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Galaxy Training for life science researchers announcement
by Daniele Parisi 29 Oct '18

29 Oct '18

Dear all, We would hereby like to announce an upcoming GALAXY TRAINING for life science researchers in GENT on NOVEMBER 6TH, organised by ELIXIR Belgium. Galaxy software framework is an open-source application that enables researchers without informatics expertise to perform computational biology analyses through the web (usegalaxy.eu [1]). The workshop will be hands-on and will introduce participants to #USEGALAXY [2] for analysis of NEXT-GENERATION SEQUENCING data (RNA-Seq or DNA-Seq). The workshop is FREE OF CHARGE. More information and registration are available at the following link: https://tinyurl.com/y8vtq6f8 [3] Please forward this information to anyone who you think might be interested. With best regards, Daniele Parisi on behalf of Paula Martinez, ELIXIR Belgium trainer -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] https://t.co/Xw3HOUZpHZ [2] https://twitter.com/hashtag/useGalaxy?src=hash [3] https://t.co/xIbYziemWT

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job adverstisement Maastricht University
by Ehrhart, Friederike (BIGCAT) 26 Oct '18

26 Oct '18

Dear all, we are looking for someone with both, bioinformatics and teaching skills: https://www.academictransfer.com/nl/50441/postdocteachergraduate-at-nutrim-… Best regards, Freddie

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SWAT4(HC)LS 2018: Semantic Web Applications and Tools for Healthcare and Life Sciences - 3-6 December 2018 Antwerp, Belgium
by Femke Francissen 25 Oct '18

25 Oct '18

SWAT4(HC)LS 2018 - Semantic Web Applications and Tools for Healthcare and Life Sciences Join us for the SWAT4(HC)LS workshop on 3-6 December 2018 in Antwerp, Belgium! ** Conference website <http://www.swat4ls.org/> / Registration <http://www.swat4ls.org/workshops/antwerp2018/registration/> ** SWAT4(HC)LS is a venue for presenting and discussing novel ideas, experiences and issues in the application of Semantic and Web technologies in the biomedical domain at large. 3 December: Tutorials <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_3rd_Tutori…> - 4-5 December: Conference <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_4th-5th_Co…> - 6 December: Hackathon <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_6th_Hackat…> Conference themes: Agriculture and Nutrition, Secondary Reuse of Healthcare Data and Open Data Keynotes: <http://www.swat4ls.org/workshops/antwerp2018/keynotes/> - Philip Bourne: How Does Data Science Impact the Semantic Web? - Dean Allemang: Semantic Web and the New Industrial Revolution - Medha Devare: Spinning a Semantic Web for Agriculture Spotlight: We have built a consistent program around agrosemantics <http://www.swat4ls.org/workshops/antwerp2018/agrisemantics/>, sponsored by the Global Open Data for Agriculture and Nutrition ( <https://www.linkedin.com/in/ACoAABuFID8BW4GSWnZGoPC0Fr19Bo4jbNzkXJo/>GODAN <https://www.godan.info/>) <https://www.linkedin.com/in/ACoAABuFID8BW4GSWnZGoPC0Fr19Bo4jbNzkXJo/>. This includes dedicate tutorials, keynote and panel discussions. Tutorials: We have setup a program of tutorials that cover pharma and healthcare industry standards such as FHIR, schema.org, CDISC, OMOP and their relations to the semantic web. Find the list of the tutorials here <http://www.swat4ls.org/workshops/antwerp2018/programme/tutorials/>. Hackathon: We are working on an hackathon <http://www.swat4ls.org/workshops/antwerp2018/programme/#December_6th_Hackat…> bringing together many of the above. Starting in 2008, SWAT4(HC)LS has been held continuously for more than 10 years, expanding from a one day workshop to a four day event composed of tutorials, conference and hackathon. SWAT4LS intends to provide an open and vibrant discussion space cross cutting across academia, industry and institutional participants. SWAT4(HC)LS is sponsored by GODAN <https://www.godan.info/> and Figshare <https://figshare.com/>. on behalf of the organizers, Femke Francissen DTL/ELIXIR-NL

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Genomics Workshop spaces @ Edinburgh Genomics: Last few spaces!
by TRAIN edgenomics-training 24 Oct '18

