Tache 1 Construction d’un simulateur. Objectifs Disposer d’un simulateur d’une population présentant un déséquilibre de liaison historique, afin d’évaluer.

Présentation au sujet: "Tache 1 Construction d’un simulateur. Objectifs Disposer d’un simulateur d’une population présentant un déséquilibre de liaison historique, afin d’évaluer."— Transcription de la présentation:

1 Tache 1 Construction d’un simulateur

2 Objectifs Disposer d’un simulateur d’une population présentant un déséquilibre de liaison historique, afin d’évaluer les propriétés distributionnelles de statistiques de test préexistantes ou développées dans le cadre de R&T, ainsi que l’efficacité de protocoles expérimentaux.

3 L’engagement Programme: Starting from existing elements - LDSO, a simulator developed by F Ytournel during her thesis (Ytournel et al (2008)) ; routines developed by F Guillaume during his thesis on the dairy cattle MAS programme – a more versatile simulation program will be developed. The software aims at generating a population of individuals similar (in terms of pedigree, and, when needed of genotypes at markers) to an existing one. The founders of this population show Linkage Disequilibrium generated by a history of mutations, selection, crosses and drift (this history being parameterized by the user). All potential causes of LD are thus represented. The population history is simulated in two steps: from the origins (generation 0) to the first individuals belonging to the known pedigree (generation N), and from founders in generation N up to the last generation N+n (from which are chosen phenotyped individuals which are the support of the QTL detection design)

4 Les moyens Partners’ contribution : ST and DR will be in charge of the practical work (which will be a part of their thesis); JME and AR will supervise from their expertise in genetics and computing sciences; FG (and F Ytournel, now post doc in Germany, who kindly accepted to contribute) will provide their software resources and know how. Methods: The programming language will be FORTRAN 90, still largely used in our field, and corresponding to the elements already existing Risks and solutions : The only risk for this type of work is a delay as compared to the planed calendar. Extra force (from JME, AR and FG) will be put on the task if this risk occurs..

5 En gros c’est fini Travail Florence, Simon et Dana Publication (et droit de référence à R&T ?) Mais on devrait pouvoir faire mieux ? –Quels besoins ? Epistasie Historique avec plus de deux lignées Autres ? –Quelles démarches ? Approche par coalescence (Bertrand) Approche intra génotype