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CAKE 3.2 Released

Tessella and Syngenta are pleased to announce that CAKEv3.2 is now available for download from the Tessella website. We would like to thank Ian Hardy of Battelle and Simon Ford of JSC International for their support during development and also all those who have reported bugs in sufficient detail for us to reproduce them.

This new version of CAKE combines the ease of use of the previous version, with substantial enhancements and many bug-fixes. The full list is available in the release notes on the Tessella site, but the key enhancements are:

• Study files that dated from version 2.2 or earlier and were opened in version 3.0 or newer could end up misbehaving with the IORE model until the file was saved and re-loaded (specifically, the IORE model was internally stuck on a parent-only topology and with default display names for compartments). This has been fixed.
• Some of the internal optimisation calculations could use incorrect values at interim steps if a metabolite initial concentration was unfixed. This could throw the final fit step off by providing unreasonable initial values to it. This has been fixed
• Implicit formation fractions (expressing formation from compartments without a sink to their final metabolite) are now explicitly stated in fit reports.
• If a fit sequence completes with formation fractions optimised to 1 from a compartment with a sink, CAKE will now draw attention to this and advise the user to consider re-running with better initial values and the sink disabled
• The mathematical model used for DFOP metabolites in versions 3.0 and 3.1 did not match that prescribed by FOCUS guidelines. This has been corrected.
• NAFTA Process fit sequences no longer use SFO fitted parameters as the basis for initial values for the DFOP and IORE stages. The IORE N value is still estimated automatically based on results from the SFO and/or DFOP stages where possible.
• The process for recommending/highlighting a representative half-life on the NAFTA Process spreadsheet has been updated to match the latest guidelines.

Additional fixes:
• DFOP models will now always report k1 as the faster rate by convention, transforming parameters after the optimisation process if required.
• Fitted values for unfixed metabolite initial concentrations are now used as initial values in subsequent steps, in common with other fitted parameters.
• Changing the Graphs for each Compartment drop-down or the Generate Advanced Reports check box on the Current Fit tab will now reload any active report with the chosen option.
• Initial values for metabolite initial concentrations are now stated in fit reports.
• It is no longer possible to use the Generate Advanced NAFTA Spreadsheet option while fits are running.
• Fixed a case where it was possible to crash the option when pasting data on the data tab in a very particular way.
• Data tab names can no longer be duplicated by double-clicking on a tab to rename it.
• Hockey stick fits and plots are now more accurate where breakpoints and/or time ranges are small.

Many more minor enhancements.

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CAKE Updates

Just for information really, but we are planning an update to CAKE in the near future as we have identified some issues with the application that we want to fix. Some of these are usability issues whilst others are to improve the fitting results with edge effects on some outlying datasets.

We hope to have an updated release available either at the end of Q4 2015 or early Q1 2016, but we will issue any update on this timeline as the planning and development process moves on

CAKE 3.1 Bug in Compartment Naming

We have come across a strange bug when naming the compartments in CAKE 3.1

If you set up A1, B1 and C1 and enter data. If you change the names of the compartments, then data disappears from the data grid. Renaming the compartment back to the default seems to restore the data.

If you set the names up first and then add the data, the parent seems to be OK, but when you add metabolite data, all the other metabolites at the same time point get the same data.

If you leave the substance names at the default, then you should experience no issues like this

We are looking into the problem and will produce a fix in the next release of CAKE

CAKE 3.1 Released

Dear all,

Tessella and Syngenta are pleased to announce that CAKEv3.1 is now available for download from http://showcase.tessella.com/.
We would like to thank Ian Hardy of Battelle and Simon Ford of JSC International for their support during development and also all those who have reported bugs in sufficient detail for us to reproduce them.

This new version of CAKE combines the ease of use of the previous version, with substantial enhancements and many bug-fixes.
The full list is available in the release notes on the Tessella site.

The key enhancements are:
• Enhanced topology – now allows for up to three primary metabolites and increased flexibility throughout the pathway.
• Biphasic metabolites – primary metabolites can now be fitted with the DFOP model where appropriate.
• Extra solver – use of this fitting routine is still transparent but can now be configured to run only the steps when it is required.
• Hockey-stick model – the default option for this model now includes an automatic pre-run to determine the best starting point for tb.
• NAFTA
o the IORE model used in NAFTA evaluations is now available
o there is an option to run the model fitting sequence in the same way as PESTDFV and generate a spreadsheet with the graphical and statistical output required by US EPA.

Additional fixes:
– Compound naming table
– Occasional missing intermediate fit reports
– Loss of data on save and re-open
– Robust metabolite statistics
– Confidence intervals all included, in line with new EFSA guidance
– Many more minor fixes

We welcome feedback on this new version, suggestions for future enhancements and details of any bugs found via the blog at https://cakekinetics.wordpress.com/.

CAKE 2.0 Released

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 (http://projects.tessella.com/cake)

1st October 2013
CAKE 2.0 has been released and is available for download from the download site at http://projects.tessella.com/cake. 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%

CAKE GUI Not Visible on Screen

There have been a few instances where the CAKE GUI does not appear on screen. CAKE is visible on the taskbar, but invoking it does not display CAKE on-screen. This has been occurring particularly on dual monitor configurations with laptops on docking stations where the screen address on start-up gets mixed up.

To solve the problem, click on the taskbar icon, the use the keyboard combination of alt-spacebar, followed by M. This makes the active window moveable with the keyboard cursor keys and allows the user to move the CAKE application back to the visible part of the screen

Problem with CAKE and Non-Default R Installation

It has been reported that with a non-default R installation (e.g. c:\R\R2.12.2), that CAKE throws an error when starting that it cannot find R.

This is described in the installation page of the online help, although it is easily missed and it does require creating a file where CAKE is installed.

To get CAKE to detect R if is installed in a non-standard place, you need to create a file called RLocation.txt in the CAKE directory (usually C:\program files\syngenta\CAKE). The file should contain one line which is the path to R, e.g. C:\R\R2.12.2 (in the case used above as an example).

There have been instances of problems with updates to the R package and CAKE not working properly. It is possible to have more than one version of R installed. If you retain the version 2.12.2 for which CAKE was tested and create the RLocation.txt file in the CAKE installation folder then you can ensure tha CAKE is pointing at the version of R for which it has been tested rather than at another R version for which testing was not carried out

In all cases seen to date, this has fixed the problems