RuleBuilder

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1 Description
2 Downloading
3 Demonstration
4 Configuration
5 Getting Started
6 Known Bugs
7 Wish List
8 Examples

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Description

RuleBuilder provides a graphical user interface to BioNetGen.

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Downloading

RuleBuilder can be downloaded from the BioNetGen Distributions page.

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Demonstration

A video demonstration of the RuleBuilder Beta.

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Configuration

With the Java Runtime Environment installed, it can be run either by double-clicking on the RuleBuilder-x.xx.jar file in the RuleBuilder directory, or typing

 java -jar RuleBuilder-x.xx.jar

from the command line.

The first thing you need to do is configure RuleBuilder with the correct paths to BNG2.pl, the BioNetGen executable, and a temporary work file. To do this, click on settings under the File menu of RuleBuilder. You will see a dialog box similar to the one below. Click Browse to find the correct file and path. The BNG2.pl file is found in the Perl2 subdirectory of the distribution. The second item in the settings window, the temp file, can be placed anywhere you have write access.

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Getting Started

Instructions for using RuleBuilder can be found here.

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Known Bugs

Using whitespace in Species or Observable names results in error when running BNG2.pl
Does not work under some versions of linux when the Gnome window manager is running. If you experience this problem, please provide specifics here.
Reading in labeled species produces spurious Molecule Types.
Valid molecules on Drawing Board with multiple component states become invalid after they are added to Molecule Types.
Fix simulation dialog box so that it can be aborted without rerunning a model.
Fix zooming. Annoying jumps.
Molecule names beginning with a number produce an error when BNG is run on the generated BNGL file because of a Perl syntax issue:

generate_network({overwrite=>1,check_iso=>1,max_iter=>25,max_stoich=>{26sProteosome=>unlimited}});

causing the BNG error

ABORT: syntax error at (eval 22) line 1, near "26sProteosome"

This problem is fixed by quoting 26sProteosome, as in

generate_network({overwrite=>1,check_iso=>1,max_iter=>25,max_stoich=>{"26sProteosome"=>unlimited}});

This is done by editing the bngl file, but a more useful solution at present is simply not to start molecule names with numbers.

Bugs that may have been fixed in Sarah's code

Importing of some BNGL files is broken. The file fceri_ji.bngl is an example.

The bug illustrated by the file fceri_ji.bngl appears to be caused by numbered reaction rules. Until it is fixed the file will import if you remove the numbers from the beginning of the reaction rule specification lines. Here is a fixed version that imports correctly into RuleBuilder.

Appearance of comment in a line causes entire line to be ignored.

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Wish List

Set up RuleBuilder as standalone app that installs easily on Windows and OS X.
Reasonable keyboard shortcuts (Sarah partially implemented these).
Default layout doesn’t permit reasonable workflow. Sarah developed a better layout and we should update to and test her modifications.
Labeling of species in plot (or some other way to make correspondence between species and indices given in plot window).
Plotting of total flux for all reactions generated by rule. This requires additional output from backend, but would be very useful in debugging.
Corresponding BNGL optionally displayed along with model elements.
BNGL text file corresponding to model displayed in separate window.
Spawning of multiple windows to handle multiple models and better data management of data collected from previous runs.
Ability to reorder items on all palettes. Currently, this is implemented only in a crude way for the Rules palette.
Search: The hardest thing to do with a big model is find the rule you are looking for.
Reorder parameters by sort. Hard to find the parameter in a list currently.
Track changes to seed species and rules so that model can be re-simulated without network generation unless these have changed. This is useful for changing model or simulation parameters.
- Allow parameter scans
Enable direct editing of BNGL model to add syntax to rules.
Highlight reaction centers.
Allow activation status of rule, seed species, or observable to be toggled using a check box.