pathwaycommons / chibe

Pathway visualization and analysis tool for Pathway Commons and other BioPAX data

ChiBE: Chisio BioPAX Editor

Chisio BioPAX Editor, or simply ChiBE, is a free editing and visualization tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio.

The tool features user-friendly display, viewing, and editing of pathway models. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art layout and visualization technologies. In addition, facilities for querying a set of integrated pathways in Pathway Commons are provided. Furthermore, visualization of experimental data, including cancer genomics data of the cBioPortal, overlaid on pathway views is supported in ChiBE. These capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers.

ChiBE is a Java application running on various platforms including Windows XP/Vista/7, Linux, and Mac OS X. It was built using Chisio 2.0 and Eclipse GEF 3.1 for graph visualization, Paxtools for accessing and manipulating BioPAX files, and PATIKAmad for experiment data analysis.

ChiBE 2.2 User's guide

For a quick guide on how to explore pathways in Pathway Commons, please see this wiki page.

Download

ChiBE is distributed under Eclipse Public License.

Below are latest builds of ChiBE.

• Latest build for Windows
• Latest build for Linux

Below are the latest releases of ChiBE 2.2 for different platforms.

• Setup file for ChiBE 2.2 for Windows XP/Vista/7: 32-bit - 64-bit

• ChiBE 2.2 distribution for Linux (see "README.TXT" for instructions): 32-bit - 64-bit

Please contact us if you need a build for another platform.

Please see the setup guide for running ChiBE from sources, and quick start guide for fast examples.

Highlights

Following are sample screenshots showing tool highlights.

Click on the figure to see the entire screenshot.

Sample Pathways

Following are images of pathway models produced by ChiBE taken from some prominent databases.

Click on the figure to see the entire screenshot.

(left) ERK/MAPK targets from Reactome (middle) Class IB PI3K non-lipid kinase events from NCI PID (right) Hedgehog signaling pathway from The Cancer Cell Map

Release Notes for Version 2.2 (June 24, 2014)

• Made architectural improvements in the core.
• Added a Data Legend for the color-coding of the currently loaded experiment data.
• Implemented an enriched-reactions query to rank reactions with a statistical measure.

Release Notes for Version 2.1 (June 26, 2013)

• Upgraded Pathway Commons interface to the latest version.
• Added support for showing/hiding compartments.
• Revised binary interaction types for SIF views.

Release Notes for Version 2.0 (January 9, 2013)

• BioPAX level 3 Support: Support for BioPAX level 3 models as well as level 2 models is now provided seamlessly in ChiBE.
• SBGN Process Description Language Compliance: Loaded pathway models are now rendered using a language mostly compliant with SBGN's Process Description Language.
• Remote Querying: Now ChiBE can send graph queries to Pathway Commons database.
• Local Querying: Loaded pathway models can now be queried to search for local relationships.
• Fetching From GEO: ChiBE now offers an alternative way for visualizing expression data on pathways, if an expression data stored in NCBI GEO is to be visualized on a pathway from Pathway Commons. With providing the GEO accession number of series file only, user will be able to visualize the particular expression set in ChiBE.
• Fetching From cBio Portal: cBio Cancer Genomics Portal is a cancer genomics analysis portal, which offers the chance to explore cancer genomes with respect to mutations, copy number alterations, mRNA expression changes, DNA methylation values, and protein levels. ChiBE enables users analysis of such data at pathway level. It collects data from cBio Portal and integrates with the model to display the alterations associated with each entity.
• Upgraded Chisio, ChiBE rendering and layout engine, to version 2.0.

Release Notes for Version 1.1 (July 10, 2009)

• Support for Mac OS X
• Improved persistence of pathway views as image
• Several minor bug fixes

Team

• Ozgun Babur, Emek Demir, B.Arman Aksoy, Nikolaus Schultz, Chris Sander, cbio at MSKCC
• Ugur Dogrusoz, Merve Cakir, i-Vis at Bilkent University

ChiBE's requirements were determined by OB, UD, ED, NS, and CS. The software design and development were mainly performed by OB, with help from MC, AA, and UD.

Acknowledgements

We would like to thank IntelliJ for providing a free open source license for IDEA.

Publications

Babur, Ö., Dogrusoz, U., Çakir, M., Aksoy, B. A., Schultz, N., Sander, C., & Demir, E. (2014). Integrating biological pathways and genomic profiles with ChiBE 2. BMC genomics, 15(1), 642.

