Biodiversity data

Virtual Research Environment

November 2024

Yvan Le Bras

Olivier Norvez

Scientific and technical coordinator
@PNDB  
@DataTerra  

Animation coordinator
@PNDB  
@DataTerra  

Table of contents


Reminder of the context and the issues


VRE : Kesaco ?


Process


Resources

Virtual Research Environment : reminder of the context and the issues

Virtual Research Environment : reminder of the context and the issues

Heterogeneity (data types, origin, standards) &
Diversity of “objects” to be linked together1

Loss of information over time2

Virtual Research Environment : reminder of the context and the issues

Computational reproducibility frequently refers to the ability to generate equivalent analytical outcomes from the same data set using the same code and software1.

[…] all raw data and metadata, code, programming scripts, and bespoke software necessary for fully replicating any analyses that lead to inferences made in a published study2.

Virtual Research Environment : reminder of the context and the issues


Data life cycle


FAIR Principles




Flux and stocks of data


Virtual Research Environment : reminder of the context and the issues

Earth is a complex system composed of subsystems involving physical, chemical and biological environments, characterized by interacting processes over a broad continuum of time and space scales.

Virtual Research Environment : reminder of the context and the issues

Gaia Data aims to develop and implement an integrated and distributed platform of services and data for the observation, modeling and understanding of the Earth system, biodiversity and the Environment.

 For more information: GAIA Data

Virtual Research Environment : reminder of the context and the issues

 For more information: GAIA Data

Virtual Research Environment : kesaco ?

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

“Research done through distributed global collaboration enabled by the internet, using very large data collections, terascale computing resources and high performance visualization” (Sir John Taylor – 2001)

“A VRE comprises a set of online tools and other network resources and technologies interoperating with each other to facilitate or enhance the processes of research practitioners within and across institutional boundaries” JISC definition

“Virtual Research Environments are innovative, web-based, community-oriented, comprehensive, flexible, and secure working environments conceived to serve the needs of modern science» Candela et al. 2013

  • Web based
  • Serve the needs of researchers communities (VRCs)
  • Open and flexible

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environments (VREs) are increasingly being used to support a more dynamic approach to collaborative working in systematics and taxonomy. Researchers who are not co-located are seeking to work dynamically together at various scales from local to international. These shared infrastructures are funded as VREs in Europe, Virtual Laboratories (VLs) in Australia and Science Gateways (SGs) in the USA and all have similar objectives.

Virtual Research Environment : kesaco ?

VRE, VL, SG…. ?

Virtual Research Environments (VREs) are increasingly being used to support a more dynamic approach to collaborative working in systematics and taxonomy. Researchers who are not co-located are seeking to work dynamically together at various scales from local to international. These shared infrastructures are funded as VREs in Europe, Virtual Laboratories (VLs) in Australia and Science Gateways (SGs) in the USA and all have similar objectives.

 For more information: LTER-Life

 For more information: BCCVL

 For more information: The science gateways research center

Virtual Research Environment : kesaco ?

Key aspects

  • Virtualisation (hiding complexity from the user);

  • access to useful resources such as datasets, software, computing power, instruments/detectors (the latter for control as well as data taking) and scholarly publications (including grey literature technical reports etc.) as well as collaboratively with other persons and organisations;

 For more information: EMBL-EBI

 For more information: Research Objects.org

Virtual Research Environment : kesaco ?

Key aspects

  • Virtualisation (hiding complexity from the user);

  • access to useful resources such as datasets, software, computing power, instruments/detectors (the latter for control as well as data taking) and scholarly publications (including grey literature technical reports etc.) as well as collaboratively with other persons and organisations;

  • interoperability across resources;

 For more information: LifeWatch ERIC

Virtual Research Environment : kesaco ?

Key aspects

  • Virtualisation (hiding complexity from the user);

  • access to useful resources such as datasets, software, computing power, instruments/detectors (the latter for control as well as data taking) and scholarly publications (including grey literature technical reports etc.) as well as collaboratively with other persons and organisations;

  • interoperability across resources;

  • support for the ‘researcher workflow’ from research idea (and checking the literature etc.) through observations/experiments to publication and subsequent discussion with citation and accreditation (maybe including management functions such as proposals and reporting to funders).

 For more information: Jisc

Virtual Research Environment : kesaco ?

Key aspects

  • Virtualisation (hiding complexity from the user);

  • access to useful resources such as datasets, software, computing power, instruments/detectors (the latter for control as well as data taking) and scholarly publications (including grey literature technical reports etc.) as well as collaboratively with other persons and organisations;

  • interoperability across resources;

  • support for the ‘researcher workflow’ from research idea (and checking the literature etc.) through observations/experiments to publication and subsequent discussion with citation and accreditation (maybe including management functions such as proposals and reporting to funders).

  • support for workflow composition (or even autonomic composition) of (2) and ideally deployment on virtualized resources (e.g. GRIDs, CLOUDs);

 For more information: Galaxy-Ecology

Virtual Research Environment : process

Virtual Research Environment : process

Choose the scale !

Virtual Research Environment : process

Then compose

Virtual Research Environment : process

issues

Virtual Research Environment : process

Personal vision

Virtual Research Environment : resources

Virtual Research Environment : resources

Collaboration oriented tools

Built on existing platform :

  • HUBzero (using Joomla)

  • Sakai (a first demonstrator project so old ;) )

  • VRE4EIC e-VRE

Specific VRE framework

Scientific articles

 biodiversitydata/vre   •    cc-by-4.0