Introduction
 Features
 Limitations
 SLIMS Basics and Concepts
 Using the tutorials
 Installing SLIMS
 SLIMS
 Starting SLIMS
 Main Screen
 Standard Commands
 Inventory
 Inventory Basics
 Browsing Inventory
 Controlled Vocabularies
 Compounds
 Browsing Compounds
 Substructure Searching
 Batches
 Plates
 Plate Reformating
 Quick Lists
 Deleting A Quick List
 cell types
 concentration
 document
 form
 dilution series protocols
 location
 order
 people
 platetype
 assay protocol
 role
 Self-Organizing Maps
 unit
 vendors
 Vocabulary
 Results
 Renaming A Project
 Experiments
 Delete An Experiment
 Extend An Experiment
 Tutorials
 Making a dilution series plate
 Browing the SMA (Spinal Muscular Atrophy) data
Making A Dilution Series

This tutorial can be followed using the "dilution.slm" database located in the SLIMS tutorial directory.  You may be requested to locate certain files located in that directory.

To make a dilution series, you will need to perform the following steps:
1. Define a dilution protocol that indicates where the compounds are plated and the concentration of each compound.
2. Add a plate using the dilution protocol so the database can load the dilution series correctly.
This tutorial walks through the process.

We have three plates
• 081321R1
• 081321R2
• 081321R3
The layout for each of these plates is as follows (all concentrations are in microMolar)

 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 A B C x x INDOPROFEN/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x D x x INDOPROFEN/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x E x x INDOPROFEN/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x F x x INDOPROFEN-analog 1/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x G x x INDOPROFEN-analog 1/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x H x x INDOPROFEN-analog 1/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x I x x Zinc Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x J x x Zinc Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x K x x Zinc Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x L x x Sodium Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x M x x Sodium Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x N x x Sodium Pyrithione/10uM 5 2.5 1.25 6.25E-01 3.13E-01 1.56E-01 7.81E-02 3.91E-02 1.95E-02 9.77E-03 4.88E-03 2.44E-03 1.22E-03 6.10E-04 3.05E-04 x x O P

1 Making A Dilution Series Protocol
First, go to the Plates inventory section and select the "Make Dilution Protocol" command.

You will see the following window:

If there is a dilution protocol that you would like to modify, you can click on "Set Dilution Template" to start from that protocol.  In this case you will click on "Set Plate Type" and select a 384 well plate.  The plate should now be the appropriate size.

Next, click on Set Dose Unit and select uM.  If you would like to add your own dose units, see the units inventory section.

There are four different types of compounds in this protocol, so you will need to add four compounds to the protocol.  To accomplish this, select the well at C5 and while holding down the left mouse button, drag the mouse to E20 and select Set New Compound.  You will see object 1 being placed in the three rows.  Compound 1 will represent Indoprofen from the above description.  We don't put Indoprofen in the protocol at this point because we may wish to reuse the same dilution protocols with different compounds in the future.

For row E you will highlights the wells from E5 to H20 and select Set New Compound, you will now see object 2 in the next three rows.  Repeat this for Compound 3 and Compound 4 until the protocol looks like this:

The next step is to set the dilution series concentrations.  Select the row from C5 to C20 and select Two Fold Dilution from the pop up menu.  Enter the starting dilution concentration, (which is 10) for this protocol, you will not need to type in the concentration at this point, just 10.  You should now see the following:

Do the following for the remaining rows D through N.  You can select "Set 2 Fold Diluton 10.000" from the pull down list instead of having to type 10 in every time.

Click on the Save button and give the protocol a descriptive name, such as "INDOPROFEN 10uM dilution columns 8-20"

 On Loading Conditions Conditions are annotations for each well used to seperate different experimental conditions.  Conditions can be any database item except batches and concentrations.  For example, if a dilution series has indoprofen with and without an addition ibuprofen, ibuprofen can be selected as a condition for the appropriate wells.  Conditions are loaded through a quicklist and any object in the quicklist can be used to annotate wells.  All wells with the same batch and conditions will be groups together in the dilution series. Below is an example of a loaded quicklist and wells annotated the addition of Alprostadil, USP.
s

2 Creating Database Plates

Not that the dilution protocol has been created, you will now want to load the dilution plates into the database.  You need to load these plates into the databsae in order for SLIMS to recognize them as dilution plates.  To load database plates, select from the Inventory menu and then click on Add Dilution Series Plates from the command menu.