Babur, O., Dogrusoz, U., Demir, E., & Sander, C. (2010). ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics, 26(3), 429-431.

chibe's Issues

Update ChiBE logo

with a higher resolution one

Original issue reported on code.google.com by [email protected] on 31 Dec 2012 at 8:55

GEO data importer does not support multiple-series-file-containing data sets.

* Start ChiBe
* Load a network
* Select Data > Fetch From GEO
* Enter GSE36139 as id and submit

It fails since the data-set consists of more than one matrix-series files. 
See: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36139

Original issue reported on code.google.com by [email protected] on 28 Sep 2012 at 4:48

Highlighting PC L3 query results

We should highlight nodes used for querying in the results of PC L3 queries.

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 9:04

"Find GoI on SIF file" does not work

rev a47d3fc39f1c:

1. Select SIF > Find GoI on SIF file
2. Select sample.sif as your network, genes.txt as your gene set; select all 
SIF rules
3. Click on "OK"

You get:

SIF view contains 55 nodes and 50 edges.
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
    at java.lang.String.substring(String.java:1937)
    at org.patika.mada.util.XRef.<init>(XRef.java:72)
    at org.gvt.action.GOIofSIFAction.run(GOIofSIFAction.java:108)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.notifyListeners(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:207)

Original issue reported on code.google.com by [email protected] on 21 Sep 2012 at 8:42

Attachments:

• genes.txt
• sample.sif

New data type (alteration)

Looks like Alteration Data has been added as a new data type to existing ones 
(Expression Data, etc.) Since it's the first of the various types, it comes up 
as default data type in dialogs (Load & Fetch operations), where Expression 
Data is more of an expected data type. Can we perhaps add Alteration Data to 
the end of this list (enum?) so Expression Data stays the defaults in such 
cases?

Original issue reported on code.google.com by [email protected] on 3 Aug 2012 at 11:55

Layout is not performed while running from jar

With certain models, layout is not performed while running the project from jar 
file. Layout is initialized but cannot go further. It throws the following 
exception if you load Interferon Gamma Signaling pathway from samples but works 
normal if you load Extracellular Matrix Organization. 

java.lang.NoSuchMethodError: org.ivis.layout.LEdge.setTarget(Lorg/ivis/layout/LN
ode;)V
        at org.gvt.layout.BiPaLayout.clearComplexes(BiPaLayout.java:87)
        at org.gvt.layout.BiPaLayout.layout(BiPaLayout.java:118)
        at org.ivis.layout.Layout.runLayout(Layout.java:243)
        at org.gvt.LayoutManager.runLayout(LayoutManager.java:266)
        at org.gvt.command.LayoutCommand.execute(LayoutCommand.java:39)
        at org.gvt.action.CoSELayoutAction.run(CoSELayoutAction.java:61)
        at org.gvt.action.OpenPathwaysAction.openPathwayInTab(OpenPathwaysAction
.java:177)
        at org.gvt.action.OpenPathwaysAction.run(OpenPathwaysAction.java:148)
        at org.gvt.action.LoadBioPaxModelAction.run(LoadBioPaxModelAction.java:2
53)
        at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
        at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection
(ActionContributionItem.java:538)
        at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContri
butionItem.java:488)
        at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionC
ontributionItem.java:400)
        at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
        at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
        at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
        at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
        at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
        at org.eclipse.jface.window.Window.open(Window.java:787)
        at org.gvt.ChisioMain.main(ChisioMain.java:207)

I did not observe this exception while working in idea.

Original issue reported on code.google.com by [email protected] on 2 Oct 2012 at 8:08

User's Guide link update

The address of "How to Use" document under the About menu should be updated to 
include 2.0, which points to the latest User's Guide.

Original issue reported on code.google.com by [email protected] on 3 Aug 2012 at 11:57

"Highlight By Name" does not use current color

Highlight something with "Highlight By Name" feature, then change the highlight 
color. If you highlight same entity with "Highlight By Name", it uses the 
previous color. Updated color is only used when "Highlight Selected" is used. 

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:55

Crash on PC level 2 neighborhood query

Query > PC (l2) > Neighborhood
Enter "PER1"
We get an exception:

org.biopax.paxtools.util.BioPaxIOException: Unexpected element at start: error
    at org.biopax.paxtools.io.SimpleIOHandler.readNameSpaces(SimpleIOHandler.java:135)
    at org.biopax.paxtools.io.BioPAXIOHandlerAdapter.convertFromOWL(BioPAXIOHandlerAdapter.java:216)
    at cpath.client.PathwayCommonsIOHandler.readBioPAXfromURL(PathwayCommonsIOHandler.java:120)
    at cpath.client.PathwayCommonsIOHandler.getNeighbors(PathwayCommonsIOHandler.java:245)
    at org.gvt.action.QueryNeighborsAction.run(QueryNeighborsAction.java:169)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:207)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:41

Bad layout

attached graphml file (provided by Ozgun) produces a bad layout (extremely long 
edges).

similar problem can be easily reproduced by querying the neighborhood of p53 in 
ChiBE (?)

