PamGene migrates to the cloud with Tercen.

Introduction

PamGene is a biotechnology company that offers an assay and instrument to detect functional kinase activity in cellular and tissue lysates through measuring peptide phosphorylation by protein kinases. The PamGene technology is used for non-invasive applications in the areas of fundamental science, translational research and diagnostics. The PamChip Assay principle can be used to deliver insights into discriminative drug responses and optimize kinase inhibitors. Through this researchers can discover novel biomarkers, targets, and pathways.

PamGene developed a software in house called BioNavigator to do data analysis on the kinase experiments but wanted to expand their functionality. Tercen is a software platform that allows wet-lab biologists to build and run sophisticated data analysis pipelines using a simple graphical interface. The platform has advanced collaboration features that enable biologists to report results and share data more quickly. Tercen has a unique ability to join the data of different disciplines, facilitating translational analysis and is unique in offering the functionality to scientific instrument makers.

Tercen uses a RAPID methodology, a set of five concrete steps to implement and customize an instrument manufacturer’s cloud strategy and key deliverables were identified for the project. 

• Reduce installation and software update support. 
• Provide more compute and storage power for clients with larger experiments.
• Handle more clients and an expansion of instrument adoption.
• Remove Kinase analysis bottlenecks.
• Remove the risk of business critical code becoming non-operatable when client operating systems are updated.

Stage 1: Requirements

In the beginning both teams met to identify the key requirements for migration of BioNavigator functionality to the Tercen platform. Two key subject areas were identified…

• PamGene proprietary software code to be embedded as is.
• General statistical functions to be replaced with Tercen general functionality.

Target deliverables were identified.

• 1Gb per day processing per instrument.
• Analysis features are to be available on all operating systems.
• Ability to integrate Matlab code.
• Branding and user experience of all elements would appear as PamGene.

Stage 2: Algorithms

The PamGene technology has proprietary algorithms developed for Quality Control, Image Analysis and Kinase Analysis. They were primarily written in R and Matlab. During the project they were wrapped into Tercen cloud-native containers (called Operators) without having to be refactored. Tercen has a data-handling system and relational algebra which works on a table-in table-out principle and makes this possible.

Algorithms were migrated for.

• Quality Control (QC-STK, QC-PTK)
• Image Analysis (PTK and STK)
• Data Analysis(ETS, MTvC)
• Kinase Analysis (TTest, UKA )

The benefits of this phase included.

• Automated memory and hard disk use controls.
• Automated regression testing for updated code.
• Version control and automated continuous integration routines on deployment.

Stage 3: Pipelines

The primary experimental designs associated with PamGene compare test conditions to a control using the proprietary code and general data analysis techniques such as t-test, scaling of data, log functions and statistical calculations.

Two primary analysis pipelines were created.

• Image Analysis (PTK,STK)
• Kinase Analysis (ETS,UKA, TTest,MTvC)

Each pipeline is version-controlled and has automated validation tests. These regression tests are automatically run when a new release is made. Proprietary PamGene operators are now separated from open-source data-analysis code and independently maintained.

• Centralized code base to support.
• Easier customer support with internet sharable analysis and client-private teams.
• Standardization and faster updates of software.

Stage 4: Interface

Visual interactions for quality control and image analysis are needed for the Kinase analysis process. Tercen provided these using Shiny interfaces in our first iteration of platform Apps. This is blended with Tercen’s powerful standard feature set for data analysis.

Functions of the user interface

• Image Checking
• Automated Grid finding
• Manual Checking of Grids

Benefits of this method.

• Eliminated difficult Matlab installation
• Allowed Users to use MAC, Windows and Linux to perform image analysis
• Easier Updates

Stage 5: Documentation

Knowledge transfer was completed with Train-the-Trainer data workshops run for the PamGene support team using real world examples. Tercen provides on-going second-line support for the team as part of the licence offering.

• Quickly get the PamGene team up to speed.
• Improve support to PamGene customers.
• Improved documentation for PamGene customers.

Results

bionavigator.pamgene.com went live on 31 Mar 2022 after a short implementation phase with internal use only.