The ISA Commons is born and presented in Nature Genetics!
Authored by more than 50 collaborators at over 30 scientific organizations around the globe, a Commentary in Nature Genetics presents the ISA Commons, a growing community that users the ISA metadata tracking framework to serve an increasingly diverse set of domains including environmental health, environmental genomics, metabolomics, (meta)genomics, proteomics, stem cell discovery, system biology, transcriptomics and toxicogenomics.
The EU ToxBank project works to use the ISA-Tab format
The ToxBank project (under the EU FP7 HEALTH) is working to establish a dedicated web-based warehouse for systemic toxicity. The system will use the ISA-TAB file format for interchange, storage and query of any investigation data, including dose-response and omics results.
The Novartis Institutes for BioMedical Research starts to use the ISA tools
The The Novartis Institutes for BioMedical Research (NIBR) is integrating an instance of selected ISA software components is also being integrated as part of an extended internal workflow for their microarray gene expression resource to facilitate research aimed at drug discovery and development.
The NCI caBIG® Nanotechnology Working Group extends the ISA-Tab
To represent and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data, this working group has developed the nano-Tab (being renamed ISA-Tab nano)
ISA down under: Bioplatforms Australia and CSIRO endorses the ISA infrastructure
The Oxford ISA developers travel to meet teams of the Bioplatforms Australia and the Commonwealth Scientific and Industrial Research Organisation (CSIRO) and run a series of training courses in Brisbane, Perth and Camberra.
The multi-institutions LINCS programme endorses the ISA infrastructure
The Harvard Medical School Library of Integrated Network-based Cellular Signatures (HMS LINCS) is beginning to use the ISA-Tab file format for storing, organizing and sharing metadata for experimental and data analysis protocols. More at the LINCS Data Working Group (DWG) page.
BGI releases updated bioinformatics software and the GigaDB based on ISA infrastructure
GigaDB is the GigaScience journal’s affiliated data base hosted by BGI to increase the sharing and reuse of large biological datasets. Through the association with DataCite, they assign data DOIs to make datasets more discoverable, trackable and citable. They also use the ISA infrastructure to maintain the highest data and metadata standards.
ISA-Tab adopted by the SNRNASM annotation guidelines
A paper published in RNA illustrates how the ISA-Tab is used to facilitate the sharing of chemical and enzymatic structure-probing data in the Single Nucleotide Resolution Nucleic Acid Structure Mapping (SNRNASM) annotation guidelines.
ISA software suite enables compliance to GSC standards
Two open-access articles describing the GSC's standard have been published in Nature Biotechnology and PloS Biology. Both include references to the ISA software suite to empower users to put GSC standards in action.
BGI announce work in progress on a new ISA-based database and journal system
GigaScience is the new system under development at BGI (previously the Beijing Genomics Institute) that combines database and journal focused on the publication and hosting of many types of "large data" types as possible; datasets will be ISA-Tab compliant and progressively the ISA software suite will be integrated. More on this on the GigaScience blog.
The public MetaboLights repository at EBI will be fully based on ISA
The developers of MetaboLights, the (BBSRC-funded) metabolomics repository at EBI have selected the ISA software suite power the public system, under development and to be launched in early 2012.
A new public resource at Harvard implements the ISA-Tab format
In March the MIND Informatics group at the MassGeneral Institure implements ISA-Tab export from the public Harvard Blood Stem Cell Repository.
Launch of the Standards-based Infrastructure with Distributed Resources (SIDR), using ISA
In February, the CNRS Institute of Biological Sciences (INSB) in France launches the SIDR, a public resource that helps raising the standardization and storage of multi-omics data. SIDR combines the ISAcreator tool with a database based on the FuGE model and serves studies in ISA-Tab format.
Launch of the NEBC ISA Data Sharing Site, fully based on the ISA
In January, the NERC Environmental Bioinformatics Centre (NEBC) launches its ISA Data Sharing Site, a public resource based on the whole ISA software suite. It works to harmonise the collection and storage of a variety of environmental studies with multi ‘omics technologies, from the NERC researchers and the community.
Launch of the Harvard Stem Cell Discovery Engine (SCDE), fully based on the ISA
In December, the Harvard Stell Cell Institute (HSCI) launches the SCDE, based on the whole ISA software suite, as a public resource bringing together stem cell-based experimental systems and high-throughput data from the HSCI researchers and the community.
Conversion to SOFT and RDF formats started
In July, the collaborative development for a new ISAconverter module that exports in SOFT - for submission to GEO public repository - has started (lead: Kimberly Begley, Harvard School of Public Health). Initial planning for an export in RDF is also ongoing (lead: Philippe Rocca-Serra, University of Oxford).
ISA paper published in Bioinformatics
Open access paper available for download here.
Endorsement as third party tools for submission to international public repositories!
In June, Pride (proteomics) and ENA (genomics) and ArrayExpress (transcriptomics) endorse the ISA tools for the preparion of submissions in Pride-xml, SRA-xml and MAGE-Tab formats, respectively.
First set of case studies from early implementers released!
In May, examples of diverse life science scenarios in which the various ISA components have been successfully tested and are being used to manage different types of studies.
ISA-Tab format implemented by other data management tools!
A growing number of other systems are implementing the ISA-Tab format, including collaborators such as SysMO-DB, XperimentR and MetWare.
New funding stream from BBSRC and NERC awarded to the ISA project (BB/I000917/1)!
The core developers (Philippe Rocca-Serra, Eamonn Maguire and Susanna-Assunta Sansone) will move to University of Oxford at OeRC to continue leading the activities along with other staff members and several UK, EU and US collaborators. Official starting date of this new phase of the project is October 1st, 2010.
Tailored ISA Worskhops - ISA infrastructure users
In January, we hosted several collaborators for the NERC Bioinformatics Center (NEBC, UK), the Netherlands Toxicogenomics Centre (Maastricht, NL) and partners of the EU Carcinogenomics project at the EBI, Cambridge, UK, funded by the UK BBSRC grant (BB/E025080/1).
'Omics Data Sharing' paper in Science, citing ISA infrastructure as exemplar project
Launch of the first installation of the BII component, as public database at EBI
Release of version 1 of the ISA software components
Tailored ISA visits - ISA infrastructure users
In May and June, we hosted several from collaborators at the EBI, Cambridge, UK, funded by the UK BBSRC grant (BB/E025080/1).
First public release of alpha and beta versions of the ISA software components
3rd ISA workshop - FuGE to ISA-Tab rendering
This 3rd workshop was be held at the EBI, Cambridge, UK, on 8-9 December, funded by the UK BBSRC grant (BB/E025080/1). Agenda:1) finalize scripts and documentation to render existing FuGE-based XMLs into ISA-Tab; 2) define plans for a mechanism to deal with new FuGE extensions (in progress and future).
2nd ISA workshop - ISA-Tab specification finalization
The 2nd ISA workshop was held at the EBI, Cambridge, UK, on 16-17-18 June, funded by the UK BBSRC grant (BB/E025080/1).
1st ISA workshop - ISA-Tab specification development
The 1st ISA workshop was held at the EBI, Cambridge, UK, on 6-8 December, funded by the UK BBSRC grant (BB/E025080/1).