Original issue reported on code.google.com by [email protected] on 30 May 2012 at 12:59

Attachments:

• badlayout.graphml

BiNOM

https://binom.curie.fr/
Investigate their support for BioPAX level3. Can they read biopax level 3 and 
write to level 3 fully?

Original issue reported on code.google.com by [email protected] on 30 Apr 2012 at 12:38

cBio alteration data settings

We should make sure min <= max for these parameters in the dialog (if it's not 
satisfied revert to original value on Enter or OK?)

Original issue reported on code.google.com by [email protected] on 3 Aug 2012 at 11:52

Selecting nodes based on expression range

We can discuss addition of a new method for selecting nodes on the graph, which 
will be useful while analyzing microarray data. This method will get an 
expression range from the user and then select nodes whose expression value is 
within this range. Instead of selecting, we can highlight these nodes or 
generate a new view consisting of these selected nodes. 
To get the input from user, we can use Slider or Scale classes of SWT. 
Alternatively, a text field based way which requires the user to write the 
minimum and/or maximum values can be followed.  

Original issue reported on code.google.com by [email protected] on 19 Jul 2012 at 2:37

Portal Data Details dialog availability

cBio Portal Data Details dialog is still available after we load expression 
data or remove data colors. It could be better if we restrict its availability 
to the cases where alteration data is loaded.
Also it is available for compartment and reaction nodes but they do not have 
associated alteration data. Maybe we can make this menu item available only for 
entity nodes, if that is possible. 

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 9:50

Icons in pop-ups/dialogs

In some windows, no icon is displayed on the title bar, while in others can't 
find the appropriate icon and displays a red square instead. We should properly 
display the ChiBE icon in all.

Ozgun, it'd be great if you can figure out the problem and pass it to Merve to 
fix if you like.

Original issue reported on code.google.com by [email protected] on 30 Apr 2012 at 12:32

No warning on sif creation with no model

When no model is loaded, we should put up a warning when the user tries to 
create a SIF view (SIF | Create SIF View ...)

Original issue reported on code.google.com by [email protected] on 15 Oct 2012 at 8:56

About box update

- Let's add cBio Portal here.
- change BCBI to Bilkent University with logo (similarly we need to make these 
changes in the User's Guide). please talk to me about what image to use for 
this.

Original issue reported on code.google.com by [email protected] on 3 Aug 2012 at 12:07

Query performed even if there are unknown symbols

PC L3 queries are performed even if there are unrecognized symbols, as long as 
the minimum required number is satisfied with known symbols. For instance, give 
one valid and one invalid symbol for Neighborhood Query and it performs the 
query with the known one. We should not continue with the query unless all the 
symbols are valid. 

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 9:15

Raw data conversion dialog next button not enabled

When I say Data --> Load Raw Data, 
choose "... has a reference ... file", click next, I load the following file as 
the reference file:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&form=text&view=data&acc=
GPL570

It recognizes several fields including the ID field, but I cannot click Next. 
Next becomes enabled only after playing with the table (no need to change 
anything).

Original issue reported on code.google.com by [email protected] on 30 Sep 2012 at 9:03

Case sensitive gene symbols

When performing querying symbols seem to be case sensitive. For instance, I can 
query neighborhood of "TP53" but "tp53" says "unknown symbol". If all symbols 
are upper case, can't we just convert all input to uppercase?

Original issue reported on code.google.com by [email protected] on 28 Jun 2012 at 12:02

Installers for Windows, Linux and Mac

Please prepare installers for these platforms. Linux and Mac ones could simply 
be a zipped distribution with proper Readme document, whereas we would like to 
have a setup executable for the Windows platform.

Make sure we specify instructions for all three platforms in the Readme file, 
including minimum requirements for running ChiBE 2.0.

Original issue reported on code.google.com by [email protected] on 4 Oct 2012 at 11:01

Legend for Nodes and Edges

We may add legends explaining what each node and edge glyph stands for, 
considering the increased number of different glyphs. This can either be a 
single legend dialog including information for both or separate dialogs for 
each. 

