Tag: Biologics LIMS

Upside foods is a fast-growing start-up working on developing cell-cultured meat for the consumer market. They have a robust R&D pipeline supported by varied teams and processes. Similar to traditional life science organizations, Upside is required to comply with regulatory requests and protocols including those from the FDA and USDA. 

Upside Foods utilize the Biologics LIMS to help answer key questions including:

• How do various growth conditions affect tissue growth?
• What combination of production variables produces the best tasting and healthiest cell-cultured meat?  

Answering these questions begins with gathering data in the lab from assays being continuously run by scientists. Prior to LabKey, Upside was using an assay data capture solution consisting of many connected moving parts including spreadsheets, manual processes, data transformations, databases and network drives. This solution was difficult to support and required lots of replication of data that was shaped differently depending on where it was stored. This system lacked:

• Central management and storage of their data 
• Audit logging and alerts for each component and the system as a whole
• Redundancy and disaster recovery
• Scalability to meet growth needs and increasing R&D complexity 

In selecting the Biologics LIMS, Upside was aiming to keep up with their many changing requirements including new instruments and assays, increasing business logic complexity and the need for a single source of truth for their data. LabKey has a number of ways to capture data including bulk import through the UI. However, Upside wanted to reduce the time and effort it took for uploading data even further, especially from high-throughput assay pipelines. They wanted to make the process as effortless as possible for their scientists. With low latency in getting instrument data loaded in the system, scientists could make faster decisions and trust the data being used for their analyses.

Presented by Jay Kasberger, Senior Manager, Software Engineering at Upside Foods, the video below describes how Upside Foods built a pipeline that leverages AWS to automate the flow of assay data.  By using Lambda and DataSync, Upside Foods reduced the work scientists have to perform to transfer runs and results into the system while keeping thorough logs and automatically alerting to any issues.

Click here to learn more about the Biologics LIMS.

Watch the presentation below:

[vc_video link=”https://www.youtube.com/watch?v=N3sIgSjshx8″]

Biopharma software is an essential tool for managing R&D data of modern biotech organizations. Biologics development is a data-driven endeavor involving many development stages and cross-functional collaboration. The inherent complexity, variety of disciplines producing data, and the sheer volume of data can easily pose a challenge to biopharma research organizations. Many research teams are using general-purpose data management tools (spreadsheets and files) or systems purpose-built for a single data type. This approach can lead to problems in tracking data and duplicating work. This blog post focuses on key considerations when selecting biopharma software for managing R&D data. 

Biopharma data management challenges include:

• Integrating data generated from disparate scientific specialties
• Difficulty in finding and highlighting important data (leading to duplication of work)
• Variabilities in data structure and conventions
• Lack of visibility into data provenance

These challenges make it difficult for biopharma researchers to answer some basic scientific questions about their data:

• Do I have the data I need?
• What is this data? (structured data model, definitions)
• Where did this data come from? (data provenance, audit history)
• How and why was it generated? (reproducibility, workflow processes)

Biopharma software can help centralize research data and enforce data standards. This allows for quick and confident answers to the questions scientists ask about their data. Along with data capture, standardizing and monitoring processes is critical to tracking biopharma R&D activity and reducing data inconsistencies.

Biopharma software should include integrated tools for data management.

The LabKey Biologics LIMS provides a central bioregistry with integrated assay data capture, workflow management, and a “data-connected” electronic lab notebook. We consider these to be the pillars of a comprehensive biopharma software solution for data management.

Bioregistry

A bioregistry helps scientists define, register, and review interconnected biological entities and their samples. By centralizing biopharma R&D data, researchers can easily find, view, and navigate through entities, their lineage, and data relationships. For example, using a bioregistry, scientists can easily find a specific molecule and see all the related sequences, samples containing it, and related assay data.

Assay Data Management

Assay data is the decision-making criteria for discovery, process development, and quality. It is generated by all contributing teams and its relevance endures throughout. Having a central, structured, and workflow-related assay data capture mechanism is essential for streamlining decision making, hand-offs, and post hoc analysis. It ensures that consistent data structures are used throughout the biopharma development process, sets expectations for needed data, and makes clear where critical data can be found.

Electronic Lab Notebook

An ELN is designed to help scientists efficiently organize and document their ongoing research. A data-connected ELN provides even more value by having access to the bioregistry, assay, and sample data captured so that additional work is not required to find and include it. This integration paradigm maintains data integrity while enabling easy data exploration and collaboration.

Workflow Management

Defining collaborative biopharma workflows helps set expectations for contributors and managers. It supports the fulfillment of material and data needs and prepares the way for process optimization, scheduling, and cross-team alignment. These workflow tools facilitate strategic experimentation, simpler data hand-off, and easier planning.

Biologics LIMS- Biopharma R&D software designed for efficient data management.

Biologics LIMS is a powerful suite of integrated tools to help scientists manage biologics research data, improve lab processes, and collaborate efficiently. The software provides biopharma researchers with streamlined registration and tracking of biological entities and samples in a central bioregistry. The bioregistry is seamlessly integrated with tools for workflow management, assay data management, and an electronic lab notebook (ELN). This combination of software tools forms a cohesive application that serves as a central hub for managing biotherapeutic development data, processes, lab notebooks, and collaboration efforts.

