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Software by Jesse R. Walsh

Tools for Systems Biology

This site is a portal to all software released by me, Jesse R. Walsh, as I complete my PhD in Bioinformations and Computational Biology in the Electrical and Computer Engineering department at Iowa State University. All software here is licensed under the GPL, so feel free to use and improve it as you see fit. Please cite me when publishing or releasing projects using any software found here.

What is Systems Biology?

Bioinformatics and Systems Biology are both rapidly gaining acceptance as important fields of science, yet both terms are still somewhat vague.  The field of Bioinformatics exists at the intersection of Biology and Computer Science and seeks to use both biological and computer science techniques in order to further our understanding of biological systems.  Bioinformatics projects will often include both biological components such as DNA sequencing, metabolomics, protein binding assays, etc., as well as computational components such as network analysis, string alignments, and machine learning methods.  A successful bioinformatician is able to bridge these two fields of science in order to achieve what neither could do alone.

As I understand it, Systems Biology really means two things. On one hand, it refers to the study of the emergent properties of a biological system that result from the interactions between individual components.  Often these interactions cannot be observed or predicted from the information obtained from each individual entity alone, and must be studied by observing the system in its entirety.  The other meaning emphasizes the word 'Systems' in the engineering sense; it refers to the application of electrical and computer engineering systems theory to biology.

Software Projects found here

Use the top menu to navigate software projects. This site includes both projects wholly designed and developed by me as well as projects in which I contributed in some significant way.