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Fred Hutch

Optide-Hunter at the Fred Hutchinson Cancer Research Center

The Optide-Hunter LIMS at the Olson Lab/Fred Huchinson Cancer Research Center

Summary

The Olson Lab at the Fred Hutchinson Cancer Research Center has developed a LIMS named Optide-Hunter for a generalized engineered protein compounds workflow that tracks entities and assays from creation to preclinical experiments. A summary of the project was published in the journal BMC Bioinformatics with the title “Laboratory Information Management Software for Engineered Mini-protein Therapeutic Workflow“.

Project Background

Gathering and integrating data from multiple locations can be difficult, particularly when protected patient data is involved and security is critical. The institution/enterprise needed to provide authorized users with access to diverse data from a wide variety of sources without resorting to piles of spreadsheets and manual alignment or home-built solutions. Researchers also needed to be able to generate visualizations and reports directly within the user interface to unlock trends and insights without leaving the combined data landscape.

Why Labkey

LabKey Server, an open source platform for scientific data integration, was a natural fit with its open data format, built-in analysis and auditing features, and flexible support for extending the platform to suit unique requirements. LabKey has its origins in the proteomics field, with success helping partners in academia, clinical research, and the biotech/pharma industry solve complex biomedical research challenges. With the free Community Edition, users can easily access all their data, structured as they uniquely require, and configurable security to ensure only authorized users have access. Developers can extend the platform using SQL, R, JavaScript, Java, and other languages via the LabKey API.

The Olson Lab decided to partner with LabKey, utilizing both custom development to extend the platform beyond current premium features, and the professional support from LabKey experts which accompanies any Premium Edition of LabKey Server. This collaboration accelerated their progress toward a solution specifically targeted to their engineered mini-protein workflow.

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The Challenge

Lab data management for complex and iterative therapeutic protein development presents significant hurdles. There are partial solutions found in pre-packaged software, but they are neither affordable nor adaptable enough for an ever-evolving academic research environment. Furthermore, many of these solutions lock down data in proprietary formats or require export and transformation in order to perform analyses.

Solution

The Optide-Hunter is used to store, extract, and view data for various therapeutics projects. It contains a compound registry, in-silico assays, high throughput production, large-scale production, in vivo assays, and data extraction from FreezerPro (a specimen-tracking database). This custom implementation was achieved using data transformation scripts and customized data import pipelines on top of core LabKey modules. Optide-Hunter also supports automated chromatogram classification. It includes HPLCPeakClassifierApp, a stand-alone application for external pre-processing of high performance liquid chromatography (HPLC) data prior to loading. The Optide-Hunter has been made available to assist other users in customizing it for their unique workflows. The ability to analyze, visualize, and interrogate the Optide data completely within LabKey Server reduces duplication and the risk of errors.

Future Work

In the future, the Optide-Hunter will be expanded to support monoclonal antibody (mAb) data, adding additional options for development of new therapies.

 

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