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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
BioNessie(G) - a Grid enabled biochemical networks simulation environment
Xuan Liu1, Jipu Jiang, Oluwafemi Ajayi
1Bioinformatics Research Centre, University of Glasgow, Glasgow, Scotland, UK. xliu@dcs.gla.ac.uk
Studies in Health Technology and Informatics
|June 19, 2008
Summary
BioNessie, a biochemical network simulator, was enhanced using UK Grid technologies. This enables larger-scale simulations, providing deeper insights into cellular processes and organismal pathways.
Area of Science:
- Biochemistry and Systems Biology
- Computational Biology and Bioinformatics
- High-Performance Computing
Background:
- Biochemical network simulations offer crucial insights into cellular mechanisms.
- The BioNessie simulator was developed at the University of Glasgow.
- Scaling simulations is essential for comprehensive biological understanding.
Purpose of the Study:
- To describe the BioNessie biochemical network simulator.
- To detail the extension of BioNessie to leverage Grid technologies.
- To support larger-scale biochemical network simulations.
Main Methods:
- Utilizing UK Grid technologies for distributed high-performance computing.
- Extending the BioNessie simulator architecture.
- Implementing parallel processing for large datasets.
Main Results:
- BioNessie successfully integrated with UK Grid resources.
- The enhanced simulator supports significantly larger-scale simulations.
- Improved computational efficiency for complex biochemical models.
Conclusions:
- The integration of BioNessie with Grid technologies enhances its capability for large-scale simulations.
- This advancement facilitates deeper understanding of complex biochemical networks.
- The developed approach provides a scalable platform for systems biology research.
