What is GeneFlow?

Geneflow is a workflow system for automating many aspects of genome data analysis in a collaborative research environment. These data may consist of genomic DNA sequence, physical mapping hybridization data, gene expression profiling data, etc. Data generation and analysis may take place at multiple facilities. The system is designed to leverage the power of the Web to tie together the various activities of data generation and analysis at multiple facilities. The system is currently being developed with the immediate goal of providing an informatics infrastructure for the Neurospora crassa and Pneumocystis carinii genome projects. The system is evolving rapidly, so this page may be updated frequently to reflect the current system status as well as the design of components to be developed in the future.

What does GeneFlow consist of?

GeneFlow consists of a number of software modules that carry out a particular function or set of functions. These modules are being developed in the Java and Perl programming languages. The modules are designed to be integrated into workflows using the METEOR workflow management system. Using METEOR workflows can be created visually, by using a graphical "drag and drop" utility. This makes it easy for non-programmers to create and modify workflows once the application modules have been developed. Additionally, METEOR, is fully web-enabled. Users of GenFlow will be able to access the different components of the application via a browser.

Availability of Software

The application modules will be made freely available for download. Use of the METEOR workflow management system requires a license from Infocosm. Alternatively, workflow applications can be created with GeneFlow software modules by hand by writing scripts.


The following image is a screenshot of the METEOR graphical workflow building utility showing a number of GeneFlow modules linked together in a workflow.

Description of Icons in Above Figure

A series of screenshots have been set up that illustrate how a user interacts with the system.


Currently GeneFlow is being developed by David Hall and John Miller with input from the fungal genomics community.