3.1.1

• Peptidome similarity calculation is now up to 30 times faster
• Add bioinformatics application note to publications
• Fix "Download Data" button of the unique peptide finder
• Fix failing Travis tests
• Update to UniProt 2016.1

3.1

• Switch to UniProt proteomes as data source for the peptidome analysis
• Loading proteomes is now 3-5 times faster
• Calculating the unique peptidome is now 5-25 times faster
• Downloading sequences from the unique peptide finder is now 3-5 times faster
• Don't abbreviate virus names in the peptidome analysis
• Mark type strains and reference proteomes in the proteome selector
• Use better default settings in the makefile to build the database
• Better invalidation rules for viruses
• Fix a bug where the API could return an error 500 in an obscure case
• Fix a bug where the invalid input would result in an error 500 when converting peptides
• Fix a bug where the TPA would crash for non-ascii input
• Update ruby on rails to 4.2.5

3.0.4

• Fix an issue where searching for a combined peptide in the TPA might cause a crash

3.0.3

• Fix a bug where peptidome analysis became unresponsive after using the "clear all"-button in IE11
• Fix an issue with the autosort tooltip in Firefox and IE

3.0.2

• Fix a bug where the Save Image popover was not clickable
• Fix a spacing issue in the peptidome clustering tooltip
• Fix an issue with the font sizes in the peptidome clustering visualisations

3.0.1

• Fix a bug where the JavaScript code crashed when updating My Proteomes

3.0

• Redesign
• Use Assemblies instead of Bioprojects as data source for the proteomes
• Add command line documentation
• Add auto-resume for a previous peptidome analysis
• Add draft genomes to the peptidome analysis
• Add type strain info to the proteomes
• Add new table based method of selecting proteomes
• Add Shift + click to expand the treeview, both on the TPA and MPA results page.
• Add autoprefixer for css
• Add notifications to indicate progress
• Add protein names to the tryptic peptide analysis results
• Add protein names to the API output
• Add the possibility to leave an email address on encountering an error
• Add the UniProt version in the footer
• Add rewritten of the uniprot parser using make files and berkeley DB
• Add copy to clipboard button for Tryptic Peptide Analysis
• Add open in UniProt button for Tryptic Peptide Analysis
• Remove drag and drop for proteome selection
• Refactored the JavaScript code to use promises were possible
• Fix an issue where the names of "My proteomes" were incorrectly abbreviated in some cases
• Fix an issue where IndexedDB was broken in Safari
• Fix an issue where the input order was not preserved for the taxonomy API call
• Fix a bug where the my proteomes popover wouldn't open once a pancore popover was shown
• Fix a bug where the pancore popover was still present after a remove all
• Fix an issue where text was selected during drag-to-reorder in the pancore graph
• Fix an issue where a few JavaScript errors were shown when loading the TPA tree
• Fix an issue where the application crashed when a user submitted non-ascii characters in the multi-peptide analysis
• Update ruby to 2.2.2
• Update rails to 4.2.3
• Update D3 to 3.5.5
• Update bootstrap to 3.3.5

2.5.2

• Add GO terms to the Tryptic Peptide Analysis
• Update to Uniprot 2015.02

2.5.1

• Fix an issue where adding "my genomes" failed

2.5

• Rewrite Treemap with D3
• Rewrite all Metaproteomics Analysis visualisation code
• Add a new full screen mode to the Metaproteomics Analysis results page with improved functionality
• Add breadcrumb navigation to the treemap
• Add breadcrumb navigation to the sunburst
• Add the option to shift-click a node in the treeview to expand all children
• Add color highlights on mouseover to the sunburst graph
• Add insdc and refseq cross references to the pept2prot api
• Add a publications page
• Improve the performance of the metaproteomics result page by reducing the page size
• Improve the sunburst image export by excluding the faded sunburst arcs from the exported image
• Incremental PRIDE dataset loading with progress bar
• Improve the tree on the TPA results page by using the number of hits instead of the number of leafs to scale the nodes + include a tooltip
• Achieve 100% test coverage
• Fix an issue with incorrect treemap bounding box
• Fix an issue with the top navigation being on 2 lines when helvetica and arial aren't installed
• Fix an issue with overlapping nodes in the new tree visualisation
• Fix an issue with header rows being imported in the database
• Fix an issue with the 'new version'-message appearing in the CLI
• Fix an issue where a serif font was used for the image export of clustered genomes
• Fix an issue where removing a genome while a genome was being removed, crashed the unique peptide finder
• Fix an issue where negative taxon id's could be returned by the API
• Update rails to 4.1.8
• Update D3 to 3.5.3
• Update bootstrap to 3.3.2