Presentation is loading. Please wait.

Presentation is loading. Please wait.

Simulating high throughput data with FBA Lots of high throughput data out there! Broad parallel screens are a new part of biological experimentation. I’ll.

Published byDaryl Leigh Modified over 10 years ago

Similar presentations

Presentation on theme: "Simulating high throughput data with FBA Lots of high throughput data out there! Broad parallel screens are a new part of biological experimentation. I’ll."— Presentation transcript:

1 Simulating high throughput data with FBA Lots of high throughput data out there! Broad parallel screens are a new part of biological experimentation. I’ll show off two types of high throughput screens you can model with FBA, using small toy examples: Library knockout screens Metabolic capability is varied Culture media remains the same Nutrient utilization screens Metabolic capability remains the same Culture media is varied

2 Gene library knockout screens You can easily test the effect of a set of gene knockouts on your model with FBA. Construct a model (optional) We’ll cheat, and use EcoCyc Identify the KB frame IDs of the knocked-out genes Edit the.fba file appropriately Decide whether you want to produce individual knockout flux summaries (can be lots of data) Run the simulation Compare the results with what you expect

3 Knockout example: isoleucine synthesis

4 Build the gene KO list Identify the KB frame IDs of the knocked-out genes Find experimental data (Baba et al. glucose minimal) Edit the.fba file appropriately Run the simulation and compare GeneFrame IDExp Essential?Sim Essential? ilvAEG10493Yes ilvBEG10494No ilvNEG10502No ilvIEG10500No ilvHEG10499No ilvCEG10495Yes ilvDEG10496Yes ilvEEG10497Yes

5 Knockout example: isoleucine synthesis Build the gene KO list Identify the KB frame IDs of the knocked-out genes Find experimental data (Baba et al. glucose minimal) Edit the.fba file appropriately Run the simulation and compare GeneFrame IDExp Essential?Sim Essential? ilvAEG10493YesNo ilvBEG10494No ilvNEG10502No ilvIEG10500No ilvHEG10499No ilvCEG10495Yes ilvDEG10496Yes ilvEEG10497Yes

6 Knockout example: isoleucine synthesis

7 Nutrient utilization screens FBA is also a great way to test whether your model will grow on different types of growth media. Construct a model (optional) We’ll cheat, and use EcoCyc Identify the KB frame IDs of the nutrients you want Create appropriate.fba files Run the simulations Compare the results with what you expect

8 Nutrient utilization screens Biolog carbon plate PM-1

9 Nutrient source example: Biolog PM-1 Col. 3 Build.fba files for each medium of interest Find experimental data (EcoCyc data) Run the simulation and compare Carbon src.Frame IDExp Growth?Sim Growth? NAcGluMIX0-421Yes GlycerolMIX0-433Yes DL-malateMIX0-445Yes D-glucosaminateMIX0-456No D-glucose-1-PMIX0-466Yes Myo-inositolMIX0-473No L-serineMIX0-484Yes 3-hydroxy- phenylacetate MIX0-495No

10 Nutrient source example: Biolog PM-1 Col. 3 Build.fba files for each medium of interest Find experimental data (EcoCyc data) Run the simulation and compare Carbon src.Frame IDExp Growth?Sim Growth? NAcGluMIX0-421Yes GlycerolMIX0-433Yes DL-malateMIX0-445Yes D-glucosaminateMIX0-456No D-glucose-1-PMIX0-466YesNo Myo-inositolMIX0-473No L-serineMIX0-484Yes 3-hydroxy- phenylacetate MIX0-495No

Download ppt "Simulating high throughput data with FBA Lots of high throughput data out there! Broad parallel screens are a new part of biological experimentation. I’ll."

Similar presentations

Instantiation of Generic Reactions by Markus Krummenacker Q1 2015.

Instantiation of Generic Reactions by Markus Krummenacker Q
Predicting essential genes via impact degree on metabolic networks ISSSB’11 Takeyuki Tamura Bioinformatics Center, Institute for Chemical Research Kyoto.

Predicting essential genes via impact degree on metabolic networks ISSSB’11 Takeyuki Tamura Bioinformatics Center, Institute for Chemical Research Kyoto.
Mammalian Cell Culture. What is cell culture, exactly?  Cells, previously growing in a human or animal modified to grow in plastic or glass In the body.

