GlycoWorkbench: Semi-Automatic Interpretation and Annotation of Mass Spectra of Glycans

Introduction

GlycoWorkbench is a suite of software tools designed for rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. The graphical interface of GlycoWorkbench provides an environment in which structure models can be rapidly assembled, their mass computed, their fragments automatically matched with MSn data and the results compared to assess the best candidate. GlycoWorkbench can greatly reduce the time needed for the interpretation and annotation of mass spectra of glycans.

Download and Installation

We are making available the next generation of the GlycoWorkbench tool as an alpha release - currently v2.0 alpha2. As this is an alpha release you will still be able to obtain the previous 1.3 release of GlycoWorkbench from the previous versions page. Please download the appropriate package from below for your operating system. The tool has been tested under Windows, Linux and Mac OS X. Windows users must have >= JRE (Java Runtime Environment) 1.6 update 20 installed as their default JRE - all other users require JRE 1.6. The latest release of the JRE 6 can be found on the Oracle homepage together with the installation guide and system requirements.

To manually launch GlycoWorkbench on the command line - please use the following command.

java -jar -Xmx300M eurocarb-glycoworkbench-1.0rc.jar

Windows

You only require the 64bit version of GlycoWorkbench if your default JRE is a 64bit (x86-64) one.

If you have installed GlycoWorkbench using the provided installation package - you'll find a corresponding entry within your start menu to launch GlycoWorkbench.

If the installer doesn't work for you - download and extract the above ZIP archive to your directory of choice; GlycoWorkbench can be launched with the enclosed executable. Please refer to the included README file, if you are having problems launching GlycoWorkbench.

News: 12/07/2010, some users are still reporting issues launching GlycoWorkbench; it appears to be an issue with some combinations of JDK and Windows that are installed. Please email info@… with the following details

  • Java version(s) (please list all) - found within Add/Remove programs (or uninstall program on newer versions of Windows)
  • Windows Version (if your not sure run the builtin program "winver") - including if it's 64bit or not.

Linux

Download and extract the correct ZIP archive into your directory of choice - run the program by clicking on the provided jar.

Mac OSX

News[13/07/2010]: Mac OSX version should work again (tested on cocoa_x86-64 build)

Run GlycoWorkbench using the provided shell script "mac_start.sh" - this requirement will be removed ASAP.

Manual

A short GlycoWorkbench_short_manual.1.2.4105.pdf ShortManual Download can also be downloaded.

How to cite

If you are using GlycoWorkbench or GlycanBuilder for preparing your articles, or if you employed the GlycanBuilder applet in your web interface, please cite:

A.Ceroni, K. Maass, H.Geyer, R.Geyer, A.Dell and S.M.Haslam: GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans Journal of Proteome Research, 7 (4), 1650--1659, 2008 ( PMID: 18311910)

A.Ceroni, A.Dell and S.M.Haslam: The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures Source Code for Biology and Medicine, 2007,2:3 ( PMID: 17683623)

Changes

2.0 Alpha 2 (Build 42) 26/07/2010

  • Fixed peak editor delete bug
  • Altered glycan contextual ribbon activation behaviour
  • UI speed ups

2.0 Alpha 2 (Build 35) 13/07/2010

  • Restored about menu .
  • Fixed Mac OSX specific issues.

2.0 Alpha 2 (Build 25) 12/07/2010

  • Added missing JNA library (Unix users affected)
  • Changed resize policy of a RibbonTask? for compatibility with Mac OSX and Linux users.

2.0 Alpha 2 (Build 15) 07/07/2010

#New Features

  • S3 support (suitability for use within GWB is being prototyped, might still be removed)
  • Automatic building of all packages and subsequent publication.

#Changes

  • Refactored the residue contextual ribbon tasks [id: 2]
  • Three packages are now created for Mac OSX (Carbon 32bit, Cocoa 32bit and Cocoa 64bit). [id:11]
  • Both 32 and 64bit packages are generated for Linux.
  • Switched Windows launcher to WinRun4J
  • New Startup script for Mac OSX (possibly to be replaced by a complete DMG)

#FIXED

  • Restored peak list paste support [id:6]
  • Fixed broken Buker peak list import [id:7]
  • Fixed exception being thrown when empty peak is deleted [id:12]
  • Fixed two UI jitter bugs [id: 16 and 17]
  • Tooltip support refactored via RichTooltip [id: 3]
  • Accelerator key support refactored via RichTooltip [id: 4]
  • Fixed some dialog boxes being too small [id: 8]
  • Converted all remaining GIF icons to PNGs [id:15]
  • Fixed high CPU load when displaying the fragment editor [id: 18]
  • Icons are now shown for terminals with unknown linkage [id: 5]
  • Fixed insert residue gallery being shown within the structure ribbon rather than the add residue gallery. (Prevented structures from being drawn from scratch). [id: 19]

Version 2.0 alpha 09/06/2010 (missing 64bit Windows Zip)

  • Cascade annotation of MSn data sets
  • Migration to Office style ribbon interface
  • Additional icons
  • Ribbon support for plugins
  • New splash screen and logo
  • Implementation of Mediawiki help system.
  • Help system, detection of internet connection.
  • Bug fixes for peak list editor (introduced in version 1.3)
  • Fixed broken jar click support (non-functional in version 1.3)

Version 1.3 21/05/2010

  • Moved user configuration into home directory
  • Initial integration of SWT browser (for future EurocarbDB integration)
  • Updated help system. (will be heavily revised in next revision)
  • Minor bug fixes.
  • Splash screen for Linux and Mac OS X users
  • Added charge field to Peak list panel

Version 1.1

Build 3480 - 22/09/2008

  • GAG profiling tool
  • in-silico fragmentation of sulfated glycans
  • graphic display of the peak list, similar to the spectra panel
  • residue properties toolbar
  • copy tables in spreadsheets with structures as compositions
  • search databases by sub-structure
  • close dialogs by pressing Escape
  • select OK in dialogs by pressing Enter
  • added executable, icons and splashscreen for Windows users
  • fixed export to SVG

see all changes

Acknowledgements

First of all, we must give a big thanks to the Glycoconjugate biochemistry group at JLUG and especially to Tobias Lehr, which have provided continuous testing and feedback to GlycoWorkbench and made it possible to reach its current level of functionality.

All my other thanks go to those projects which have provided free of charge some great Java libraries, sharing the result of their work with all the developers community. Many features of this software would not be possible without their effort. We should always remember to support open source and open access policies.

The component for loading raw spectra files have been realized using the fantastic library developed by Jayson Falkner and his colleagues at ProteomeCommons. They are working really hard to extend the support to all available formats in close collaboration with the MS instrumentation vendors. These guys really need all the appraisal and the support from the mass spectrometry community.

The components for displaying graphs have been realized using the !JFreeChart library, from the !JFree collection of Java free software projects.

The export to SVG, EPS and PDF has been made possible by the Batik toolkit from the Apache XML Graphics Project, part of the Apache Software Foundation for open source software.

The new look of GlycoWorkbench alpha 2 has been made possible by the Flamingo and Substance libraries created by Kirill Grouchnikov (pushing-pixels.org). All new artwork within GlycoWorkbench alpha 2 was created by Claire Strain-Damerell using Inkscape.

Last but not least we thank the  GlycomeDB Project for hosting the new web presence of GlycoWorkbench?.

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