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CAKE 2.0 Released

October 1, 2013

15 January 2014
A bug fix was implemented in CAKE 2 to solve a problem with the substance table below the topology schema in the user interface. This now links the substance name with the topology ID thoughout the application (previously they got mixed up). The updated installers are downloadable from the download site (

1st October 2013
CAKE 2.0 has been released and is available for download from the download site at This update fixes several bugs that were in CAKE 1 including:

CAKE not starting on a visible part of the screen
Failure to fit due to problems with the covariance matrix
Errors with some versions of R. CAKE 2 ring-fences its own R environment independant from a standalone R installation
The order of replicate data points remains constant
DFOP half-lives are displayed, not just the k rates
When using MCMC and random seeds, the seed used is now written to the report file

Enhancements over CAKE 1 were also made including:

Final fits are automatically shown at the end of a run
The default graphing option is “Yes, always”
All final outputs can be output as a group rather than singly
User defined names can be added to the metabolic topology
Graphs can be produced from fixed parameters
Metabolites are no longer constrained to zero at time zero
90% confidence intervals are specified as well as 95%


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