Mammalian Cell Culture. What is cell culture, exactly?  Cells, previously growing in a human or animal modified to grow in plastic or glass In the body.
The Effects of an Increasing Dilution Rate on Biomass Growth and Nitrogen Metabolism of Saccharomyces cerevisiae Kasey O’Connor Ashley Rhoades Department.

The Effects of an Increasing Dilution Rate on Biomass Growth and Nitrogen Metabolism of Saccharomyces cerevisiae Kasey O’Connor Ashley Rhoades Department.
Darwinian Genomics Csaba Pal Biological Research Center Szeged, Hungary.

Darwinian Genomics Csaba Pal Biological Research Center Szeged, Hungary.
Metabolic functions of duplicate genes in Saccharomyces cerevisiae Presented by Tony Kuepfer et al. 2005.

Metabolic functions of duplicate genes in Saccharomyces cerevisiae Presented by Tony Kuepfer et al
Intro to BEopt w/ EnergyPlus

Intro to BEopt w/ EnergyPlus
Using Pathway-tools for phenotype- directed curation Jeremy Zucker Broad Institute of MIT and Harvard Boston University.

Using Pathway-tools for phenotype- directed curation Jeremy Zucker Broad Institute of MIT and Harvard Boston University.
MGH-PGA Genomic Analysis of Stress and Inflammation: Pseudomonas aeruginosa Strain PA14 Non-Redundant Mutant Library Nicole T. Liberati, Dan G. Lee, Jacinto.

MGH-PGA Genomic Analysis of Stress and Inflammation: Pseudomonas aeruginosa Strain PA14 Non-Redundant Mutant Library Nicole T. Liberati, Dan G. Lee, Jacinto.
The activity reaction core and plasticity of metabolic networks Almaas E., Oltvai Z.N. & Barabasi A.-L. 01/04/2006.

The activity reaction core and plasticity of metabolic networks Almaas E., Oltvai Z.N. & Barabasi A.-L. 01/04/2006.
Experimental and computational assessment of conditionally essential genes in E. coli Chao WANG, Oct 11 2006.

Experimental and computational assessment of conditionally essential genes in E. coli Chao WANG, Oct
Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Göteborg University.

Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Göteborg University.
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states Speaker: Zhu Yang 03.05.2006.

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states Speaker: Zhu Yang
A synthetic gene- metabolic oscillator Fung et al. 2005.

A synthetic gene- metabolic oscillator Fung et al
Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Dept. of Cell and Molecular Biology Göteborg University.

Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Dept. of Cell and Molecular Biology Göteborg University.
Metabolic/Subsystem Reconstruction And Modeling. Given a “complete” set of genes… Assemble a “complete” picture of the biology of an organism? Gene products.

Metabolic/Subsystem Reconstruction And Modeling. Given a “complete” set of genes… Assemble a “complete” picture of the biology of an organism? Gene products.
Lecture #23 Varying Parameters. Outline Varying a single parameter – Robustness analysis – Old core E. coli model – New core E. coli model – Literature.

Lecture #23 Varying Parameters. Outline Varying a single parameter – Robustness analysis – Old core E. coli model – New core E. coli model – Literature.
Functional Genomic Hypothesis Generation and Experimentation by a Robot Scientist King et al, Nature 2004 427:247-252 Presented by Monica C. Sleumer February.

Functional Genomic Hypothesis Generation and Experimentation by a Robot Scientist King et al, Nature : Presented by Monica C. Sleumer February.
Insights into carbon assimilation in ectomycorrhizal fungi through use of 13 C-labeled glucose and amino acids Megan Grass 1, Janet Chen 2, Andrew Ouimette.

Insights into carbon assimilation in ectomycorrhizal fungi through use of 13 C-labeled glucose and amino acids Megan Grass 1, Janet Chen 2, Andrew Ouimette.
Unique Flexibility in Energy Metabolism Allows Mycobacteria to Combat Starvation and Hypoxia Berney, Michael, and Gregory M. Cook. Unique Flexibility.

Unique Flexibility in Energy Metabolism Allows Mycobacteria to Combat Starvation and Hypoxia Berney, Michael, and Gregory M. Cook. "Unique Flexibility.

Similar presentations

Ads by Google