News
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
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
- fixed
- A bug where the JavaScript code might crash while updating My Proteomes
- 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
- 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
- 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:
update 2.5.2: update to Uniprot 2015.02
- A new full screen mode
- A new treemap implementation
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:
Unipept 2.5.1
- 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
Unipept 2.5.1
- fixed
- An issue where adding "my genomes" failed
- 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:
update: fixed an issue where the Metaproteome Analysis crashed when "SEQUENCE" was present in the input
- A full API and documentation
- A new treeview for the Tryptic Peptide Analysis
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:
Unipept 2.4.1
- 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
Unipept 2.4.1
- fixed
- Image exports
- fixed
- An issue with the spacing of the changelogs
- updated
- Use the PRIDE API instead of BioMart
- fixed
- An issue preventing the genomes table being reorderd by dragging
Unipept 2.3
posted on 2014-08-02
Unipept 2.3 includes these major updates:
update 2.3.1: update to Uniprot 2014.05
- A new visualisation for the multi-peptide analysis
- Improved "my genomes" feature
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
- updated
- Uniprot to 2014.05
- updated
- The list of refseq genomes
Unipept 2.2
posted on 2014-06-07
Unipept 2.2 includes these major updates:
update 2.2.2: fixed a crash when exporting multi-peptide results
- 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
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:
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.
- 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 2.2.2: fixed a crash when exporting multi-peptide results
update 2.2.3: fixed an issue with "filter duplicate peptides" not behaving as expected.