This tutorial will walk you through adding compounds to the
database. Open the "addcompounds.slm" tutorial database.
The data you will need to follow this tutorial is in the "Compound
Libraries" directory. You can either select the "Tutorial Data"
folder from the start menu, or browse to "C:\Program
Files\SLIMS\tutorial\Compound Libraries". (This is the directory
only if SLIMS has been installed in the default location)
Windows Tutorial Instructions:
To start with an empty database you can select
SLIMS/tutorial/addcompounds database from the Start Menu. To
locate the datafiles, select the SLIMS/Tutorial data from the Start
that completing this tutorial will alter this database. The file
of compounds to be added can be found in the installed tutorial
directory. You can open this by selecting SLIMS/Tutorial
directory from the Start Menu.
To add compounds and to add batches to the database, select the Add
Compounds command from the compounds command pane. The wizard
steps through the compound loading. Adding compounds to the
database is somewhat complicated, fortunately it only needs to be done
once in a while. SLIMS only loads compounds from MDL sd files
which are industry standard files used to deliver structural
information as well as information like plate layout, vendor
information and catalogue numbers. SLIMS saves all of this
information, but some information is more important than others.
SLIMS requires a basic set of information to be able to load a
molecule. A molecule is loaded in two phases. The first
phase is called a compound. This contains the basic information
about the compound including the compounds catalogue number and
vendor. The second phase is called a batch. A batch is
essentially the physical representation of the compound. For
example if you purchase aspirin twice from the same company, you will
receive it in two different batches that reference the same
compound. The compound wizard assumes that you are loading in
batches of compounds. Batch information includes the batch's
location, initially in a plate or vial, but you can edit the location
table to add locations more specific to your laboratory, the amount of
the batch and the amount unit of the batch. SLIMS has a small
number of units that it understands, you can add more units to the unit
If the compounds are stored on plates then SLIMS can also read in the
plate information from the SD file and create plates in the database.
The next page asks for the location of the compound file.
Remember, SLIMS only accepts MDL sdf files.
Selecting the Compound File
Clicking on the browse
button will open up a file browser in order to find the compound
file. Select the ACL.sdf file from the Compounds Library
If you installed SLIMS onto your C: drive, then the ACL.sdf file will
be located at:
C:\Program Files\SLIMS\tutorial\Compound Libraries\ACL.sdf
The next page specifies the options for loading compounds into the
Compound Loading Options
There are several options when loading compounds into the
database. These options are detailed on the wizard page.
You will want to have the following options selected, Use SD files
to add plates, Stop on
errors and Automatically add
A full description of loading options are as follows:
Completly Scan File - SLIMS
displays a report of the fields inside the SD file to allow for
selection of the appropritate fields from within the SD file.
Appropriate fields include the name
of the compound, the vendor and
so on. When this option is selected, SLIMS completely scans the
SD file to find all the data fields. This is useful when an SD
file contains different fields for each compound. For large SD
files this is usually not recommended since the complete scan can be
time consuming. If this option is not selected, only the first 10
compounds will be scanned.
Use SD file to add plates to database
- SD files are also used to keep track of both the chemical compound
and the plate layouts. If plate information is included with the
SD file, in addition to loading the compound structure into the
database, SLIMS can load the plates into the database as well.
The plate information should include the barcode (or plate), row and column locations in seperate fields
although SLIMS provides some limited
functionality for retrieving this information from a single field.
Stop on errors and remove loaded
compounds - By default, SLIMS stops loading compounds when any
error is detected and removes any compound, batch or plate that has
been loaded from the selected file. Unchecking this option will
load all loadable molecules from the SD file. This is not
recommended, it is much safer to only load completely loadable files
and not load them piecemeal.
Automatically add ne suppliers to
database - If you are loading an SD file that is a combination
of multiple different vendors, you may want to automatically include
vendors into SLIMS vendor list. This will not include their
relevant information such as website url or contact information, but
can be useful anyway. You will have to update this information
yourself after loading the SD file.
Scan the SD File
The next step is perform a scan of the SD file. This
brief view of the data fields inside the sdfile so that the proper
fields can be selected prior to loading.
Sometimes, the plate, row and column fields are combined into a single
field. The selections at the bottom of the window can be used to
split up a single location field into the desired plate row an column
fields. Let's take a typical example. Let's suppose that
the SD file has a field named "LOCATION" and the data inside this field
looks something like "ACL0001/A/1". This usually means that the
barcode is ACL0001 the row is "A" and the column is 1. Remeber
that wells inside plates usually have rows indicated by letters and
columns indicated by numbers.
Scan the fields and note where the plate identifiers are. You
will need a barcode and row and a column to describe the well.
Sometimes the well or both the barcode and the well are stored in one
field. Slims would prefer to have
fields for the plate (barcode) and the row and column for the
compound. You can use the "Choose a field" and "split on" options to
split a field into a plate barcode and well. In the example
below, the NAME column has been selected
to be split using the "\" character. The order of the new fields
are "plate" then "row" then "column". This will add three new
fields to be selected from "SLIMS_plate", "SLIMS_row" and
"SLIMS_col". These will be available when during the plate field
selection screen which is described below.
Leaving the "Choose a field" entry blank will not add any new fields.
Select The SD Fields to
include in the database
After the review of the datafields, the proper data can be selected
before loading into the database. The database is set up to
ensure that certain data is entered for each compound. This is
usually controlled by the database administrator. Data that must
be entered is highlighted in yellow on the screen.
Either a field from the SD file
can be selected, or a default value can be entered for each
field. Fields highlighted in yellow are mandatory fields that
must be filled out before the compounds can be loaded. The
compound and batch selection field is shown below. To load the
ACL library you can fill in the fields as shown.
Selecting the Fields for
If plates are being added to the database, the same
applies. To load the ACL plates, select the fields shown below.
Finally the compounds are ready to be loaded into the database.
Clicking on the next button will start the loading process. If
any error occurs during the loading process, a log message is displayed
showing the error. Some of the errors can be quite cryptic since
they involve processes buried deep inside SLIMS. You can copy and
paste from the log file when sending error reports back to SLIMS
When the load is complete you will be able to browse the newly loaded