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CAKE 3.2 Released

February 29, 2016

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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