1. Selecting a dilution protocol
2. Locate or enter the barcodes of the plates to load.
3. Identify the compounds represented by object 1, object 2... in the dilution protocol
4. Load the plates into the database
2a Selecting the Dilution Protocol

You must enter the dilution database plates into SLIMS before a dilution analysis can be completed.  Loading a dilution assay is identical to loading a normal assay except that dilution plates are automatically identified and dilution series are calculated.

To create a database plate, select Add Dilution Series Plates from the plates command menu.  You will first be presented with the available dilution series protocols.

Select the protocol that you just created.  The following window will appear:

2b Locate or enter the barcodes of the plates to load

To make a plate, you will need to specify the compounds used in the protocol.  The actions menu in the lower left allows you to create plates in two ways, you can read the output from a robotic fluidics robot such as a Zymark Hit List or you can create the plates by manually specifying the compounds.  Click on the Make Hit List Manually from the actions menu.  You will be requested to enter the number of plates that you want to create:

We will be creating three plates.  The window should now look like:

There are three barcodes in the upper left hand window.  We will like to change these to our barcodes, so click on the first barcode, wait a second and click on it again.  You will now be able to change the barcode to 081321R1  You can now go ahead and change the rest.

2c  Identify the compounds for each dilution plate

You will now enter the compounds that belong on each plate.  Select the first barcode, the window should look like:

Notice that there is room for four compounds.  Remember that this particular protocol only takes four compounds

There are two ways to make dilution plates, manually and automatically.

Making Dilution Plate Manually

Tedious Methods

The simplest but most time consuming way is to find the batch (or compound) you are interested in in the batch or compound view, select the row and drag the row over to the batch window in the protocol.  If you drag a batch, the associated structure will appear in the window.  If you drag a compound and there is only one batch for the compound, the compound will appear in the window, otherwise you will have to select the appropriate batch from a list.

The next method is slighly less tedious, but requires you know the plate, row and column of the plate where your batch is located.  These are usually discovered in a hit picking process.  For hit picking, when you are making a dilution series, you are actually using batches from other plates.  You can either drag a compound or a batch from the compound or batch inventory menu to the batch_id cell or enter a source barcode, row and column to select a compound.

Less Tedious Method
Many robotic systems output a hit picking list that you can read to get the plate, row and column information.  SLIMS only supports the Zymark format currently.  Additional, the Results view can output the current list of compounds in a hit list format.

How to find compounds in the database

Here is an one way to find out where a compound is plated  Remember that automatically generated hit lists will know the source plate, row and column.  Go to the compounds inventory menu, and select search.  In the menu, we can search for any compound whose name contains indoprofen.

Select the desired compound and click either Locate Plates or Get Batches from the command menu  Locate Plates will indicate where the compounds are plated, if the compounds are not in plates, we can find out the batches using Get Batches.  The latter might be appropriate if we are creating the plates manually.

An example of searching the compounds for PYRITHIONE and viewing the results of get batches is shown below.

We discover that Indoprofen is plated in NINDS002 at E3 and, in our case, has batch number 5382.  Either enter NINDS002, E and 3 in the window or drag the compound into the batch_id window.  To drag inventory items,  click on the row number, hold the mouse button down and move the pointer over to the batch_id cell.

Similarly locate Zinc Pyrithione, INDOPROFEN-analog 1and the Sodium Pyrithione.

You can copy and paste the selected values from one plate to another as opposed to repeating the tedious process.

Remember to enter these values for EVERY plate!  The dilution plate window should now look like this:

The final step is to click on "Add Plates".  SLIMS will not load the plates if it detects any errors, if it doesn't, congratulations!  You are done!

To load these plates into the database, you will use the standard add results command.  We will briefly walk you through the process of adding dilution plates.

Navigate to the results section and click on the add button indicated below.

Type in a descriptive name:

Now double click on the newly added project and click on the Experiments tab (or simply double click on the newly created project):

The project has no experiments, so click on the Add button to add the dilution experiment that you just created the protocols for.