LabKey Biologics helps scientists:

• Speed up decision-making with unified ELN, bioregistry, workflow, and assay data management tools
• Centralize and connect data for a holistic view of your data landscape and interrelationships
• Manage and optimize lab processes with a workflow tool designed for biopharma R&D

Click here to learn more about LabKey Biologics and take a product tour.

From cell lines and constructs to their vectors and insert sequences, biotherapeutic development involves many moving parts that need to be defined and connected. Using spreadsheets to manage this data and their inter-relationships is a highly inefficient and error-prone endeavor. Without a central bioregistry to capture and track all of these pieces, researchers could end up with data that is inaccurate, redundant, and insufficient. 

A bioregistry is a structured data repository that helps scientists answer a multitude of questions during the biotherapeutic development process. By efficiently attaining answers to those questions scientists can make data-driven decisions, increase efficiency, and trust the integrity of their data. Time is precious in biotherapeutic development and reducing duplicative efforts and time wasted in finding entity information can be highly advantageous to most organizations. 

Adopting a bioregistry can provide biopharma organizations with the following benefits:

• Centralization of information for critical biological entities and protection of intellectual property
• Eliminating duplication and improving data integrity by verifying the uniqueness of entities upon registration
• Creation of links between samples, entities, electro nic lab notebooks and entity creation processes (protein, expression, purification, characterization)

The LabKey Biologics Bioregistry

LabKey Biologics includes a fully integrated bioregistry as part of a suite of integrated software tools for biotherapeutic development. The bioregistry captures complete entity and sample information for molecular entities, nucleotide sequences, protein sequences, expression systems, constructs, vectors and cell lines. Researchers can easily navigate through entities and their relationships. For example, researchers can find a specific molecule and see the component sequences, the samples of that molecule and the assay data associated with those samples.

Click Here to learn more about LabKey Biologics and take a tour!

[vc_video link=”https://www.youtube.com/watch?v=AcUj-EN254U” align=”center”]Developing biopharmaceuticals is an increasingly important endeavor in the drug discovery efforts of almost every major pharmaceutical company. High-yield, stably expressing cell lines are of critical importance for economically viable biopharmaceutical production processes. Tracking CLD processes can be challenging due to the number of clones generated, as well as the high number of tests performed to identify producer cell lines suitable for industrial, large-scale manufacturing processes.

In this presentation at the LabKey User Conference, Bo Zhai of Janssen Research & Development explains how he implemented LabKey Biologics to map the entire cell line development process with proper lineage tracking. The platform also assisted in associating the molecule entity as well as analytical testing information with samples at different CLD stages to effectively reduce the clone selection timeline.

About LabKey Biologics

LabKey Biologics is a flexible LIMS software platform providing biopharmaceutical researchers with an intuitive suite of tools for biological entity registration, workflow management, and integrated data exploration. The platform provides researchers with a complete data landscape by tracking generations of proteins, plasmids and physical samples, and connecting design data to related assay results. Learn more about LabKey Biologics by exploring the features below:

Bioregistry – Capture structured data of all biological entities and samples.

Electronic Lab Notebook – Create data-rich notebooks with a fully integrated ELN.

Biologics Assay Management – Integrate experiment data from any assay, connecting results to sample details and lineage information.

Biologics Workflow Manager – Manage and optimize your Biologics development processes

Media Registration – Define standard recipes and available raw ingredients to facilitate consistent media preparation.

Request a Demo or Start a Trial to learn more about LabKey Biologics.

[vc_video link=”https://youtu.be/2WpQ_ncpsMQ” el_width=”80″ align=”center”]Centralizing biologics assay data so it can be easily viewed and analyzed in a single place is one of the core challenges biotherapeutic research teams encounter. Without centralized assay data, teams must turn to time-consuming and error-prone manual integration methods to collaborate and maximize the value of their analytical data.

LabKey Server’s robust mechanisms for defining assays and uploading assay data are helpful for bringing analytical data into a single system, but our biologics software– LabKey Biologics, takes this one step further and provides valuable structure and connections that help biologics research teams understand how that analytical data fits into the larger context.

LabKey Assay Designs: Standardizing Analytical Data Structures

LabKey Biologics allows teams to define or customize biologics assay designs (many editable assay design templates come pre-defined within the system) to capture assay data in a specific structure. Some teams using LabKey Biologics may need to define only a few assay designs to support their research, while others working in a more complex environment may need to define 100+.

When building an assay design, laboratory teams can choose to add fields specific to batches, runs and results to provide additional context for their data. LabKey supports a wide variety of field types (including integer, float, boolean, and text) and users can configure aliases, validation rules, and a variety of other characteristics for each.

