FCModeler

This FCModeler picture shows a sample metabolic network for the plant hormone Gibberellin. For more pictures click here.

Project Abstract

The FCModeler project focuses on the dynamic display of directed graphs for projects such as metabolic networks and computer networks. Graph theory is used to analyze complex networks for common cycles and path search between nodes. The goals of this program are to:

Capture the intuitions of biologists and provide a modeling framework for assessing large amounts of information
Test effects of hypotheses

Use graph theoretic approaches to analyze network structure and behavior and search for critical paths in the network
Develop simulation tools based on fuzzy methods that model changes in the network

The graphical display program is written in Java. The modeling software is currently implemented in Matlab with an XML interface between the packages. The software is freely available for noncommercial use. If you improve the code, please share your innovations with the rest of the user community.

FCModeler Current Development

NEW Version of software available.
Continue to develop simulation tools using R
Develop more graph theoretic analysis.
Consistency checking for different type of “omics” data

Software / Files / Documents Used in this Project

Version 2.0 : Self-installing version for windows 2000 and XP; requires the Java 2 SDK, version 1.4.1 or above. (April 19, 2004)

This version represents a major upgrade

Different file format for files to accommodate the different levels of information available about a graph; ranging from graph structure to annotation and links.
Complete subgraph selection capabilities based on pathway names, cycles, paths, and P-neighborhoods.
Links to the open-source program R for data computation, generation of animation files, and performing network modeling.
Sample Data Files (from the MetNet Project): (Leave the files zipped for use with FCModeler)

Version 1.0 Software: (requires the Java 2 SDK version 1.3.x (http://java.sun.com/j2se/1.3/))

FCModeler v1.0 Jar Files (with layout program for Windows 2000) , Java documentation of code
FCModeler layout programs (Linux) (Mac)
FCModeler User's Manual

Note: This software uses the dot layout routine from the graphviz opensource software developed at AT&T labs (http://www.research.att.com/sw/tools/graphviz/) and the diva information software infrastructure. (http://www.gigascale.org/diva/)

Project Participants

Dr. Julie A. Dickerson (Electrical and Computer Engineering)	Dr. Eve Wurtele (Botany)
Mr. Zach Cox (MS, graduated 8/2002)	Mr. Paul Jennings (Undergraduate Research Assistant) Computer Engineering
Mr. Adam Tomjack (Undergraduate Research Assistant) Computer Science	Dr. Daniel Ashlock (Mathematics)
Ms. Josette Etzel (Ph.D. Student, Computational Biology)
Mr. Pan Du (Ph.D. Student, Electrical Engineering)

Project Funding

This work has been supported by

Proctor and Gamble Corporation
National Science Foundation (This material is based upon work supported by the National Science Foundation under Grant No. 0209809) Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation."
Iowa State University Plant Sciences Institute

Publications

J.A. Dickerson, Z. Cox, “Using Fuzzy Measures to Group Cycles in Metabolic Networks,“ North American Fuzzy Information Processing Society (NAFIPS) Annual Meeting, Chicago, IL, July, 2003.
Poster from ISMB 2002 J.A. Dickerson, Z. Cox, A.W. Fulmer
J.A. Dickerson, D. Berleant,Z. Cox, W. Qi, D. Ashlock, E.S. Wurtele, and A.W. Fulmer, "Creating and Modeling Metabolic and Regulatory Networks Using Text Mining and Fuzzy Expert Systems," in Computational Biology and Genome Informatics, edited by Jason T. L. Wang, Cathy H. Wu, Paul Wang, World Scientific Publishing:Singapore, pp.207-238, 2003.
J.A. Dickerson, Z. Cox*, E. Wurtele, A.W. Fulmer, "Creating metabolic and regulatory network models using fuzzy cognitive maps," IFSA World Congress and 20th North American Fuzzy Information Processing Society (NAFIPS) International Conference, Vancouver, British Columbia, Volume 4, 2171-2176, July, 2001.
J.A. Dickerson, D. Berleant, Z. Cox*, W. Qi, and E. Wurtele, "Creating Metabolic Network Models using Text Mining and Expert Knowledge," Atlantic Symposium on Molecular Biology and Genome Information Systems and Technology (CBGIST 2001), 26-30, Durham, North Carolina, March, 2001.

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