| Title: |
Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python Modules |
| Language: |
English |
| Authors: |
Kaste, Joshua A. M. (ORCID 0000-0003-1942-0315); Green, Antwan; Shachar-Hill, Yair (ORCID 0000-0001-8793-5084) |
| Source: |
Biochemistry and Molecular Biology Education. 2023 51(6):653-661. |
| Availability: |
Wiley. Available from: John Wiley & Sons, Inc. 111 River Street, Hoboken, NJ 07030. Tel: 800-835-6770; e-mail: cs-journals@wiley.com; Web site: https://www.wiley.com/en-us |
| Peer Reviewed: |
Y |
| Page Count: |
9 |
| Publication Date: |
2023 |
| Sponsoring Agency: |
US Department of Energy, Office of Science; National Science Foundation (NSF), Division of Graduate Education (DGE); National Institute of General Medical Sciences (NIGMS) (DHHS/NIH) |
| Contract Number: |
DESC001826; 1828149; T32GM110523 |
| Document Type: |
Journal Articles; Reports - Research |
| Education Level: |
Higher Education; Postsecondary Education |
| Descriptors: |
Science Instruction; Teaching Methods; Prediction; Metabolism; Programming Languages; Kinetics; Biochemistry; Models; Computer Simulation; Lesson Plans; Lecture Method; Workshops; Undergraduate Students; Graduate Students; Doctoral Students |
| DOI: |
10.1002/bmb.21777 |
| ISSN: |
1470-8175; 1539-3429 |
| Abstract: |
The modeling of rates of biochemical reactions--fluxes--in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint-based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to-date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C-metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands-on computer laboratory component of a four-day metabolic modeling workshop and participant survey results showed improvements in learners' self-assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level. |
| Abstractor: |
As Provided |
| Notes: |
https://github.com/Gibberella/Metabolic-Modeling-Lessons |
| Entry Date: |
2023 |
| Accession Number: |
EJ1400899 |
| Database: |
ERIC |