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Thursday , September 24, 2020

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Newsletter IFB brief
Institut Français de Bioinformatique news

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Dear colleagues, 
 

The research effort to fight the Covid-19 pandemic is probably unprecedented internationally. Unsurprisingly, it comes up against the problems encountered in other areas of biology and health : lack of accessibility and interoperability of data and tools and lack of transparency which limits coordination and induces excessive redundancy of work. In the case of Covid, there is also the difficulty that extremely diverse communities (doctors, epidemiologists, biologists, modelers, data scientists, bioinformaticians) encounter in understanding each other in order to cooperate

This difficult context offers the IFB the opportunity to make a valuable contribution.

Indeed, on it own scale, it has set up an organization allowing very different professions (clinicians, biologists, modeler, IT specialists, web specialists, database managers, trainers) to cooporate in projects of European scope (ELIXIR, RDA, etc.) In addition, the IFB has developed shared IT infrastructures, the primary purpose of which is precisely to meet the computational needs of biologists and clinical researchers. Finally, and perhaps above all, the "FAIRification" (Findable, Accessible, Interoperable and Reusable) of tools and data at European level is one of its primary objectives.

In this newsletter, you will also find a focus on Galaxy France initiaves, as well as upcoming Actions, Training and Events. 


 

Christophe Antoniewski, on behalf of the Task-force Covid-19

 

IFB HIGHLIGHTS

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The Covid-19 Task Force of the IFB focuses its efforts  around the following operational objectives: 
  • Developing a web portal of French resources for Covid-19, which will be federated with ELIXIR resources and EBI COVID-19 Data Portal and linked to international resources (bio.tools, TeSS).
  • Providing rapid support to COVID-19 research projects by connecting them to computational resources (NNCR) and appropriate expertises in the IFB (reference pages web covid 19).
  • Fostering collaborations between the relevant actors: Inserm, CNRS, Aviesan, REACTing, HAL, RDA, etc.
  • Beyond, the Task Force will adapt the IFB's fundamental objectives to the context of Covid-19: FAIRification of data and tools.

Different actions will help achieve these objectives: definition of annotation standard and specifications, user support to enhance data annotation quality, facilitation of data submission to open access databases, training courses, hackathons, annotathons, responses to calls, etc.

These are complex and time-consuming tasks, but they also represent an opportunity to show the value of the IFB, to provide significant support to researchers committed against covid-19 and, beyond that, to be in solidarity with our society. We need you all ! 

 
Celebration of the 35 most cited Paris Saclay University scientist in 2019

We are proud of Hadi Quesneville (URGI - INRAe) is in the group of 35 highly cited scientists from Paris-Saclay University

Survey by the Committee for Open 

A survey is available on the uses and practices of digital tools among researchers in France. It should be open until the end of the month and you are invited to answer and disseminate it

 quick tour of the FRENCH GALAXY INSTANCES 

Generalist main domain for NGS analysis. Different French teams are developing and deploying customised instances of the Galaxy platform, which can serve a broad diversity of researcher communities. Since April 2020, IFB has deploys a national portal available to all communities, which will also serve as entry to the specific instances
 
ProteoRE (Proteomics Research Environment) is a Galaxy-based instance for the interpretation of proteomics and transcriptomics data for biomedical research. 21 tools allow researchers to apply a large range of dedicated bioinformatics tools and data analysis workflows, share their analyses, and enable reproducibility while keeping tracks of the overall process
 
 
The user-friendly pipeline FROGS (Find, Rapidly, Otus with Galaxy Solution) analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. It produces abundance table of OTUs and their taxonomic affiliation


PiRATE

A Pipeline to Retrieve and Annotate Transposable Elements. Each tools used by PiRATE are automated into a stand-alone Galaxy. This PiRATE-Galaxy can be used through a Virtual Machine, which can be download here

 
Thematic subdomain dedicated to metabolomics analysis
 
Dedicated to RNA-seq analysis and local bioinformatics tools (kissplice,/TEtools, priam_search, kissplice/kissDE)
 
Generalist NGS domain and local NGS tools 
 
NGS data analysis and microbial genomics
 
A Galaxy instance dedicated to small RNA (miRNAs, siRNAs, piRNAs, tRFs, viral RNAs, ...) analyses and functional genomics
 
A catalog of bioinformatic tools available across a collection of public Galaxy instances
 


 

Other tools

A new release v.1.2.0 of CulebrONT pipeline is now available. CulebrONT is a snakemake pipeline to prokaryotic or eukaryotic genome assemblies using oxford nanopore technology. Check the SouthGreen platform repository and documentation A new version of SouthGreen platform tool GreenPhylDB has been released with 46 plants. A key innovation is the support of 19 pangenomes as a first step toward comparative pangenomics.


