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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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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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