protocol

Protocols are created when adding experiments to projects.

To create a new protocol, click on the "Make Protocol..." button in the command pane. To view an existing protocol, click on the "View Protocol..." button in the command pane. You can also create new protocols while adding results.

The process of generating a protocol is described here as a supplement to the process of adding results.

How to add a new protocol:

• Navigate to the protocol inventory and click on the "Make Protocol" button.
• The first thing you will need to do is to select a plate type for your protocol. SLIMS only cares about the size of the plates as far as the plate type is concerned, you will be able to load results using the same protocol even if the are created with many different plate types.
• The next step is to select the wells that contain the control compounds. To do this click an initial cell and, while holding the mouse button down, drag the mouse over the appropriate controll wells. Then release the mouse. At this point you will be given a list of options indicating what type of control wells you would like to create.
  • + positive control well(s)
  • - negative control well(s)
  • x collect no data from this well
  • clear clear the well
• Select how you would like to combine the control wells. You can choose to use the control's mean value or median values.
• Finally, select a scoring scheme. You can select to compute a percent inhibition for each well, a percent enhancement or a fold increase. These are computed as follows, x is the value read from the plate, P is the combined positive controls and N is the combined negative controls.  Both the percent inhibition and percent enhancement are centered on zero.  The negative controls are at -100% and the positive controls are at 100%
  
• Percent Inhibition
  (1 - (x - N)/(P - N)) * 100 - 100
• Percent Enhancement
  (x - N)/(P - N)) * 100 - 100
• Fold Increase
  x/N