Original issue reported on code.google.com by [email protected] on 19 Jul 2012 at 2:10

Fine-tune layout parameters

We should fine tune layout parameters such as desired edge length (30 looks 
good).
Currently there is no single point from which we can change these, maybe a 
change in the class structures might also achieve this.

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 6:59

Find GoI on SIF

We should consistently rename this feature under the SIF menu. I think we use 
"Paths Between" instead of "GoI" now. Both the menu item and the dialog title 
should be changed. We should also put a one liner (explanation) for this at the 
beginning of the dialog like we did(?) with some queries.

Original issue reported on code.google.com by [email protected] on 19 Sep 2012 at 1:11

Context menu PC queries are level3

Need to specify the fact that PC queries available under node context menu are 
level3: "... (Level 3)"

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:23

Saving should ensure .owl extension

When saving a model, if user enters some name not ending with .owl, ChiBE does 
not handle it and uses whatever name is given. 

ChiBE shouldn't save files without .owl extension. If the user ended the file 
name differently, then it should add .owl to the end of the file name.

Original issue reported on code.google.com by [email protected] on 30 Sep 2012 at 7:24

Legend menu item name and title inconsistent

let's consistently name them "Legend"

Original issue reported on code.google.com by [email protected] on 13 Sep 2012 at 10:25

Web page screenshots

Screenshots in tool web page needs to be updated for 2.0

Original issue reported on code.google.com by [email protected] on 28 Dec 2012 at 1:13

Detection when the user mixes L2 and L3

ChiBE can work with BioPAX L2 and L3, but cannot mix them. So if user starts 
with a level, they cannot merge with another level, or cannot query a database 
of different level. However, the related actions are not doing this check, and 
if user mixes levels, an exception is thrown. These checks should be placed in 
the appropriate actions. The current level can be checked using:

main.getOwlModel().getLevel()

and the error message can be displayed using:

MessageDialog.openError(main.getShell(), title, message);

Original issue reported on code.google.com by [email protected] on 12 Apr 2012 at 4:33

Update Documentation

We need to update the User Manual in line with latest changes

Original issue reported on code.google.com by [email protected] on 30 Apr 2012 at 12:30

Sample models

We will need some sample models (both l2 & l3) checked in to the sources and to 
be distributed with the installers. Pass it on to Merve if you like.

Original issue reported on code.google.com by [email protected] on 19 Sep 2012 at 10:40

Update query documentation.

Update documentation about PC L3 queries offered in pop-up menu.

Original issue reported on code.google.com by [email protected] on 4 Oct 2012 at 1:09

Query names and explanations inconsistent

Can we please go over all queries, their menu item names, dialog titles and 
explanations to be consistent?
For instance, we still have "GoI" in query window titles instead of "paths 
between".
In the explanation of "paths between" queries (both local and l3), can we add 
"of specified length limit" after "Find all paths"?
Similarly modify the explanation for PoI (Paths from to).

Original issue reported on code.google.com by [email protected] on 21 Sep 2012 at 11:37

Extra layout calls on query in new window

When we make a query to show results in a new window, before the new window is 
opened and query results are laid out and presented in this new window, a 
layout (sometimes multiple successive ones) is performed *in the window from 
which query was made*. 

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:34

Document alteration data feature

Now that we have a way to query and show alteration data from cBio Portal, we 
should document this feature (under Experiment Data chapter).

Original issue reported on code.google.com by [email protected] on 3 Aug 2012 at 12:08

SIF view are closing unnecessarily while loading an owl

Start ChiBE
Load any SIF file.
Click on Load BioPAX Model button.

Now it asks you if you want to save the file. If you say yes, nothing happens. 
It works as if cancel pressed. If you say no, then your SIF tab is closed upon 
loading the BioPAX model.

How should it behave:

When there is no BioPAX file loaded, it shouldn't bother with saving the graph 
or closing existing tabs while loading a new BioPAX file.

Original issue reported on code.google.com by [email protected] on 20 Sep 2012 at 7:42

Zoom with scroller

Emek thinks that if ChiBE can zoom in and out with mouse scroller, this would 
be cool.

Current scroller action is to scroll. We can implement this for ctrl+scroll.

Original issue reported on code.google.com by [email protected] on 15 Feb 2013 at 10:32

Raw data conversion wizard freeze in Mac

Arman showed me that after doing "Data --> Load Raw Data" in Mac, the wizard 
appears but the application is frozen.

