How Congruence Therapeutics Made Data Processing ~1,000x Faster with KNIME

The Challenge: Manual Processes Hindering High-Value Scientific Work 

Congruence Therapeutics, located at the Mila Quebec AI Institute in Montreal, is a biotech company that develops drugs to fix misfolded proteins that cause disease. 

They integrate machine learning, artificial intelligence, and wet lab science through their own discovery engine and develop proprietary therapeutics and computational tools to optimize drug discovery.

As part of their ongoing efforts, Congruence identified a bottleneck in their operations: efficiently cleaning and restructuring assay data exported from plate readers. 

The company frequently runs biological assays using 384-well plates to experiment, then test and analyze the data. The plate readers generate data into an Excel file, but the raw output requires substantial reformatting before scientists can begin analysis. Assay scientists — trained in experimental biology — were spending significant time on repetitive tasks such as copying, pasting, and reshaping datasets.

“What has to happen is the assay scientist slowly cuts and pastes [data] for hours into a format that can allow them to do the analysis. And so it's a perfect case for KNIME.” Lee Fader, Vice President at Congruence Therapeutics.

This process consumed a portion of each scientist’s week and delayed downstream analysis. 

“It’s a really far too common example of how we get caught using old habits to do routine tasks that can be automated. To me, it’s the kind of thing that when I identify the problem, I salivate with excitement over the possibility of building a KNIME workflow to solve the problem”. 

The Solution: Automating Routine Data Processing with KNIME Visual Workflows

Previously scientists would write macros or VBA code to run the analysis, but this was extremely complex, time-consuming, and the file size would cause the macros to break. To address this, the team developed a KNIME workflow and deployed it through KNIME Business Hub. The solution included:

• File upload and cleaning: Simplified import of raw assay data and extraction of relevant rows.
• Data app deployment via KNIME Business Hub: Allowed for visual exploration, filtering of results, and export preparation.
• Curve viewer and quality control: Enabled inspection of positive/negative controls and individual assay curves via an interactive JavaScript view.

The output was formatted for direct use in a specific graphing application called Prism, eliminating the need for manual reorganization. Regular usage led to iterative improvements of the output, with scientists requesting new features to extend functionality. In the end, colleagues used this solution to push their work forward instead of spending hours doing manual and error-prone work in Excel. 

The Results: ~10% Time Savings per Experiment, per Scientist, per Week

Automating assay data processing delivered measurable results for Congruence Therapeutics:

• Complex, time-consuming tasks can now be carried out 1,000x faster.
• Scientists reclaimed 8–10% of their time per assay per week.
• With 5 or 6 scientists running 2 assays per week, automation has the potential to produce a savings of about the cost of one scientist's annual salary (equating to approx. $300,000/year in the US)

“The other key thing that I think is amazing is how much time savings and process improvement we've been able to realize with KNIME,” says Lee. ”Twenty percent in time spent analyzing data per week per person is quite amazing, actually. It's a whole day where they could be planning an experiment or running another experiment or analyzing data, something like that.”

Deploying the data processing workflow on KNIME Business Hub made it accessible to all lab scientists, including those without prior KNIME experience or deep data science or analytics expertise. 

The centralization of workflows ensured consistency and streamlined tool management: 

“We have the [KNIME Business Hub] in the background and it has been churning away very consistently, managing all our tools for design, prioritization of our synthesis work at contract research organizations, and interaction with our consultants. It’s all in the background on the KNIME Hub running smoothly.” 

With the time back, Lee is able to get creative and search for more use cases where KNIME can be used to save time and money.

Enabling a Culture of Automation & Process Optimization

Lee continues to spearhead internal knowledge-sharing sessions to show others at Congruence how they can use KNIME to operate more efficiently. His initiative helps maximize the value of data analytics investments by empowering more users to build, share, and scale data solutions efficiently across the organization. Congruence Therapeutics is using KNIME not only as a data tool, but as a platform for scientific enablement and operational efficiency.

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