This is the Linux app named AMBIENT to run in Linux online whose latest release can be downloaded as ambient-1.3.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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AMBIENT to run in Linux online
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DESCRIPTION
IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest!AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism.
For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific.
Audience
Science/Research
Programming Language
Python
This is an application that can also be fetched from https://sourceforge.net/projects/ambient-bio/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
