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


SLIMS results are loaded by specifying a set of plate data files that belong to a specific experiment.  Each experiment belongs to a project and a project can contain multiple experiments.  Each experiment is a unique set of data created under different experimental conditions.

Experiments can be so-called primary experiments or secondary experiments that may include dilution series data.

Results are divided into three parts.

Projects -> Experiments -> Results

Opening up a project reveals the underlying experiments and opening up a result reveals the underlying results.  A project can be opened by double clicking on the project or by single clicking and then clicking on the experiments tab.

Double clicking on a project will go to the experiements tab.  Double clicking on an experiment will go to the results tab.  Otherwise, you can select the desired project, click on the experiements tab then click on the desired experiment and then click on the results tab.

Results themselves have multiple views depending on the type of result.

The SMA data that can be loaded from the dilution tutorial looks as follows:

Note the additional tabs (which are either at the bottom of the screen or below the project, experiment and results tabs).  These tabs include

Here a user can enter comments about the experiment including various protocol information and otherwise.
Hhis shows the plates that were loaded and various information including the probability of systematic error and the correction performed on the plate
The raw uncorreced data from every well on every plate.  The batch_id specifies the compounds analyzed.  Empty batches are most likely the positive and negative controls.
This is the same as the raw data except that each plate has been corrected for systematic error.
These results are taken by combining replicate data from the raw results
These results are taken by combining replicate data from the spatial error corrected results.

Some views share some similar commands. The commands that are relevant to the raw, normalized, results and corrected data are:

Substructure Search
Allows the user to draw a piece of a molecule and search the result set for this fragment.  If a row is selected, the initial molecule depicted is the selected row.  This makes for easy searches for analogue structures.
Find Similar
if a row is selected, clicking on the view similar button will perform a similarity sort on the data in the experiment and show the results based on the most similar compound to the least similar compound.  The most similar compound gets a score of 0 and the least similar gets a score of 1.0
Get Plates
Find the plates that a given compound or selection of compounds are located.  This is great for hit picking!
View Correction
See the difference between the spatially corrected data and the raw data.  This will show you if the systematic error was actually significant or not.
Plot some data in the view.  You will be asked to select the columns for the X and Y axes.  Points in the plot are linked back to the view so that clicking on a point will highlight the row in the view that the point was derived from.
Add Plot
Add a plot to the current plot
Plot Dilition
If the data is a dilution series then plot the dilution series for the selected compound.  For this to work the row must be seleted by clicking on the number beside the row.
Add Dilution
Add a plot to the dilution series plot.
Perform an analysis of the currently displayed view.  Analysis are either automatically  finding all analog compounds, generating a self organizing map from the selected compounds or placing the viewed compounds onto an existing self organizing map.
Export the data to a csv file.  No images or compound data is stored in the dataset.
To Excel
Export the data to Microsoft Excel including images.  Excel must be installed for this to function properly.  Dilution series views will output specially formatted dilution series reports.
Export the view as an MDL SD file.

Plate view commands:

View Plate
View the selected plate.  Clicking on a well in the plate viewer will show the compound that is in the well.
Analyze Plate
Show a plate view with the systematic error tool.  The systematic error tool is a plot of frequencies and shows a histogram of the power distribution.  Removing frequencies with high amplitude will reduce the systematic error in the plate.
This view only shows the plate with respect to where the compounds are placed.  Controls are not shown in this view.
View All
View all the plates in the dataset.  This is good for finding outlier plates or getting a good overall view of the assay.  Eventually you will be able to reject plates from this view, but that will be in the next revision of SLIMS.  A good overview of the View All functionality is here.

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