Source code


Added by Richard Challis on December 16th 2015

The source code for all our projects is available on Atlassian_Bitbucket_Logo or GitHub

Our Ensembl plugin for ensembl.lepbase.org is available at bitbucket.org/lepbase/lepbase-ensembl

Our Ensembl mirror setup scripts are available at github.com/lepbase/ensembl-easy

Our Ensembl data import pipeline (which includes search indexing) is available at bitbucket.org/lepbase/lepbase-import

We have written a generic GFF parsergithub.com/rjchallis/gff_parser, which we use in our import pipeline to accommodate, validate and correct the diversity of GFF formats used in Lepidopteran genome projects

Our SequenceServer fork with changes to allow hierarchical taxon display and closer integration with our Ensembl instance is available at bitbucket.org/lepbase/lepbase-sequenceserver

Our assembly statistic visualisations are based on our github.com/rjchallis/assembly_stats javascript project

We have written an API training environmentbitbucket.org/lepbase/lepbase-workshopfor use in training workshops, which we intend to make more widely applicable as an introduction to the Lepbase API

Our WordPress theme for this site is available at bitbucket.org/lepbase/lepbase-wordpress

 

Lepbase uses many other open source bioinformatics projects, including:

The EBI‘s Ensembl genome browser powers ensembl.lepbase.org

blast.lepbase.org is powered by the Wurm Lab‘s SequenceServer 

Community annotations at webapollo.lepbase.org are made possible by Web Apollo