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MOST: a software environment for constraint-based metabolic modeling and strain design
James J Kelley1, Anatoliy Lane1, Xiaowei Li1
1Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ 08102, USA and Phenomics and Bioinformatics Research Centre and School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA 5095, Australia.
Bioinformatics (Oxford, England)
|February 14, 2015
Summary
MOST, a user-friendly software, now offers the fastest gene knockout algorithm (genetic design through branch and bound) through an intuitive interface. This tool integrates flux balance analysis for optimizing metabolic pathways and product yields.
Area of Science:
- Metabolic Engineering
- Computational Biology
- Systems Biology
Background:
- Flux Balance Analysis (FBA) is a key method for predicting metabolic behavior.
- Genetic Design through Branch and Bound (GDBB) is the fastest algorithm for identifying gene knockouts to enhance product formation.
- Previous GDBB accessibility was limited to command-line interfaces, posing challenges for non-programmers.
Purpose of the Study:
- To introduce MOST (Metabolic Optimization and Simulation Tool).
- To provide a user-friendly interface for GDBB and FBA.
- To facilitate the optimization of metabolic pathways for increased product yield.
Main Methods:
- MOST implements GDBB within an intuitive, Excel-like graphical user interface.
- The software integrates FBA for metabolic modeling.
- It supports Systems Biology Markup Language (SBML) and CSV file formats.
Main Results:
- MOST makes the GDBB algorithm accessible to users without programming expertise.
- The software streamlines the process of identifying gene knockouts for metabolic pathway optimization.
- It enhances the usability of advanced computational tools in systems biology.
Conclusions:
- MOST democratizes the use of GDBB for metabolic engineering applications.
- The tool simplifies the prediction and implementation of genetic modifications for improved product synthesis.
- It represents a significant advancement in making complex metabolic modeling tools accessible to a wider scientific audience.
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