Creating Experiments

Learn how to create experiments

User Guide: Creating Experiments in Foundry Portal

Overview

Here’s how the experiment creation process works:

1. Create a draft experiment. You can refine this draft at any time, with no payment commitment.

2. Submit for review. When you’re ready, click the “Move to Review” button.

3. Receive your quote. Our team will review your experiment and prepare a final quote.

4. Confirm and start production. After reviewing the quote, confirm to start the production process.

1. Creating a New Draft Experiment

Initial Setup

To begin creating a new experiment, locate the navigation sidebar and click the “New Experiment” button.

Required Information

1. Experiment Name

Start by choosing a descriptive name for your experiment. This name will be used throughout the system for tracking and reference purposes, so make it specific enough to identify the experiment’s purpose.

2. Assay Type Selection

Select the type of assay you want to perform from the available options. Each assay type has its own pricing structure and specific requirements, including its own minimum order size. You’ll find detailed documentation links next to each option to help you understand the differences.

3. Target Configuration

You have two options for configuring your target:

Using a Catalog Target:

Our database contains pre-validated targets that you can select from. Using a catalog target offers several advantages:

• The supplier information is automatically filled in

• We’ve worked with this supplier before

• Quality control data is available

Creating a Custom Target:

If you’re working with a custom target you can’t find in the catalog, you’ll need to provide:

• The target name (required)

• The amino acid sequence (required)

• A supplier URL (optional, but recommended)

• Any additional notes about special handling or considerations

4. Protein Designs Upload

You can upload your protein designs using one of two methods:

CSV Upload:

When using a CSV file, you’ll need to include:

• A column for sequence names

• A column for amino acid sequences

• An optional column for marking controls

Our CSV mapping tool will help you match your columns to our required fields, and we’ll automatically validate the sequence formats.

FASTA Upload:

If you prefer FASTA format:

• The sequence headers will become your sequence names

• The sequences will be automatically parsed

5. Selecting Controls

After uploading your sequences, you’ll be able to designate certain sequences as controls (if you have a “Control” column in your CSV with boolean values, controls will be selected automatically)

6. Configuration Options

Finally, configure the experimental parameters:

• Set the number of replicates (the default is duplicate; triplicate is available as an add-on)

• Add any additional notes or special requirements

• The estimated price is for your information only and will most likely change after our review. For instance, it does not include the target cost or potential discounts, which will be added to your final quote

2. Draft Mode

In draft status, you can freely edit your experiment. The system updates price estimates, saves progress without commitment, and provides instant feedback on parameter validity.

3. Moving to Review

When you’re ready to proceed with your experiment, the review process begins.

Initiating Review

The review process starts when you click the “Move to Review” button.

• Your experiment details will be locked during review

• Our team will assess the technical feasibility

• A final quote will be prepared

• You’ll receive notifications about the review progress

During Review

While your experiment is under review, you’ll see a status indicator showing “In Review”. During this period:

• The experiment details are locked to maintain consistency

• You’ll receive email updates about the review progress

• Our team may reach out with questions or suggestions

If you need to make changes during the review period, you can use the “Remove from Review” button to:

• Return the experiment to draft status

• Make necessary modifications

• Resubmit to Review when ready

After Review: Quote, ETA and Confirmation

After your experiment is approved, you’ll receive a quote and an estimated timeline.

Quote: A detailed cost breakdown, including discounts, fees, and the total price, will be provided.

Timeline: You’ll also get a start date and estimated completion date (ETA) for your experiment results.

4. Confirming your Experiment

When confirming the experiment, you commit to pay the full amount of the quote. The confirmation process is simple but crucial:

Review the Quote: Access and download the complete quote PDF from the experiment page.

Final Confirmation: Click “Confirm Experiment,” acknowledge the terms and timeline, and submit your confirmation.

Post-Confirmation

Once confirmed, the process moves forward automatically:

• The experiment status updates to “In Production.”

• Materials are ordered to begin your experiment.

• The experiment appears under “Active Experiments” on your dashboard.

Timeline and Milestones

Here’s what to expect:

1. Waiting for Materials (5–10 days):

We’ll order the required gene fragments and target.

2. In Production:

Once all materials arrive at our lab, we’ll begin protein expression and proceed with the steps specific to your selected assay type.

3. Data Analysis and Validation:

Lab-generated data undergo rigorous processing and quality control (QC) to ensure reliability. If results are unclear, we’ll initiate re-runs as needed.

4. Done:

Results are delivered via the Foundry Portal, including a full data package with raw lab data.

Order size

The minimum order size depends on the assay. Binding screening and affinity characterization need 24 sequences per target. Expression, thermostability, enzyme activity and epitope binning need 20 sequences.

The minimum is per target, not per project. Splitting 24 designs across two targets does not meet it: each target needs its own 24 sequences.

Two points that come up often:

• The designs do not have to be related. They can be variants of a single protein, or 24 unrelated sequences. What matters is that they are all being tested against that target.

• Replicates do not count toward the minimum. The minimum counts distinct sequences, so 10 designs run in duplicate does not meet it.

Expression is included with binding assays. It is not a separate line you need to add. See Binding for what each assay covers.

If you have fewer designs than the minimum, contact us. We run smaller pilots and benchmarks.

Controls

You do not need to provide an expression control. Expression is read out by split-GFP against our own internal calibration, so a dedicated expression positive control is not required.

For binding, we do recommend a positive control. The simplest way is to include your control sequence alongside your designs. During sequence upload there is a field to mark a sequence as a control.

Controls count toward your sequence total. An order of 20 sequences with one control contains 19 designs.

For newly onboarded targets we do not automatically hold validated positive-control binders. A new target may need a feasibility step before the main experiment.

Plate layout: to fit controls on the same plate as the designs, the design total needs to be 90 or fewer, or 120 or more.

Check that your control is compatible with our platform before you upload it: see Supported protein formats.

Replicates and concentrations

Binding experiments run at multiple target concentrations, in duplicate by default.

Assay	Target concentrations	Replicates
Binding screening	2, plus a zero-concentration blank	Duplicate
Affinity characterization	4, plus a zero-concentration blank	Duplicate

The zero-concentration blank is always included, and it is what the other curves are referenced against.

Triplicate is available as an add-on. See our services page for cost.

The lab may add replicates at its own discretion when a first pass is borderline. This is why some sequences in your results have more replicates than others.