Tool assembly: IFB
What is the IFB data management tool assembly?
The IFB is the French national Bioinformatics Infrastructure that supports research projects in Life Sciences by provisioning a bioinformatics environment, which consists of IT infrastructure (such as storage and computing resources), software and training, distributed across the country. The IFB federates around 20 bioinformatics platforms which make physical, operational and human resources available to researchers in a synergistic and efficient way. Each platform brings its own IT infrastructure and bioinformatics expertise to create a better support network, distributed over the country, for Life Sciences research activities.
IFB data management tool assembly supports data management activities of scientists during all the phases of their projects, from planning to publication.
Who can use the IFB data management tool assembly?
IFB and the underlying infrastructure are accessible to researchers in France and their foreign collaborators. Researchers that would like to know more about IFB services can find specific contact details at the unified IFB help desk page and get support through the dedicated help pages. Depending on the resources, fees may apply. It is therefore advisable to contact them during the planning phase of the project.
The way you can access the IFB depends on the type of resources (for instance, cluster or cloud), and there will be different authentication procedures (local, national or international). For example, the Biosphere cloud federation uses the EduGAIN federation for authentication, while useGalaxy.fr uses the ELIXIR AAI authentication. To have additional information on how to access the IFB contact the help desk.
For what can you use the IFB data management tool assembly?
Data management planning
IFB recommends DMP-OPIDoR or DSW as tools for writing a Data Management Plan (DMP).
DMP-OPIDoR is hosted and maintained at Inist-CNRS and is tailored to meet the needs of many French academic institutes. You will find many DMP templates, in French and/or English, created by funders and academic institutes. A dedicated team offers training and support for DMP templates and DMPs. They can be reached via this contact form. The machine actionable version of DMP-OPIDoR allows the production of structured standardized DMP content. It enables the integration of information from funding agencies such as the French National Agency (ANR), and also integration and interactions with computing infrastructures provided by IFB and Genci, the organization in charge of the three supercomputing centres in France. DMP OPIDoR is freely accessible to anyone. First, one has to create an account (login, password). Then this account can be linked to the Renater identity federation. For support about OPIDoR, you can check the cat-OPIDoR support providers page.
DSW is a tool to collaboratively compose data management plans through customisable questionnaires. IFB has used DSW to develop templates for France Bioimaging (FBI data management plan) and for Hosted Scientific Service Management Plan (HSSMP).
Although they are not part of IFB, other infrastructures in France can also help you generate new data. Specifically, some facilities can assist you with in vivo and in vitro experiments, synthetic biology, omics techniques, imaging, structural biology and other techniques and expertise. To find the adequate facility you may use the Ministry search engine or the IBiSA directory of french facilities in Life Sciences.
Once your data have been generated by the facility, you will need to transfer it to your local system or to the IFB infrastructure, if you intend to use the IFB’s compute services. In both cases it is a good practice to get in touch with IT support (local or IFB), especially if the volume of your data is large.
If you have to reuse previously generated data, keep in mind that the different IFB platforms provide many specialized databases. A list of the databases is available here. These databases are, for the most, freely available.
To support data collection along with standard metadata, IFB is providing SEEK instances available at URGI and GenOuest.
Data processing and analysis
IFB infrastructure gives you access to several flavours of computing resources, according to your needs and expertise:
- Several clusters hosted either at IFB-Core or on any of the member platforms. You can request accounts on any of the member clusters.
- The Galaxy France portal operated by IFB members in complement of the Galaxy Europe.
- The cloud federation Biosphere allows the deployment of ready-to-use appliances (virtual machines with all required software installed for analysis) for several scientific domains (Genomics, Bioimaging, Metabolomics, etc.). A list of the different appliances is available on the RainBio catalogue. You can log in here using your academic credentials.
Each of the computing resources offers its own storage solution tailored for the needs of the users (fast access, capacitive). You may have to choose a resource according to what its service offers and also according to its proximity to your own location in order to benefit from better support and also better data transfer speed.
IFB infrastructure can also help you with bioinformatics analysis of your data. Many of the IFB member platforms can provide expertise for data analysis in many domains (genomics, metagenomics, transcriptomics) as well as software development. To check the expertise of the platforms, you can use this catalog. A list of the tools developed by all IFB members is available here.
Data sharing and publishing
It is good practice to publish your data on repositories. IFB encourages researchers to browse the list of ELIXIR deposition databases for biomolecular data to find the appropriate repository.
The french scientific community benefit from Recherche.Data.Gouv a national Dataverse repository. This repository is associated with thematic reference centres and data management clusters. IFB is the reference centre for Life Science.
If you are a member of INRAE (one of the stakeholders of IFB infrastructure), you can access the institutional instance of the Dataverse platform Data INRAE. Data INRAE can be used by researchers to store and describe datasets during the project, and to share them according to specific sharing settings.
You can also browse cat-OPIDoR for an overview of the different services related to data management provided by IFB infrastructure and its stakeholders in France.
Compliance monitoring & measurement
IFB infrastructure promotes the implementation of the FAIR principles. To this end, IFB provides and encourages the use of the FAIR-Checker, a web interface aimed at monitoring the level of FAIRification of data resources. This tool uses the FAIRMetrics APIs to provide a global assessment and recommendations. It also uses semantic technologies to help users in annotating their resources with high-quality metadata.
How to write a Data Management Plan (DMP). Data organisation
Best practices to name and organise research data. Data storage
How to find appropriate storage solutions. Data publication
How to prepare data and find repositories for publication. Documentation and metadata
How to document and describe your data. Data analysis
How to make data analysis FAIR.
Relevant tools and resourcesSkip tool table
|Tool or resource||Description||Related pages||Registry|
|DATAVERSE||Open source research data respository software.||Data storage Researcher Data Steward: research Data Steward: infrastructure||Training|
|ELIXIR Deposition Databases for Biomolecular Data||List of discipline-specific deposition databases recommended by ELIXIR.||Data publication Researcher Data Steward: research Data Steward: infrastructure COVID-19 Data Portal NeLS CSC||Standards/Databases|
|FAIDARE||FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI.||Researcher Data Steward: research Plant sciences Plant Phenomics Plant Genomics||Tool info|
|FAIRDOM-SEEK||A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes.||Data storage Data Steward: infrastructure NeLS Microbial biotechnology Machine actionability Plant Phenomics Plant Genomics||Tool info Training|
|Galaxy||Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.||NeLS Marine Metagenomics Data analysis Researcher Data Steward: infrastructure Galaxy||Tool info Training|
|OpenStack||OpenStack is an open source cloud computing infrastructure software project and is one of the three most active open source projects in the world||Data storage Data analysis TransMed||Training|
|PHIS||The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis.||Plant Phenomics Plant sciences||Training|
Online questionnaire for the development of data management plans - repository of DMPs.
|Researcher Data Steward: research Data management plan|