Tag: Biologics LIMS

There is no single test that is run to assess the safety, stability, and scalability of a biologic treatment. Instead, these key characteristics are measured using a variety of analytical and observational tests. In order to assess the biologic’s viability as a therapeutic, scientists must be able to analyze all of these data points in conjunction with one another. When R&D teams are utilizing spreadsheet based systems for data management, this aggregate analysis requires manual integration of data from multiple datasets stored in a variety of formats.

Manually integrating datasets can pose a number of productivity challenges for R&D teams.

1. Manual integration is often a time-consuming process that can take valuable time away from your scientists.
2. It is difficult to ensure that data is integrated in a consistent manner across projects and team members.
3. Manual manipulation of data means a higher chance of human error.

LabKey Biologics automates the integration of datasets, and prepares data for analysis in an efficient and reliable manner. Automating the integration of data with LabKey Biologics can enhance R&D productivity in the following ways.

Saving Your Scientists Time

LabKey Biologics stores R&D data including molecular entity definitions, sample details, and analytical results in a consistently structured manner, preparing it for seamless integration with related data of other types. The system then automatically builds relationships between related data, so that scientists can easily explore data through the UI or export integrated data for analysis using external tools. Automatically building connection between structured data types saves scientists hours of time that would be spent on manually integrating data, and allows them to dedicate more time to analysis.

Ensuring Consistent Data Processing

Relationships between data types stored in LabKey Biologics are defined on a global level, ensuring that data connections are built consistently across all projects. Users can also design custom grid views of data to surface data points of interest in a single grid. These custom views can be saved and applied across groups of samples or experiments, ensuring that data is presented consistent across a research project.

Minimizing Human Error

Perhaps the most straight-forward benefit of utilizing LabKey Biologics for research data integration is minimizing the potential for human error. Manual integration can lead to copy/paste mistakes, problemattic auto-formatting, and other errors that can be hard to detect and significantly hinder analysis. Using LabKey Biologics to integrate datasets eliminates the risk of these types of errors during the integration process, and provides additional mechanisms to protect against human error during data analysis including audit logging of data access and transformations.

With LabKey Biologics, biopharma R&D teams can automate data integration, accelerating the integration process and ensuring the generation of high quality datasets. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.

Developing a safe and effective biotherapeutic involves the collection of data from many different team members and research functions. At larger biopharma organizations, there are often multiple team members working on similar tasks in a functional area.

In order for collaborative R&D to operate efficiently, team members need visibility into what data has been generated across the research group. LabKey Biologics provides a central hub for storing R&D data with an easy to navigate structure and dynamic querying capabilities to help team members locate data of interest. Providing greater visibility with LabKey Biologics can enhance R&D productivity by:

Preventing Duplicate Work in the Lab

There are several ways in which the visibility into previously generated data provided by LabKey Biologics can prevent duplicate work in the lab. Perhaps a bench scientist is interested in understanding what protein expression occurs under a particular set of conditions. Unbeknownst to them, an experiment testing that same protein expression was completed 6 months earlier by another team member. Using LabKey Biologics, this researcher could search historical experiments with those same conditions and view their results, saving them the time and resources of conducting a new experiment.

LabKey Biologics can also prevent teams from running duplicate experiments on the same sample. Each sample in LabKey Biologics stores a complete record of all of the assays that have been run against them. Technicians can use this information to verify that an assay has not already been run.

Protecting Against Dirty Data

A lack of visibility into your team’s previously generated data can also lead to duplicate records in your bioregistry. LabKey Biologics provides easy mechanism for searching/sorting existing data to locate previously registered entities, and also conducts an automated uniqueness check on each entity registered in the system. These tools ensure that related data is connected to the correct entity from the start, and removes the need for downstream data clean-up.

With LabKey Biologics, biopharma R&D teams can reduce redundant experimentation saving valuable time and resources. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.

