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Team:UNAM-Genomics Mexico/Modeling/ExtremePathways
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| - | '' | + | ==Introduction== |
| + | The bounded right-hand null space of the stochiometry matrix generates a convex cone, generated by convex vectors. These generating vectors, id est those that conceptually border the cone, are the Extreme Pathways. Any solution within the steady state flux distribution can be represented as a linear combination of said pathways. For more on this, consult chapter 9 of [http://dx.doi.org/10.2277/0521859034 "Systems Biology: Properties of Reconstructed Networks", by Bernhard Palsson]. | ||
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| + | ==Our Work== | ||
| + | Since our pathway was adding a novel metabolite (H2), we hypothesized the transgenic pathway might represent an Extreme Pathway. We found two tools used in calculating these Solution Space Bordering Vectors, both by [http://gcrg.ucsd.edu/Downloads/Extreme_Pathway_Analysis Palsson's Lab] ExPa and its bigger cousin X3. These calculations have been running for a week, with no end in sight. Should they finish before the Regional, we'll talk about it in the Presentation (or update this at the Wiki-Thaw...). Anyhow, getting the data into the format acceptable by ExPa required another round of parsing, and another [https://2011.igem.org/File:UNAM-Genomics_Mexico_ParserV4.m script]. If your interested in our parsing adventures, you may read more [[Team:UNAM-Genomics_Mexico/Modeling/FBA#Parsing_v4|here]]. The final ExPa compatible file is [https://2011.igem.org/File:UNAM-Genomics_Mexico_hmedina_Data.txt here]. | ||
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| + | ==Results== | ||
| + | Currently, the simulation is still running. The log file is over 100Mb long, so we're not inclined to upload it here. Should the simulation finish within the foreseeable future, we'll present the results during the Regional Presentation. | ||
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Latest revision as of 02:33, 29 September 2011
Introduction
The bounded right-hand null space of the stochiometry matrix generates a convex cone, generated by convex vectors. These generating vectors, id est those that conceptually border the cone, are the Extreme Pathways. Any solution within the steady state flux distribution can be represented as a linear combination of said pathways. For more on this, consult chapter 9 of [http://dx.doi.org/10.2277/0521859034 "Systems Biology: Properties of Reconstructed Networks", by Bernhard Palsson].
Our Work
Since our pathway was adding a novel metabolite (H2), we hypothesized the transgenic pathway might represent an Extreme Pathway. We found two tools used in calculating these Solution Space Bordering Vectors, both by [http://gcrg.ucsd.edu/Downloads/Extreme_Pathway_Analysis Palsson's Lab] ExPa and its bigger cousin X3. These calculations have been running for a week, with no end in sight. Should they finish before the Regional, we'll talk about it in the Presentation (or update this at the Wiki-Thaw...). Anyhow, getting the data into the format acceptable by ExPa required another round of parsing, and another script. If your interested in our parsing adventures, you may read more here. The final ExPa compatible file is here.
Results
Currently, the simulation is still running. The log file is over 100Mb long, so we're not inclined to upload it here. Should the simulation finish within the foreseeable future, we'll present the results during the Regional Presentation.
