This 10 second gif will give you the basic idea. Download the template files from github and modify to fit your needs.

We begin the phactor™ HTE workflow by navigating to https://phactor.cernaklab.com. The landing page, Settings, displays terms of service and privacy policy associated with use of the software. This stage simply asks for a name for the experiment, its throughput (24 or 96 wells), and the desired reaction volume for each well (typically 100 µL at these throughputs). Clicking ‘Create Screen’ takes the user to the next stage, Factors.

The Factors stage is largely optional – inputting the experimental design in terms of reagent distributions allows for automated plate design. For instance, a 24 well experiment may screen 4 ligands and 6 catalysts. Inputting 4 and 6 into the respective textboxes indicates to the software that these reagents will be screened and should expect the corresponding chemicals to be added. Factors assigned 0 are ignored and factors assigned 1 are distributed into each well. As mentioned, this step is optional, and the reaction array can be designed entirely by hand in the Grid stage as desired.

Additionally, the Factors stage of the workflow expects input regarding experimental metadata and anticipated products. Stir rate, temperature, and solvent can be recorded here in addition to user defined commentary. Clicking the Set Products’ button displays a popup with fields to describe expected products and side products. Currently, the expected product and two side products are supported. Each product or side product should be input with an associated SMILES and descriptive name. This form can be automatically populated with a csv with the following headers: [Well, main_product_name, main_product_smiles, side_product1_name, side_product1_smiles, side_product2_name, side_product2_smiles], where the Well column dictates the location of the products via well label (e.g., A1, D6, etc.). Examples and templates for this file can be found in the ‘input_product_input’ folder of the provided GitHub repository. Notably, this step is optional and is only necessary to automatically generate analytical files in the Grid stage. Clicking save records the information and takes the user to the Chemicals stage.

The Chemicals stage collects information regarding substrates and reagents planning to be used in the reaction array. Chemicals input here need not be included in the actual experiment. If screening factors were defined in the previous stage, the checklist in the bottom left indicates the amount of chemicals currently added and the number of chemicals expected to automatically design the plate. Once all factors are satisfied, the checklist turns fully green. Chemicals can be added manually via the form at the bottom of the page, and each reagent should be associated with a descriptive name, molar mass, desired reaction molarity, overhead or amount to prepare multiplier, SMILES, density, and reagent/factor type. The “screen?” checkbox indicates whether the compound should count towards the automatic plate distribution. This option is given should the user wish to automatically generate parts of the reaction array and manually adjust other portions in the Grid stage. Chemicals can be automatically added via a small example library of common reagents provided by clicking the “Add From Database” button. Here a searchable database of chemicals associated with a molecular weight, SMILES, and descriptive name is shown. Checking the boxes and assigning a reaction molarity and factor type then clicking “Add” will add the selected chemicals to the experimental reagent list. Again, chemicals can be added to this stage via CSV template with the following headers: [atp, chemicalName, chemtype, density, factor, molarMass, molarity, order, smiles], where atp (amount to prepare) is the overhead multiplier, chemtype is the factor type, and order is the anticipated order of addition into the reaction well. It is necessary for chemtype to be one of the factor types defined in the protocol (e.g., Nucleophile, Catalyst1, etc.). CHECK THE TEMPLATE FILES IF YOU ARE UNSURE. Examples and templates for this file can be found in the ‘chemicals_input’ folder of the provided GitHub repository. Should screening factors be defined and met, clicking “Run” takes the user to the Grid stage and automatically populates the experimental design. Otherwise, clicking the forward arrow will proceed to the Grid stage.

The Grid stage is an interactive wellplate where reagents can be manually added or removed from one or multiple wells. Clicking on a well shows detailed information about reagents added to that well and dragging over or clicking multiple wells allows for bulk edits to be made to the design. Stock solution recipes are shown in the table on the left, and true weights of reagents can be added to recalculate solvent volumes to achieve the correct stock molarity. Hit record weights to save the true weighted masses of the reagents. The download buttons provide a variety of CSV outputs to integrate with analytical or robotic instrumentation. Typically, the user will download the ‘Wellplate recipe’ and send this file to a printer to set up the experiment.

Once the experiment is complete and analysis data has been collected, the Analysis stage can visualize a series of outputs. Here, a CSV file is required with the following headers: [Sample Name, product_smiles, product_yield, product_name] where Sample Name is the well label (e.g., A1, A2, D6, etc.). Optionally, the headers [side_product1_smiles, side_product1_yield, side_product1_name, side_product2_smiles, side_product2_yield, side_product2_name] are supported for full report display. Again, examples and templates for this file can be found in the ‘analysis_input’ folder of the provided GitHub repository. Additional columns can be added for any analytical method. Various outputs can be displayed three at a time by choosing the headers for the heatmaps. The heatmaps are interactive, and clicking a cell displays the inputs, outputs, output value, and molecular structure of the product in the well.

Finally, the Report stage provides a series of outputs displaying information regarding the performed experiment. Full output requires information regarding side product1 and side product 2, but minimally only main product information is the ‘Download Results CSV’ button. Again, check the template files if you are unsure.