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Helis Academy Course: FAIR Data Stewardship - digital data scholarship for wetlab scientists, 27-29 May, 2019, Niel, Belgium
by Celia van Gelder 12 Apr '19

12 Apr '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 wetlab 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 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. We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course. * On day one trainees will investigate data management plans, which types are there and how they should be used. * 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. * 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. 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/> . You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course 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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Register now: Statistics for Omics course - 24-28 June 2019 - Amsterdam
by Femke Francissen 10 Apr '19

10 Apr '19

Together with the Amsterdam UMC (location VUmc) we are organising the 4-day course: Statistics for Omics Date: 24, 26, 27 and 28 June 2019 Location: VUmc, Amsterdam This introductory course gives an overview of many statistical tools to analyse omics data. The course can be followed by researchers with a minimum or elementary background in quantitative data analysis (see ‘Pre-requisites’ below). Participants will learn and practice commonly used tools including: • Tools to explore datasets including clustering, principal components and network analysis; • Models to answer basic statistical questions: differential behaviour (e.g. mRNA expression) and multiple testing, also using Bayesian models; • Models for classification and prediction, including penalised regression; • Models for emerging technologies: radiomics and single-cell sequencing data. Methods will be applied on experimental data in practical hands-on sessions using the statistical software R. Insight about how methods work is given in an intuitive way wherever possible which, combined with some formalisation and the practical work, makes theory accessible and helps cement concepts. Slides and instructions for the practical sessions will be made available electronically to participants. Pre-requisites: Participants are assumed to be familiar with the following at the start of this course: • Basic R, including how to use functions and packages; • Basic statistics: mean, variance, standard deviation; • Probability distributions: normal; • Statistical testing: t t -test, Wilcoxon test, significance level, p p -value, null & alternative hypotheses; • Measures of association: Pearson correlation, regression. For whom? The course is tailored for PhD students and researchers (such as pathologists, psychological biologists, human geneticists, oncologists, neuro-geneticists) whose research involves experiments that generate omics data. It can also suit researchers with a quantitative background looking for a short introductory course. Participants who successfully complete the course receive 3 ECTS. Read more and register! Femke Francissen Community manager BioSB research school www.biosb.nl

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2019 Galaxy Community Conference, 1-8 July, Freiburg Germany
by Dave Clements 10 Apr '19

10 Apr '19

*2019 Galaxy Community Conference (GCC2019)1-8 July, Freiburg, Germanyhttps://galaxyproject.org/gcc2019 <https://galaxyproject.org/gcc2019>* *Deadlines22 April: Oral Presentation and Lightning Talk abstracts due <https://galaxyproject.org/events/gcc2019/abstracts/>.17 May: Early registration ends <https://galaxyproject.org/events/gcc2019/registration/>The 2019 Galaxy Community Conference (GCC2019) <https://galaxyproject.org/gcc2019>, the tenth annual gathering of the worldwide Galaxy <https://galaxyproject.org/> community, will be held 1-8 July in Freiburg, Germany. GCC brings together hundreds of faculty, clinicians, other 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 many opportunities for networking.Presentations will cover the full spectrum of Galaxy applications, enhancements and deployments. If you are working in data intensive science research then there will not be a better place to share your work, learn from others, and find new collaborators.Present your work!Abstract submission <http://localhost:8080/events/gcc2019/abstracts/> for talks, lightning talks, demos and posters is now open. If you work in data-intensive life science (or in other fields using Galaxy) then please consider presenting your work at GCC2019. This is an ideal chance to present to 200+ researchers, all addressing common challenges in data intensive science. Review of oral presentations starts on 22 April, in a little over a month. Submit an abstract (or two) now <http://localhost:8080/events/gcc2019/abstracts/>!RegistrationEarly registration <https://galaxyproject.org/events/gcc2019/registration/> starts at €49/day for students and postdocs, and €79 / day for other academics and non-profit researchers. Early registration ends 17 May, when rates go up by 60%. So, register early <https://galaxyproject.org/events/gcc2019/registration/>.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 and 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 platform is domain agnostic and is now used in domains as diverse as natural language processing, constructive solid geometry, and social science.We hope to see you in Freiburg!GCC2019 Organizers <https://galaxyproject.org/events/gcc2019/organizers/>* -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/

