This version provides the following:

• Submissions via the RESTful interface.
• Support for allele retirement.
• Querying of isolates by allele designation or sequence tag count.

This is a minor release that provides the following:

• Option to ignore previously defined profiles when batch uploading.
• Option to automatically refresh scheme caches in isolate databases when batch uploading.
• Option to relax auto allele definer CDS checks for use with pseudogenes.
• More efficient handling of previously tagged peptide loci in Genome Comparator analyses.
• Fix to isolate database SQL setup file.

This version provides performance improvements for scheme breakdown analysis and offloads large Locus Explorer, Exports, and Two Field Breakdown analyses to the offline job manager.

There are also minor tweaks to the automated submissions system.

As Sourceforge file upload is currently unavailable, this version can be obtained from https://github.com/kjolley/BIGSdb/releases

This is a major release that provides the following:

New functionality

• RESTful interface to facilitate access to data within BIGSdb databases by third-party tools. Authentication is supported by OAuth 1.0A to allow access to password-restricted resources.
• Web-based data submission system that allows users to submit data (alleles, profiles, isolates) to curators via the web. The interface supports data generated by NGS tools.
• Command line contig uploader script allows data to be uploaded to the database outside of the web interface.... read more

This version introduces a large number of improvements.

General

• New submitter class of user allowed to upload and curate their own data, or
  data from members of their user group, but no other records.
• Removal of access control lists (ACL) which were not widely used and
  complicated to administer. Their purpose has been largely removed by the
  introduction of submitter accounts.
• Project options to select whether to include individual projects in
  isolate info pages and in a new project description page.
• Option to set base isolate id number - this is useful if there is a plan
  to merge isolate databases in the future as you can use different sequences
  of id numbers.
• Support for diploid MLST schemes in seqdef database.
• New allele status of 'ignore' (while previously they were either 'confirmed' or 'provisional')
  to enable an allele to be defined but not shown in public interface or used in analyses.
• Optionally include seqbin id and position in Sequence Export output.... read more

This version speeds up searches by size of the sequence bin due to a new table that stores seqbin stats. This table is updated automatically by database triggers.

There is also now support for record versioning. Records can be replicated apart from the sequence bin and old versions hidden by default. This facilitates storing and comparing multiple genome versions for an isolate. See http://bigsdb.readthedocs.org/en/latest/curator_guide.html#isolate-record-versioning for more details.... read more

This release fixes a memory leak in Genome Comparator.

Also, the autotagger now sets the BLASTN word size to the length of the smallest allele as it is only looking for exact matches. This speeds up the search.

This version introduces support for multiple allele designations at a locus and the removal of pending designations.

The autotagger and auto allele definer scripts are now multi-threaded, allowing you to run them on multiple cores. Autotagger jobs are split by isolate among the threads (so a single isolate will only run on one thread), while auto definer (scannew.pl) jobs are split by locus.

MAFFT is now the default sequence aligner (MUSCLE is still supported). This is significantly faster. To use this, make sure it is installed (v6.840+) and set the mafft_path attribute in bigsdb.conf to point to the mafft executable.... read more

This is a minor release that prevents unnecessary warning messages appearing in the bigsdb.log file due to Perl features that have been designated as experimental in Perl version 5.18. This is the version installed with Ubuntu 14.04.

Please also note that the Bio::Biblio module used in the bigsdb_getrefs.pl script is no longer part of BioPerl (since BioPerl 1.6.920). If installing on Ubuntu 14.04, this module will need to be installed from CPAN - the easiest way to do this is using cpanminus (install this using the Linux package manager, then type 'cpanm --sudo Bio::Biblio').

This version includes improvements to Genome Comparator handling of truncated loci.

Excel files are also generated now for analysis results from various plugins and submission templates.

Please note that there is a new Perl module dependency: Excel::Writer::XLSX. This will need to be installed if not already present on the system. Most up-to-date Linux distributions should have a package for this, otherwise it should be installed using CPAN.

This version improves support for UNICODE character sets so that accented characters in places and names should always be properly displayed.

The tagging process following a scan has also been improved making this step very much faster following a large scan job.

Please note that there is a new folder in the BIGSdb/lib folder (CGI), so ensure this is included when updating libraries.

This version contains a number of improvements largely geared to running offline jobs. These can now be listed and cancelled by the submitting user.

There is also an offline new allele definer that looks for new alleles within genomes and can define these automatically within a linked sequence definition database.

Please note that the schemas of the isolate, seqdef and jobs databases have changed. Please use the upgrade SQL scripts to upgrade old databases.

This version provides performance improvements.
Please note that legacy BLAST support has now been removed.

This version creates pages in HTML5, rather than XHTML, in order to utilise modern browser features, including client-side validation of curation forms.

Isolate queries can now be filtered by multiple projects and/or publications whereas this was previously limited to single values. Filtering can also be performed based on size of the isolate sequence bin.

New alleles can now be batch uploaded in FASTA format whereas previously these had to be formatted in tab-delimited text.... read more

This version runs scan jobs as a forked background process. This allows jobs to be started, bookmarked and returned to later. Scan jobs can also be stopped by the user.

There have also been interface improvements that render information pages better on small screens and mobile devices.

This version allows the option of schemes containing loci that may have ambiguous alleles. This is useful for ignoring loci in which a subset of profiles may have paralogous loci. There is also a new contig export plugin.

Please note that the schemas of the isolate and seqdef databases have changed. Please use the upgrade SQL scripts to upgrade old databases.

There have also been changes to Javascript plugins with the upgrade to jquery v1.9.1.

This version mainly introduces some core genome analysis to the Genome Comparator plugin.

This version introduces database partitioning. Present datasets with constrained choice of loci, schemes and isolate records. Datasets can also be associated with additional specific metafields.

Please note that the schemas of the isolate and seqdef databases have changed with new tables defined to support the new functionality. Please use the upgrade SQL scripts to upgrade old databases.

This version contains support for materialized views for sequence definition database schemes to improve performance with large MLST schemes.

There is also now support for adding flags, e.g. internal stop codon etc., to allele definitions. These flags are automatically transferred over to an isolate database during tag scanning.

There is also a new RulesQuery plugin that can be used to define how to scan a pasted-in genome and extract data in a specified format.... read more

This version contains mainly improvements to the GenomeComparator plugin.

This version has an improved sequence query function that enables MLST sequence type or any other locus information to be determined directly from a whole genome assembly (multiple contigs).

The Genome Comparator plugin now also generates a distance matrix and a splitsgraph to graphically display relatedness of analysed genomes.

This version introduces a TagStatus plugin that displays a schematic representing the schemes and loci that have been designated and tagged.

This update fixes a few minor bugs and introduces more options for the offline autotagger script.

This version introduces BLAST database caching for seqdef databases when querying on 'all loci' and the ability to cache scheme data within an isolate database for improved performance.

It also includes a new offline autotagger script to tag exactly matching alleles outside of the web interface.

This version enables searching of isolates by sequence tag status. The isolate query form has also been refreshed using hideable elements to facilitate the addition of new options without cluttering the screen.

A new javascript JQuery plugin is required so please ensure that jquery.coolfieldset.js is added to the javascript directory if upgrading.