Overview
The Comparator is an integrated package of Java tools for performing a quantitative analysis on a collection of data sets. Core tools for the system are focused around data entry, transformation, and analysis. Additional tools can be created and linked with the Comparator. Domain users customize the Comparator by adding and removing tools.
JigCell is a suite for cell cycle modeling that includes the Comparator. The cellcycle module is the collection of Comparator tools used by JigCell. This module customizes entry of experimental data, supports dynamic data collection from models using the JigCell Model Builder and Run Manager, and performs objective-based comparisons.
Papers Describing the Comparator
NA Allen, L Calzone, KC Chen, A Ciliberto, N Ramakrishnan, CA Shaffer, JC Sible, JJ Tyson, MT Vass, LT Watson, JW Zwolak. Modeling Regulatory Networks at Virginia Tech. OMICS: A Journal of Integrative Biology, 7(3):285-299, 2003.
NA Allen, CA Shaffer, MT Vass, N Ramakrishnan, LT Watson. Improving the Development Process for Eukaryotic Cell Models with a Modeling Support Environment. In Proceedings of the 2003 Winter Simulation Conference, pp. 782-790, 2003.
NA Allen, CA Shaffer, N Ramakrishnan, MT Vass, LT Watson. Improving the Development Process for Eukaryotic Cell Models with a Modeling Support Environment. SIMULATION: Transactions of the Society for Modeling and Simulation International, 79(12):674-688, 2003.
NA Allen, KC Chen, CA Shaffer, JJ Tyson, LT Watson. Computer Evaluation of Network Dynamics Models with Application to Cell Cycle Control in Budding Yeast. IEE Systems Biology, 2006 (to appear).
Other JigCell Papers
MT Vass, NA Allen, CA Shaffer, N Ramakrishnan, LT Watson, JJ Tyson. The JigCell Model Builder and Run Manager. Bioinformatics, 20(18):3680-3681, 2004.
NA Allen, CA Shaffer, LT Watson. Building Modeling Tools that Support Verification, Validation, and Testing for the Domain Expert. In Proceedings of the 2005 Winter Simulation Conference, pp. 419-426, 2005.
TD Panning, LT Watson, NA Allen, CA Shaffer, JJ Tyson. Deterministic Global Parameter Estimation for a Budding Yeast Model, 2006 (to appear).
User Information
Information on installing the Comparator is part of the main JigCell distribution.
Testing
Smoke tests quickly exercise the system with minimal user input. Going through the system tests more throughly exercises the Comparator.
Getting Started
The Comparator can be used as a standalone application or as an analyzer in the BioSPICE Dashboard. Most users run the Comparator as a standalone application.
- Walkthrough using the Comparator as a standalone application
- Walkthrough using the Comparator in the BioSPICE Dashboard (not recommended)
Release Information
Releases are made on a regular basis rather than waiting for the completion of specific features. All original code is released under the DARPA BioCOMP Open Source License. The core modules are in the compare package. A set of addon modules for cell cycle modeling is in the cellcycle package. This package require the compare package to run or build. The default configuration for JigCell uses the cellcycle modules. Other components of JigCell are available from the main JigCell distribution. The Comparator is built using the JigCell build system.
Downloads
- Latest BioSPICE release
- Latest JigCell release
Change Logs
- Changes for versions 6.1.0 to current
- Changes for versions 6.0.0 to 6.0.5
- Changes for versions 5.0.0 to 5.0.5
- Changes for versions 4.0.0 to 4.0.5
- Changes for versions 3.0.0 to 3.0.3
- Changes for versions 2.0.0 to 2.0.5
- Changes for versions 1.1.0 to 1.1.8
- Changes for versions 1.0.0RC1, 1.0.0, and 1.0.1
Future Plans
JigCell has a bug tracker that holds all of the bug reports and feature requests that we've gotten. There is a queue specifically for Comparator issues.
Before the bug tracker was in use I kept a list of "blue sky" features. This list is no longer being updated.
Programming Resources
General
| Getting started with Comparator development | HTML | - |
|---|---|---|
| Overview of current Comparator modules | HTML | - |
| API documentation for all Comparator classes | HTML | |
| Cross-referenced and syntax highlighted source code | HTML | - |
| Design rules to keep in mind when working on the Comparator | HTML | - |
| Debugging the Comparator | HTML | - |
Working with Comparator Data
| Organization of data in the Comparator and how to access it | HTML | - |
|---|---|---|
| Existing data sources and how to use them | HTML | - |
| Using data elements | HTML | - |
| Sequence diagram of a transform evaluation | - | PS |
| File formats used by the Comparator | HTML | - |
Diagrams
| Package design for Comparator (Notes) | PASTA | PNG |
|---|---|---|
| Current package dependencies for Comparator (Notes) | PASTA | PNG |
| Package design for JigCell (Notes) | PASTA | PNG |
| Current package dependencies for JigCell (Notes) | PASTA | PNG |
| Data flow diagram for the Comparator | FIG | PS |
| Data flow diagram for Compare2 | FIG | PS |
| Data flow diagram for the JigCell | FIG | PS |
| User workflow diagram for the JigCell | FIG | PS |
| Comparator wiring diagram [out of date] | FIG | PS |
| Simplified Comparator wiring diagram [out of date] | FIG | PS |
| List of JigCell components used in the diagrams [out of date] | DOC | PS |
