Keywords: Algorithmes ; bases de données ; modélisation ; bioinformatique ; imagerie biologique ; génomique ; transcriptomique ; proteomique ; agronomie ; cancer ; pathogènes ; morphogénèse
Since october 2012, the Institute of Computational Biology (IBC) is an inter-disciplinary institute involved
in research, development, and education in the field of computational biology. IBC develops innovative meth-
ods and software to analyze, integrate and contextualize large scale biological data in the fields of biology,
health, agronomy and environment. IBC is a multidisciplinary research center that brings together the forces of
Montpellier area in computational biology. Over the years, 64 permanent researchers, 21 postdoctoral fellows,
more than 44 PhD students and engineers have participated to our research initiatives. The initial consortium
included 14 labs and one company Accobiom, but over time 3 more labs joined us and a startup company Se-
qOne was created.
Research was organised in five areas (corresponding to workpackages of the initial project):
1. HTS: Methods for high-throughput sequencing analysis
2. Evolution: Scaling-up evolutionary analyses
3. Annotation: Structural and functional annotation of proteomes
4. Imaging: Integrating cell and tissue imaging with Omics data
5. Databases: Biological data and knowledge integration.
These areas correspond to topics where computational challenges arise due to the needs for processing large
(sometimes huge) datasets. Indeed, recent dramatic technological improvements allow most life science labs to
acquire such data sets, the processing & analysis of which remains a bottleneck. The most confonding example
being the deluge of sequence data that has occured since the advent of Next Generation Sequencing techniques
Twice during the period, we have launched an internal call for research projects led by young researchers.
Seven subprojects were selected and funded.
Our goals were to develop algorithms, databases, statistical procedures, or models that we can turn into pro-
grams, software, or web-services, which can then solved questions arising in life sciences. As outcome, over
226 publications in international journals and proceeding of conferences were published during these almost 6
years in computer science, math or biology areas, and a some more are still to come (see our publication list).
Moreover, we have developed 40 software, programming libraries or R packages that are available to the end
users, mostly life scientists or engineers, and bioinformaticians. Some of these can be used directly for free as
web services (e.g. on the ATGC bioinformatics or on SouthGreen platforms) or through programmatic inter-
faces (as for ontologies portal AgroLD). Future efforts are planned to support those tools that attract numerous
users – some of our tools are clearly already exploited by the international community. Another outcome is a
maturation project launched in 2014 that gave rise to a startup company (SeqOne), as well as several software
licences. All planned deliverables, and some more, were completed.
IBC has become the privileged place for computational biology in the region, a fact that is strongly sup-
ported by the frequency and attendance of our seminars, the number of foreign visitors, the quality of appli-
cations received for PhD and postdoc grants. Thanks to offices provided by the University of Montpellier, we
could host well-known senior scholars as foreign visitors in very good conditions. For instance, researchers
from New-york and Barcelona have joined IBC after several visits, and we carry on collaboration with parisian
colleagues. IBC members have also received invitations as keynote speakers for major conferences. A lot of
efforts were dedicated to training students and to organized visible, both international or local, scientific events
such as summer schools, workshops, hackatons and conferences (~20 altogether, not counting the annual IBC
IBC members have launched and head complementary projects funded by ANR, European Commision, the
Fondation pour Recherche Medicale, the Association for Cancer Research, or Agropolis Foundation (and much
more). About 10 of these large projects are on-going as of november 2018 and some will last till 2023. IBC
was privileged to get feedback from an external scienfific board, the members of which we thank for their avail-
ability, help, and comments. As the IBC board has collaborated to the writting and conception of the MUSE
Excellence initiative project, we hope that the IBC can carry on its tremendous scientific work within this new
framework in the future.
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
Reference Number: 11-BINF-0002
Project Region: Occitanie
Discipline: 5 - Bio Med
PIA investment: 2,000,000 €
Start date: September 2012
End date: September 2018
Project coordinator : Eric RIVALS
Etablissement coordinateur : Université de Montpellier
Partenaire(s) : CNRS délégation Occitanie Est, CIRAD - Paris, INRIA Sophia Antipolis (Valbonne), IRD Marseille, INRA Montpellier, Acobiom