Smit (Wageningen University) Registration for the course is open! Find out more information at the course website. BioSB Education Programme This course is part of the BioSB Education programme, the Netherlands Bioinformatics and Systems Biology research school, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl.

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PhD position in Bioinformatics with joint doctoral degree from universities of Mainz and Maastricht
by Lenz, Michael 23 Apr '19

23 Apr '19

Dear colleagues, We are looking for a Bioinformatics PhD candidate for a project entitled "Multifaceted data analysis of coagulant activity in arterial/venous thrombo-inflammation", which is part of the TICARDIO innovative training network. Please see the attached pdf file as well as the TICARDIO homepage (www.ticardio.eu<http://www.ticardio.eu>) for more detailed information. Thanks in advance for forwarding this e-mail to any potentially interested candidates! Best wishes, Michael Lenz ----------------------- Dr. Michael Lenz Postdoctoral researcher University Medical Center of the Johannes Gutenberg University Mainz, and Computational Biology and Data Mining group, Johannes Gutenberg University Mainz, Mainz, Germany -----------------------

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Bioinformatics job opportunity in Cambridge
by Adrian Liston 18 Apr '19

18 Apr '19

May you please add this job opportunity to the Benelux bioinformatics mailing list? https://babrahaminstitute.livevacancies.co.uk/#/job/details/77 We have a post-doc opportunity for a data scientist to join an immunology lab. No immunology experience needed - you bring the data skills and we'll teach you the immunology! Regards, Adrian Adrian Liston Senior Group Leader, Lymphocyte Signalling Babraham Institute, Cambridge The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms>

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Fwd: Tenure Track Bioinformatics Innsbruck
by Lieven Sterck 15 Apr '19

15 Apr '19

> From: "Sigrid Neuhauser" <Sigrid.Neuhauser(a)uibk.ac.at> > To: "Sigrid Neuhauser" <Sigrid.Neuhauser(a)uibk.ac.at> > Sent: Monday, 15 April, 2019 11:35:58 > Subject: Tenure Track Bioinformatics Innsbruck > Dear all, > the Institute of Microbiology in Innsbruck ist hiring – we are looking for a > tenure track fellow in bioinformatics – see the attached job description. > The positon scope is very broad and open to attract as many bright minds as > possible. The person we are looking for should have experience in working with > bioinformatics data of microorganisms (including bacteria, archea, fungi, > protists) in the widest sense. So a good track record either in > genomics/transcriptomics or biodiversity or network analyses or metabolomics > will make you a promising canditate. > More info can be found here: > https://lfuonline.uibk.ac.at/public/karriereportal.details?asg_id_in=10452 > If you have any questions, please do not hesitate to get in touch! > Please forward to any prospecitve PostDocs or anybody who you think might fit > for this positon! > Best regards > Sigrid > PS: apologies for cross posting! > ------------------------------------------- > Dr. Sigrid Neuhauser > Institute of Microbiology > University of Innsbruck > Technikerstraße 25 > 6020 Innsbruck > e-mail: [ https://zmail.psb.ugent.be/Sigrid.Neuhauser@uibk.ac.at | > Sigrid.Neuhauser(a)uibk.ac.at ] > tel: +43 (0)512 507 51259

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Fwd: [ISCB - Student Council Symposium 2019] CALL FOR ABSTRACTS
by Daniele Parisi 15 Apr '19

15 Apr '19

-------- Original Message -------- SUBJECT: [ISCB - Student Council Symposium 2019] CALL FOR ABSTRACTS DATE: 2019-04-12 19:03 FROM: Nilson Coimbra <nilson.coimbra(a)gmail.com> TO: Alexander Monzon <lascs(a)iscbsc.org> Dear colleagues, On behalf of the ISCB Student Council Symposium 2019 Organizing Team We invite you to submit an abstract for oral and/or poster presentation for the 15th Symposium of the International Society for Computational Biology Student Council, to be held on the 21th of July, 2019 in Basel, Switzerland, as a satelite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB [1]). http://symposium.iscbsc.org [2] The deadline for submitting an abstract for oral and poster presentation is on 6th of May, 2019 at 11:59 (GMT). ### ABSTRACTS GUIDELINES ### The abstract should not exceed 350 words and must be structured into three separeate sections: Background: the context and purpose of the study; Description: the main findings; Conclusions: brief summary and potential implications. ######################## All abstracts will be considered for poster and oral presentations and the outstanding ones will be awarded. Travel Fellowships are available and all candidates with submitted abstracts are encouraged to apply. If you are ready to submit, check: https://easychair.org/my/conference.cgi... [3] to proceed with the submission. We hope to see you in the beautiful Basel, Switzerland in 21th July, preceeding the ISMB 2019. Amel Bekkar Chair, 15th ISCB Student Council Symposium 2019 Nilson Coimbra - SCS 2019 Co-chair Co-Chair, 15th ISCB Student Council Symposium 2019 -- NILSON DA ROCHA COIMBRA PhD. Candidate - Bioinformatics Bioinformatics Graduate Program - UFMG - Brazil _Download the world_ [4] 0000-0001-9407-4761 -- DANIELE PARISI PhD student at ESAT-STADIUS, KULeuven, Yves Moreau's group Board member of RSG Belgium Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] https://www.iscb.org/ismbeccb2019 [2] http://symposium.iscbsc.org/?fbclid=IwAR2LNEKao3PttaGOMhCppkfoxH6SFuHNHngje… [3] https://l.facebook.com/l.php?u=https%3A%2F%2Feasychair.org%2Fmy%2Fconferenc… [4] http://orcid.org/0000-0001-9407-4761

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