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SLIMS Online Help
Introduction
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SLIMS Basics and Concepts
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SLIMS
Starting SLIMS
Main Screen
Standard Commands
Inventory
Inventory Basics
Browsing Inventory
Controlled Vocabularies
Compounds
Browsing Compounds
Substructure Searching
Adding Compounds
Batches
Adding Batches
Plates
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
concentration
document
form
dilution series protocols
location
order
people
platetype
assay protocol
role
Self-Organizing Maps
unit
vendors
Vocabulary
Results
Adding a project
Renaming A Project
Experiments
Add An Experiment
Delete An Experiment
Extend An Experiment
Tutorials
Adding Compounds and Batches
Adding Results to the Database
Making a dilution series plate
Browing the SMA (Spinal Muscular Atrophy) data

Compounds


Browing Compounds

The compound structures are displayed in the view along with the following properties:
  • smiles - the smiles string for the compound
  • name - the name of the compound, either user supplied or the drug name
  • vendor - the vendor of the compound, this comes from the vender table which is a controlled vocabulary
  • library - this is a user supplied tag to annotate compounds purchased at different times
  • catno - the vendor's catalogue number of the compound
  • mw_total - molecular weight of the compound
  • mw_active - the molecular weight of the smallest fragment of the compound
  • num_atoms - the number of atoms in the compound
  • num_bonds - the number of bonds in the compound
The compound view has the following commands available:
  • Substructure Search - Search the current compound view for a substructure.  This command opens up a new dialog box where a substructure can be entered.  If a row is selected, then the view is opened with the substructure from the current row.  Exiting this dialog starts the substructure search.
  • Find Similar - Sorts the compounds based on their similarity to the currently selected compound.
  • Locate Plates - Display all the plates where the currently selected compounds are found.
  • Search - Search for properties in the view
  • Sort - Sort the view
  • Export - Export the selected view to a csv file.  This doesn't save images.
  • Export To Excel - Export the selected view to Excel.  Excel must be installed on your computer.  This really should only be used for relatively small views.
  • To SDF - Export the current view as a MDL Structured Data File.  This is a standard format for transporting chemical structures and their related data fields.
  • Load QuickList - Join the current view with the given quicklist.   Used from the compound view, this shows all compounds stored in the quicklist.
  • Add Compounds - Add Compounds to the database.  This is also how batches are added to the database.
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