Developing a biologic therapeutic requires the coordinated efforts of many team members. From concept to confirmation, each stage involves the generation, analysis, and dissemination of large quantities of data between the members of your research and development team.

Creating a central point of access for data generated across team members streamlines data sharing and significantly improves your team’s productivity. LabKey Biologics serves as a “single source of truth” for R&D data, from details about molecular entities to the samples that have been generated and the experiments that have been run. One of the productivity benefits of implementing LabKey Biologics is the clarity it provides to team members about where to store data and where to find data.

Team Members Know Where to Store Their Data

Without a data sharing hub, team members often find themselves relying on several different distribution methods to disseminate data to different groups, adding steps to the data sharing process and slowing productivity. Providing a central system for data storage that is accessible by all team members provides data generators with a consistent, repeatable process for distributing data. With LabKey Biologics, team members can centrally manage all of the data they generate about entity designs, biological samples, and analytical results, as well as group data by experiment and add relevant metadata to enhance discoverability.

Team Members Know Where to Find Data

A central point of access for research data eliminates the wasted time searching for data in a variety of different storage locations (emails, local drives, cloud-based file shares…). Team members using LabKey Biologics can rely on the consistent data structures established by the system to locate data of interest and omni-bar searching to easily locate row level data within datasets.

With LabKey Biologics, teams can reduce the time spent on tedious 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.

High-Throughput Data Generation Requires High-Tech Data Management

Historically, one of the primary challenges faced by drug development teams was generating enough data to conduct authoritative research. Innovative technologies introduced over the last decade have all but solved this, but R&D teams now face an equally daunting challenge: efficiently managing and analyzing the massive amounts of data produced by high-throughput technologies. These technologies have outpaced the data management systems of many organizations, creating a bottleneck at the point of analysis and slowing R&D productivity.

Team-Based Science Brings Data Sharing Challenges

The shift to team-based approaches in research has also compounded the challenges of handling massive datasets. For maximum productivity, teams must work across disciplines, which often means sharing data with geographically dispersed team members and collaborators. Some of the common challenges that arise in this type of high-volume, collaborative environment include:

• The lack of a central point of access for data generated across team members.
• The lack of visibility into what data has already been generated.
• The lack of a reliable method for handing off data to other team members.
• The lack of automated data integration tools, requiring team members to manually integrate data from multiple sources.

While some of these challenges can be solved through well documented processes and communication standards, LabKey Biologics is specifically designed to enable this type of team-based science. Over the course of the next few months, we will be discussing each of these barriers, the challenges they cause, and how R&D teams can overcome them with the help of LabKey Biologics. Subscribe to the LabKey blog to follow along.

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Team-based approaches to research are becoming increasingly popular in R&D labs as collaborative efforts help increase overall productivity and drive deeper insight. Research managers are responsible for ensuring that research activities executed by multiple team members operate efficiently and produce high quality results. In a multi-person environment, it can be challenging for research managers to achieve a comprehensive view of the all activities in their lab as data can easily become siloed.

As team-based research becomes more critical in science, research managers are in need of productivity tools that help facilitate communication and collaboration amongst lab members and provide them with a comprehensive look at their lab’s overall operations. LabKey Biologics provides a centralized system for managing of ongoing research and storing completed data analyses generated across team members. Some of the key tools to support team-based science include:

Configurable Work Request System

A configurable system for requesting work within LabKey Biologics facilitates the generation of work requests, their assignment, and the handoff of any resulting data for common laboratory tasks like sample preparation or assay data collection. LabKey Biologics maintains a persistent relationship between the task request and the resulting data, providing team members with helpful context about the data’s generation. For example, a user can easily navigate from an assay data grid within the system to the original request for the data, allowing them to see who requested this data and why. Specific samples, as well as, registered entities like protein sequences or cell lines, can also be tied to unique work requests.

