- BBClist - maillist.psb.ugent.be

[Gtpb] Training Assistant (recruiting)
by Pedro L. Fernandes 17 May '18

17 May '18

Training Assistant for Biodata.pt (recruiting) http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=100246 -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] PDA18 - Course announcement / Reminder
by GTPB Administration 16 May '18

16 May '18

Course Announcement / Reminder PDA18 Proteomics Data Analysis with Lennart Martens, Harald Barsnes and Lieven Clement Key terms: Proteomics data, identfication, quantification, statistics IMPORTANT DATES for this Course Deadline for applications: May 20th 2018 Course date: May 28th - June 1st 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The core focus will be on shotgun proteomics data. Quantification through isobaric labels (iTRAQ, TMT) and label-free precursor peptide (MS1) ion intensities will also be introduced. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: this is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PDA18/ Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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CODATA-RDA Research Data Science Summer School & Advanced Bioinformatics Workshop - call closes 21st of May
by Alexander Botzki 16 May '18

16 May '18

Dear collegaues, On behalf of Celia van Gelder, I would like to forward this announcement: Deadline approaching for CODATA-RDA Schools in Trieste in 2018 - 21st of May: * The CODATA-RDA Research Data Science Summer School, 6-17 August 2018, for information and application please look at http://indico.ictp.it/event/8329/overview * An Applied Bioinformatics workshop, from 20-24 August, that will focus on applying machine learning in bioinformatics. Application via: http://indico.ictp.it/event/8561/ Best regards Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl<mailto:celia.van.gelder@dtls.nl> websites: www.dtls.nl<http://www.dtls.nl/>, www.biosb.nl<http://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

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Data Carpentry workshop June (Brussels)
by Kim DE RUYCK 15 May '18

15 May '18

Dear, [ https://www.elixir-belgium.org/training | ELIXIR Belgium ] is organizing a Data Carpentry workshop on 12-13 June 2018 in Brussels. This workshop teaches the core skills for working with data effectively and is designed for people with little to no prior computational experience. More information can be found [ https://inbo.github.io/2018-06-12-bru-datacarpentry-inbo-elixir/ | here ] . Kind regards, Paula Andrea Martinez Data science and bioinformatics trainer [ https://tess.elixir-europe.org/events | TeSS ] - find our events

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Jalview workshop 28.05.2018
by Eva-Maria Krammer 14 May '18

14 May '18

==== JALVIEW workshop, May 28 ==== Bilille organizes a one-day tutorial on the bioinformatic software Jalview (www.jalview.org <http://www.jalview.org>). Jalview is a comprehensive and user-friendly platform that allows to create and analyse multiple sequence alignments. This tutorial is for all scientists working with protein, RNA and DNA sequence data. Participants will learn how to use Jalview, and explore its capabilities for working with 3D structure, phylogenetic trees and annotation from public databases. - Date: May 28, 2018 (from 9:30 to 16:00) - Venue: Cité Scientifique, Villeneuve d'Ascq, France - Program and registration: https://wikis.univ-lille1.fr/bilille/jalview_2018 The instructor is James Procter, coordinator of the Jalview project (Division of Computational Biology, School of Life Sciences University of Dundee, UK). Registration is free, but mandatory (max 25 people). On the behalf of the organizing committee, Eva-Maria Krammer

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NETTAB 2018: Building a FAIR Bioinformatics environment - Call for Abstracts for oral communications - Submit within May 20, 2018
by Frederik Coppens 14 May '18

