Creating an Efficient and Transparent Laboratory and Data Management Process to Expedite the Formalization of Internal R&D Standard Operating Procedures (SOPs) (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.
The Standard Operating Procedure (SOP) is necessitated by the need to standardize the process of data collection at all levels by providing clear, concise and prescriptive procedures on the use of standard Data Collection Tools (DCTs) for the data collection, collation and aggregation.
You can categorize SOPs into three different types: step-by-step, hierarchical steps, and flowcharts. Some business processes are better suited for certain types than others, depending on their complexity. Let's take a closer look at each SOP format.
We recommend including the following elements in your SOPs: header, purpose, scope, references and related documents, definitions, roles and responsibilities, procedure, appendices, revision history, and approval signatures (as required).
Standard operating procedures provide the policies, processes and standards needed for the organization to succeed. They can benefit a business by reducing errors, increasing efficiencies and profitability, creating a safe work environment and producing guidelines for how to resolve issues and overcome obstacles.
Typically, the SOP is two pages long, single-spaced, written in 11-point typefaces, and broken up into five to eight paragraphs. Your overall narrative should be organized logically and coherently, with each paragraph addressing a particular topic or theme connected to your academic and professional ambitions.
Examples of Standard Operating Procedures include guidelines for onboarding new employees, steps for handling customer service inquiries, protocols for software updates or deployments in IT, and procedures for emergency responses or safety measures in a manufacturing setting.
Good Laboratory Practice (GLP) and Standard Operating Procedures (SOPs) provide guidelines for proper operation of equipment, maintenance and sanitation, reporting structures, and related activities. These practices are routinely employed at large academic and research-based institutions.
Introduction: My name is Tyson Zemlak, I am a excited, light, sparkling, super, open, fair, magnificent person who loves writing and wants to share my knowledge and understanding with you.
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