Home
SLIMS Online Help
Introduction
Features
Limitations
SLIMS Basics and Concepts
Using the tutorials
Installing SLIMS
SLIMS
Starting SLIMS
Main Screen
Standard Commands
Inventory
Inventory Basics
Browsing Inventory
Controlled Vocabularies
Compounds
Browsing Compounds
Substructure Searching
Adding Compounds
Batches
Adding Batches
Plates
Adding Plates
Adding Dilution Series Plates
Plate Reformating
Quick Lists
Adding a Quick List
Deleting A Quick List
Adding Items To Quick Lists
cell types
concentration
document
form
dilution series protocols
location
order
people
platetype
assay protocol
role
Self-Organizing Maps
unit
vendors
Vocabulary
Results
Adding a project
Renaming A Project
Experiments
Add An Experiment
Delete An Experiment
Extend An Experiment
Tutorials
Adding Compounds and Batches
Adding Results to the Database
Making a dilution series plate
Browing the SMA (Spinal Muscular Atrophy) data

protocol

Assay data plates are converted into results through the use of a protocol. Protocols define how microtiter results are combined and converted into normalized scores.

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

This HTML Help has been published using the chm2web software.