Wasabi plugin system update 1.2019

Wasabi plugin system allows to add custom command-line tools to the Wasabi interface via plugin JSON API.

Both the plugin system and included plugin files have been updated. See http://wasabiapp.org/plugins for more details.

  • JSON API additions (“version”, “debug”, “disable”, “dirpath” option, syntax shorthands)
  • Selections can now change option groups/configurations (with two-way sync for value changes)
  • FastTree plugin added
  • Bug fixes and improvements both client- and server side
  • Also: server code now supports Python 3, and Wasabi import dialog accepts Wasabi dataset IDs

The latest Wasabi is ready to use on our public server and its source files are available from GitHub repository or Wasabi downloads

Wasabi updates 10.2018

Thanks for testing Wasabi and reporting issues on the Wasabi GitHub page.

We’ve got progress:

  • Added tree scalebar and domain restriction option for import URLs
  • Fixed data export bugs together with numerous other reported issues (undo, rendering etc.)

The latest Wasabi is ready to use on our public server and its source files are available from GitHub repository or Wasabi downloads

Wasabi updates 8.2018

Wasabi has improvements in tree annotation and plugin support:

  • Support for tree labels (e.g. bootstrap values)
  • Faster tree import and rendering
  • New URL parameters for customizing Wasabi (see http://wasabiapp.org/rest)
  • Browse shared analysis library folders without Wasabi user account
  • Updated Wasabi plugin API (see http://wasabiapp.org/plugins)
  • Added MAFFT aligner plugin

The latest Wasabi is ready to use on our public server and the source files are available from GitHub repository or Wasabi downloads

Wasabi updates 12.2017

The issue reporting for Wasabi has moved to the Wasabi GitHub page.

Some of the improvements and bug fixes in recent Wasabi updates:

  • Fixed issues with importing certain fasta headers.
  • Fixed issue with importing tree and sequence from separate web addresses.
  • Fixed issues with tree rendering (tree drawing overflow, 0-length branches, annotations etc.).
  • Added support for serverless cross-origin data import (CORS and JSONP)
  • Custom metadata parsing from NHX trees (see NewickMeta dictionary)
  • Tree node and branch coloring (PhyloXML “color” or NHX “C” and “BC” tags)

The latest Wasabi is ready to use on our public server and its source files are available from GitHub repository or Wasabi downloads

Wasabi outage

Wasabi was offline 20.-21. March due to unexpected changes in wasabiapp.org nameserver settings. The issue has been resolved and hopefully stays that way.

Wasabi update 9.2016

We have released Wasabi maintenance update.

Changes include:

  • Wasabi can now import Ensembl EPO alignments crossing block boundaries
  • Bug fixes and optimizations (e.g. improved Ensembl genetree support, server can provide data in jsonp format etc.)

The updated Wasabi is ready to use on our public server and its source files are available from GitHub repository or Wasabi downloads

Wasabi integrated to Ensembl genome browser

The world’s largest genome browser Ensembl (http://ensembl.org) has integrated Wasabi to provide interactive visualization of the Genetree datasets.

To see Wasabi in action, click on any node in a genetree (e.g. BRCA2 genetree) and click “Wasabi viewer”. The selected subtree together with the sequence alignment will be visualized in a pop-up Wasabi window.

See also an illustrated example in Ensembl release notes.

Wasabi integrated to ConSurf server

In addition to our public server, Wasabi can be added to other web services for customized integration.

The ConSurf server is using Wasabi to provide interactive visualization for the result alignments and phylogenetic trees.

Here’s an example results page with Wasabi link: http://consurf.tau.ac.il/2016//Gallery/2POL_A/output.php

And the article describing ConSurf: http://nar.oxfordjournals.org/content/44/W1/W344.full

 

Wasabi update 1.2016

Have a great year in 2016! Here’s an update for you:

  • New stuff
    • Import genetrees and alignment blocks also from Ensembl Genomes
    • Extended tree metadata import (EC/AC codes etc.)
    • Licensing changed from GPL to AGPL
    • New attribute (“check”) added to the plugin system and Pagan plugin
    • Sequences can now be removed from treeless dataset
  • Bug fixes
    • Fixed newick import
    • Sequence window position now retained after translation
    • Fixed server communication errors in userless (standalone) mode
    • Fixed a bug where tree was lost when saved to analysis library

New Wasabi is ready to use on our public server and its source files are available from GitHub repository or Wasabi downloads

Wasabi article published!

Great news! The first article describing Wasabi and few of its use cases has been published in Molecular Biology and Evolution.

 

You can now read the article online and cite it in publications:
Veidenberg, A., Medlar, A. and Löytynoja, A. (2015) “Wasabi: an integrated platform for evolutionary sequence analysis and data visualisation.” Mol. Biol. Evol.