News

Unipept 3.2

posted on 2017-06-27

Unipept 3.2 includes these major updates:
  • https and rails 5 support
  • an updated database based on UniProt 2017.05
Check the release notes for a full list of changes.

Unipept 3.2 changelog

posted on 2017-06-27

Unipept 3.2 consists of 147 commits and 150 changed files with 1,983 additions and 1,350 deletions. This includes these updates:
added
a configure script for the make file
added
ec number and go term information to the database
improved
the performance of downloading proteome data
improved
the error resilience of the make file and scripts
fixed
an issue where not all type strains were added to the proteomes
fixed
an issue where the unique peptide finder could crash when requesting 0 sequences
updated
the publications section and about page
updated
to https and http2
updated
to rails 5
updated
to ruby 2.4
updated
to UniProt 2017.05

Unipept 3.1

posted on 2016-06-08

Unipept 3.1 includes these major updates:
  • a faster peptidome analysis based on UniProt proteomes
  • an updated database based on UniProt 2015.12
update 3.1.3: update to UniProt 2016.05
Check the release notes for a full list of changes.

Unipept 3.1 changelog

posted on 2015-12-11

Unipept 3.1 consists of 84 commits and 75 changed files with 1,158 additions and 921 deletions. This includes these updates:
added
UniProt proteomes as data source for the peptidome analysis instead of assemblies
added
Type strains and reference proteomes markers in the proteome selector
improved
The loading speed of proteomes by 3 to 5 times
improved
The unique peptidome calculation speed of proteomes by 5 to 25 times
improved
The sequence download speed of peptidomes by 3 to 5 times
improved
The taxon invalidation rules for viruses
fixed
an issue where virus names were abbreviated in the peptidome analysis where they shouldn't
fixed
a bug where the API could return an error 500 in an obscure case
fixed
a bug where the invalid input would result in an error 500 when converting peptides
fixed
a bug where the TPA would crash for non-ascii input
updated
rails to 4.2.5
3.1.1 - 2016-02-01
added
Our Bioinformatics publication
improved
The peptidome clustering to improve speed up to 30 times
fixed
An issue with the "Download Data" button of the unique peptide finder
updated
UniProt to 2016.01
3.1.2 - 2016-02-23
updated
UniProt to 2016.02
3.1.3 - 2016-06-08
added
Protein download from the Unique Peptide Finder
updated
UniProt to 2016.05

Unipept 3.0

posted on 2015-07-31

Next to a new design, Unipept 3.0 includes:
  • a command line tool
  • a completely rewritten Peptidome Analysis
Check the release notes for a full list of changes.

Unipept 3.0 changelog

posted on 2015-07-31

Unipept 3.0 consists of 438 commits and 337 changed files with 10,504 additions and 5,978 deletions. This includes these updates:
added
A completely new redesign
added
Use Assemblies instead of Bioprojects as data source for the proteomes
added
A command line tool and documentation
added
Auto-resume for a previous peptidome analysis
added
Draft genomes to the peptidome analysis
added
Type strain info to the peptidome analysis
added
A new method of adding proteomes to the peptidome analysis
added
Shift + click on a node to expand all treeviews
added
A notification system
added
Protein names to the tryptic peptide analysis results
added
Protein names to the pept2prot API output
added
The possibility to leave an email address on encountering an error
added
The UniProt version in the footer
added
A rewritten version of the uniprot parser using make files and berkeley DB
added
Copy to clipboard button for Tryptic Peptide Analysis
added
An open in UniProt button for Tryptic Peptide Analysis
fixed
An issue where the names of "My proteomes" were incorrectly abbreviated in some cases
fixed
An issue where IndexedDB was broken in Safari
fixed
An issue where the input order was not preserved for the taxonomy API call
fixed
A bug where the my proteomes popover wouldn't open once a pancore popover was shown
fixed
A bug where the pancore popover was still present after a remove all
fixed
An issue where text was selected during drag-to-reorder in the pancore graph
fixed
An issue where a few JavaScript errors were shown when loading the TPA tree
fixed
An issue where the application crashed when a user submitted non-ascii characters in the multi-peptide analysis
updated
ruby to 2.2.2
updated
rails to 4.2.3
updated
D3.js to 3.5.5
updated
bootstrap to 3.3.5
3.0.1 - 2015-08-01
fixed
A bug where the JavaScript code might crash while updating My Proteomes
3.0.2 - 2015-08-03
fixed
A bug where the Save Image popover was not clickable
fixed
A spacing issue in the peptidome clustering tooltip
fixed
An issue with the font sizes in the peptidome clustering visualisations
3.0.3 - 2015-08-07
fixed
A bug where peptidome analysis became unresponsive after using the "clear all"-button in IE11
fixed
An issue with the autosort tooltip in Firefox and IE
3.0.4 - 2015-08-12
fixed
A bug where searching for a combined peptide in the TPA might cause a crash

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.