Allcyte: Improving drug targeting with single cell imaging

About Allcyte

Allcyte, using its high-content imaging platform, Pharmacoscopy, aims to bring personalized cancer medicine to patients and physicians, and helps pharmaceutical companies focus their target and immunomodulatory drug development.

Industries: Healthcare & Life Sciences
Location: Austria

About CLOUDPILOTS

A Google Cloud partner since 2011, CLOUDPILOTS Software & Consulting GmbH enables digital transformation and cloud-based collaboration.

With Google Cloud Platform and CLOUDPILOTS, Allcyte built an infrastructure capable of analyzing, storing, and data mining tens of thousands of microscopic images of cancer patients’ cells per day.

Google Cloud Results

  • Records, stores, and analyzes up to 100 terabytes of imaging data every year
  • Deploys analysis software quickly, efficiently, and reliably with Google Kubernetes Engine
  • Enables rapid and heavy scaling without large upfront costs thanks to flexible pricing

Processes a minimum of 100 gigabytes of images daily

Recording and analyzing tens of thousands of microscopy images of cells from cancer patients per hour, the biotech startup Allcyte is bringing unprecedented insight into how drug treatments affect individual patients. Allcyte was started in 2014 as a project at the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences, where it could take advantage of the institute’s professionally maintained computing resources to record, process, and analyze microscopic images showing how drugs interact with single cells.

“Moving from an academic environment, time was a factor for us. If our platform goes down for even a couple of days, the backlog in our processes could take weeks to catch up. We chose Google for its reliability and because we could deploy our software quickly, to always be able to perform necessary analyses.”

Dr. Gregory Vladimer, Scientific Co-founder and CSO, Allcyte

By the start of 2017, Allcyte had developed into an independent startup. However, the company needed a powerful infrastructure if it was to continue its work outside an academic environment. To do that, it turned to Google Cloud Platform.

“Moving from an academic environment, time was a factor for us. If our platform goes down for even a couple of days, the backlog in our processes could take weeks to catch up,” says Dr. Gregory Vladimer, Scientific Co-founder and CSO at Allcyte. “We chose Google for its reliability and because we could deploy our software quickly, to always be able to perform necessary analyses.”

Rapid scaling and stable performance

Combining cutting-edge microscopy techniques with powerful data analytics, Allcyte’s strength lies in Pharmacoscopy, its high-content imaging technology. Using primary samples from patients with blood cancer, treating them with drugs, and then recording tens of thousands of images at the single cell level, Allcyte can very quickly predict the clinical effectiveness of large libraries of drug treatments. This enables physicians to take the most suitable course of action for each individual patient, and can help focus research on pre-clinical drugs into specific indications. After the first pass, all images are continually stored for Allcyte’s future analysis.

What makes the company’s solution work is the scale of its operations. Since it started, Allcyte has screened more than 150 billion cells, generating more than 200 terabytes of data. All this requires an incredibly powerful infrastructure to process, store, and analyze the images quickly enough to treat patients in a clinical context, as well as provide longer term research material. At CeMM, Allcyte could take advantage of a professionally maintained, on-premises university compute cluster. After it went independent, however, the company knew that it needed a new solution to stay viable. As a startup with limited resources, recreating the on-premises solution it had at CeMM was not feasible so Allcyte looked to the cloud for a solution.

“The best thing about Google Kubernetes Engine is how simple it is to set up and get going. If we had tried to do this with an on-premises solution it would have taken much longer just to get even the infrastructure set up correctly.”

Bernhard Fieglmueller, Senior Cloud Consultant, CLOUDPILOTS

Allcyte met with representatives from Google to see how it could replicate Allcyte’s architecture with Google Cloud Platform. Encouraged by Google’s investment in health and life sciences, Allcyte software engineer Oscar Lopez teamed up with Google Cloud Partner CLOUDPILOTS to implement the new cluster-based architecture, running on Google Kubernetes Engine, for easy scaling and automation. CLOUDPILOTS and Allcyte used Google Container Builder to replicate its deployment pipeline, allowing for speed without sacrificing stability.

Keeping the huge amounts of data and staying within budget limits was made possible by using Google Archival Cloud Storage: Nearline. Meanwhile, Google Stackdriver Monitoring, Google Stackdriver Error Reporting, and Google Stackdriver Logging have helped Allcyte find errors and react to them faster than ever before. Using G Suite, and Google Hangouts in particular, has made collaboration between CLOUDPILOTS and Allcyte very easy and helped the migration go smoothly.

“The best thing about Google Kubernetes Engine is how simple it is to set up and get going,” says Bernhard Fieglmueller, Senior Cloud Consultant at CLOUDPILOTS. “If we had tried to do this with an on-premises solution it would have taken much longer just to get even the infrastructure set up correctly.”

“Using Google Kubernetes Engine, we don’t have memory or data limits for our jobs, and this allows us to think bigger and start to combine our data with other datasets out there to create better analysis algorithms. We’re really glad we came to CLOUDPILOTS and Google. The service has been fantastic.”

Dr. Gregory Vladimer, Scientific Co-founder and CSO, Allcyte

Built to last, ready to expand

With Google Cloud Platform, Allcyte has been able to rebuild and improve its infrastructure on a cloud-based platform designed for stability and rapid growth. During the migration process, the company has been processing a minimum of 100 gigabytes of data a day. Flexible pricing from Google and the ability to scale quickly means that, even as a startup, Allcyte has been able to migrate without incurring heavy upfront costs or compromising on performance.

By December 2017, Allcyte and CLOUDPILOTS successfully replicated its crucial data pipeline without disrupting its normal workflow. “I’m impressed with how robust the new pipeline has been,” says Dr. Vladimer. “We’re pushing jobs to it every day with no issue.”

Allcyte is currently working on its data storage capacity. The ability to store and quickly retrieve image data, long after its primary clinical or experimental use, is vital to the Allcyte mission of supporting drug development. Using Google Cloud Storage, the company will be able not only to store the 100 terabytes of data per annum it expects to generate, but also keep vast amounts of it accessible and ready for analysis, which was not possible with the company’s older on-premises solution. Looking ahead, Allcyte is keen to experiment with Google Cloud APIs for healthcare as well as Google Cloud AI machine learning tools to see what additional insights it can extract. As Allcyte continues to grow, it can rely on CLOUDPILOTS and Google to give it the right tools to help it adapt and expand to even greater things in the future.

“Using Google Kubernetes Engine, we don’t have memory or data limits for our jobs, and this allows us to think bigger and start to combine our data with other datasets out there to create better analysis algorithms”, says Dr. Vladimer. “We’re really glad we came to CLOUDPILOTS and Google. The service has been fantastic.”

About Allcyte

Allcyte, using its high-content imaging platform, Pharmacoscopy, aims to bring personalized cancer medicine to patients and physicians, and helps pharmaceutical companies focus their target and immunomodulatory drug development.

Industries: Healthcare & Life Sciences
Location: Austria

About CLOUDPILOTS

A Google Cloud partner since 2011, CLOUDPILOTS Software & Consulting GmbH enables digital transformation and cloud-based collaboration.

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