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Optide-Hunter

Laboratory Information Management Software for Engineered Mini-protein Therapeutic Workflow

Optide Hunter

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“. Learn more in this case study, then try Optide-Hunter for yourself.

Project Background

Protein-based therapeutics are a fast-growing class of novel medical interventions in areas such as cancer, infectious disease, and inflammation. The protein engineering process involves key strategies for optimizing desired therapeutic properties such as reduced immunogenicity, increased stability for storage, increased target specificity, etc. The Olson Lab experiments with nature-inspired bioengineered mini-proteins modified with synthetic chemistry to produce “Optides” (optimized peptides), which hold promise for improving the performance of potential therapies.

Development of protein therapeutics requires many iterations of modification and testing. It is critical to track details about sample sources, lineage, assay outcomes, and more in a queryable way. Scaling up these processes requires a cost-effective, flexible data management system. The Olson Lab has sought to construct such a system from limited resources, as they are a non-commercial organization.

Challenge

Integrating lab data for the complex and iterative therapeutic protein development process 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.

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.

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.

Benefits

Optide-Hunter, built on the LabKey Server platform, can be instantly used and adapted by new users without a big financial commitment. In fact, you can try the Optide-Hunter yourself now using either a read only example or by creating your own 30-day hosted trial version where you can upload your own data.

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.

Explore the Optide-Hunter

You can explore it right now using our read-only version, complete with some example data. Get started with the steps below.

  1. Open the Optide-Hunter by clicking the button above. It will open on a new tab.
  2. Click the Optides project icon at the bottom of the page.
  3. Here you see the uploaded data files and a menu of options along the top.
  4. Select Compounds Registry > Samples to see the list of sample sets. Click Purpose of Compounds Registration for Production in the right hand column to learn how to register homologues, variants, and constructs.
  5. Next, select HTProduction > Assays from the top menu bar and click Importing Flow Cytometry Data to learn how you would upload data to the NovoCyte assay.
  6. Note that you can explore our example here, but cannot make changes or add your own data to this shared read-only server.

After exploring our example, if you would like to create your own server for uploading data and making changes, you can create a 30 day hosted Trial of your own. Start your trial here, and choose the “Optide-Hunter – Case Study” option when you create your site.

You can find additional information about getting started using the Optide-Hunter in wikis throughout the server.

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