BIGSdb version 1.12.0 released

BIGSdb version 1.12.0 has been released and is available for download from Sourceforge and GitHub. This is the genomics platform that runs the PubMLST databases. Since the release of version 1.11.0, we have introduced the following:

New functionality

  • Submissions of new allele, MLST profile, isolate and genome data can be made to curators via the RESTful interface.
  • Support for allele retirement so that identifier re-use can be prevented if an allele has been removed.
  • Relaxed auto allele definer CDS checks for use when designating new pseudogene alleles.
  • Support for querying by allele counts of individual loci or total number of allele designations across the genome.


The isolate querying interfaces have been merged so that browsing, querying and retrieving by lists of attributes are all combined on a single page. The principal advantage of this is that this allows the further combination of subqueries to build more complex searches. You can now, for example, paste in a list of isolate ids or any other attribute and then filter these based on provenance or allele designation/scheme criteria. Query form elements can be shown or hidden at will so that the basic form remains uncluttered and additional forms shown only when needed. This has been developed with mobile use in mind so that the query experience on phones and tablets remains positive.

Isolate querying

Combine query form elements to build complex searches

Performance improvements

  • Larger analysis jobs for the Locus Explorer, Export and Two Field Breakdown plugins are now queued and run offline.
  • Faster scheme breakdown analysis.
  • Improvements to scheme caching so that caches are (optionally) updated automatically in the background following a batch isolate upload.
  • Efficiency improvements when comparing peptide loci in Genome Comparator analyses.

Full documentation can be found at