From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Thu May 3 14:50:30 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Thu, 3 May 2018 14:50:30 +0200 Subject: [ELIXIR-ITA_ml] [BITS2018/ELIXIR-IIB] Workshop on Docker and Reproducibility - 25-26 June - Turin (Italy) Message-ID: COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. ELIXIR-IIB is pleased to announce the upcoming Workshop on Docker and Reproducibility, a satellite event held jointly with the BITS Annual Meeting 2018. IMPORTANT DATES: Deadline for applications: 30 May 2018 Course date: 25-26 June 2018 FEE: 100? Places on the workshop are limited to 24. The candidates with an adequate profile will be accepted on a first-come first-served basis, until we reach 24 participants. Chosen participants will be notified by email. VENUE: University of Turin, Molecular Biotechnology Center, Via Nizza, 52 - 10126 Torino (Italy) COURSE DESCRIPTION: Docker is a container framework for Linux that allows a developer to make easier the creation, deployment, and execution of applications by using containers. Recently it is becoming a promising approach to computational biology research reproducibility by: - Saving time and expenses on human and computational resources allocated to already performed analysis; - Boosting communication between computational biologists working on similar topics; - Enhancing transparency within the community; - Granting open access computational knowledge to the community. During the workshop the participants will learn the core concepts of docker and how to easily embed bioinformatic pipelines/workflows into a docker container. Full details at: https://elixir-iib-training.github.io/website/2018/06/25/BITS_Docker_Torino.html Should you have any question, do not hesitate to contact the local organiser Dr. Marco Beccuti (beccuti a di.unito.it) and/or the ELIXIR-IIB Training Team (elixir.ita.training a gmail.com). We apologise for cross-posting. Please, email us back with the word REMOVE as the subject line, if you don't want to receive messages from ELIXIR-IIB Training anymore. Kind regards, the Organisers. -- *ELIXIR-IIB Training * https://elixir-iib-training.github.io/website/ -------------- parte successiva -------------- Un allegato HTML č stato rimosso... URL: From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Thu May 3 15:09:13 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Thu, 3 May 2018 15:09:13 +0200 Subject: [ELIXIR-ITA_ml] ELIXIR at ECCB 2018 Message-ID: -------------- parte successiva -------------- Un allegato HTML č stato rimosso... URL: From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Thu May 3 18:31:03 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Thu, 3 May 2018 18:31:03 +0200 Subject: [ELIXIR-ITA_ml] rita casadio Annuncio Gordon Conference Message-ID: <5490a593-58f5-814e-cde1-282a88145110@unibo.it> Gentilissimi sperando di fare cosa gradita vi invio l'annuncio di una Gordon Conference di possibile interesse per la comunitŕ grazie dell'attenzione per dettagli visitate il sito: https://www.grc.org/human-genetic-variation-and-disease-grs-conference/2018/ Rita Casadio -- Rita Casadio Biocomputing Group Phone: +39 051-2094005 Fax: +39 051-2094005 http://www.biocomp.unibo.it -------------- parte successiva -------------- Un allegato non testuale č stato rimosso.... Nome: GRC_program_2018.pdf Tipo: application/pdf Dimensione: 4417263 bytes Descrizione: non disponibile URL: From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Thu May 3 18:34:48 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Thu, 3 May 2018 18:34:48 +0200 Subject: [ELIXIR-ITA_ml] rita casadio Annuncio Gordon Conference Simposio Message-ID: Gentilissimi sperando di fare cosa gradita vi invio l'annuncio di una Gordon Conference di possibile interesse per la comunitŕ grazie dell'attenzione per dettagli visitate il sito: https://www.grc.org/human-genetic-variation-and-disease-conference/2018/ Rita Casadio -- Rita Casadio Biocomputing Group Phone: +39 051-2094005 Fax: +39 051-2094005 http://www.biocomp.unibo.it -------------- parte successiva -------------- Un allegato non testuale č stato rimosso.... Nome: GRC_program_2018.pdf Tipo: application/pdf Dimensione: 4417263 bytes Descrizione: non disponibile URL: From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Wed May 9 14:44:04 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Wed, 9 May 2018 14:44:04 +0200 Subject: [ELIXIR-ITA_ml] Fwd: [Compute] Cloud Resources through Helix Nebula project In-Reply-To: <44013c61-3961-75e1-9496-aa1a7e977b09@ebi.ac.uk> References: <44013c61-3961-75e1-9496-aa1a7e977b09@ebi.ac.uk> Message-ID: Dear Elixir, EMBL have been part of the Helix Nebula Science Cloud project over the last 