Task Management for Bench Scientists

When tasks are assigned to users within LabKey Biologics, they are added to a dynamic workflow dashboard for that user. User-specific dashboards display tasks that are in that user’s work queue, as well as the tasks that they have assigned to others and their statuses. Research managers can use this dashboard view to monitor team member workloads, understand instrument usage, and plan for the future needs of the lab.

Experiment View of Assay Data

In order to keep experiments on track, research managers need the ability to see all of the analytical data that has been generated for each experiment. LabKey Biologics makes all assay data relevant to an individual experiment available directly from the experiment detail page. Users can easily search, sort, and filter integrated assay data for easy location of specific analytical results.

See how LabKey Biologics can help your team work together more efficiently and derive powerful insight from your integrated data. Explore LabKey Biologics free for 30-days in our hosted trial environment, or contact us to request a demo.

Over the past few months, the LabKey team has made several key enhancements to the LabKey Biologics application to help teams organize and visualize data relationships. Take a look at some of these recent enhancement below.

Group Sample and Assay Data Using the Biologics Experiment Framework

An experiment framework has been added to LabKey Biologics that allows users to group all the data relevant to a single experiment. Teams can define a name and description for each experiment, add samples, and upload analytical results.

Navigate Between Generations of Samples with the New Lineage Grid View

In addition to the existing lineage visualizations, LabKey Biologics users can now view all of the ancestors and descendants of a particular sample in an easy to navigate lineage grid. This grid view is particularly helpful when viewing lineage data for samples with large quantities of related samples or lengthy derivation history.

Auto-Register Sequences During GenBank File Import

Improvements to LabKey Biologics import process enable to the auto-registration of multiple sequences when a GenBank file is uploaded. With these changes the full sequence of the plasmid, the coding sequences, and the resultant protein sequences are now auto-registered.

Want to see these features in action

Explore LabKey Biologics free for 30-days in our hosted trial environment, or contact us to request a demo.

Cell culture is a central component of protein development and the media used during this process can have a significant impact on its performance. In the R&D environment, media technicians are responsible for both the precise production of cell culture media and the optimization of media recipes to maximize qualities such as growth and stability.

Capturing the detailed information about recipes, ingredients, and batches needed to optimize media production is one of the key challenges faced within protein engineering. The advances in cell culture technologies in recent years have quickly outpaced simple spreadsheet and database-based systems for storing media recipes and batch IDs. Today’s media technicians need software tools to consistently structure data about media recipes, ingredients and batches, so it can be easily accessed and queried on demand.

LabKey Biologics provides essential tools to help protein engineering teams overcome key challenges in cell culture media development, including:

Detailed Recipe Registration

Registering a recipe in LabKey Biologics allows technicians to specify all of the information needed for its execution including ingredients, ingredient concentrations, steps for creating the mixture, expiration time, and other key aspects. The system also allows the creation of mixtures that contain other mixtures, even when you don’t know all of their underlying concentrations or ingredients (as is often the case with vendor-supplied mixtures).

Media technicians have a number of different methods available for registering media recipes, depending on their complexity and scale. Technicians can create recipes individually using the media registration UI or they can register many recipes at once using bulk upload features or programmatic registration via LabKey Biologics API.

Consistent Batch Preparation

LabKey Biologics helps minimize formulation errors by auto-calculating the amounts for each ingredient in a recipe based on a target mixture amount. As a technician prepares a batch of mixture, they are prompted to input the actual amount of each ingredient used, as well as the raw material ID. If the media technician needs to use multiple bottles of a raw ingredient to fulfill the formulation, the system will allow them to register multiple raw materials for a single ingredients.

Following the Media Trail

The structured data captured in LabKey Biologics allows R&D teams to track the complete lineage of each individual sample, and present lineage as a visualization or grid. Sample characteristics, assay results, and relevant media details are tied together allowing media technicians to troubleshoot problematic raw materials, better optimize their batches, and improve upon media recipes to improve protein yield.

