Tag: Biologics LIMS

[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.
Learn More & Register

LabKey User Conference & Training – Basel

June 4-5, 2019 | 2 Days
Basel, Switzerland
Learn More & Register!

LabKey User Meeting – London

June 6, 2019 | FREE
London, UK
Learn More & Register!

Labkey User Conference & Workshop – Seattle

October 3-4, 2019 | 2 Days
Seattle, Washington, USA
Learn More & Register!

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More on the Blog

Barriers to R&D Productivity: Manual Data Integration Strategies

Barriers to R&D Productivity: Lack of Visibility into Previously Generated Data

Barriers to R&D Productivity: Lacking a Central Point of Access to Data

Barriers to R&D Productivity: What’s Slowing Down My Research?

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.

[vc_cta h2=”Explore LabKey Biologics” h2_font_container=”color:%23116596″ h2_use_theme_fonts=”yes” h4=”Sign-up for a free, hosted trial.” add_button=”bottom” btn_title=”Start Trial” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_shape=”round” btn_align=”left” use_custom_fonts_h2=”true” btn_link=”url:https%3A%2F%2Fwww.labkey.com%2Flabkey-biologics-trial-sign-up%2F|||”] Explore LabKey Biologics free for 30-days in a secure, hosted environment. Sign-up for a LabKey Biologics trial to explore sample data, register entities, create samples, and more. [/vc_cta]

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.