ISA software suite
The three first applications are launched by Java Web start
During the first launch, a directory named ISA_metadata will be created in your home directory. This last one will contain all configurations and ISA-tab files created with this software suite.
ISA (Investigation / Study / Assay) infrastructure is the first to suggest a general format and a free software suite for biologists and bioinformaticians in order to:
- Facilitate experimental metadata local management (ie sample characteristics, technology and type of measurement, sample-related data) for studies using one or more technologies;
- Encourage users to use ontologies and "minimum information checklists";
- Standardize the studies to submit them in public repositories such as international ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics).
The ISA-Tab format has been developed in synergy with several international collaborators and with MAGE-Tab, Fuge, PSI and biomedical formats such as SDTM. The decision on how to regulate its use (i.e. the choice of fields or controlled vocabularies) is controlled by external agencies community, such as MIBBI and OBO Foundry .
For more information on this software suite or on the ISA-Tab format, visit the ISA website.
Create an experiment : ISA tools
Java Application for curators to customize and regulate the fields displayed in ISAcreator, by declaring some required fields and specifying allowed values (e.g. from a set of ontologies term).
Friendly Java application with which the "experimentalists" can include or edit experimental metadata and validate the ISA-Tab files formatted according to the specified configuration (via the ISAconfigurator).
Java application to validate and convert ISA-Tab files into several other tabular or XML formats to submit into public repositories such as ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics).
Browse an experiment : BII
Relevant EBI systems, such as ArrayExpress , Pride and ENA-Reads
are built to respectively store microarray experiments, proteomics and NGS (next-generation sequencing).
These systems have different submission and download formats and use various representations of the metadata and terminologies. Nothing yet exists for metabolomics and other biomedical/environmental assays.
BioInvIndex infrastructure aims at being a single entry point for researchers willing to submit their experiences and/or easily download sets of similar data.
BII web application
is a web interface providing all experiments
deposited in the database
(maintained by the administrator).
The user can search a study / experiment, consult the associated details and download the related files.