With the right tools, cell culture media technicians can consistently produce media batches and iterate media recipes to maximize performance. Request a demo to see this functionality in action and learn more about how LabKey Biologics can help accelerate your biotherapeutic R&D.

The focus of pharmaceutical and biotech research has seen a significant shift in recent years. Many research teams are no longer driving towards building small molecules, but are instead focused on designing new protein-based therapeutics. Protein engineers at these organizations are often responsible for the structural design of target molecules as well as the experimental protein production and characterization of their designs.

To support this work, protein engineers need biologics software tools to capture details about molecular components such as proteins, antibodies, plasmids and cell lines, as well as the detailed steps of the development process. LabKey Biologics provides an easy to use system for centralizing this information and additional tools to help facilitate protein design including:

Uniqueness Verification

There are a number of entities that might be critical for a research organization to register in a bioregistry. These could include:

• Protein Sequences
• Nucleotide Sequences
• Molecules (ex: Antibodies)
• Plasmids
• Cell Lines

Each of these entities is checked for uniqueness when they are registered in LabKey Biologics.  This prevents dirty data caused by duplicate records and reduces duplicate work for protein engineers. Uniqueness checks are in place for all entity types, whether you are registering a single sequence or a molecule composed of multiple protein sequences.

Uniqueness checks are also run on data auto-registered during the import of a GenBank file. In that case, LabKey Biologics will register plasmids during the import of a GenBank file, but also auto-register any regions that translate to protein sequences. If a protein sequence already exists, the system will register only the relationship between the plasmid and that protein sequence, not create a new sequence.

Classification by Protein Engineers

LabKey Biologics includes a classification engine that can identify, predict, and calculate various characteristics of registered molecules. This saves protein engineers valuable time manually assigning classifications.

The system automatically detects many regions and features of protein sequences including leader sequences, variable regions, constant regions, and CDRs. LabKey Biologics can also be trained to recognize additional sequence classifications, for example, by registering a leader sequences as a “Leader” within the system, it will recognize future leader sequences that match it.

LabKey Biologics can also recognize heavy chains and light chains and predict their type,  based on the amino acid sequence of a registered protein, as well as the isotype of the overall antibody.

For all of these classifications, whether LabKey Biologics is detecting subsequences on the amino acid sequence or the type of overall sequences, the protein engineer can always override the classification engine if the prediction is incorrect.

Integration with Other Systems

Often times, protein engineers are using another application to design proteins or plasmids. LabKey Biologics makes it easy to bring this data into the system, either via APIs or by bulk upload. Regardless of the registration method, the same classification and uniqueness checking features apply to all registered entities.

To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal.

When analyzing biologics assay data, scientists often need to look beyond the results at related data to answer their research questions. Comparing lineage characteristics like which expression system was used to generate an experiment sample or details about the sample itself, such as the buffer used in it, can uncover crucial data patterns and insights.

This type of data exploration requires data to be captured in a structured manner and integrated into a central system where it can be easily accessed, queried, and analyzed.

Structuring Data for Maximum Value

LabKey Biologics provides tools to ensure that data is correctly structured and consistently stored. For each data type within the LabKey Biologics application, users are able to configure a specific structure, indicating the names of fields as well as their type. Because this data is consistently structured, a user can pull together relevant data from different sources for an integrated view of their data during analysis.

For example, when looking at the results for a specific assay type, such as optical density, a user can add details about the samples themselves to the assay results data grid. This might include the buffer used, the expression system used to create it, or the name of the antibody (or other molecule) that was being produced.

Customized Data Views for Quicker Access

Users can customize the default assay data grid view to include these additional look-up columns. Customized default views provide quick access to all the data relevant to the user’s research, instead of having to join data each time they view the dataset. Users can also sort, filter, and search the data in these additional columns the same way they can with native assay data fields.[vc_cta h2=””]To see this functionality in action, request a demo! To learn more about LabKey Biologics check out our documentation and resources on the LabKey Support Portal. [/vc_cta]