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Friday , February 12, 2021

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Newsletter IFB brief
Institut Français de Bioinformatique news

Edito

Dear colleagues, 

For many years now, IFB has been the French node of the European distributed infrastructure for life-science information, ELIXIR. This membership has opened great opportunities to collaborate with european colleagues on the development of resources and services at the EU scale but also to give more international visibility and impact to French national resources.

A very good illustration of this impact is given by the ELIXIR-CONVERGE project, coordinated by the ELIXIR Hub and in which IFB is a partner. This 3-year long project started in 2020 and it aims to start a coordinated support for the development of data management plans (DMPs) and their implementation. This service will rely both on ELIXIR central and national resources such as dedicated tools, archives, training and expertise. A network of data stewards is being developed for coordination in the long run.

On January 31st, a collaborative website has been designed to guide life scientists in their efforts to better manage their research data following the FAIR Principles : the ELIXIR Data Management Kit. It gives a precious overview of the problems and resources for data management applied to Life Sciences and it different facets. Go and visit it ! The version online is a beta version that will be improved during the project. But it is also meant to be continuously improved by its users. The next step is the linking of the ELIXIR Data Management kit with the Data Stewardship Wizard to facilitate the actual delivery of a data management plan.

The second example is the Beyond 1 Million Genomes (B1MG). The aim of this project is to create legal guidance, best practices and recommendations to construct infrastructure enabling the commitment of 23 European Member States to give cross-border access to one million sequenced genomes by 2022 (1+ Million Genomes Initiative). If you wish to be involved, don't hesitate to visit B1MG Stakeholder Portal

The B1MG, as well as CONVERGE, are embedded in the Open Science objective, to make knowledge accessible for all. Both projects promote the unhindered dissemination of research outputs and aims to improve research efficiency by supporting data discovery, accessibility, interoperability, and re-use. 

Anne-Françoise Adam-Blondon, Victoria Dominguez Del Angel & Angela Saenz

 

IFB HIGHLIGHTS

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MuDi4LS 
The PIA3 project Shared digital spaces for life sciences (MuDiS4LS) outlines the IFB's next roadmap. The budget allocated to the project is 16.5 M€. More information in the press release (french version)
 

Virus-Host (Eco)- Systems Biology Special Issue 
You are working on virus-host relationships SARS-CoV-2, Covid-19, viruses with -omics, mathematical or phylosophical point of view. Feel free to submit a manuscript to the Virus-Host (Eco) Systems Biology Special Issue
 

ISfinder- associated developments

TnCentral. A Prokaryotic Transposon DataBase and KnowledgeBase (M. Chandler, K. Ross, A. Varani, and Protein Information Resource, Heorgtown University). Including a subset of data from ISfinder

TnPedia. An Encyclopedia of Prokaryotic Transposable elements. (M. Chandler, K. Ross, A. Varani). Also integrated into TnCentral. Entirely update and replaces "Information (General Information; ISfamilies)" from ISfinder
 

 ELIXIR PROJECTS AND EUROPEAN INITIATIVES 

Open letter - Support data sharing for COVID-19
EMBL-EBI has initiated a call for data sharing to accelerate COVID-19 research and prepare for future outbreaks. Niklas Blomberg, EMBL's DG Edith Heard, EMBL-EBI's directors Erwan Birney and Rolf Apwiler, Guy Cochrane, Christine Durinx and hundreds of other scientists have already signed it. We encourage all ELIXIR members to sign the letter in support of open data 



International Day of Women and Girls in Science 
At the initiative of ELIXIR, you have discovered all day yesterday, February 11, the stories and celebration of the defenders of equality in the scientific world. Follow all the ELIXIR stories of this day with #ELIXIRforEquality


