Short description of BAMBOO, the Inria Project-Team that preceded ERABLE
The application of mathematics to biology has a very long history, much longer than the relation between computer science and genomics that in the late twentieth century gave birth to the terms of bioinformatics and computational biology. Although its experimental part prevented many from getting much involved with the discipline, biology has held a deep fascination to people with a mathematical mind. Beyond the much expressed cliché that computers are essential to analyse the huge masses of data being produced by sequencing and other high-throughput experiments, it is the high level combinatorics underlying most of life processes that has cast a spell on the imagination of mathematicians and computer scientists alike. The combinatorics of life is unexpectedly diverse and its complexity goes much beyond what any human imagination could or would wish to consider. Polymorphisms within a same population add another level of difficulty that may lead one to legitimately wonder if living systems have a structure simplifiable into some general principles.
Bioinformatics and computational biology as such are reaching a stage where they stand poised to go in different directions. On one hand, increasing computing power is indeed required and may be attained by the production of more efficient software or hardware. On another hand, the need to get at simplified representations of biological systems remains as acute as it was more than three hundred years ago when some of the first mathematical models were proposed (by Thomas Malthus) to better understand populational biology phenomena. The route adopted by BAMBOO attempts to deal with the huge amount of data and with the broadness of picture this offers, while at the same time trying to arrive at increasingly more detailed models, and thereby at a better and finer understanding of biological systems at any scale, from genotype to phenotype, and back.
This route has broad exploratory objectives that are as model- or hypothesis-free as possible, and aims to bring to light unexpected or contradictory knowledge. This is a first objective of BAMBOO. There is however enough structure, at different levels, in the data to arrive in a step-wise manner at an increasingly more detailed and realistic picture of the various processes that, alone or in relation with others, create and maintain life. The route therefore asks for a constant dialog between exploratory forays into the data, and precisely defined and controlled statistical or experimental investigations. We do not aim to arrive at models as detailed as those obtainable for small scale systems although some such could be attained in a few cases. Our goal, and this will represent the second main objective of BAMBOO, is rather to arrive at an accurate even if rough scaffolding model that could provide a more precise and complete picture of biological systems than has been tried before. Evolution will represent both the main investigative means to arrive at such a general model and a major purpose of the undertaking, together with getting at biological function. Evolution will be understood in a very general sense, that is, classically as the changes selection imprints on the molecular texts, and, something which is less usually considered, as the changes on the way such texts are read by the cellular machinery. Moreover, we shall attempt to take into account not just the genetic but also the epigenetic (heritable but not encoded in the DNA sequence) and cultural variations that have taken place in the history of life.
- Arriving at good models for the different questions addressed that are both biologically realistic and mathematically well-defined and elegant
- Designing combinatorial and stochastic text, tree and graph algorithms that are efficient (complexity analysis) and practical (software development)
- Developing good theories for random models in a biological context
- Maintaining a constant dialog with wet-lab experiments
The main objectives of BAMBOO are impossible to reach if they do not involve people from both the theoretical and experimental parts of biology and of such related areas as biochemistry, from various backgrounds and specialities within mathematics, and from both theoretical and practical computer science. The team is therefore strongly interdisciplinary and gathers people from the INRIA Grenoble – Rhône-Alpes, the Laboratory of Biometry and Evolutionary Biology (LBBE – CNRS UMR 5588) at the University Claude Bernard, Lyon 1, and the Functional Biology, Insects and Interactions Unit (BF2I) at the National Institute of Applied Sciences (INSA) of Lyon. BAMBOO is located at the University of Lyon 1 and INSA Lyon, both on the Doua Campus of Lyon.
The biological and biochemical expertises in the team range over all the kingdoms of life, bacteria, archea and eukaryota including the so-called higher species such as vertebrates, and cover also deep knowledge of symbiotic systems that are essential for understanding evolution and function (symbiosis refers to the long-term interaction between two organisms). It ranges from field and experimental aspects to theory. The methodological (mathematical and computational) expertises concentrate around text and graph algorithmics, and combinatorics, with strong components in modelling (discrete, stochastic and dynamic), computational and statistical data analysis, statistics, and knowledge representation.
Main international relations
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Computação e Estatística, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
- Laboratório Nacional de Computação Científica, Ministério da Ciência e da Teconologia, Petrópolis, Rio de Janeiro, Brazil
- Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Firenze, Italy
- Dipartimento di Informatica e Sistemistica, Università di Roma “La Sapienza”, Roma, Italy
- Dipartimento di Informatica, Università di Pisa, Pisa, Italy
- Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Centrum Wiskunde & Informatica, Amsterdam, Netherlands
- Knowledge Discovery and Bioinformatics Group, INESC-ID, Instituto Superior Técnico, Lisbon, Portugal
BAMBOO stands for Biology, Algorithmics and Mathematics, Besides Other Occupations that hold the attention of any scientist and enable him/her to pursue his/her research objectives. As a vegetal, bamboos are the fastest growing woody plants in the world. Their growth rate (up to 60 centimeters (24 in.)/day) is due to a unique rhizome-dependent system, but is highly dependent on local soil and climate conditions. Bamboos have a variety of uses, for cuisine, medecine, construction, etc. They may serve as musical instruments, such as a flute. Didgeridoos, which are wind instruments of the Aborigines of northern Australia, are also sometimes made of bamboo. May its music, like that of BAMBOO, please your ears.