2009/01/19 by Anastasia C. Deckard, Anastasia Deckard, Frank T. Bergmann +5 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN) #q-bio.MN
paper · pdf · doi:10.48550/arxiv.0901.3067
17 pages, 6 figures
arxiv created 2009/01/19 · openalex publication_date 2009/01/19 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable time (< 20 days). We have currently generated over 47 million unique reaction networks. All currently generated sets of networks are available and as new sets are completed they will also be made available. Also provided are programs for translating them into different formats, along with documentation and examples. Source code and binaries for all the programs are included. These can be downloaded from (http://www.sys-bio.org/networkenumeration). This library of networks will allow for thorough studies of the reaction network space. Additionally, these methods serve as an example for future work on enumerating other types of biological networks, such as genetic regulatory networks and mass-action networks that include regulation.