ASaiM

Lessons learned from developing a framework for biologists


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

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

# 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