Original issue reported on code.google.com by [email protected] on 7 Nov 2012 at 7:53

Tag sources for 2.0

Repository needs to be tagged for version 2.0 (need to wait a little bit longer 
until release candidates are verified in different platforms)

Original issue reported on code.google.com by [email protected] on 28 Dec 2012 at 1:14

Experiment data values table columns too narrow

Load an experiment data and go to Data --> Data Selection --> Values.

Values are unreadable because column width is small, values are long, and their 
alignment is to the center. I cannot even manually adjust the column widths 
because even I resize the window, the table stays fixed. There are several 
points that can be improved here:

- Print values to a few significant digits
- Set column width to fit the number in it (may not be good for large numbers).
- Align numbers to the left so we can read the important part even if cannot 
see the whole.
- Dynamically resize the table when the window width is changed.

Original issue reported on code.google.com by [email protected] on 30 Sep 2012 at 7:45

Improve description of neighborhood query

Query > PC (l2) > Neighborhood
We are not allowed to specify a distance for this query but the explanation 
implies that. I guess we do a fixed distance neighborhood query here; can we 
specify that distance explicitly here?

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:43

Query is performed after closing the query dialog

PC L3 "Pathways with keyword" and "Object with RDF ID" queries perform a query 
after the window is closed with the keyword supplied in previous turn. 

Original issue reported on code.google.com by [email protected] on 2 Oct 2012 at 8:17

Consistent naming of query operations

We should consistently name each query operation as discussed earlier.

Original issue reported on code.google.com by [email protected] on 30 Apr 2012 at 12:33

Delete Pathway does not work properly with L3 models

Choose an L3 model which has nested pathways. Deleting a pathway does not 
delete its name from Open Pathway dialog and if you try to open the pathway, it 
throws a Null Pointer Exception. 
I can provide an example model if needed. 

Original issue reported on code.google.com by [email protected] on 21 Sep 2012 at 12:04

Rename Bothstream

We could rename it to "Both Streams" or "Up and Down Streams"

Original issue reported on code.google.com by [email protected] on 26 Sep 2012 at 8:22

SBGN-compliance

How far are we from being SGBN-complaint? We don't need to support SBGN PD 
notation fully but supporting the basics would be nice. Please investigate how 
much work is involved to do so.

Original issue reported on code.google.com by [email protected] on 30 Apr 2012 at 12:35

Template Reaction Node disappears after duplicating pathway

Use local queries to generate a pathway. When you duplicate it, template 
reaction nodes are not present in the duplicated pathway. 
With pathways generated by PC L3 queries, they disappear from duplicated 
pathway after updating it.

Original issue reported on code.google.com by [email protected] on 21 Sep 2012 at 11:32

Cannot save images as .gif

If you try to save pathway or image as a gif file, you get the following 
exception and an empty gif file is generated:

org.eclipse.swt.SWTException: Unsupported color depth
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.internal.image.GIFFileFormat.unloadIntoByteStream(Unknown Source)
    at org.eclipse.swt.internal.image.FileFormat.unloadIntoStream(Unknown Source)
    at org.eclipse.swt.internal.image.FileFormat.save(Unknown Source)
    at org.eclipse.swt.graphics.ImageLoader.save(Unknown Source)
    at org.eclipse.swt.graphics.ImageLoader.save(Unknown Source)
    at org.gvt.action.SaveAsImageAction.run(SaveAsImageAction.java:139)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:400)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
    at org.eclipse.jface.window.Window.open(Window.java:787)
    at org.gvt.ChisioMain.main(ChisioMain.java:207)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)

I did a quick search about this exception and found this information: "Saving 
an ImageData as a GIF is expected to work if your image data is of bit depth 1, 
4 or 8." So it seems these images does not satisfy this depth requirement. 
Should we try to find an alternative way of saving as gif files or omit gif 
file option? What is your suggestion?

Original issue reported on code.google.com by [email protected] on 27 Sep 2012 at 1:45

Decrease compartmentless molecules.

We can improve ChiBE view by assigning compartmentless objects to the most 
likely compartments. For instance if they are related to a reaction with 
molecules in a compartment, we can move them there.

Original issue reported on code.google.com by [email protected] on 15 Feb 2013 at 10:36

Portal Data Details dialog is not updated

Load alteration data and remove some of the samples using "Data | Data 
Selection". If alteration frequency changes after this operation, node color 
and tooltip values are updated accordingly but the frequencies in "Data 
Details" pop-up dialog remains same.  

Original issue reported on code.google.com by [email protected] on 24 Sep 2012 at 9:04