 

 ELIXIR PROJECTS AND EUROPEAN INITIATIVES 


Ensuring that EU-funded coronavirus research results are accessible to all. View supporting organisations, download and endorse the manifesto

IFB actively participates to the European Data Portal and ELIXIR federation of Covid-19 Task Forces

EOSC-Life launches 2nd Training Open Call

Apply bv November 13, 2020 for funding for development and delivery of courses and capacity building


Implementation Studies
 
The ELIXIR Galaxy Community is addressing an new Implementation Study call. The plan is to focus on data management in Galaxy. If you have any interest in this topic, let us know


 EVENTS

 
European Research and Innovation Days
From September 22nd to 24th, 2020 - Online.

Niklas Blomberg will introduce ELIXIR's work with a specific emphasis on health data and Covid-19. Join the panel discussion on September, 23rd, Hub3 Digitalisation at 10:30 am CEST. 


Best Practices in Research Data Management and stewardship Workshop

ELIXIR-FR and ELIXIR-LU are pleased to announce this online event. This training takes place on October, 5th to 8th 2020 at 9:30 to 12:00 CEST. The registration is free but compulsory


 

Job vacancies

Business Development Officer

IFB-core platform


Biostatisticians and/or bioinformaticians 

The C3BI platform (Institut Pasteur) offers 4 opportunities


IE CDD in bioinformatics

Fixed-term contract at the Reproduction and Development of Plants Laboratory ENS in Lyon


IR CDD at the ARTbio plaform

Bioinformatics of Genomic Variants in Children and Young Adults with Acute Myeloid Leukemia 


Training and Outreach

University Diploma in Integrative Bioinformatics (DUBii)

The next session of the DUBii will take place in March 2021 (courses in Université de Paris) and in April-May 2021 in IFB platforms (tutored personal project of trainees). Applications are open until November the 15th. IFB Contact


Bioinformatics for the processing of sequencing data (NGS)

Understand the principles of high throughput sequencing data analysis methods, and understand the results obtained, the parameters and their impact on the analyses. This training will take place from 21st to 25th September in Montpellier, organised by the LIRMM and the ATGC platform.


CNRS Workshop Single-Cell 2020

The third edition of the Training Workshop, focusing on the study of heterogeneous cell populations from a genomic, transcriptomic and epigenomic point of view, will be held from September 27th to October, 2nd 2020, at the Roscoff Biological Station.


9th AVIESAN - IFB - Inserm school of bioinformatics

Initiation to the processing of genomic data obtained by high-throughput sequencing (NGS) from 4th to 9th October 2020 at the Roscoff Biological Station. This edition of the school, structured around three thematic worshops in parallel sessions (RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq), tackles new technolohical challenges (data integration, factorial methods for integrative analysis). It includes a personalised tutorship customized to each participant's projects (Bring Your Own Data). 


Molecular phylogeny - advanced training

Three days of training, from October, 5th to 7th 2020, in Montpellier, to be able to test hypotheses, adjust models and understand evolution on a molecular scale.


Transposable Elements annotation and/or manual curation training

From November, 24th to 27th, 2020 in URGI-INRAe, Versaille. Deadline for pre-registration: October 1st, 2020. 


The ABiMS platform

ABiMS has planned its next training session which will take place coming November and December. It will include the following modules: Linus for Beginners, Advanced Linus, Cluster Usage, Git for Beginners, R for Beginners, Statistics with R, Galaxy for Beginners. Contact 


Training material for ProteoRE

It's available via the Galaxy Training Network and TeSS



Publications


Characterization of accessory genes in coronavirus genomes. Virology Journal, 2020. 


Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. Rice 13, 2020.