Within the CEBA, ongoing research aims at making available for researchers a set of mathematical and computing tools in order to facilitate the treatment of biological data. A working group in mathematics and informatics applied to biodiversity (MIAB) was set up to meet these growing needs, in particular with the ‘Virtual Biodiversity Lab’ project developed and supported by the CEBA.
This should advance knowledge on Amazonian biodiversity more rapidly.
Make computer tools available for the CEBA community, essentially to support ecology and epidemiology, and then enhance and extend them progressively according to scientists’ needs. This is the aim of the approach selected by the team made of four researchers and engineers from the Biogeco laboratory and members of the CEBA: Alain Franc (coordinator), Philippe Chaumeil, Jean-Marc Frigero and Yec’han Laizet.
The team develops several tools:
– databases: for example, a database on French Guiana trees was designed, in collaboration with Daniel Sabatier and Jean-François Molino, researchers at the Amap laboratory, to which the Cayenne herbarium is attached, and Henri Caron (Ecofog laboratory), all members of the CEBA. This database was made available for CEBA members and is accessible of the websiste of the Réseau de Systématique (Systematics network) called R-Syst1. A researcher can question the database to identify an individual with its DNA sequence.
– applications that process large volumes of data like DNA sequences. When combining for instance the applications Disseq (distance measuring) and Delic (visualisation), the user can check if the hierarchical structure of diversity suggested by taxonomy is coherent with the distances between DNA sequences. The calculated result is presented in the form of a graph in MDS (Multidimensional Scaling) with series of dots with the same color, corresponding to closely-related taxa in terms of phylogeny.
Note that Disseq is one of the three pilot applications that were deployed with the recently-launched E-Biothon2 platform.
Screenshot – result of the calculation made by the application Declic on 1000 individuals of French Guiana tree, leading to the positioning of ten families. We note a mix of both continous and cluster structures.
© Alain Franc & al. – Biogeco
To facilitate the use of these tools, the team of researchers offer a shared computer working environment, that can be adapted according to the needs, via a simple web portal. These tools created within the ‘Virtual Biodiversity Lab’ project are available on the Galaxy3 server which is already used by the Genome-Transcriptome facility of Bordeaux (PGTB). This server proposes standard tools, as well as those specifically created by the MIAB working group and by the PGTB.
The online access is simple and practical: no need to use the computer’s random-access memory (RAM) nor its processing power. As for the Next-generation sequencing (NGS) data, their treatment requires high-performance computing resources, that are available neither in the laboratories, nor on the Galaxy server. Yec’han Laiezt is now working to build gateways to high-capacity computer platforms. The aim is to make the data treatment imperceptible for the user: he accesses the tool without wondering about the complex computer process that are hiding behind.The platform evolves thanks to the users’ feed-back on their needs concerning the software to the MIAB team. The team then develops specific applications.
Thus, the CEBA members have the opportunity to characterise French Guiana biodiversity more rapidly and reliably. This applies to ecology with the study of plants, fungi and amphibians for example, but also in epidemiology in order to identify the viruses in some species as well as species that play a role of vectors in the transmission of some diseases.
The MIAB research group presented its works several times to the CEBA teams, during specific missions in French Guiana and during the annual CEBA meetings in 2012 and 2013. The researchers who work on molecular taxonomy have positive feedbacks and already use the available tools, that will diversify.
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Contact:
Alain Franc, coordinator of the MIAB working group
alain.franc@pierroton.inra.fr, 0033 557 122 813
Useful links:
1. R-Syst: http://www.rsyst.inra.fr/fr/content/le-r%C3%A9seau (Open-access database starting today)
2. E-biothon press release: http://www2.cnrs.fr/presse/communique/3313.htm (in French)
3. Galaxy server: https://galaxy-pgtp.pierroton.inra.fr/
