Automated Prism-based Assay Data Analysis

Scirex is now able to automate GraphPad Prism based data processing from plate-reader output file to curve-fitting results and charts and result capture into a database.

Prism is a great tool for biological assay data analysis; it’s very flexible and has powerful data visualization features. The automation support, however, is limited and it’s not a strong data management tool; often you and up having your results in many different files and need to manually maintain an Excel file summarizing the results.

With the Prism automation features in Scirex, you can now enjoy the flexibility and data analysis power of Prism without sacrificing automation and data management.

Elements of this approach are discussed in two previous blog articles, here and here. A discussion about the challenges of managing research can be found in this blog article, and our general approach to assay data management is discussed here.

Automated Analysis Process

You start by registering the experimental setup in Scirex, by selecting your input samples and specifying the plate layout (the Assay Plate is auto-generated from the input samples and the sample layout):

The plate layout template consists of sample positions and concentration/dilution. This template can be reused in subsequent experiments.

Once you have performed the experiment, you upload the raw plate readings by dropping the reader file on the assay step details page. The Scirex database will now contain one result-set representing the raw data and one result-set representing data series:

As can be seen in this screenshot, the raw data contains the direct measurements in plate format, whereas the data series are generated by Scirex based on the plate layout. The two result-sets are linked and the raw data contains a cross-reference to the original data file, providing you with full data traceability.

Once you have the data series in Scirex, you can use the PrismWrapper application to automatically run Prism and capture the results back into Scirex. You start by selecting the data series result-set and the Prism template file:

The Scirex PrismWrapper client will download the data series, generate a new Prism file, run Prism to perform the analysis, thencapture the results and charts back into Scirex. Once this process has completed (it typically takes a few seconds), the curve fit result can be found in the Scirex website:

Manual Processing Options

There may be cases where the fully automated processing doesn’t yield the right results, e.g. because of the need to exclude outliers or try alternative fitting model or parameters. You may also need to work manually with the Prism files when preparing charts for presentations or reports.

The automated processing involves the creation of regular Prism files that you can also work with manually, e.g. by modifying the curve fitting or by creating new charts.

If you modify the curve fitting, you can upload the results in Scirex as a second curve-fitting result-set. You will have both the automated and manual processing results in the database and the option to choose which of the curve fits from the two sets to release as the final results.

Why Use the Scirex to Run Prism?

The automated data processing using Prism templates provides lots of benefits while retaining the flexibility you are used to when working with GraphPad Prism:

  • Full traceability, from compound through samples and assay experiments to different curve fitting results, data series, raw data and the original reader output files. This traceability includes support for different curve fittings on the same data series, useful e.g. for evaluating different analysis models and parameter sets
  • You can very easily change the template, including curve fitting model and parameters as well as generated charts, simply by editing the Prism file used as a template
  • Automated the preparation of Prism files from reader output saves time and reduces the risk of manual processing errors
  • Easily search for results and generate charts and reports than combine data from different experiments, including automated tools for monitoring assay performance
  • Data sharing with your colleagues is easier because the results go into a shared database. You still control visibility of the results, since you can cancel individual results, and result-sets are only visible to the project once it’s marked as “published”
  • The data processing is integrated with the workflow features in Scirex, including the ordering process, further improving data traceability and reducing the need for manual data handling in emails and files