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Printable Handouts
Navigable Slide Index
- Introduction
- Talk outline
- Modeling in systems biology
- Computational metabolic modeling types
- Constraint-based metabolic modeling
- Modeling approaches: Constraint-based
- CBM & GSMM
- Applying constraints
- Flux balance analysis defenitions
- Flux balance analysis - optimal solution
- Principle of flux balance analysis
- Flux balance analysis - applying balance contraints
- Flux balance analysis - applying bound contraints
- Find optimal point in solution space
- FBA: Single solution
- FBA: Unbounded
- FBA: Degenerate solutions
- What can we calculate using FBA?
- Flux variability analysis (FVA)
- Limitations of FBA
- Data integration - public data base
- Data integration
- Kinetic metabolic modeling & flux balance analysis
- Modeling approaches to metabolism
- Kinetic modeling: Basic concepts
- Kinetic modeling
- Kinetic modeling: sample
- Kinetic modeling: Labeled metabolomics
- Labeled metbolomics model
- Kinetic modeling: Limitations
- Computational tools for metabolic flux analysis
- Applications and examples
- Computational modeling examples
- I: Predicting growth properties
- II: Predicting flux distributions
- III. Predicting gene essentiality/dispensability (1)
- III. Predicting gene essentiality/dispensability (2)
- III. Predicting gene examples
- IV: Bioengineering
- Further readings
- Thanks
Topics Covered
- Modeling in systems biology
- Computational metabolic modeling types
- Constraint-based metabolic modeling
- CBM & GSMM
- Principles of flux balance analysis (FBA)
- Flux variability analysis (FVA)
- Data integration
- Kinetic modeling
- Computational modeling examples
Links
Series:
Categories:
Therapeutic Areas:
Talk Citation
Cascante, M. and Marín de Mas, I. (2018, April 30). Metabolomics flux on the genome scale [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 2, 2024, from https://doi.org/10.69645/TARL8044.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Marta Cascante has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
- Dr. Igor Marín de Mas has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
Other Talks in the Series: Bioinformatics for Metabolomics
Transcript
Please wait while the transcript is being prepared...
0:00
Hi.
I am Marta Cascante.
I am Professor of Biochemistry and Molecular Biology at
the Department of Biochemistry and Molecular Medicine at the University of Barcelona.
I study molecular basis of integrating experimental and computational approach,
the framework of system biology and systems medicine,
with a focus on metabolic adaptations accompanying essential cell phase and
pathological alterations associated with multi-factorial disease, such as cancer.
Long-term goal of our research is to develop new therapies and new bio-markers.
Hi I'm Igor Marin.
I'm a Computational Biologist,
and I'm currently a Postdoctoral Researcher at
the Institute of Environmental Assessment and
Water Research run by the Spanish Research Council.
My specific interest lies in the section of computational method and self systems.
More specifically, my research is focused on developing and applying methods based on
computational modeling to study the metabolic and
signaling mechanics underlying cellular disorders.
So, today we are going to introduce
computational modeling and metabolic flux concepts
in the context of systems biology approach.
1:15
This stuff is divided in four parts.
First, we will briefly explain
the main concepts that has been explained in the previous talk.
Next, we will introduce the constraint-based modeling approach.
In the third part, we will talk about the kinetic modeling approach.
Finally, we will present some application and examples of computational modeling.
In our previous talk,
we introduced the concept of computational modeling in the framework of systems biology.