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Open Bioinformatics Position in Zürich
by Lynn Verbeke 05 Apr '19

05 Apr '19

Dear all, there is an open position (full time and permanent) in the Bioinformatics team of Biognosys. See https://www.biognosys.com/about/career for more information. Kind regards, Lynn

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ELIXIR Course "Single cell RNA-seq data analysis with R" 27.-29.5.2019 in Finland
by A.Mahfouz＠lumc.nl 05 Apr '19

05 Apr '19

FYI ----------------------------- Dear all, Please note that registration is now open for the ELIXIR EXCELERATE course "Single cell RNA-seq data analysis with R" which takes place 27.-29.5.2019 at CSC in Espoo (Helsinki), Finland. This hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is organized by ELIXIR Finland in collaboration with ELIXIR Sweden, Norway, Germany, Netherlands and France, and it is free of charge. The application deadline for the course is 16.4.2019. Participants are selected based on their motivation description, and we will also do our best to ensure that every country / research group gets at least one representative in the course. For registration and more information, please see the course website at https://www.csc.fi/web/training/-/scrnaseq. Best regards, Eija Eija Korpelainen, Ph.D Product Manager, ELIXIR-FI Training Coordinator Data analytics, Bioinformatics CSC - IT Centre for Science P.O.Box 405, 02101 Espoo, Finland Phone +358 50 381 9726

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[Mittelerde Meeting 2019] Call for Abstracts Open
by Daniele Parisi 04 Apr '19

04 Apr '19

-------- Forwarded Message -------- SUBJECT: [Mittelerde Meeting 2019] Call for Abstracts Open DATE: Thu, 4 Apr 2019 15:50:01 +0200 FROM: Mittelerde 2019 <me19(a)mailbox.tu-dresden.de> TO: me19(a)mailbox.tu-dresden.de Dear Colleagues, after the great success in Mittweida, the tradition continues for the fourth time. We are delighted to announce the MITTELERDE MEETING 2019. The meeting will be held on 13-14 JUNE 2019 at the BIOTEC, TU DRESDEN. Registration will be open until 7 June 2019. You can submit your contribution until 17 MAY 2019. There are a few highlights that render this year's Mittelerde Meeting a must attend: * Invited speakers: * Andreas Beyer, Cologne * Yves Moreau, Leuven * Peter R. Wills, Auckland * Mittelerde speakers: * Andreas Dahl * Marc Thilo Figge * Michael Hiller * Florian Jug * Dirk Labudde * Yixin Zhang * Extend your stay in Dresden and join us for: the Dresden Long Night of Science [1] and the famous cultural festival Bunte Republik Neustadt [2] REGISTRATION & SUBMISSION: HTTPS://TINY.CC/ME19 Topics: * protein sequence & 3D structure * RNA sequence, secondary & 3D structure * protein-protein and protein-RNA interactions * genomics, NGS analyses & genetic variation * deep sequencing * computational chemistry * systems biology * image analysis * text mining & ontologies * related fields of bioinformatics If you have any questions do not hesitate to reply to this message. We enjoy hosting the conference and would appreciate to see you in Dresden. You can find a PDF version of the call and a poster for advertisement attached. PLEASE FEEL FREE TO DISTRIBUTE THEM IN YOUR INSTITUTES. Best regards The organizing committee -- Mittelerde Meeting 2019 Conference Office Technische Universität Dresden Center for Molecular and Cellular Bioengineering (CMCB) BIOTEC Tatzberg 47/49 01307 Dresden Germany Tel: +49 (0)351-463-40068 Email: me19(a)mailbox.tu-dresden.de Webpage: https://webapp.biotec.tu-dresden.de/e/me19 -- 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] http://www.wissenschaftsnacht-dresden.de/english/ [2] http://www.brn-dresden.de/index.php