24 Oct '18

Dear Budding Bioinformaticians We have a very limited number of spaces remaining on two introductory level bioinformatic workshops here at Edinburgh Genomics this November: Bioinformatics for Genomics 19-23 November: This weeklong workshop, taught by our experienced team of bioinformaticians, covers everything you need to know to get a footing with genome informatics. Starting with an introduction to Linux and then an introduction to R on days one and two, we will get you up to speed with the languages of bioinformatics. Day three covers some more involved genome analysis in the form of genome annotation in R along with a foray into data visualisation with R, then day four and five are focused on RNA-seq data analysis. This broad introduction is perfect for those new to genome analysis that want to be able to analyse their own data or contribute to collaborations using genomic data. For more info see: https://genomics.ed.ac.uk/services/bioinformatics-genomics To sign up: https://www.surveymonkey.co.uk/r/B4G_191118 R for Genomics 26-28 November: R for Genomics gives a comprehensive introduction to the R programming environment using genomic data examples. By the end of this two day course you will be familiar with Rstudio, loops, functions, genomic annotation data and be able to make beautiful graphs using ggplot2 ready for your next publication. No prior experience necessary for this beginner friendly course. For more info see: https://genomics.ed.ac.uk/services/r-genomics To sign up: https://www.surveymonkey.co.uk/r/R4G_261118 There are only a few places left on these courses so if you're interested act quickly, they are first come first served! Not the courses you're looking for? Tell us what courses you would like to see in the future by completing our training needs survey: https://www.surveymonkey.co.uk/r/7M6QB2D Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics 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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CENTURI postdoctoral call now open - Marseille, France
by BAUDOT Anaïs 24 Oct '18

24 Oct '18

Dear Colleagues, CENTURI is recruiting up to 10 highly motivated postdoctoral fellows to work in an interdisciplinary life science environment. The available postdoctoral projects will be displayed on the "Recruitment" part of our website, with more projects being added to our website up until November 15. Candidates can either apply to one of the advertised CENTURI projects or submit their own project, providing that they meet the application criteria and that their application is supported by the host lab(s). These projects should be submitted to: postdocproject(a)centuri-livingsystems.org Deadline for application and project submission for postdoc candidates: November 30, 2018 More information about the projects and application: http://centuri-livingsystems.org/recruitment/ <http://centuri-livingsystems.org/recruitment/> We invite you to share this call with your professional network. Best regards, CENTURI management team

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Fwd: CENTURI is recruiting a lead data analyst/scientist - Marseille, France
by BAUDOT Anaïs 24 Oct '18

24 Oct '18

> Begin forwarded message: > > From: <info(a)centuri-livingsystems.org> > Subject: CENTURI is recruiting a lead data analyst/scientist > Date: 22 October 2018 at 11:03:45 CEST > To: undisclosed-recipients:; > > Dear Colleagues, > > CENTURI is recruiting a lead data analyst/scientist within CENTURI’s technology transfer platform. The lead data analyst will help shape the data sharing and analysis platform and will be able to learn from, as well as distribute his/her knowledge in the CENTURI community. > > More information about the offer: http://centuri-livingsystems.org/job-offer-data-analyst/ <http://centuri-livingsystems.org/job-offer-data-analyst/> > > > CENTURI offers a three-year contract from the Aix-Marseille Université. > > Deadline for application: November 23, 2018 > > > We invite you to share this this call with your professional network. > > Best regards, > CENTURI management team --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

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Data scientist position at Eindhoven University of Technology
by Bosnacki, D. 22 Oct '18

22 Oct '18

Eindhoven University of Technology has a vacancy for a data scientist at the Biomedical Engineering Department and the Institute for Complex Molecular Systems (ICMS). For more information please go to: https://jobs.tue.nl/nl/vacature/data-scientist-materialsdriven-regeneration…

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1-week course single-cell transcriptomics and epigenomics in Roscoff (France)
by Morgane Thomas-Chollier 19 Oct '18

19 Oct '18

Date : 3rd February 2019 – 8th February 2019 Place : Roscoff, France Deadline registration: 15th November This one-week class focuses on the large-scale study of heterogeneity across individual cells from the genomic, transcriptomic and epigenomic points of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. A wide range of single-cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. It is not necessary to have personal single-cell data to analyse. Deadline registration: 15th November http://www.france-bioinformatique.fr/en/evenements/sincellTE_2019 -- The organizing committee: Erwan Corre, Marc Deloger, Marie-Agnès Dillies, Agnès Paquet, Antonio Rausell, Nicolas Servant, Morgane Thomas-Chollier Morgane

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Exciting postdoc opportunity in Bordeaux
by Nikolski Macha 19 Oct '18