Centralizing Assay Data In the System

Once an assay design has been built in LabKey Biologics, data can be added to the system using that design to provide its structure. There are a number of different ways to load your assay data into LabKey Biologics including:

• Automatically uploading via the LabKey API
• Manually uploading spreadsheets
• Pasting spreadsheet-type data
• Entering data into a form

The first strategy, automatically uploading, leverages the APIs of LabKey Biologics to allow other instruments or file systems to talk directly to the system. The other three strategies involved a manual process suitable for varying use cases. If you have a large spreadsheet to integrate, you might want to use the manual upload method or paste the tabular data directly into the application. If you just have a couple of values you want to enter, simply entering the data into a form in the LabKey Biologics UI might be the simplest strategy.

Leveraging Sample Lineage for Context

As you know, analytical data generated during experiments is tied to a specific sample. Because the lineage of samples is tracked in LabKey Biologics, the application will automatically query sample lineage when data is uploaded and present relevant biological entities side-by-side with analytical data in the bioregistry. Showing the sequence or molecule information adjacent to the analytical data, allows scientists to easily ask questions of their data and conduct comparisons with other sequences that are seen in different experiments.

Ready to see this functionality in action? Watch the quick look video above. For more information or to request a demo- Click Here

The drive to discovery of new biologic therapeutics involves massive amounts of data passing step by step through a lengthy and sometimes iterative process involving large or distributed teams. Economies of scale and team member specialization can reduce the overhead of research and development, but only when every transfer of data is clear and efficient, with reliable audit logging to track the process.

Modern data collection techniques and processes can overwhelm data management solutions and handoff procedures that weren’t designed for the volume of modern high-throughput research.

• How do you know you have all the necessary data for an experiment or analysis task?
• How can you tell if you have the right version of data?
• What other tasks have been completed on this data, and was anything learned in a related experiment that I should know about?

Traditional methods for transferring data, such as email or direct meetings with collaborators, may not suffice when questions arise later. Recording exactly what happened and capturing all ad hoc sharing of information will prevent other team members wasting time tracking down answers.

LabKey Biologics is specifically designed to make data handoffs seamless and consistent. Sharing a central data repository and using common and fully audited workflow procedures means everyone involved, including new team members, can easily find required data and learn everything they need to know about it.

Centralized access to data makes collaboration seamless

Using a data sharing hub, team members never need to wonder where to find the data they need. Clear and consistent gathering of experiment metadata means that not only do they see what they need, they immediately know when it’s ready for the next task or experiment. With LabKey Biologics, team members share access to the entity designs, biological samples, and analytical results they need for further research.

Tasks assignments are clear in a workflow request system

Ensuring that everyone knows who is doing which tasks and in what order is critical to efficient research. Team members using Biologics can rely on the workflow request system to clearly track responsibilities – avoiding both duplication of effort and the risk of missing key steps.

Self-service access to past work of others

When teams are large and distributed, even knowing who to ask about past work can be complex. By keeping all details about every experiment with the data itself, teams using LabKey Biologics ensure that everyone has the information they need at their fingertips.

With LabKey Biologics, R&D teams reduce the time spent on repetitive data management tasks and devote more time to discovery. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.[vc_column width=”1/6″][vc_column width=”2/3″][vc_cta h2=”Upcoming Webinar” add_button=”bottom” btn_title=”Register for a Session” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_align=”center” btn_link=”url:https%3A%2F%2Fzoom.us%2Fwebinar%2Fregister%2FWN_EKhv0KeiSQaOrav-oOEmCg||target:%20_blank|”]Join LabKey Product Manager, Ryan Luce, Ph.D, for an introduction to LabKey Biologics! Explore the entity registration, data integration, and workflow management capabilities of the LabKey Biologics system.[/vc_cta][vc_column width=”1/6″]

LabKey has continued to improve and enhance the LabKey Biologics application with the release of version 19.1! We continue to work with our users to prioritize the most needed features and solutions for R&D teams.

Highlights

• Users can now create a custom chart or a view of a data grid once, and then see that view anywhere that’s relevant within Biologics. This allows you to design a report or graph, but be able to repeatedly see that analysis filtered to the samples in any particular experiment.
• Media and batch creation enhancements better match real world needs for flexibility with clarity. Import ingredient and raw material information in bulk, include “unknowns” for mixtures when necessary, and enter additional ingredients to a recipe during creation of a batch.
• Sample set operations have also been improved, with easier-to-read views of associated assay data as well as improved performance for importing and updating samples.
• Scientists need the flexibility to store arbitrary file types with their work, including published articles, SOPs, supplemental datasets, and images. You can now attach any number of files to a specific experiment, providing context and analysis of what occurred.

View Full Release Notes >

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Upcoming Events

Webinar: Intro to LabKey Biologics: May 2, 2019

Join LabKey Product Manager, Ryan Luce, Ph.D, for an introduction to LabKey Biologics! Explore the entity registration, data integration, and workflow management capabilities of the LabKey Biologics system.
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LabKey User Conference & Training – Basel

June 4-5, 2019 | 2 Days
Basel, Switzerland
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LabKey User Meeting – London

June 6, 2019 | FREE
London, UK
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Labkey User Conference & Workshop – Seattle

October 3-4, 2019 | 2 Days
Seattle, Washington, USA
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