Section: Scientific Foundations
A short introduction to bioinformatics
Studying life at macromolecular level (DNA, RNA, protein or metabolites) involves multiple researches in mathematics and informatics  :
Data and Knowledge management. Multiple technologies are producing raw data that have to be cleared and assembled into meaningful observations. It is the realm of statistical studies, with sophisticated normalization procedures, most of them being included in routine treatments. Information is produced in a highly distributed way, in each laboratory. Standardization, structuring of data banks, detection of redundancies and inconsistencies, integration of several sources of data and knowledge, extraction of knowledge from texts, all these are very crucial tasks for bioinformatics. High throughput techniques are also a source of algorithmic issues (assembling of fragments, design of probes).
Comparative genomics. Referring to a set of already known sequences is the most important method for studying new sequences, in the search for homologies. The basic issue is the alignment of a set of sequences, where one is looking for a global correspondence between positions of each sequence. A more complex issue consists in aligning structures. More macroscopic studies are also possible, involving more complex operations on genomes such as permutations. Genotyping studies consider Single Nucleotide Polymorphism data, which correspond to mutations observed at given positions in a sequence with respect to a population. Analyzing this type of data and relating them to phenotypic data leads to new research issues. Once sequences have been compared, phylogenies, that is, trees tracing back the evolution of genes, may be built from a set of induced distances.
From structural analysis to systems biology. This large domain aims at extracting biological knowledge from Xome studies, where X varies from genes to metabolites. Biological sequences and networks of components in the cell must verify a number of important constraints with respect to stable and accessible conformations, functional mechanisms and dynamics. These constraints result in the conservation during evolution of "patterns" and types of interactions to be deciphered. Many advanced researches consider now the study of life as a system, abstracted in a network of components governed by interaction laws, mostly qualitative or quantitative for reduced systems.