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Thursday , December 10, 2020

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Newsletter IFB brief
Institut Français de Bioinformatique news

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Dear colleagues, 

Conceptualizing the research life cycle as embedded in an Open Science culture is slowly gaining traction in all aspects of our lives as researchers and engineers. Open Science may be defined as 

It [Open Sciencerelies on the combined effects of technological development and cultural change towards collaboration and openness in research.

If anything, even if unfortunately, this momentous year of 2020 has shown us the critical necessity of mutualising our efforts and resources towards a common goal, that of apprehending the Covid-19 pandemic. Beyond the obvious benefits of the shared endeavours, exemplified by the IFB, ELIXIR, the RDA and many others, we know that transparency is the foundation of trust: the ultimate incentive for fostering and consolidating an Open Science philosophy and adapting our practices to it. 

Mutualisation of resources and the subsequent offer of services to the life science community is the core of IFB's purpose. The many services currently proposed are the embodiment of this commitment to collaborative practices and openness; they thrive to support and grow the Open Science culture of our community.

We acknowledge that the demand is huge and utterly diverse, but we keep consolidating our portfolio of all things open and FAIR (tools, infrastructures, training, news, ...). We are planning to implement and deploy an IFB portal dedicated to Open Science, a portal whose primary audience will be our end-users. Its aim will be to accompany scientists in the management of their scientific data , from the drafting of the data management plan to the brokering processes concluding the data life cycle. The portal is also intended as a repository of resources related to Open Science, and a collaborative space for the community. 

This will be the last newsletter for this year, and what a year ! We are left to wish you, your loved ones, your friends, your colleagues, a good and healthy transition into the year to come. We are looking forwards to meeting you on the other side of 2020 ! 
 

Paulette Lieby, Thomas Denecker & Jean-François Dufayard 

 

IFB HIGHLIGHTS

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Practical course : Bioinformatics investigation about SARS-CoV-2 origins
 
The phylogeny of coronaviruses was used as a study case for a course on phylogeny inference addressed to students of a Bachelor in Sciences and Humanities. This course reproduces the analyses and figures of the article "Tracing the origins of SARS-CoV-2 in coronavirus phylogenies" published in French and in English (in press). It covers the classical basic concepts of first course in bioinformatics: biological databases, pairwise alignments, sequence similarity searches, multiple alignments, tree inference. The teaching material (data, tutorials) has been conceived to be re-usable, and is available here 
 
 
PIPprofiler tool
 
Profiles of Percent Identical Positions (PIP) have been recently used in many publications about coronavirus phylogeny. Thomas Denecker ans Jacques van Helden, Hélène Chiapello and François Gerbes developed and deployed a user-friendly and highly interactive web tool to generate PIP profiles between a reference sequence (e.g. the full genome of SARS-CoV-2 or the sequence of the spike protein) and a set of query sequences (e.g. a selection of coronavirus genomes, or their spike protein sequences). The tool can be used online via shiny server running on the IFB-core cluster, and as a cloud appliance on BioSphere. A cloud instance has been used for the course "Bioinformatics investigation about SARS-CoV-2 origins" (see above) and it ran swiftly with a group of 20 students

 
How FAIR is my data?
 
The IFB interoperability working group is happy to share with you the FAIR-checker web tool. It allows to systematically evaluate your favorite web resources against a set of FAIR maturity indicators. It provides recommendations to enhance the FAIRness of your resources, as well as a framework to propose new metrics. The code is open-source and available here. We are welcoming any feedback and potential contributions
 
 
In Novembre 2020, the CNRS Research Data Plan was released, which is in line with the need to accelerate development towards Open Science. This document should be considered as a framework to take in consideration for IFB future projects

 
IFB General Assembly 2020 
 
The IFB's General Assembly took place on 26 November 2020. The morning session was open and devoted to a selection of highlights. The afternoon session was reserved for IFB member platforms. Find all the slides right here 



 
Creation of the LIRMM, to which the ATGC platform is attached, PEWO can be easily extended by community developers whenever a new tool is published or made available. Recently, a group of researchers from Germany proposed and implemented the integration of the tool App-Spam. Only a few months after PEWO release, App-Spam is now part of PEWO
 
