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Printable Handouts
Navigable Slide Index
- Introduction
- Talk outline
- Systems biology & models
- Recent approaches of biology
- The human genome project
- Genome projects
- What is the aim of systems biology?
- What is a model?
- Computational modelling
- Why do computational modelling?
- Part 2
- Genome-scale metabolic network models
- Metabolic models - various types of information
- MM 1: Reaction stoichiometry and directionality
- MM 1: Examples
- MM 2: Sub-cellular localization
- MM 3: Transport and exchange reactions (1)
- MM 3: Inputs
- MM 4: Gene-protein-reaction (GPR)
- MM 4: GPR associations
- MM 5: Biomass composition
- MM 5: Biomass composition - equation
- Escherichia coli metabolic network
- Human metabolic network
- GSMM are available for a number of organisms
- GSMM building
- Part 3
- SBML models
- SBML models data base
- Structure of SBML structure
- SBML structure
- SBML structure: metabolism
- SBML structure: reactions
- Modelling approaches to metabolism
- Further readings
- Thank you
Topics Covered
- Recent approaches in system biology and modeling
- Different compartment and building of genome scale metabolic network models
- Using system biology markup languages (SBML) to represent metabolic models
- Main concepts in SBML model building
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Talk Citation
Cascante, M. and Marín de Mas, I. (2018, March 29). Metabolomics flux introduction [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 21, 2024, from https://doi.org/10.69645/WZBH3344.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
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0:00
Hello. I am Marta Cascante.
I am Professor at Biochemistry and Molecular Biology at
the Department of Biochemistry and Molecular Medicine at the University of Barcelona.
I study molecular basis of disease,
integrating experimental and computational approach into
a framework of system biology and system medicine with a focus on
metabolic adaptation accompanying essential sulfates of
pathological alterations associated with multi-factorial disease, such as cancer.
Long-term goal of our research is to develop new therapies and new biomarkers.
Hi. I'm Igor Marin.
I am a computational biologist,
and I am currently a Postdoc Researcher at
the Institute of Environmental Assessment and Water Research,
run by the Spanish National Research Council.
My research interest lies at the intersection of computational methods and solar systems.
More specifically, my research is focused on developing and applying tool space and
computational modeling to study
the metabolic continual mechanism underlying cellular disorders.
So today, we are going to introduce computational modeling and metabolic fluxes,
concepts in the context of systems biology approach.
1:19
This lecture is organized in three parts.
First part, the introduction to the concept of systems biology and modeling.
After, we will talk on the genome-scale metabolic network modelings, and finally,
we will introduce you on how to store and exchange models with SBML files.
First, we will talk on what is system biology.