ABiMS Developments

Software engineering as carried out by ABiMS aims to provide research teams and user communities with databases or tools that best suit their needs. Below is a short alphabetically ordered list of such software applications that have been developed by ABiMS team members.

CBM : The Cahiers de Biologie Marine are a journal published by the Station Biologique de Roscoff. The web application allows users to browse/search through the journal issues, and subscribers to download PDF files of every article. It also provides back-end enabling the library personnel to manage article upload, subscriptions and collect statistics about article popularity.

ChanneLIS : The Channel Library Information System was an INTERREG-IV funded project resulting in the development of the ChanneLIS database. This database collects bibliographic information about channel-related literature with an emphasis on “grey literature”. The Web application allows searching for bibliography entries from classical criteria (authors, publishers, publication dates…) but also from more specific criteria such as pre-defined channel geographical areas, taxon names or thesaurus terms. The back end provides functionalities for curating these bibliographical entries after their automated extraction from local databases/files.

Cyanorak : Cyanorak is an information system supplemented with a set of analysis tools dedicated to the comparative genomics of marine cyanobacteria. It hosts data about clusters of proteins computed by an ABiMS developed pipeline from about 100 genomes of completely sequenced cyanobacteria. The web application allows browsing/searching for specific clusters and/or proteins. It also provides a back-end for curators to enhance the quality of sequence and cluster annotations.

GISM : Upon the request of the Service Mer, the ABiMS platform has developed the Gestion des Interventions du Service Mer web application. It has been designed to support the collection and management of information related to service requests about the usage of resources provided by the Service Mer (species collection, scientific diving, vessel usage and reservation). Users describe their needs by filling a form which is then processed with the application’s backend by members of the Service Mer.

High-Frequency Data Repository : For several years now, oceanographic data is collected by researches of the Station Biologique de Roscoff by various pieces of equipment (Ferryboxes on board of two ferries, sensor-equipped buoys, underwater probes, weatherstations). ABiMS has developed a data repository integrating measurements coming from these sources and offering consolidated views to the general public (graphs retracing the evolution of sensor values over time), as well as an access to the raw data with means to extract subsets of the series to scientific partners of the project.

Inventaires : The need to collect observation data related to local species has led to the development of the Inventaires web application. Its current version, entirely re-developed by the ABiMS team, stores detailed information about over 3,000 observed specimen covering about 1,800 taxons. The web application provides the functionalities for “observers” to add descriptions of specimen they spot in the field. Visitors can use the application to look for these observations using various criteria (location, taxon or other).

Pelagos : The Pelagos database is the result of a collaborative effort driven by the Pése`u(des Stations et Observatoires Marins (RESOMAR). It stores biodiversity data from coastal pelagic ecosystems (including time series). One of its goals is to exploit the biological information that has been acquired to answer scientific questions for instance relative to factors controlling distribution and abundance of pelagic organisms on different spatial and temporal scales.

Renkañ : The Renkañ application is used by the planktonic symbiosis research team at the Station Biologique de Roscoff to organize and share information on Radiolarians specimens available in the lab. Samples are composed mainly of single cells collected and isolated worldwide before to be processed in the lab. Information on collection procedures, location, morphology and molecular markers are provided for each specimen.

SulfAtlas : Widespread in nature, sulfated biomolecules are highly diverse in chemical structure and biological function. The SulfAtlas database describes the families and subfamilies of structurally-related sulfatases. Subfamilies are created based on phylogenetic analyses and essentially correspond to different substrate specificities. The database describes over 4,500 sulfatases distributed in over 70 families and subfamilies.

Tadoussac : Tadoussac is a LIMS-like web application (with restricted access). It has been developed to manage information about overexpression and crystallization experiments. This information includes description of plasmids and genes, and results of expression experiments.

TARA Data Portal : In order to provide a means to look for publicly available data related to data collected during the TARA cruises, the Tara Data Portal harvests dataset descriptions from various sources and offers a web interface to query these descriptions according to a wide range of criteria (data type, geolocation, data provider). It also offers the possibility to extract subsets of a selected set of reference data (rows / columns of more comprehensive datasets).

Wisca : WiseScaffolder (WiSca) is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common thread for the manual improvement of scaffolds.