Table 1.
Major service developments in 2012
| Development | Utility |
|---|---|
| 11 face-to-face training events and creation of new training materials | http://www.ebi.ac.uk/ena/about/training |
| Application-specific checklists | Framework for community developers to develop specifications for external applications and pipelines for ENA validation and presentation of data (e.g. http://www.ebi.ac.uk/ena/about/epigenomics_submissions) |
| Checklists for annotated sequence submissions | Checklists that define Webin submission templates for annotated sequences (https://www.ebi.ac.uk/embl/genomes/submission/app/login/login.jsf) |
| Creation of genome assembly storage layer | Improved and more granular support for assembly information including compliance with AGP2 (http://www.ebi.ac.uk/ena/about/genome_assembly_database) |
| Creation of search warehouse and launch of ENA query builder and search | See below and http://www.ebi.ac.uk/ena/about/browser |
| Extension of ENA sequence search to include reference sequence data directly from Ensembl and Ensembl Genomes | Provision of rapid interactive and programmatic sequence search service to all sequences in ENA and the Ensembl and Ensembl Genomes resources (http://www.ebi.ac.uk/ena/search/#Search) |
| Inclusion of capillary sequencing instruments into the raw sequence storage layer (SRA) | Raw capillary sequence submissions are now supported in the Sequence Read Archive (SRA) storage layer in ENA (http://www.ebi.ac.uk/ena/about/sra_preparing_metadata) |
| Inclusion of sample checklist support for raw data submissions in Webin | Provision of tabular sample checklist functionality in the Webin system that greatly simplifies the submission of sample annotation for different sample types (https://www.ebi.ac.uk/ena/submit/sra/#home) |
| Launch of raw sequence data file uploader/downloader utility | Support for simple and managed upload and download of raw sequence data files—available as interactive and command line clients (e.g., http://www.ebi.ac.uk/ena/data/sradownload/SRA-FileDownloader.jnlp) |
| New services for genome assembly submissions | Tools and workflow for the submission of assembly information (http://www.ebi.ac.uk/ena/about/genome_assembly_submissions) |
| Release of CRAM sequence data compression technology | See below and http://www.ebi.ac.uk/ena/about/cram_toolkit |
| Simplification of transcript shotgun assembly submissions | Simplification of submission process for the growing body of transcriptomes assembled from shotgun data (http://www.ebi.ac.uk/ena/about/TSA-submission-instructions) |