The add results wizard should open.  Click on the next button to get the plates page:

Locate the Indoprofen Analog Plates Files.  (For a default install, these will be located in C:\Program Files\SLIMS\tutorial\Indoprofen Analog Plates).  Add all the plates in the Indoprofen Analog Plates folder.

Since we created the dilution series plates, everything should be ok and ready to load.

You should still inspect all of the plates by clicking on the View All button.  Click on the "Larger" button a couple of times to get a larger plate view:

There is definitely a dilution series here!  Close this window and click on Next.

Now we need to tell SLIMS how each plate well is going to be scored against the controls.  Select the "Standard Percent Enhancement" protocol from the drop down menu.  Make sure that the controls are in the proper locations:

Click next.  The next window allows setting the options for correcting spatial systematic errors cause by various experimental problems such as robot error or plate evaporation.  Since we are doing a dilution series, you can turn off this feature:

Clicking on next will load the plates!  Click on the finish button.

Now you want to see the results, so double click on the Indoprofen Analogs Dilution Series Experiment.

Go to the dilution series by clicking on the dilution tab:

To plot one or more dilution series, select the row you would like to plot, and click on the Plot Dilution button from the commands menu:

Clicking on the "To Excel" button will make a nice Microsoft Excel report for all of the dilution compounds that can be used to make production quality graphs.

 Batch ID Vendor Catalogue Number Name 707 Default (change me to your lab) 1500351 INDOPROFEN Therap cat:  Analgesic; anti-inflammatory Average Standard Deviation Concentration Unit Values 266.8053 128.8492 0.000153 uM 86.69309 261.6199 187.6671 261.2778 419.2037 453.5741 94.42066 297.0805 339.7112 186.2945 144.3043 0.000305 uM 51.13885 69.98259 161.1792 444.3889 131.2037 175.6481 398.7384 47.8548 196.5158 200.7631 79.10405 0.00061 uM 168.1123 173.6232 154.4239 308.9815 332.6852 204.9815 84.5828 229.9645 149.5127 111.2319 134.0815 0.001221 uM 75.67127 149.8019 38.69486 -65.2407 93.57407 374.1667 243.9561 -21.4474 111.9102 181.9883 82.55665 0.002441 uM 229.9767 151.0463 232.4655 223.3519 282.0185 90.61111 26.86737 156.7271 244.8306 153.3065 164.3937 0.004883 uM -67.7901 151.224 145.7131 144.2407 124.3889 546.9074 67.74913 92.89033 174.4352 210.6915 217.2419 0.009766 uM -37.2134 13.62912 300.7296 269.2778 466.3148 531.7963 208.1026 -99.4944 243.0816 144.9745 134.0784 0.019531 uM 91.31514 -39.3467 166.1568 116.6852 304.8333 305.1296 9.596466 306.2625 44.13828 221.1837 178.2353 0.039063 uM 84.55983 -56.946 332.5506 135.9444 134.463 446.7593 149.0754 274.7814 489.4653 109.2628 264.0296 0.078125 uM 196.0224 -71.701 116.9142 43.7963 188.3889 -299.315 683.3804 8.284751 117.5943 -82.6853 119.2155 0.15625 uM -29.5693 -233.828 -16.592 -128.352 79.64815 -272.648 -2.42758 8.50337 -148.902 -140.932 399.902 0.3125 uM -280.76 -153.654 -593.46 -154.722 -424.944 618.6111 -88.1263 -537.388 346.0512 -598.308 236.1525 0.625 uM -576.927 -309.559 -909.359 -602.13 -444.796 -988.204 -324.453 -529.737 -699.604 -769.036 342.6402 1.25 uM -1069.53 -97.8334 -678.79 -1182.87 -391.759 -927.759 -853.73 -741.36 -977.687 -1506.41 457.3553 2.5 uM -1191.66 -1414.41 -1523.2 -1276.2 -1998.57 -2259.31 -769.343 -1839.92 -1285.07 -1559.61 321.5183 5 uM -1217.44 -1136.37 -1352.36 -1933.39 -2081.83 -1661.09 -1358.52 -1715.31 -1580.2 72.59174 215.8984 10 uM -117.21 6.873819 83.31543 193.1296 -247.759 500.6852 160.6622 -67.3574 140.9865