News

Unipept 2.5

posted on 2015-02-25

Unipept 2.5 includes a completely rewritten Metaproteomics Analysis results page with:
  • A new full screen mode
  • A new treemap implementation
Check the release notes for a full list of changes.
update 2.5.2: update to Uniprot 2015.02

Unipept 2.5 changelog

posted on 2015-02-25

Unipept 2.5 consists of 191 commits and 151 changed files with 3,995 additions and 15,187 deletions. This includes these updates:
added
A new full screen mode to the Metaproteomics analysis results page
added
Breadcrumb navigation to the treemap
added
Breadcrumb navigation to the sunburst
added
The option to shift+click a node in the treeview to expand all its children
added
A highlight effect when hovering over sunburst slices
added
insdc and refseq cross references to the pept2prot api
added
Incremental PRIDE dataset loading
added
A new page with an overview of our publications
improved
The responsiveness of the Metaproteomics Analysis (full rewrite)
improved
The treemap visualisation (own implementation using D3)
improved
The sunburst image export by excluding the faded slices from the exported image
improved
The Tryptic Peptide Analysis tree by using the number of actual hits for the node size and include tooltips
fixed
An issue where removing a genome while a genome was being removed, crashed the unique peptide finder
fixed
An issue where negative taxon id's were returned by the API
fixed
An issue with overlapping nodes in the new tree visualisation
fixed
An issue with a "new version"-message appearing in the CLI
fixed
An issue where a serif font was used for the image export of clustered genomes
fixed
An issue with the top navigation being on 2 lines when helvetica nor arial were installed
updated
rails to 4.1.8
updated
D3.js to 3.5.3
updated
bootstrap to 3.3.2
This is the first unipept version to achieve a 100% test coverage.

Unipept 2.5.1
fixed
An issue where adding "my genomes" failed
Unipept 2.5.2
added
GO terms to the peptide page
updated
UniprotKB to 2015_02

Unipept 2.4

posted on 2014-10-07

Unipept 2.4 includes these major updates:
  • A full API and documentation
  • A new treeview for the Tryptic Peptide Analysis
Check the release notes for a full list of changes.
update: fixed an issue where the Metaproteome Analysis crashed when "SEQUENCE" was present in the input

Unipept 2.4 changelog

posted on 2014-10-07

Unipept 2.4 consists of 438 commits and 206 changed files with 9,015 additions and 4,048 deletions. This includes these updates:
added
An API and documentation
added
A reset button to the visualizations of the metaproteomics analysis results
added
A new treeview visualization to the tryptic peptide analysis results
improved
The organisation of the tryptic peptide analysis page
improved
The export of the phylogenetic tree by hiding the internal nodes on export
fixed
The database to account for bigger uniprot accession numbers
fixed
The database to account for bigger EMBL and Refseq cross references
updated
Ruby on Rails to 4.1.4
updated
D3.js to 3.4.11
The single peptide analysis was renamed to tryptic peptide analysis and multi peptide analysis was renamed to metaproteomics analysis.

Unipept 2.4.1
fixed
Image exports
fixed
An issue with the spacing of the changelogs
Unipept 2.4.2
updated
Use the PRIDE API instead of BioMart
Unipept 2.4.3
fixed
An issue preventing the genomes table being reorderd by dragging
Known issues: the list of GO terms was disabled because it's missing from the database.

Unipept 2.3

posted on 2014-08-02

Unipept 2.3 includes these major updates:
  • A new visualisation for the multi-peptide analysis
  • Improved "my genomes" feature
Check the release notes for a full list of changes.
update 2.3.1: update to Uniprot 2014.05

Unipept 2.3 changelog

posted on 2014-08-02

Unipept 2.3 includes these updates:
added
A treeview visualization to the multi-peptide analysis results
added
EC numbers and GO terms to the single peptide analysis results
added
Links to PRIDE and PeptideAtlas on the single peptide analysis results
added
The option to add multiple genomes at a time to the my genomes feature
added
Copy to clipboard buttons where appropriate
added
The option to add unlimited genomes to the my genomes feature
added
A progress bar to the multi-peptide analysis page
improved
The parsing of a peptide list by stripping #-symbols
improved
Cleaner layout by removing most gradients and drop shadows
improved
Clustered order now gives more predictable results
fixed
A bug where filtering the selection tree of the peptidome analysis was case sensitive where it shouldn't be
fixed
A bug where loading the /organisms page resulted in an error
fixed
A bug where only loading 'my genomes' into the peptidome analysis caused an error
fixed
A bug where having 2 genomes with the same name caused the phylogenetic tree to crash
fixed
An issue where some image assets failed to load
fixed
A small inaccuracy with the UPGMA calculation
updated
Bootstrap to 3.2
updated
D3.js to 3.4.8
Unipept 2.3.1
updated
Uniprot to 2014.05
updated
The list of refseq genomes
Known issues: the list of GO terms was disabled because it's missing from the database.

Unipept 2.2

posted on 2014-06-07

Unipept 2.2 includes these major updates:
  • The Peptidome Clustering feature including the ability to add your own genomes to the Peptidome Analysis
  • An (optional) fixed color scheme for the sunburst visualisation
Check the release notes for a full list of changes.
update 2.2.2: fixed a crash when exporting multi-peptide results

Unipept 2.2 changelog

posted on 2014-06-07

Unipept 2.2 includes these updates:
added
Peptidome clustering
added
myGenomes to peptidome analysis
added
Fixed color option to the sunburst graph
added
The option to disable individual lines in the unique peptide finder
added
Full screen support for Internet Explorer 11
added
Links to the bioproject pages where appropriate
added
Invalidation "metagenome" NCBI taxa
improved
The design of the unique peptide finder: abbreviations for organisms names, use icons where possible, better help texts, ...
improved
The loading of the unique sequences in the unique peptide finder
fixed
A bug where the genome size was not shown by default
fixed
A bug causing the LCA to be root in some cases in the unique peptide finder
fixed
A bug where matching children weren't shown while filtering on the multi-peptide results page
fixed
A bug where the custom drag cursors weren't shown in Internet Explorer
fixed
A crash when using autosort without genomes
fixed
An issue with the full screen view of the peptide finder graph
fixed
An issue where the download dialog didn't disappear by pressing the escape key
updated
Rails to 4.1.1
updated
Ruby to 2.1
updated
Bootstrap to 3.1.1
updated
D3.js to 3.4.6
update 2.2.1: fixed deployment issues
update 2.2.2: fixed a crash when exporting multi-peptide results
update 2.2.3: fixed an issue with "filter duplicate peptides" not behaving as expected.

Unipept 2.1

posted on 2013-12-23

Unipept 2.1 includes these major updates:
  • A fresh coat of paint
  • Lots of bug fixes and performance improvements
Check the release notes for a full list of changes.

Unipept 2.1 changelog

posted on 2013-12-23

Unipept 2.1 includes these updates:
added
A fresh coat of paint for most of the pages
added
Support for high resolution (retina) displays in all images and icons
added
An option to download the data in the unique peptide graph as a Microsoft Excel compatible CSV file
added
An option to download the sunburst and unique peptide graph as an SVG file
improved
Rewrite of all file download code to improve the user experience
improved
Smoother dragging in the unique peptide graph
improved
Custom taxonomy tree implementation on the multi-peptide result page
fixed
A bug where the download button stayed disabled after downloading the results on the multi-peptide page
fixed
A bug with full screen mode on the unique peptide page
fixed
A bug where dragging a node triggered a popover in some browsers
updated
Bootstrap to 3.0.3
updated
D3.js to 3.3.10