SLIMS Basics and Concepts
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.
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
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:
Setting the default format for reading plate files
- 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
Plate files come in as at least as many flavors as plate reader vendors.
SLIMS has a default format that it can easily read.
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:
ACL001, DAUGHTER001, ASSAY001
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.