BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing in bioinformatics field. The software automates the update cycle and the supervision of the locally mirrored databank repository.
It is made of 2 packages, biomaj and biomaj-watcher.
Biological knowledge in a genomic or post-genomic context is mainly based on transitive bioinformatics analysis consisting in an iterative and periodic comparison of data newly produced against corpus of known information. In large scale project, this approach needs accurate bioinformatics software, pipelines, interfaces and numerous heterogeneous biological banks, which are distributed around the world. An integration process that consist in mirroring and indexing those data is obviously an essential preliminary step which represents a major challenge and bottleneck in most bioinformatics projects; BioMAJ aims to resolve this problem, by proposing a flexible and robust fully automated environment.
Biomaj package is the core of the software. It is in charge of downloading some data from a remote or local site via different protocols (ftp,http,...), and to apply some processes on downloaded data.
In case of error, a new update can be launched on failed process, without redownloading all the data. A console and a command-line interface display the status of each data bank, its location, size...
the watcher is the web front-end of the core software. It provides a cron management to automate the updates, a direct access to update logs, display status and statistics on data banks. Anonymous users can have read access to the list of the banks. Authenticated users (local or ldap) can edit bank properties, create transformations workflow...
Community resource sharing
The web site of biomaj provides many bank property examples as well as a number of post-process programs for common bioinformatics tasks (blast indexing, emboss ...). Those files come from the software team but also from the Biomaj community (http://biomaj.genouest.org/?page_id=22)
Software and information are available at:
Source code is available at:
This project is a collaborative effort between two French Research Institutes INRIA (Institut National de Recherche en Informatique et en Automatique) & INRA (Institut National de la Recherche Agronomique).
Active Contributors are:
- Romaric Sabas ( Plate-forme genouest – INRIA ), Olivier Sallou ( Plate-forme genouest – INRIA ), David Allouche (Unité de Biometrie Intelligence Artificielle – INRA ), Olivier Collin ( Plate-forme genouest – INRIA )