 
The Prospective Symposium on Data Science, Artificial Intelligence and Biology organised by the CNRS took place on 2 December 2020, in which the IFB was particularly involved, especially as the institute will launch several activities related to AI in 2021. The slides are available here, and the videos of the keynote talks will soon be available
Oxford Nanopore Seminar series 
Julie Orjuela (IRD, South Green) was invited to present Culebront in the seminar entitled "Analysis pipelines for nanopore sequence data" on the 6th October 2020. The video is available here




 

 ELIXIR PROJECTS AND EUROPEAN INITIATIVES 


Every week, news about the European bioinformatics community of ELIXIR can be found, including the initiatives of each member node. In the last weekly brief, you will find the new ELIXIR podcast "Venture into standards - lessons from the toilet paper industry"

 
The Swiss Institute of Bioinformatics (SIB) which is also the Swiss node of ELIXIR, reshaped their bioinformatics portal, which provides a convenient access to >160 bioinformatics databases and software tools in different domains including several new Covid-19 resources

 
It covers various topics of interest for bioinformatics training: Summary of GOBLET AGM 2020; Education Summit 2020 & 2021; Member Highlights: 2020 Bioinformatics Community Conference (BCC2020); Bioinformatics Critical Guides & Pratical Guides

 
This report scopes the issue of the reproducibility of scientific results, based on a field review and on an expert seminar on the opportunity of policy action in Europe

 
New publishing Platform by European Commission 

The EC will launch the Open Research Europe (ORE). It will be a scholarly publishing platform that will provide Horizon 2020 and Horizon Europe beneficiaries with a no-cost full open access peer-reviewed publishing service. It will span across all fields of research

 
Report of the sixteenth plenary of the RDA virtually held in Costa Rica, November 2020. Find here the general overview, the tab/chairs sessions, and the conference sessions

 EVENTS

 
Biogenouest Webinar

On December 15th, Biogenouest is organising a scientific day around the FAIR bioinformatics axis "FAIR tools and environments for bioanalysis"  


Plant Data Management webinar

This presentation will cover the usage of MIAPPE, which has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plan scientists in the management of experimental data. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples 


FAIRplus Innovation and SME Forum

The 2nd FAIRplus Innovation and SME Forum is aimed at companies working with life science data or planning to provide FAIRification services, and anyone interested in FAIRification of their data


ELIXIR-UK All Hands 2020

The annual ELIXIR-UK All Hands brings together people working at ELIXIR-UK consortium member institution for this two-day meeting: 10 & 11 December 2020 - Virtual


Montpellier Omics Days 2021

The 9th edition of the MOD will be held on 9 and 10 February 2021. Due to the health crisis, the conferences and workshops will take place online


Paper Cuts Day

Galaxy organises an Worldwide Contribution Fest to fix annoying but easy-to-fix bugs



 

Job vacancies

Community liaison officer and project monitoring 
Evry, France

Head of documentary resources
Nomenclature of rare diseases and associated genes. Paris, France

PhD position
An association study by whole-genome sequencing (WGS) on inherited cardiac arrhythmia. Nantes, France

Biological data processing engineer, internal mobility position
Bordeaux, France



Training and Outreach

Python and the Pandas module for manipulating and processing data
27th until 29th January 2021, Montpellier. Contact


Admin training Galaxy 
25th until 28th January 2021, online



Publications
 
Tekman, M., Batut, B., Ostrovsky, A., Antoniewski, C. et al. 2020. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.  GigaScience.


Hufsky, F., Lamkiewicz,K ., Almeida, A., Navratil, V., et al. 2020. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.  Briefings in Bioinformatics. 


Guignon, V., Toure, A., Droc, G., Dufayard, JF., Conte, M., Rouard,M. 2020. Green PhyIDB v5: a comparative pangenomic database for plant genomes. Nucleic Acids Research


Vandenbrouck, Y., Pineau, C., Lane, L. 2020. The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology. J Proteome Res


Lagardère, M., Chamma, I., Bouihol, E., Nikolski, M., Thoumine, O. 2020. FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins Nature Scientific Reports 


Gautreau, G., Bazin, A., Gachet, M., Planel, R., Burlot, L. et al.  2020. PPanGGOLiN : Depicting microbial diversity via a partitioned pangenome graph PLOS Computational Biology 









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