Applications are now being accepted for integrating thematic digital research service providers into EOSC-Pillar and EOSC-Portal. The Open Call closes on 28 February 2021, 23:59 CET
This website-based toolkit, a collaborative effort from all ELIXIR Nodes, is designed to guide life scientists and data stewards in managing their research data. The RDMkit will get its public beta release on 31 March 2021. We envision this to become a flagship resource for ELIXIR in research data management, covering all aspects relevant to life sciences. ELIXIR Hub is inviting ELIXIR colleagues, including Platforms, Communities and Focus Groups, to help us with content, feedback and revisions, and to join the editorial team and the band of contributors. Register for the early-bird demo webinar / 1 March 2021, 2pm CET


 EVENTS

All Hands ELIXIR-FR 2021
The next ELIXIR France All Hands meeting will take place virtually on 16 February 2021. This meeting will bring together members of the ELIXIR french community and collaborators from partner organisations. In a series of plenary sessions, the participants will review achievements and activities for 2020, as well as on-going projects, and discuss priorities for the future. Contact for additional information.



Innovation and SME Forum: Data-Driven Innovation in the Agritech Sector
Reminder of the event organised by ELIXIR-FR and ELIXIR-BE (Belgium), in partnership with Bayer and Emphasis from 10 to 12 March 






 

 Job vacancies 

Web Applications Developer 
Paris, France



all IFB job opportunities


 training and outreach 

At the beggining of this year, the IFB/ELIXIR-FR announces its training offer for the year 2021 around the FAIR theme (Findable, Accessible, Interoperable, Reusable)

Open Science and DMP training
from 15 to 19 March - informed audience
from 16 to 19 November - beginners

Training "FAIR principles applied to bioinformatics"
from 28 to 30 June - for bioinformaticians and bio-analysts

More information 




Training in Toulouse using command line 
Places are still available. Next Sessions: Linux (22th March), Cluster (23rd March), extract information in large files with sed and awk (24th March), awk programming (25th March), nfcore workflows (26th March), RNAseq analysis with statistics (1éth April), short reads alignment and variant calling (15th and 16th November).


Galaxy training 
A 5-day Global Galaxy Course is organized by GTN (Galaxy Training Network), a virtual event showcasing a wide variety of tutorials and involving IFB's trainers. The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq) and Proteomics. February 15-18, 2021 (all time zone), cost free).



 Publications 


Sempéré, G,. Pétel, A., Abbé, M., Lefeuvre, P., Roumagnac, P., Mahé, F., Baurens, G., Filloux, D. 2021. metaXplor : an interactive viral and microbial metagenomic data manager. Giga Science


Ashraf, U., Benoit-Pilven, C. Navratil, V., Ligneau, C., Fournier, G., Munier, S., Sismeiro, O., Coppée, J-Y., Lacroix, V., Naffakh, N. 2020. Influenza virus infection induces widespread alterations of host cell splicing.  NAR Genomics and Bioinformatics


Sallard, E., Halloy, J., Casane, D., Decroly, E. van Helden, J.  2021. Tracing the origins of SARS-COV-2 in coronavirus phylogenies : a review.  Environ Chem Lett


Sharma, V K., Jinadatha, C.,  Lichtfouse, E., Decroly, E., van Helden, J., Choi, H., Chatterjee, P. 2021. COVID-19 epidemiologic surveillance using wastewater.  Environ Chem Lett


Ison, J., Ienasescu, H, Rydza, E., Chmura, P. Rapacki, K., Gaignard, A., Schwämmle, V., van Helden, J. Kalaš, M., Ménager, H. 2021. biotoolsSchema : a formalized schema for bioinformatics software description. Gigascience


Ksouri, N., Castro-Mondragón, J.A., Montardit-Tarda, F., van Helden, J., Contreras-Moreira, B. Gogorcena, Y. 2021. Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants : the peach example. Plant Physiology


Yang, Y., Bocs, S., Fan, H., Armera, A., Baudoin, L., Xu, P., Xu, J., This, D., Hamelin, C., Iqbal, A., Qadri, R., Zhou, L., Li, J, Wu, Y., Ma, Z., Emmanuel I, A., Rivallan, R., Liu, N., Xia, W., Peng, M., Xiao, Y. 2021. Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance. Commun Biol









Editor in chief  Claudine Medigue & Jacques van Helden
Redactor in chief Suzanne Lauriou