DNA Assembly

Why Construct Assembly with Synthace?

The advancement of DNA assembly is changing many fields of biotechnology, from vaccines to biomaterials. Highly efficient methods require automation that can keep up with the higher throughput. As construct assemblies utilize more parts, the number of possible outcomes increases and the throughput increases, necessitating automation. Programming devices for these processes can be a challenge, especially for complex assemblies requiring multiple parts.

Robust, reproducible designs

Synthace simplifies performing complex assemblies by automatically programming liquid handling steps, liquid transfer calculations, and providing full sample traceability.  

Calculate

Synthace automatically calculates all liquid handling steps, making changing protocols and assemblies easy

Trace

Synthace provides in silico experimental preview giving full sample traceability

Report

Synthace’s Assembly Design Report gives estimated probabilities of assemblies, improving fidelity and efficacy

Pain points and current processes

  • Current practices

    With Synthace

  • Experiment inputs

    Current practices

    • Hard to translate construct design into executable steps for a liquid handler, especially for multi-part assemblies
    • Can’t easily link metadata to samples with Excel

    With Synthace

    • Flexible sample setup allows the user to easily define all constructs, mastermixes, competent cells, and other parts in design file
    • Synthace programs all liquid handling steps allowing for more complex experiments
  • Experiment planning

    Current practices

    • Designing construct experiments requires time consuming planning and research
    • Volume transfer steps require time consuming calculations
    • Changing assemblies and experiment parameters is difficult

    With Synthace

    • Plan your experiment remotely, from anywhere
    • Flexibly change experimental parameters and protocols with Synthace's intuitive interface and dynamically reprogram the automation
    • Synthace’s assembly report estimates probabilities of different assemblies fidelity and efficiency
  • Experiment execution

    Current practices

    • User needs to understand liquid handling hardware details to modify execution

    With Synthace

    • Simply send the generated method to the automation for execution through SynthaceHub
    • Synthace provides a fully fledged automation method that can be run in the native software, providing more than just a worklist
  • Data aggregation

    Current practices

    • Linking design to output data requires manual input
    • Keeping track of samples throughout experiment can be tedious and time consuming

    With Synthace

    • Synthace enables full sample provenance as all samples are tracked throughout
    • Assembly results files, plate layouts, device instructions, reagents, and Assembly Report all found on one page
  • Experiment outputs

    Current practices

    • Difficult to compare data and methods with previous runs
    • Sharing experimental protocols between lab members and devices can be challenging

    With Synthace

    • Previous data sets stored in the cloud for easy access
    • Share flexible workflows between team members at different sites and between different automation devices

Protocol walkthrough

Basic concepts

Translate human-readable actions into machine instructions

Simple building blocks...

Elements are a key concept in Synthace. They translate human-readable actions into machine instructions. You can define how the experiment will be performed through the element input parameters.

Elements form the visual user interface to Synthace’s planning engine. Synthace interprets your requirements and translates these into complex robot instructions. Input volumes are also calculated and the labware needed is determined.

...translated into complex robot instructions

You can create workflows in Synthace by connecting elements together to specify the flow of physical materials and information.

A simple workflow example is connecting an element where liquids and their properties are defined (e.g. liquid names, concentrations, pH, and so on) with an element that aliquots these liquids onto a plate as desired.

Define experiment

Easily define and modify your experiment

Define your assemblies to automate the design

Synthace’s device-agnostic software automatically converts assembly design into instructions for any device you are using

Quickly view entire experiment in silico

See how Synthace calculates all liquid transfer steps in order to give the desired assemblies

Overview of entire experiment

Synthace’s Execution Details page aggregates plate layouts, labware and reagents required, Assembly Report and a full set of device-specific instructions

Preview in silico

Preview your runs in detail at your desk

Synthace’s execution preview shows a layout of your device, and clearly shows where labware needs to be placed and the amount and location of your reagents.

The preview also shows every liquid handling action in order of execution with a useful step-by-step time estimate. This minimizes the chances of errors, and gives you an immediate estimate of walk-away time. Hovering over individual transfers will indicate the selected liquid handling policies. 

Output

Keep track of your assemblies

Presents the required labware

Synthace’s Assembly Report automatically keeps track of the parts and lengths of your assembly as well as calculates your assembly's fidelity without the need for additional software. This increases the assembly's robustness and reproducibility. Keeping all experimental files and reports on one page reduces manual data matching which can be slow and error-prone. 

Introducing Synthace, the world’s most powerful software platform for performing biological experiments

​​Intelligent software for the dynamic use of laboratory automation

Sophisticated experiments made simple

FAQs

Synthace for DNA Assembly is available on:

  • Tecan's Freedom EVO®
  • Hamilton's Microlab® STAR and STARlet
  • Gilson's PIPETMAX®
  • FORMULATRIX®'s MANTIS®

The Synthace planning engine parses the high-level inputs specified in your workflow, including the experimental design, selected labware and deck layout. The planning engine converts these instructions into low-level instructions such as the liquid handling steps and the exact labware positions on your predefined deck layout.

Yes, custom deck layouts can be chosen in Synthace. The user can define multiple deck configurations for the same liquid handler mode.

SynthaceHub automatically sends log and configuration files to the cloud for storage in your organization’s private data repository in Synthace from the liquid handler’s native software.

Although calendar integrations are not yet available in Synthace, the estimated run times as calculated by Synthace’s planning engine provide an accurate timing for you to ensure that you have booked enough time on your desired devices to execute your experiments.

Synthace will work out the changes necessary to implement your workflow. You simply need to upload your deck configuration and re-simulate — Synthace will use your new worktable layout to determine the necessary instructions.

Synthace comes with its own library of different liquid handling policies for all types of liquids. You can select different liquid handling policies for each of the liquid handling steps. Different samples can have different policies, and these policies can be linked to your liquid classes on certain liquid handling devices.

Yes, Synthace’s cherry picker is one example of that. Another example would be DOE runs with hard to change factors where we would need to run across two workflows.

Experimental results can be searched and accessed by everyone in your group/organization who has an account in Synthace. If you would like to discuss access control and data security in more detail, please drop us an email or use the “Request a demo” button above.

Trusted by

We were founded by a team of biologists in 2011 as a bio-process service provider, optimizing the existing bio-processes of our clients using a multi-factorial experimental approach. We used automated robotic equipment to run our high-dimensional, complex experiments.

Synthace has helped us improve our business and think outside the box, and its platform has allowed us to do many things we previously couldn’t” André Raposo Group Lead - Computer-Aided Biology (CAB) group at Oxford Biomedica
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