Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
ELIXIR-NL Course: Bioinformatics for Translational Medicine using Galaxy Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam ( <https://goo.gl/maps/CphwJEFDegt> O|2 Lab Building, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/ Application form: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/enrollment-galaxy-workshop-2018/ TARGET AUDIENCE This course consists of two parts, each of which you could register separately in the <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> application form. Part 1 (Day 1 and 2): biomedical & translational medicine researchers/students who are keen on bioinformatics Part 1 and 2 (Day 1, 2 and 3): educators in the bio domain who would like to start using Galaxy in their courses as an introduction to bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts, each of which you could register separately. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognized researchers in the fields of biomedicine, bioinformatics education, and Galaxy workflows. The confirmed speakers include Remond Fijneman (Day 1), a scientist in oncology from NKI; Björn Grüning (Day 2), the leader of Galaxy training network, who is also actively involved in Bioconda, and Jaap Heringa (Day 3), the scientific director of the Netherlands Bioinformatics Centre. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analyzing patient-derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: * Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. * Reference-based RNA-Seq data analysis * Module detection in differential gene expression in meta transcriptomics samples. * Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy * How to teach bioinformatics workflows. * How to prepare training material development. Day 1 - Wed Oct 17 Day 2 - Thu Oct 18 Day 3 - Fri Oct 19 Morning <http://galaxyproject.github.io/training-material/topics/introduction/> Introduction to Galaxy <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Network analysis with microbiota metatranscriptome Teaching bioinformatics workflows <https://shiltemann.github.io/> Saskia Hiltemann <https://hi-it.org/> Chao Zhang <http://www.few.vu.nl/~feenstra/> Anton Feenstra Keynote I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching <https://www.nki.nl/people/fijneman-remond/> Remond Fijneman <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://www.cs.vu.nl/~heringa/> Jaap Heringa Afternoon <http://galaxyproject.github.io/training-material/topics/transcriptomics/> RNAseq <http://galaxyproject.github.io/training-material/topics/metagenomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/> Galaxy training material development <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann Evening Social dinner About the instructor: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Björn Grüning, Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Correction: An earlier version of this announcement mentioned that you dont need to bring your own laptop, this is NOT TRUE. We regret the error. You do need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants own expenses) Should you have any question about this course, please contact Celia van Gelder ( <mailto:celia.van.gelder@dtls.nl> celia.van.gelder@dtls.nl) 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@dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl 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.
POSTDOCTORAL POSITION in STRUCTURAL BIOINFORMATICS, PROTEIN DESIGN and STRUCTUROMICS The structural bioinformatics group of the Université Libre de Bruxelles, Belgium (3BIO-BioInfo - Prof. M. Rooman) is seeking candidates for a postdoctoral position. Research context: Maintaining the stability and interactions of structured proteins is a necessary condition for them to properly fulfill their function. On the other hand, designing variants with optimized stability or affinity is a way to create new functional proteins that are stable in various conditions, even outside their physiological range. Considering that experimental techniques are slow and costly, the challenging development of efficient bioinformatics tools, capable of predicting the change in protein stability and protein-protein affinity upon mutations, could guide and limit the experiments that must be performed to identify relevant mutants. Such tools possess a large series of applications in all the biotechnological sectors that use proteins for their unique properties. They also present a fundamental interest as they shed some light on the relations between protein sequence, structure and function, a longstanding problem in protein science. Furthermore, understanding how natural evolution guided protein mutations and led from ancient to current proteins, and what exactly drives this evolution, is another motivating issue. Although stability and natural evolution are obviously linked, their exact relation is complex and far from known. Despite the few systematic and large-scale investigations probing into this relation, the residue mutations likely to optimize protein stability and affinity are nevertheless often chosen on the basis of the sequence conservation in homologous protein families. Objective: The goals of this project consist in deepening the understanding between natural evolution and protein stability and affinity, and to take advantage of this relation to improve, on the one hand, the stability and affinity predictors, and on the other hand, the models that mimic protein evolution. Offer: One full time postdoctoral positions for 18 months starting between October and February 2018, financed by the FNRS Fund for Scientific Research, with the possibility of extension through an FNRS postdoctoral research grant or a Marie Curie EC grant. The candidate can not have lived in Belgium for more than 18 months in the last 3 years. Required: - PhD degree in Sciences (Bioinformatics, Bioengineering, Physics, Chemistry, Informatics). - Good programming and computer science skills, preferably in C. - Good communication skills in English. - Good publication record in peer-reviewed scientific journals. Desirable: - Experience in the area of protein structural bioinformatics and/or machine learning. Contact: Please submit a 1) cover letter detailing your background and interest in the position, 2) a full C.V. and 3) at least two references (with name, email, address, phone number) via email to Prof. M. Rooman (mrooman@ulb.ac.be).
participants (2)
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Celia van Gelder -
Marianne Rooman