Category: Products & Services

12 Dec 2018
LabKey Biologics software for managing biologic R&D workflows

Increasing R&D Productivity with Central Research Management Tools

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

Workflow management software for bench science, managing laboratory workflows in LabKey Biologics

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 dashboard for bench scientists and workflow tools in LabKey BiologicsTask 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.

Group all assay data by experiment in LabKey BiologicsExperiment 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.

27 Nov 2018
software for integrating data from rare disease research

Built for Science: Pooling Data for a Better Understanding of Rare Disease

Rare diseases are broad in phenotypic traits and far reaching in impact. Today, approximately 7,000 different rare diseases affect an estimated 350 million individuals worldwide.¹ Difficulty in the understanding, diagnosis, and treatment of rare diseases stems from a lack of available data about any one disease at any one research site. The volume of data needed to produce authoritative discovery about any one rare disease requires the collaborative pooling of phenotypic, genotypic, and clinical information from many disparate sources.

LabKey is helping research networks advance understanding about rare diseases by providing a flexible platform to help overcome key data integration challenges including:

Software for integrating data from multiple clinical sitesIntegrating Data from Multiple Clinical Sites

Researchers and clinicians need access to a substantial pool of data in order to identify disease trends and determine appropriate treatment for patients. In the case of rare disease where the occurrence of a disease within the population is not commonly seen, integration of data from multiple clinical sites is essential to identifying a patient’s course of treatment.

LabKey Server facilitates the collection and integration of rare disease data from multiple clinical sites by providing:

  • Operational data portals for data collection and preparation at clinical sites.
  • Data processing pipelines for transferring data to an integrated repository.
  • De-identification of personally identifiable information in clinical datasets.

Framework for structuring disease data for collaborationAchieving Consistent Data Structures for Disease Data

In order for data to be integrated in a meaningful way, data generated at each clinical site must follow a consistent data structure. When data is structured correctly, researchers can query across data sources identify patterns in disease.

LabKey Server provides tools to help teams structure rare disease research data correctly during collection, and QA features to combat human error including:

  • Data entry forms for clinical data collection tied to underlying data structures.
  • Spreadsheet templates for offline data collection and bulk upload to LabKey data structures.
  • Quality control features like lookups, aliases, and validators identify and correct errors found in data prior to integration with other sources.

Tools for secure data sharing in rare disease researchProviding Access to Integrated Data

Integrating data collected from patients of rare disease helps clinicians make data-driven treatment decisions and research teams understand the genesis of the disease and the potential pathways to its cure. The data access needs of these different interest groups often vary, and the ability to control access to data at a granular level is essential to maintaining patient privacy without hindering research progress.

LabKey Server provides tools to control access to rare disease data and ensure appropriate use including:

  • Role and group-based permissions for managing access to projects and folders.
  • The ability to flag and remove PHI fields from data sets for collaborators without PHI-level permissions.
  • An audit log that captures all access of and actions taken against a dataset.

 

Explore LabKey Server

With the right tools, research networks have the ability to more effectively understand and treat rare disease. Sign-up for a free trial to see how LabKey Server can help your team overcome these and other key research challenges.

Related Resource

Blog Post

Genomics England and LabKey: Creating and Securing “A Dialogue Between the Clinical Context and Researchers”

Genomics England has been working with LabKey to develop a LabKey Server-based data management and exploration portal that would facilitate the knowledge sharing dialogue between clinicians and researchers as part of the UK’s 100,000 Genomes Project. The initial phase of this collaboration centered around providing clinicians and researchers access to centralized phenotypic and sample information gathered from rare disease patients and their families at sites across the UK while ensuring security and privacy of patient information.

