From Optflux
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.
The edit can be undone.
Please check the comparison below to verify that this is what you want to do, and then save the changes below to finish undoing the edit.
Latest revision | Your text | ||
Line 30: | Line 30: | ||
<br><br> | <br><br> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
==File Definitions== | ==File Definitions== | ||
Line 49: | Line 37: | ||
<br><br> | <br><br> | ||
− | <b>COBRA Maps</b>: maps developed for COBRA Toolbox. There are, at the moment,several maps on this format for many of the models hosted in the BiGG knowledgebase (http://bigg.ucsd.edu). These maps can be used on | + | <b>COBRA Maps</b>: maps developed for COBRA Toolbox. There are, at the moment,several maps on this format for many of the models hosted in the BiGG knowledgebase (http://bigg.ucsd.edu). These maps can be used on di�erent models that have similar pathways, with a correct mapping of the identi�ers between the layout and the BiGG model. |
− | The | + | The fi�les are text tab-delimited �les divided in four sections, and since they were created to map a metabolic model for a ME tool, the conversion to the metabolic layout presented in this work was relatively straight forward. These �les contain the notion of molecules (metabolites/currency), reaction nodes (transformations) and reactions (reaction nodes). |
<br><br> | <br><br> | ||
<b>SBGN PD</b>: SBGN (http://www.sbgn.org/) is a visual language developed by biochemists, modellers and computer scientists that aims at being the standard for visual representation of biological processes. | <b>SBGN PD</b>: SBGN (http://www.sbgn.org/) is a visual language developed by biochemists, modellers and computer scientists that aims at being the standard for visual representation of biological processes. | ||
SBGN defines three visual languages: Process Description (PD), Entity Relationship (ER) and Activity Flow (AF). This plugin supports PD language files. You can learn more about these maps by downloading this [http://sourceforge.net/projects/sbgn/files/SBGN%20Process%20Description%20language/Level%201%20Version%201.3/sbgn_PD-level1-Manual-v1.3.pdf/download file]. | SBGN defines three visual languages: Process Description (PD), Entity Relationship (ER) and Activity Flow (AF). This plugin supports PD language files. You can learn more about these maps by downloading this [http://sourceforge.net/projects/sbgn/files/SBGN%20Process%20Description%20language/Level%201%20Version%201.3/sbgn_PD-level1-Manual-v1.3.pdf/download file]. | ||
+ | |||
+ | <br> | ||
At the moment SBGN-PD maps are only supported entities of the type "simple chemical" (for metabolites) and "process" (for reactions). Clone nodes are considered currency metabolites. | At the moment SBGN-PD maps are only supported entities of the type "simple chemical" (for metabolites) and "process" (for reactions). Clone nodes are considered currency metabolites. | ||
Line 64: | Line 54: | ||
This can be made using the Import KGML interface that the plugin provides: | This can be made using the Import KGML interface that the plugin provides: | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
<br><br> | <br><br> | ||
+ | <b>XGMML</b>: |