GCAT 6.3.1 Production Release

GCAT 6.3 makes input file format more flexible by ignoring any columns that GCAT does not recognize, such as Time or OD. It also fixes bugs.

GCAT 6.3.0. Bug fixing release.

 • Enabled ignoring any columns that GCAT does not recognize as Time or OD

 • Fixed bugs

Average blank

• Enabled use of average OD of control wells as the blank value at each time point. This makes it possible to account for potential changes in the OD of blank media during the course of an experiment, e.g. due to evaporation. This happens when a user checks Average OD of blank wells at each time point option under the Media background menu.
• It is now possible to define only one limit, e.g. upper or lower, for the heat map color scale ranges. The other limit is set automatically to the lowest or highest value of the corresponding growth curve parameter in the dataset. This happens when only one value is specified in the Heat map ranges menu, while the other is left blank.
• Improved error handling and reporting. R errors are now correctly passed to Rails. The users can display the R errors by pushing the Full console message button on the error page. They can also send the error and other debugging info to GCAT developers by email by pushing the Send button. When sending the error to the development team, a user can optionally identify self by providing an email address and a name.
• When media background is set to the first OD reading, GCAT automatically changes default inoculation timepoint to 2. This happens when a user checks the Take the first OD reading of each well to be the blank option in the Media background menu.
• Substantially refactored the Rails code and added unit tests.
• Back-end R package is now available in a ready-to-install archive form.

AUC fixed

Fixed AUC display on well plots.

AUC

Implemented Area Under the Curve (AUC) calculation.

GCAT 6.0.2

Changed default OD transform options to be more appropriate for most users:

• By default, the user is expected to enter a custom blank OD value into the Media background menu. It remains possible to use the first reading in the well as blank. It is also possible to set blank value to 0.
• The default OD Transform is now log(x). It remains possible to select log(x+0.1) or log(x+delta), with delta specified by the user.
• The default Inoculation time point index is now 1, e.g. it is assumed that the first OD reading in the well is post-inoculation and not that of blank media. However, GCAT generates an error if Media background is set to the first OD reading while Inoculation time point remains 1, as these two choices are inconsistent with each other.

Note: when the log(x) transform is used for OD, all data points where OD < blank.OD are discarded.

Enabled specification of value ranges for heat maps. Setting these ranges consistently in different GCAT runs will result in heat maps with identical color scales, facilitating comparisons between experiments.