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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 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 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 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

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.