JigCell Run Manager User's Manual

The JigCell Run Manager (JCRM) allows a user to define a set of specifications for simulation runs using a spreadsheet interface. Each row of the spreadsheet describes the information necessary for a single simulation run. While this is not the only way that JCRM can be used, the typical use is to create an ensemble of simulation runs related to a specific biomolecular reaction model, where each run differs from the others in only minor ways. Thus, JCRM provides support for defining simulation runs in terms of minor differences from other simulation runs, with the potential of building up a hierarchy of such differences. This makes it easy to define small parameter changes that affect many simulation runs.

JCRM serves two chief purposes. The first is to let users provide the specifications needed to run a simulation that matches a particular experiment. The second is to let users organize related simulation runs, and then run and view the results of either the entire ensemble or of a single simulation.

JCRM Manual - Table of Contents
1 - Overview 2 - Interface Components 3 - JCRM Menu Bar
4 - JCRM Spreadsheets 4.1 - Runs Spreadsheet 4.1.1 - Parents Editor
4.1.2 - Changes Editor 4.2 - Basal Parameters Spreadsheet 4.3 - Basal Initial Conditions Spreadsheet
4.4 - Simulator Spreadsheet 4.5 - Plotter Spreadsheet

1 - Overview

Cell cycle modeling often involves defining a model, which captures the differences among potentially hundreds of mutations of the wild type organism. This is represented by a simulation run for each such mutation, where each simulation run differs from others in a small number of parameters. JCRM allows users to express a hierarchy of simulation runs that define the minor differences between runs. That is, one run might be identical to a base run, except for changes to a few parameters or initial conditions. Hierarchies can be built up, whereby a given simulation inherits the differences from the wild type from one or more other runs. Developers of sophisticated cell cycle models do not want to have to edit all such simulation runs (and there could be hundreds of these) when they wish to change one or two parameter values shared by all such runs. JCRM's run hierarchies avoid this problem.

JCRM provides a sophisticated mechanism for keeping track of logical relationships among simulations done on a single model to fit a variety of experiments and allows the modeler easily to explore the parameter space of a model over a complicated set of simulations.

Run Manager Example

Figure 1. A simulation ensemble for budding yeast cell mutants.

2 - Major Interface Components

On startup JCRM screen will appear as in Figure 2. JCRM has two main user interface components: the menubar and the tab bar. The tab bar is disabled until a run file has been loaded.

Spreadsheet Interface
Figure 2. JCRM on start up.

3 - JCRM Menu Bar

The JCRM Menu Bar has three items: RunManager, File, and Edit. Only the first two are enabled when there is no run file loaded.

4 - JCRM Spreadsheets

JCRM manages the description and execution of ensembles of simulation runs using a tabbed spreadsheet interface. To specify a simulation run, the user must provide a model, a parameter set, an initial condition set, and a simulator parameter set. Each of these is specified using its own tab. Thus, there are five tabs in the JCRM interface. These are each described below.