2.4.3

• Fix an issue where reordering the genomes table by dragging caused a crash

2.4.2

• remove all uses of PRIDE BioMart and use the PRIDE API instead

2.4.1

• Add support for Travis
• Fix image exports
• Fix the spacing of the changelogs
• Fix a bug in the genome_cache tests

2.4

• Add an API and documentation
• Add tests for the ruby on rails app
• Add a reset button to the visualisations
• Add the new treeview to the tryptic peptide analysis page
• Improve the organisation of the tryptic peptide analysis page
• Improve phylogenetic tree export by hiding internal nodes
• Improve the LCA calculation code by rewriting everything in java
• Rename single peptide analysis to tryptic peptide analysis
• Rename multi peptide analysis to metaproteomics analysis
• Fix the database to account for bigger uniprot accession numbers
• Fix the database to account for bigger EMBL and Refseq cross references
• Update rails to 4.1.4
• Update D3 to 3.4.11

2.3.1

• Disable the GO terms because they are missing from the database
• Update to Uniprot 2014.05

2.3

• Add treeview to the multi-peptide analysis result page
• Add ec numbers and go terms to the single peptide analysis result page
• Add links to PRIDE and PeptideAtlas on the single peptide analysis result page
• Add the option to add multiple genomes at a time to the my genomes feature
• Add copy to clipboard buttons where appropriate
• Add the option to add unlimited genomes to the my genomes feature by switching to indexedDB storage
• Add a progress bar to the multi-peptide analysis page
• Improve the multi-peptide analysis input parsing by stripping #-symbols
• Improve the design by removing most of the gradients and drop shadows
• Improve the stability of the clustered order
• Fix a bug where filtering the selection tree of the peptidome analysis was case sensitive where it shouldn't be
• Fix a bug where loading the /organisms page resulted in an error
• Fix a bug where only loading 'my genomes' into the peptidome analysis caused an error
• Fix a bug where having 2 genomes with the same name caused the phylogenetic tree to crash
• Fix an issue where some image assets failed to load
• Fix a small inaccuracy with the UPGMA calculation
• Update bootstrap to 3.2
• Update D3.js to 3.4.8

2.2.3

Fixed an issue with "filter duplicate peptides" not behaving as expected.

2.2.2

Fixed a crash when exporting multi-peptide results

2.2.1

Fixed the deploy scripts

2.2

• Add peptidome similarity feature
• Add myGenomes feature to peptidome analysis
• Add full screen support for IE11
• Add links to the bioproject webpage in the peptide finder graph tooltips and genomes table
• Add an option to disable individual lines in the unique peptide finder by clicking on the legend labels
• Add an option to use fixed colors for the sunburst graph allowing to compare the results of multiple samples
• Add rails errors log via email
• Make most of the logging optional by using settings
• Improve the design of the genomes table
• Improve the loading of the unique sequences in the unique peptide finder
• Less clutter in the peptide finder graph by abbreviating names
• Fix a bug where the genome size was not shown by default
• Fix a bug causing the LCA to be root in some cases in the unique peptide finder
• Fix a bug where the custom drag cursor wasn't shown in Internet Explorer
• Fix a bug where matching children weren't shown while filtering on the multi peptides result page
• Fix a crash when trying to sort without genomes
• Fix an issue with the full screen view of the peptide finder graph
• Fix an issue where the download dialog didn't disappear by pressing the escape key
• Update to capistrano 3
• Update bootstrap to 3.1.1
• Update D3.js to 3.4.6
• Update ruby to 2.1
• Update rails to 4.1.1