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 Basics and Concepts

Selecting a row of data

When selecting items in SLIMS for further processing, the entire row must be selected.  To select a row, simply select the number to the left of the dataview so that the entire row is highlighted.  For example, this is necessary when plotting dilution series.

SLIMS maintenance

Like most Laboratory Information Management Systems, SLIMS has simple parts and difficult parts.  The main intention of SLIMS is to make life easier for the Biologist.  SLIMS accomplishes this by providing easy ways to created assay protocols for analysis and for annotating data.  SLIMS also provides utilities to export data to Microsoft Excel in case users need analysis routines and better plotting capabilities than SLIMS provides.

One thing to remember is that every object in SLIMS has a unique id that is generated by the system.  This ID is simple a number specifying the order that the object was loaded into the system.  No two objects have the same number.  This number is also used as a default identifier, that is a compound may have an id 45786 that SLIMS uses to identify the compound if the user hasn't supplied a name.  This is useful in cases where two compounds have the same name, i.e. Aspirin.  The ID helps to determine exactly what version of Aspirin is being viewed.

As with all such systems, there are elements within SLIMS that complicated by there very nature.  While not terribly complicated, these tasks should first be performed on an empty database for practice.  See the various tutorial sections spread throught the manual.

The tasks that should be performed by a reasonable experienced administrator include:

Importing compounds and plate data into SLIMS.  

The main issue with importing compounds is not the actual act of loading compounds into SLIMS, but importing compounds into SLIMS and keeping track of their plate locations.  Many users get confused by the difference between a compound and a batch for instance.  A compound is just a representation of a particular structure given by a supplier such as prostaglandin purchased from SIGMA.  The batch represents the physical location of the compound and may exist in several different places, such as when transferred from one plate to another.  The batch helps to identify the "paper trail" of the compound.   The compound loader can load the compound and also can load the batch.  In this case, the batch indicates the plate and  well for the purchased compound.

SLIMS only loads files in MDL's SD format.  A good program for converting between different formats is OpenBabel.  SLIMS supports loading plate locations in the following formats:
  • The barcode and row and column locations are in different fields inside the compound file
  • The barcode, row and column fields are seperated by a single character such as in: ACL/A/04
Setting the default format for reading plate files

Plate files come in as at least as many flavors as plate reader vendors.  SLIMS has a default format that it can easily read.

Default Format
File name:  <barcode>.csv
Where <barcode> is the plate's barcode.

The file format is simply a matrix of data where each row is located on a different line and the plate reader values are seperated by commas.  Each value must be a number.

For example, a 384 well plate file looks like:


where a1,a2 would be the numeric values in the respective wells.

It is not always easy to generate these formats, however, and SLIMS does support the creation of plugins that can be written in SLIMS scripting language to generate plates.  This is slighly complicated however and the SLIMS developers are in the process of collaborating with the Society of Biomolecular Screening to develop an XML based plate format that can be output by any plate reader and read by any analysis system.  This, unfortunately, is in an early stage of development.  If you have format that you would like SLIMS to read by default, please contact the SLIMS maintainer and appropriate arrangements can be made.

Dealing with barcodes

Barcodes are one of the fundamental units of data inside SLIMS.  A barcode defines where the compound batches are inside a plate that is analyzed.  They also keep track of plate transfers for fluidics handling.  Without barcodes, SLIMS is not very useful.  Keeping track of barcodes is a fundamentally tedious and boring task.  However, it must be mentioned again, that it is a necessary task.  Furthermore, SLIMS uses the batch in a plate to keep track of duplicates in order to use replicate statistics on the processed data.

The plate transfer file is fairly simplistic and can be accessed via the plate inventory.  The file is again a comma seperated value file and each row contains plate history starting from the initial barcode.  Remember that the initial barcode must exist in the database.  An example is:


This means that ASSAY001 contains the same compounds as DAUGHTER001 and that DAUGHTER001 contains the same compounds as ACL001.

Quick and dirty loading of data

During the loading process, you can manually input barcodes for your plates.  All you have to specify is the parent plates that exist in the database.  These plates can be selected through a pull down menu, but the process can be fairly tedious.

Finally, SLIMS does provide a blank plate with default empty compounds for users who just want to quickly load data.  The compounds are labeled "blankA1" through "blankO24".  The SD file for loading these compounds is also used in the compound loading tutorial.  Users can simply select blank1 as there plate barcode to quickly load plates.  It should be noted, that all plates during the load are considered duplicate plates so this method really shouldn't be used very often.

This HTML Help has been published using the chm2web software.