Adding parameters to a Setup

Adding parameters

The newly created Setup has several tabs with different types of information. In the following we will walk through what each tab controls and how to add content and thereby configure the behaviour of the Setup. This part is important! It has an impact on:

1) what data you can upload to the experiments under the Setup and 

2) what part of the experimental data you can get into the SAR tables and hence your analysis.

Let’s initiate with a high level explanation of what the different tabs contain:

• Details: This is just the META data you entered as you created the Setup - name etc
• Raw Parameters:
  This is where you define the parameters (fields/columns) you want to capture from the experiments. So basically the columns headers of the data file you get back from the experiments (the data providers). So this is where the “raw data” or the actual delivered/uploaded data go.
  There a two sub groups of Raw parameters: Group and Data.
  The Group parameters are the values that might repeat in the data set, for example the compound and the dose:
  
  The raw parameters are the values that will be varying for each line, for example the Animal number and the value we measure:
  
• Result Parameters:
  This is similar to the above “Parameters” in the sense that this is also where you define the parameters/columns but here as the final result from the experiment. Hence, this is where the derived data from the experiment go. As an example the raw data could be conc/effect or conc/inhibition values - then the final results (the derived) data would be the ED50 or IC50 and here you would then have parameters like: Compound, Batch, IC50 (and maybe others).
  
  
  NOTE: IF you receive an excel sheet with a final result table from your lab or data producers then you can decide to load all that directly into the result parameters as that is then the “final results data from that experiment”. 
• Constants:
  Constants are the parameters that provide meta information about the experiment. A set of constants might be “Species”, “Strain”, “Study ID”.
  When you create contents, imagine a spreadsheet with your experiment, each column being a parameter. If a columns value would be the same for all rows, then that parameter would be a constant in your setup.

• SAR:
  Here you can pick those Constant parameters that will make experiments based on the Template different. In our example we have defined three constants: “Species”, “Strain”, “Study ID”. Different values in Species and Strain will make experiments incomparable, so we pick those two parameters.
  
  Experiments having different “Study ID” will not have any influence on the values the experiment will produc, so we leave that one out.

• Experiments: This is basically a list of all the experiments run and uploaded under this Setup. Nothing to configure here. It is naturally empty from the start as there are not experiments here yet

• Results: This is a table to help you answer the question “show me everything tested under this Setup (assay/model). So all results across experiments. But no aggregation if the same compound has been tested more than once. Simply a merge of all the rows from all the experiments

Now with the above overview information let’s get to the first Parameter tab and add the relevant / needed parameters.

Adding relevant parameters / information to the tabs:

1. Select the “Parameters” tab
2. Click the “+” icon in the top right corner to add a new parameter. The following window appears:

You now - naturally - need to add/select values for the individual fields. Some of these are straightforward, others require some extra reading below. 

1. Add a name and a description
2. Select an Experiment Role and a Hypothesis role (read the Parameters section to understand what this means)
3. Select a Data type (numeric, text, data or Entity/lookup table) and a Unit. Note: Depending on the choice of data type selected other configuration options appear. To learn more about these settings read the “Individual parameter config…” section below.
4. Mark the parameter required if relevant. Note: IF a parameter is marked “Required” you cannot upload data without it!
5. Sort order - meaning in what order do you want the columns to appear in a data view, this can also be changed by dragging the rows up and down in the parameters table.
6. Plugin name and Safe name you cannot edit
7. Group name - used to group parameters in the experiment viewer. Parameters with the same group name will be displayed in a column group.