14 May '18

Submission deadline end of this week ! NETTAB 2018 Building a FAIR Bioinformatics environment October 22-24, 2018, Genoa, Italy http://www.nettab.org/2018/ <http://www.nettab.org/2018/> Submission deadline for abstracts for oral communications: Sunday May 20, 2018. CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS NETTAB 2018 is organised in collaboration with ELIXIR Nodes of the UK and Italy as well as the Italian Society of Bioinformatics, BITS. The main focus will be on FAIR principles in bioinformatics, a challenging topic that we hope will attract many researchers from all over the world, including but not limited to, Bioinformaticians, Biologists, Computer Scientists, and others working or interested in the above research scope. The FAIR Guiding Principles for scientific data management and stewardship, published in 2016, has sparked worldwide interest across the biology community: from grassroots to policymakers, and from data providers to publishers. In order to make the FAIR concept a reality, we need to answer many questions, like: What is FAIRness? How to make FAIR data a reality? How to facilitate the translation to FAIR data? How to measure it? On these topics, there are many ongoing projects, such as EOSCpilot, FAIRmetrics, FAIRsharing, and GO-FAIR. Now is the perfect time to discuss on these topics and related actions, and to move on from FAIR principles to FAIR practice. The workshop will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics. TOPICS Methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics including, but not limited to: FAIR concept • Specification and revision of components, conceptual issues. • Criticisms and review of FAIR principles Development tools • FAIR Web Services, metadata for FAIR tools, revision of standard formats. FAIRification methodologies • FAIRification best practices and training • Experiences of FAIR methods • Best practices and lessons learned from domains outside bioinformatics. • FAIRness evaluation • FAIRness validation and correction tools. • FAIR metrics: Levels of FAIRness, FAIRness scores, FAIRness minimal levels. FAIR environment • Integration and interoperation of FAIR data and systems. • FAIR and its demonstrated contribution to open science and reproducible results • FAIR principles and practices of research outputs other than data: workflows, scripts, tools, models, training materials, SOPs etc • Surveys of FAIR resources and methods FAIR value • Examples of FAIR in practice and the benefits of FAIR resources • Related initiatives to FAIR: for example Data Commons and EOSC • The economics of FAIR • Incentives for FAIR stewardship throughout the data lifecycle The topics of NETTAB 2018 also include the usual topics of NETTAB workshops. INSTRUCTIONS AND DEADLINES Submission of abstracts for oral communications: Sunday May 20, 2018 Notification: Monday June 18, 2018 Abstracts of maximum four A4 pages must be submitted through EasyChair at: https://easychair.org/conferences/?conf=nettab2018 <https://easychair.org/conferences/?conf=nettab2018> . See full instructions at: http://www.igst.it/nettab/2018/submissions/instructions-for-authors/ <http://www.igst.it/nettab/2018/submissions/instructions-for-authors/> . KEYNOTE SPEAKERS Michel DUMONTIER, MaastrichtUniversity, The Netherlands Frederik COPPENS, Gent University , Belgium Patricia PALAGI, SIB, Switzerland Christine DURINX, ELIXIR, Switzerland GUEST SPEAKERS Rob HOOFT, DTLS, The Netherlands Rafael JIMENEZ, ELIXIR, UK Marco ROOS, LUMC, The Netherlands Amnon SHABO, Siemens, Germany Tutorial/Hackathon programme under definition. WORKSHOPS ORGANIZORS Carole Goble, University of Manchester Paolo Romano, Ospedale Policlinico San Martino, Genoa Mauro Giacomini, University of Genoa SCIENTIFIC COMMITTEE The Scientific Committee is being defined. Many invitations are still pending. Oya Deniz BEYAN, Fraunhofer FIT, Germany Jan Willem BOITEN, Lygature, The Netherlands Robin CHAMPIEUX, Oregon Health & Science University, USA Michael CRUSOE, Common Workflow Language, Lithuania Peter DOORN, DANS-KNAW, The Netherlands Michel DUMONTIER, Maastricht University, The Netherlands Leyla Jael GARCIA CASTRO, EMBL-EBI, United Kingdom Mauro GIACOMINI, University of Genoa, Italy Carole GOBLE, University of Manchester, United Kingdom Alasdair GRAY, Heriot-Watt University, United Kingdom Paul GROTH, Elsevier Labs Paolo MANGHI, CNR/ISTI & OpenAIRE, Italy Patricia PALAGI, Swiss Institute of Bioinformatics, Switzerland Helen PARKINSON, EMBL-EBI, United Kingdom Paolo ROMANO, Ospedale Policlinico San Martino, Italy Susanna Assunta SANSONE, Oxford eResearch Center, United Kingdom Kees VAN BOCHOVE, The Hyve, The Netherlands Mark WILKINSON, UPM, Spain Katherine WOLSTENCROFT, Leiden University, The Netherlands Paolo Romano on behalf of Workshop Organizors Paolo Romano Ospedale Policlinico San Martino Genova, Italy Skype: p.romano Email: paolo.romano(a)hsanmartino.it <mailto:paolo.romano@hsanmartino.it> - paolo.dm.romano(a)gmail.com <mailto:paolo.dm.romano@gmail.com> CON TE LA NOSTRA RICERCA PUO' DIVENTARE CURA DEVOLVI IL TUO 5 X 1000 AL SAN MARTINO! FINANZIAMENTO DELLA RICERCA SANITARIA CODICE FISCALE 02060250996 5xmille.ospedalesanmartino.it <http://www.ospedalesanmartino.it/sostienici.html> Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Exciting postdoc opportunity in Copenhagen
by Magali Michaut 14 May '18

14 May '18

You want to be happy and do some cool work? ;-) Here is your chance: cancer stem cell research with exciting single cell data in the capital of happy people! Check it out and/or spread the word: http://jobportal.ku.dk/alle-opslag/?show=147220 <http://jobportal.ku.dk/alle-opslag/?show=147220> If you have questions about our group, please contact me. Looking forward to hearing from you, Magali

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2 positions for Computational Systems Biology Postdoc at Institut Curie
by Alexander Botzki 12 May '18

12 May '18

Dear colleagues, We are looking for brilliant postdocs to join our Cancer Computational Systems Biology group. Please could you spread the word about this opportunity and forward the attached announcements to whoever might be interested? Many thanks in advance. Best wishes Emmanuel Emmanuel.Barillot(a)curie.fr

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FW: Data Carpentry workshop June (Brussels) & ELIXIR Train the Trainer August (Antwerp)
by Alexander Botzki 08 May '18

08 May '18

Dear all, ELIXIR-BE<https://www.elixir-belgium.org/> is hosting two events that might be of your interest or that you might be able to recommend to people around you. The first one is a Data Carpentry workshop in Brussels, next month (June 12-13) https://inbo.github.io/2018-06-12-bru-datacarpentry-inbo-elixir/ The second is an ELIXIR Train the Trainer workshop in Antwerp, last week of (August 20-21) https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-tickets-45… Please don't hesitate to contact me if you have any questions. Kind regards, Paula Andrea Martinez Data science and bioinformatics trainer TeSS<https://tess.elixir-europe.org/events> - find our events [Image removed by sender.]

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[Gtpb] PDA18 - Course announcement / Reminder
by GTPB Administration 07 May '18

07 May '18

Course Announcement / Reminder PDA18 Proteomics Data Analysis with Lennart Martens, Harald Barsnes and Lieven Clement Key terms: Proteomics data, identfication, quantification, statistics IMPORTANT DATES for this Course Deadline for applications: May 20th 2018 Course date: May 28th - June 1st 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The core focus will be on shotgun proteomics data. Quantification through isobaric labels (iTRAQ, TMT) and label-free precursor peptide (MS1) ion intensities will also be introduced. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: this is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PDA18/ Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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