SLIMS Online Help
SLIMS Basics and Concepts
Using the tutorials
Installing SLIMS
Starting SLIMS
Main Screen
Standard Commands
Inventory Basics
Browsing Inventory
Controlled Vocabularies
Browsing Compounds
Substructure Searching
Adding Compounds
Adding Batches
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
dilution series protocols
assay protocol
Self-Organizing Maps
Adding a project
Renaming A Project
Add An Experiment
Delete An Experiment
Extend An Experiment
Adding Compounds and Batches
Adding Results to the Database
Making a dilution series plate
Browing the SMA (Spinal Muscular Atrophy) data

Adding an Experiment

Adding an experiment is the crux of the SLIMS system.  To add an experiment you must have the following:

  • plate files with barcodes (If the plate does not have barcodes, you can set the barcodes manually)
  • the barcodes must be present as a SLIMS plate.  That is, SLIMS must have the plate barcode loaded into the inventory system as a copy of a plate (see plate reformating)
To add an experiment, click on the results navigation menu and then select the project to which you would like to add an experiment.  You should see something like the following:

The experiments tab should be highlighted and the menu items should include, "Add", "Extend" and "Delete".

Selecting "Add" should reveal the following dalog

Enter an experiment name and the following wizard will appear:

The first step is to locate the plate files that you wish to load.

To add plates you can drag them to the main window or add them one at a time using the Browse for Files button.  Additional commands are as follows:

Manually Set
Allows you to set the parent barcode of the plate files for the purposes of loading into the database.  This is useful when the plate barcodes have not been loaded into the database.

Manually setting compounds allows you to your plates by selecting a parent plate for each new plate.  The parent plate is used to indicate what compounds are in which wells for the plates.
clears the loaded plates.
View All
shows all the selected plates in a multiple plate view allowing you to see all the plates at the same time, check for systematic errors and reject plates from the experiment.
Make Reader
If the some files are not readable, this wizard allows you to make a reader for the file.  A walkthrough guide is available here.
Remove  Selected
Remove the selected files from the view.
View Selected
View the plate with the standard plate viewer.

If you would like to follow along with the rest of the tutorial, please install the tutorial package and select the "Add Experiment" database.  This database contains all the compounds you will need to load the primary SMA data that is located by default in the "C:\Program Files\SLIMS\tutorial\primary SMA screen data\NINDS C33A 02-07-02" directory.  You can browse to this directory or simple drag all the plate files to the main window.  Add all the files that begin with NINDS.

The screen should now look like:

It is a good idea to click on "View All" to get an assay level view of the data.  The following screen should apear:

Clicking on a plate will update the plate information window with the filename and barcode of the selected plate.  For this screen, there is some obvious plate effects for some of the replicates.  (There are six replicate plates for every plate)  You can make the plates larger by clicking on the larger button and smaller by clicking on the smaller button and reject the plates by clicking on the "Reject Plate" button.  All rejected plates will be removed from the analysis.  The various options in the View All button are available here.

If any plate file cannot be read, it will be highlighted.  Clicking on the View selected button will show the text of the file if it cannot be read.  Otherwise, it will show the plate file in graphical format.  You may make new file readers for plates that cannot be read.

Once all the plates are readable, clicking on the next button will allow you to set the scoring protocol.

At this point you can select an existing protocol or create a new protocol for reading the assay plates.

Protocol are relatively simple affairs.  To create a protocol you need to specify:
  1. the plate type (i.e., the size of the plate to form the scoring protocol
  2. the location of the positive and negative controls
  3. how to deal with replicates
  4. the scoring system to use
For this protocol, select a 384 Well Plate.  The window will now update to have the correct number of plates and wells:

Select the computation as "Percent Enhancement" and the replicate statistic as "median"

Next click on well A1 and, while holding the mouse button down, drag the mouse to P2.  A popup menu will appear. 

Select Positive Controls from the menu.  The window will now look like this:

Next, make the

For the SMA data, make the protocol look as follows:

Note:  to select wells for positive and negative controls, simply click on the first well, hold the mouse button down and drag over the selected region.  When the mouse button is released, you will see a pop-up menu where you can select the type of control.

When you click on OK you can select the name for this protocol.  A good suggestion is "Standard Percent Enhancement".

The window will now reflect your choice of protocols

Clicking on the next button will reveal the correct systematic errors options.

If either the positive or negative controls should be the average of the plate, you can correct their systematic errors.  If either the positive or negative controls should be radically different from the average response of the plate, leave them unselected.  If you would like to view the plates again, simply click on the back button until you get to the plates page.  From there you can click on the view all button.

For the case of the SMA data, the positive controls are essentially no effect so it is safe to correct these wells.  The negative controls are wells with no cells, so these wells should not be corrected.  You can click on the BACK button to select View All from the plate selection window in order to get an idea about how the plates are loaded.

It is always safe to leave the positive and negative controls unselected, although the plate corrections might not be as good.

Once you have decided, click on Next and the plates will be loaded.

When the data is loaded you can select finish and select the experiment you just loaded.

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