Software engineering activities involving ABiMS aim at providing targeted communities with applications or databases that closely fit their needs and cannot already be found on the market. The majority of software development deals with Web applications allowing local or remote research groups to browse, search or annotate scientific data. Stewardship of this data can be the responsibility of the ABiMS platform, but some Web applications also tap in existing reference data sources. Scientific domains related to software engineering activities include comparative genomics (the Cyanorak database), oceanography (High-Frequency data repository), biodiversity time series (the Pelagos database), or an integration effort of data from these domains (the Tara Oceans Data Portal). Moreover, development projects related to digital libraries have also been achieved by ABiMS : the Cahiers de Biologie Marine web application dedicated to a journal edited by the Station Biologique de Roscoff, and the ChanneLIS web application, an INTERREG-IV funded project.
Finally, ABiMS has also developed some command-line tools in collaboration with local research teams. The WiSca utility is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data.
Software engineering efforts undertaken by ABiMS try to adhere as closely as possible to the values and the principles of agile software development. Practically, user representatives are associated at each stage of the project, and participate in the definition and prioritization of functionalities to be designed and developed in each iteration or sprint. They are provided with means to assess the conformity of what has been developed from early on, through working prototypes and can thus give precious feedback to enhance mutual understanding and enhancement of the deliverables.
Please find here a short list of software applications that have been developed by ABiMS team members.