19 Oct '18

Three more weeks to apply to this computational postdoc position in epigenomics with exciting methylation data and more ! Check it out and/or spread the word: https://www.sfbi.fr/content/investigating-methylome-grape-and-oak-under-wat… If you have questions about our group, please contact me. Looking forward to hearing from you, Macha Nikolski ======= Investigating the methylome of grape and oak under water stress Global climate changes that includes several environmental constraints including drought, is a major concern that affects plant survival both in agro-systems and forest ecosystems. Indeed plants have evolved a wide range of mechanisms to cope with adverse environmental conditions that often lead to rapid and integrated reprogramming of gene expression patterns. Recent works have evidenced that epigenetic regulations, including DNA methylation, are essential to the responses of plants to environmental constraints, and may contribute to their long term adaptation to adverse conditions. In this context the METDRY project addresses the question of the potential involvement of genomic DNA methylation in the adaptation and responses to drought in woody perennial plants using grape and oak as representatives of cultivated plants and forest ecosystems respectively. It is based on the comparative analysis of methylomes, transcriptomes and small RNA populations in a drought sensitive and drought tolerant species in grapevine and oak and aims at identifying differentially methylated regions (DMRs) and gene expression profiles linked to long term adaptation to drought. The main objectives of the project are: 1. To analyze the genome wide distribution of 5mC in a drought sensitive and tolerant species in oak and grapevine, and determine similarities and differences between these contrasted phenotypes in each genus. 2. To determine changes in DNA methylation landscape induced by drought in the sensitive and tolerant species in each genus. 3. To investigate if DNA methylation contributes in a similar way to the responses to drought stress and to long term adaptation to drought in plants from natural population (oak), and in plants that have been selected by breeders over several generation (grapevine). 4. To implement a robust bioinformatics data analysis pipeline for BS-seq data and integrative approaches including BS-Seq, RNA seq, and Small RNA seq data. Applicants should be highly motivated and have a PhD with expertise in bioinfomatic and strong background in (epi)genomics . Knowledge in plant sciences is strongly recommended. Qualifications: We seek a bright, highly motivated, and enthusiastic bioinformatician with a background in epigenomics or genomics and an interest for plant biology. Candidates with other backgrounds such as molecular biology, with a strong interest in bioinformatics, are also invited to apply. Experience with NGS technologies and pipeline development is required. Applicants should have demonstrated abilities to work in a Linux environment and have experience in handling NGS data. Programming (Python, Perl, etc.) is required and knowledge of biostatistics is appreciated. A high standard of spoken and written English is appreciated, as are good communication skills. Ability to work autonomously, as well as part of a team, and to interact with scientist from different background including molecular biologist, plant physiologist and bioinformaticians is required. Applicants will have to share their time between three different laboratories. Contact: philippe.gallusci(a)inra.fr <mailto:philippe.gallusci%40inra.fr> (0557575847/0680945152) gregoire.le-provost(a)inra.fr <mailto:gregoire.le-provost%40inra.fr> (0557122773) macha.nikolski(a)u-bordeaux.fr <mailto:macha.nikolski%40u-bordeaux.fr> (0557571247) Links: UMR EGFV: https://www6.bordeaux-aquitaine.inra.fr/egfv/ <https://www6.bordeaux-aquitaine.inra.fr/egfv/> CBIB: https://cbib.u-bordeaux.fr/ <https://cbib.u-bordeaux.fr/> UMR BIOGECO: https://www6.bordeaux-aquitaine.inra.fr/biogeco <https://www6.bordeaux-aquitaine.inra.fr/biogeco> -- Head of Bordeaux Bioinformatics Center Research Director LaBRI / CNRS CBiB - Université Bordeaux 146, rue Léo Saignat, 33076 Bordeaux www : http://www.labri.fr/perso/macha/ <http://www.labri.fr/perso/macha/> tel : +33 (0)5 57 57 12 47

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EuBIC Winter School 2019
by Bittremieux Wout 18 Oct '18

18 Oct '18

We kindly invite you to participate in the EuBIC Winter School 2019 on January 15th-18th 2019 in Zakopane, Poland on proteomics bioinformatics [1]. It is the third of its kind and has proven to successfully bring together scientists in the field of proteomics and bioinformatics for proteomics to discuss challenges specific to this field. The registration is opened [2] until November 16th (early bird) / December 16th (regular). The Winter School will start with an educational day dedicated to workshops and trainings in established proteomics tools and workflows. The following days, internationally renowned invited speakers will give lectures and practical workshops covering the aspects of identification, quantification, result interpretation, and integration of MS proteomics data. This year’s special focus is the Challenges in Quantification and DIA. In order to share and discuss our work, we invite all interested conference attendees to submit an abstract for a poster. A selection of abstract submissions will additionally be chosen for short talks. Yours sincerely, on behalf of the organization committee, Wout Bittremieux [1] https://www.proteomics-academy.org/eubic-winter-school-2019 [2] https://www.proteomics-academy.org/registration

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