2 years to procure commercial cloud resources for 'big science'. We are now entering the phase where the procured cloud resources will become available for use beyond the current test cases. Access to these cloud resources will require an ELIXIR ID and you will need to be allocated cloud resources for you to use. We are expecting to have access from June for about 6 months to significant resources (~1000 cores & 1PB of storage) from a number cloud providers that are part of the consortium. EMBL is co-funding these cloud resources (with the EC) as part of this per-commercial procurement project and agreed to let projects from the ELIXIR community use a portion of these cloud resources. Access and use of these cloud resources will be coordinated through the TSC team at EMBL-EBI. If you have cloud workloads that are ready or can be made ready please get in touch with me. Your local ELIXIR node may be able to help migrate or tune your workloads for the cloud resources. A training session will take place at the ELIXIR All Hands meeting in Berlin in June. We do not foresee any charge for the use of these cloud resources. Please feel free to forward this within your node, to other communities or platforms. Thanks Steven -- Steven Newhouse, Head of Technical Services European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Office:+44(0)1223 49 4651 Mob:+44(0)7825 995027 URL: http://www.ebi.ac.uk/ _______________________________________________ Compute mailing list Compute a elixir-europe.org https://lists.elixir-europe.org/mailman/listinfo/compute From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Mon May 14 11:23:06 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Mon, 14 May 2018 09:23:06 +0000 Subject: [ELIXIR-ITA_ml] NETTAB 2018: Building a FAIR Bioinformatics environment - Call for Abstracts for oral communications - Submit within May 20, 2018 Message-ID: NETTAB 2018 Building a FAIR Bioinformatics environment October 22-24, 2018, Genoa, Italy 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 . See full instructions at: 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 - paolo.dm.romano a 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 -------------- parte successiva -------------- Un allegato HTML č stato rimosso... URL: From elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it Mon May 14 15:30:18 2018 From: elixir-ita_ml.elixir-ita.cnr.it a srv00.area.ba.cnr.it (General ELIXIR-Italy Mailing list) Date: Mon, 14 May 2018 13:30:18 +0000 Subject: [ELIXIR-ITA_ml] Integrative Bioinformatics 2018 at Rothamsted Research, 13-15th June, 2018 Message-ID: Cari colleghi, vi prego di far circolare questo annuncio, che spero sia di interesse per molti di voi. Paolo Romano (===) Dear colleague we encourage you to join us at IB 2018 at Rothamsted Research (13-15th June). Registration includes attendance at the symposium; refreshment breaks; lunches; a conference networking party at the historic Rothamsted Manor on the evening of Thursday 14 June; and a shuttle service between Rothamsted Conference Centre and the Aubrey Park Hotel. Recently we have made attendance more attractive and: *Workshop admission (13 June) is now included in the registration cost *Half-price tickets available for students and BBSRC-funded postdocs A draft full programme is on the registration website and here... *https://docs.google.com/document/d/1E7D4_CS0vlldEcEuknXjEnSBZSZCJvbI5w1FdFh-gG4/edit#heading=h.x8imy73570r8 Extended the submission deadline for flash talks to May 7 and for posters May 18. There are now less than 45 days to the Integrative Bioinformatics Symposium at Rothamsted with an exciting line-up of invited speakers and workshops. Please Register at http://ib2018.eventzilla.net Invited Speakers include: Prof Christine Orengo, Prof Gos Micklem, Prof Carole Goble, Prof Chris Evelo, Dr Paul Groth, Dr Bjoern Gruening, Dr Oliver Stegle, Dr Tamás Korcsmáros, Dr Simon Jupp, Dr Gancho Slavov, Dr Dietrich Rebholz-Schuhmann, Dr Evangelia Petsalaki Invited Workshop speakers: Matthias Lange (IPK), Cyril Pommier (INRA URGI), Marco Brandizi (Rothamsted), Ajit Singh (Rothamsted), Mark Needham (Neo4j), Kevin Dialdestoro (Genestack), Mike Sternberg (Imperial), Rob Davey (Earlham) Workshops *From FAIRer Data to FASTer Discoveries using applications from plant genomics and phenomics *Phyre and PhyreRisk - Integrating genetic variant data with experimental and predicted protein structures and their complexes *COPO - A portal for plant scientists to describe, store and retrieve data more easily Paolo Romano Ospedale Policlinico San Martino Genova, Italy Skype: p.romano Email: paolo.romano a hsanmartino.it - paolo.dm.romano a 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