Galaxy services

Sigenae's Galaxy instance: from system administration to software engineering

Galaxy (https://galaxyproject.org) is an analysis web interface whose development began in 2006-2007 with a first version distributed in mid 2010. It is actively maintained by the "Galaxy project" team at Penn State, Johns Hopkins University, Oregon Health & Science University for people who want to process (bio)computer data without specific computer skills.
The four main objectives of galaxy are: accessible, reproductible, transparent genomic science, and community centered.

An active community around Galaxy develop tools and share within the Galaxy ToolShed.
Galaxy can be used by researchers in different ways : on their personnal computer, or via remote web servers. A free public web server Galaxy is provided by the Galaxy Project, but for production environment with huge amount of data and heavy computations, the best is to setup a local instance of this web service, closer to our local data storage et HPC cluster.

System administration services outside Galaxy.
Many of the projects carried out by Sigenae have their deliverables presented via a website, hosted on virtual machines managed by Sigenae.
Sigenae can also advise users on the IT infrastructure to be put in place to meet their needs, or even set it up in collaboration with Genotoul BioInfo.

Sigenae software engineering: a question of granularity.
Software development at Sigenae is goal-driven. If software building blocks already exist to conduct bioinformatics analysis, a workflow type development will be favored. If there are missing software building blocks, they will be developed in the language best adapted to the type of processing.
In some cases, we rewrite a software solution for performance reasons. Optimization can simply consist of a change of programming language, better input/output management, use of databases, parallelization by splitting the input data files into sub batches if possible, or by fine parallelization (multi processing, multi threading).

Sigenae's role is therefore not limited to bioinformatics analysis and presentation of results, the team is able to develop and implement complete IT solutions to meet the needs of the researcher.