SLIMS Online Help - Make a Dilution Series

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.

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Conditions are an adv

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 Plates from the Inventory menu and then click on Add Dilution Series Plates from the command menu.

Loading dilution plates involves the following steps:

Selecting a dilution protocol
Locate or enter the barcodes of the plates to load.
Identify the compounds represented by object 1, object 2... in the dilution protocol
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:

2d Loading Plates into the Database
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.

3 Adding the results
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