News

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 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 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 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 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 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 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 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 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 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.