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case study

Creating an Efficient and Transparent Laboratory and Data Management Process to Expedite the Formalization of Internal R&D Standard Operating Procedures (SOPs)

by Brigitte Ganter, Ph.D. | posted on June 05, 2024

Developing new medicines for traditionally difficult protein targets requires new approaches that can easily be compared to building an airplane from scratch and learning to fly it. Think Bioscience is exactly at this stage. They are utilizing synthetic biology to both identify new natural products that can act as starting points for new therapeutic development and also help screen through those newly identified natural products in an efficient way. Think Bioscience’s approach is unique, in that they are optimizing their entire laboratory and data management processes (see Figure 1) while also formalizing their internal R&D Standard Operating Procedure (SOP). In other words, they are trying to fly the plane while still building it.

Figure 1: High-level description of Think Bioscience’s approach to optimizing their entire laboratory and data management processes.

To scale and standardize their proof-of-concept (PoC) processes and ensure all data collected follows a rigorously established SOP, all disparate data points (including metadata) are tracked and linked back to each specific experiment available within a centralized database. Think Bioscience needed to modernize, adapt, and improve their internal Excel spreadsheet-based processes to accommodate their need to manage all entities and data in one single source of truth. The Unified Platform L7|ESP®, with its Workflow Orchestration system, was identified as the perfect solution to bring organization, efficiency, and scalability to this process while formalizing the internal SOP process. Furthermore, to identify new protein targets using plasmid libraries and ensure efficient screening and identification of sequences of interest, and to be able to search through existing libraries in bulk, Think Bioscience took advantage of the plasmid editor (see Figure 2), data ingest app, and search capabilities available as open-source components in the L7|HUB to create an efficient and transparent process.

Figure2: Plasmid editor available as an open-source component in the L7|HUB.

L7|ESP Is the Solution to Overcome their Challenges

CHALLENGES L7|ESP PROVIDES THE SOLUTION

Tracking and collecting large disparate data at scale

 
  • Flexible and fully featured LIMS software that captures all process information
  • Integrates sample-specific information to inform all business processes
  • Collects, tracks, manages, and stores all disparate data types across all experiments within one platform
    • Stores large sequence data files, chemical structure data, in vitro assay data, including metadata
    • Links disparate data collected to central experiment
    • Handles any data size, including gigabytes of data
    • Removes the requirement for manual tracking
  • Tracks all processes, instruments, and samples, including location
  • Uploads scale-level modifications via the ingest app

Formalizing SOPs While Still Developing the Experimental Details

 
  • Quickly reflects SOP rewrites
  • Collects, tracks, and stores disparate data types across all experiments
  • Provides the plasmid editor to generate and track plasmids with DNA variants to be used for screening purposes
  • Streamlines library screening and data generation
  • Executes experiments
  • Provides bulk method of creating plasmids and libraries with metadata
Understanding Process Efficiencies and Inefficiencies
  • Functions as an organizational data hub that supports easy data retrieval
  • Supports querying and mining large data to inform process details
  • Saves downstream analytics time
  • Organizes all NGS data metrics associated with in vitro data
Managing Data Integrity Risk
  • Removes the need to work with many different tools
  • Centralizes library generation, data collection and tracking, and data querying
    • Registers all libraries, samples, and experimental details
  • Functions as the single source of truth
  • Improves data reporting and transparency
  • Organizes data and makes them accessible, following FAIR data principles
Maintaining all Plasmid Data
  • Stores high-throughput plasmid data
  • Integrates plasmid database (DB)
  • Removes the requirement for manual plasmid data tracking
Efficiently Creating and Managing the Many Relationships Between DNA and Chemical Products
  • Creates a seamless integration and experience to relate plasmid design, modification, and creation to LIMS features and business processes
  • Provides plasmid editor for bulk plasmid creation
  • Uses the plasmid as the most pivotal entity and assigns children and sibling relationships to designated plasmid libraries
    • Shows the parent/child relationship at an entity level
  • Queries every single data point and cross-examines it with any data point
  • Creates plasmid samples and libraries, assigns the plasmid to a library, and associates it with all metadata
  • Manages all NGS data associated with in vitro data
  • Scales and expands to accommodate plasmid data throughput process needs
Scaling the PoC
  • Integrates and manages all laboratory instruments/equipment, robotics, supplies, and other resources
    • Removes the requirement for manual instrument/equipment tracking
Ensuring Adherence to Data Provenance
  • Ensures highest standards of compliance, traceability, and sample/data provenance
  • Provides an audit trail for each entity from sample to screening
    • Controls all field changes

L7|ESP Value-Add

The Unified Platform, L7|ESP, with its Workflow Orchestration system, brings organization, efficiency, and transparency to Think Bioscience’s R&D SOP implementation process, facilitating disparate data collection, tracking, and storing. L7|ESP also streamlines library screening and data generation, integration of a plasmid editor, plasmid libraries with associated metadata, and efficient data mining and retrieval of its organizational data hub. The system not only allows for better data tracking, but also enables scalability, transparency, and connectivity between team members involved in rewriting SOPs to formalize internal processes. In other words, L7|ESP is helping Think Bioscience fly faster.

The Unified L7|ESP Platform, with its Workflow Orchestration system, is the ideal solution for us to modernize, adapt, and improve our internal excel spreadsheet-based processes to formalize our SOPs and to manage all entities and data in one single source of truth. 

Joel Kralj

Director Platform Innovation, Think Bioscience

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ABOUT THE AUTHOR

Brigitte Ganter, Sr. Director of Product Marketing

Brigitte Ganter, is currently Sr. Director of Product Marketing at L7 Informatics. Prior to her work at L7, Brigitte had founded enlightenbio LLC where she oversaw as General Manager all aspects of the company’s activities with particular focus on product management and product marketing services, including market research reports. Brigitte holds a PhD from the Swiss Federal Institute of Technology, Zurich (ETH Zurich) and conducted her post-doctoral work at Stanford University. Her broad industry experience includes positions of increasing responsibility predominantly in the role of Director of Product Management at several biotechnology/technology startups (Iconix Biosciences, Ingenuity System [now a Qiagen company], DNAnexus).