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PhD Positions in Computational Cancer Research and Data Science at the German Cancer Research Center (DKFZ)
by Graduate Program 04 Apr '19

04 Apr '19

Dear Colleague, I would like to draw your attention to our International PhD Program at the German Cancer Research Center (DKFZ) in Heidelberg, which might be of interest to your students who are seeking further research in the area of Data Science, (Bio-)Informatics, Computational Biology etc. The next application deadline is 31st May 2019 and more information can be found in the attachment and at www.dkfz.de/phd<http://www.dkfz.de/en/phd-program/index.html?campaign=phd/compmsc>. I would be very grateful if you could forward this information to potential PhD students at your institution. If you would prefer not to receive similar e-mails in the future, please do not hesitate to contact me. Many thanks and best wishes, Franziska --- --- --- Dr. Franziska Schmidt Graduate School Project Manager German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany [cid:image003.jpg@01D4EAE8.368A1BC0]<http://www.dkfz.de/en/phd-program/index.html?campaign=phd/compmsc>

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Postdoc (research Associate) position in the filed of clinical and translational medicine informatics
by Venkata Pardhasaradhi SATAGOPAM 04 Apr '19

04 Apr '19

Dear all We are looking for a Postdoc (research Associate) in the area of clinical and translational medicine informatics at Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. Please refer the below URL for more details and how to apply http://emea3.mrted.ly/24zuq Best regards, Venkata — Dr. Venkata Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-36421 venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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Postdoc in Marseille, France on machine learning, gene regulation and diseases
by GONZALEZ Aitor 03 Apr '19

03 Apr '19

Dear colleagues, We are proposing a two-year Postdoc position related to the bioinformatics analysis of disease specific gene regulatory loci. The objective of this Postdoc project is to develop a disease specific-model of common regulatory variants. This model will be used to predict new gene regulatory single nucleotide polymorphisms (SNPs) and genomic regions involved in these diseases. The resulting predictions will be use to investigate the shared and specific contributions of the genome to these disease classes. Details of the project and host labs can be found here: http://centuri-livingsystems.org/pdp2019-06-2/ This Postdoc project is part of the Postdoc Programme of the Turing Centre for Living Systems (CENTURI). The deadline of the application is: April 26, 2019 and the application procedure is explained here: http://centuri-livingsystems.org/recruitment . The Postdoc candidate should have a Doctoral degree in an area related to Mathematics, Computer Science, Biophysics, Bioinformatics or Population Genetics with interest and/or experience in statistics, machine learning, data analysis and human genetics. We expect the candidate to have at least one publication in a peer-reviewed journal relate to any of these topics. The Postdoc candidate will work under the joined supervision of a bioinformatics scientist (Aitor González, TAGC, Marseille, France), a geneticist (Pascal Rihet, TAGC, Marseille, France) and an statistician (Badih Ghattas, I2M, Marseille, France). We encourage candidates to contact us (AG, PR and BG) in advance for further information and/or guidance for the application. Thank you for sharing this offer with motivated candidates. Sincerely yours, Aitor González, Pascal Rihet and Badih Ghattas -------------------------------------------------- Aitor GONZÁLEZ Aix-Marseille Université UMR1090 TAGC 163, avenue de Luminy - case 928 13288 Marseille cedex 09 Tel +33 (0)491 82 87 48 Fax +33 (0)491 82 87 01 http://www.aitorgonzalezlab.org/

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Two ELIXIR Belgium courses in May - 13+14 and 15 of May: Carpentry Genomics and Open Software Best practises
by Alexander Botzki 02 Apr '19

02 Apr '19

Dear all, I would like to send you more information about two ELIXIR training course taking place 13, 14th of May and 15th of May in Ghent. Data Carpentry Genomics Registration: https://training.vib.be/data-carpentry-genomics 4 OSS - Best practises in Open Software Registration: https://training.vib.be/4-oss-best-practises-open-software Trainers: Mateusz Kuzak, Toby Hodges Location: Ghent 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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