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 Compounds

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 Menu. 

Note 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.

Adding Compounds
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 controlled vocabulary.

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.

Page 1

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 directory.

Windows Note:  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

Page 2

The next page specifies the options for loading compounds into the database.

Compound Loading Options

There are several options when loading compounds into the database.  These options are detailed on the wizard page.

options page

You will want to have the following options selected, Use SD files to add plates, Stop on errors and Automatically add new suppliers.

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 shows a 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.

Plate Selection

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 three independent 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.

Compound Fields

Selecting the Fields for loading Plates

If plates are being added to the database, the same procedure applies. To load the ACL plates, select the fields shown below.
Plate Selection

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 developers.

Page 7

When the load is complete you will be able to browse the newly loaded compounds.
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