Lessons learned from developing a framework for biologists
ASaiM logo

Bérénice Batut — October 16th, 2015

PhD thesis in bioinformatics and computational biology

  • Contribution to aevol project
  • Development of simple Python scripts

Post-doc in bioinformatics

  • Development of ASaiM project
# ASaiM project
## Objectives Development of a bioinformatics environment to analyze data from gut microbiota

Gut microbiota

Gut microbiota

Community of microorganism species that live in the digestive tracts

"Forgotten" organ

Metagenomic: study of microbiota

### Complexity * Short sequences * Sequence variability * Uncomplete reference databases *Need for numerous treatments to extract useful information*
Example of workflow to sort sequences given their type
Example of workflow to sort sequences given their type
# ASaiM framework
Bioinformatics framework to generate workflows to analyze data from gut microbiota
### First tested approach Simple Python scripts
### Third tested approach Homemade approach * Configuration file * Workflow description * Web interface for generation * Python scripts to execute workflow in configuration file
### Final approach Galaxy * Open-source project based on Python * International development community * Web interface * Galaxy Tool Shed
### ASaiM framework * Configuration of a Galaxy server * Development of wrappers for tool integration * Development of scripts to use Galaxy and API