Read the Post >

 

¹https://globalgenes.org/

20 Nov 2018
New features added to LabKey Server v18.3 for scientific data integration and analysis

What’s New in LabKey Server v18.3

We are excited to announce the release of LabKey Server v18.3! This release includes a variety of enhancements designed to make integration and analysis of data more efficient and secure, including:

  • Support for multiple R engines for a single site. Users can now select an alternative to the default R engine for individual projects as well as declare an R engine as a sandbox environment, isolating it for security purposes.
  • Integration with RStudio Pro* allows users to view, edit, and export LabKey Server data in the RStudio Pro interface.
  • Navigation improvements have been made to project and custom menus to help improve the user experience.
  • Antivirus scanning* automatically checks all file uploads, attachments, archives and other content for viruses during import.
  • Enhancements to visualization tools allow users to specify multiple y axes for scatter and line plots, hide trend lines and data points on time charts, and include visualizations in study participant views.
  • Additional QC Trend reports* including Moving Range and Cumulative Sum plots have been made available for GPAT/file-based assays.
  • ETL definition editor enhancements* provide automatic code completion and allow administrators to define a new ETL using an existing definition as a template.
  • Support for Java 11 allows LabKey to run on both Oracle Java SE 11 and Oracle OpenJDK 11.*

Check out the 18.3 Release Notes for the full list of enhancements included in this release!

Download LabKey Server v18.3 >

*Premium feature, please contact your LabKey account manager for additional information and configuration support. If you’re interested in learning more about premium subscriptions, please contact us.

**Oracle Java SE 8 is supported as well, but will be removed in 19.1.

16 Nov 2018
Java release cadence, LabKey Server

The Java Shake-Up: What it Means to LabKey and You

LabKey Server is a Java-based web application. Recent changes to Oracle’s Java licensing model and release schedule require changes by software providers like LabKey, as well as application administrators. Below LabKey’s VP of Product Strategy, Adam Rauch, explains the recent changes, how LabKey plans to address them, and what actions need to be taken by teams running LabKey Server to ensure on-going stability and support.

Recent Changes to Java Release Cadence and Licensing

Last year, Oracle announced several significant changes to the Java release and support model that introduce complexity to the previously straightforward process of deploying a Java runtime. Organizations will need to make decisions and revise their upgrade processes, but we believe these changes will lead to a stronger Java platform, one that will be more responsive and easier to support in the long term.

Perhaps the biggest news is that Oracle now requires a paid subscription for all use of the Oracle Java Runtime (“Oracle Java SE”) in production environments. Starting with Java 11 (released September 2018), organizations are required to pay up to $25 per CPU per month for production server or cloud use of Oracle Java SE. This seems to apply to everyone… no exceptions for academic, non-profit, or small organizations. With a subscription, Oracle will provide long-term support (LTS) for designated versions of their runtime (Java SE 8, 11, 17).

With Java 9, the release cadence transitioned from major versions every five or six years to more incremental feature releases every six months. According to Oracle, this new time-driven release model allows more rapid innovation, but it also means organizations will need to upgrade more quickly to keep pace with the changing platform.

This diagram (brought to you by the LabKey Visualization API) helps illustrate this change, with each bar capturing the time Oracle publicly supported (or plans to support) each version:


Note that in addition to more rapid and shorter releases, Oracle has eliminated the overlap between versions. Under the new model, public support for previous releases ends immediately upon release of a new version. As a result, Java 9 was end-of-lifed (no further support) the day Java 10 was released and Java 10 was end-of-lifed the day Java 11 was released.

Other Options and LabKey’s Response

As a Java-based web application, every deployment of LabKey Server is affected by these changes. You can certainly move to a paid subscription with Oracle, but many of you have told us you want a free Java option. LabKey has heard you and, starting with LabKey Server release 18.3, you now have the ability to deploy with a completely free, open-source Java runtime.

This is possible because Oracle has embraced OpenJDK, the open source implementation of the Java platform. Oracle recently contributed its remaining commercial features to the OpenJDK project and now builds its subscription Oracle Java SE from the OpenJDK sources. In fact, Oracle distributes two versions of OpenJDK: the Oracle Java SE requiring the commercial license and a production-ready open-source build of OpenJDK licensed under GPLv2 with the “Classpath Exception” (“Oracle OpenJDK”). The code is the same; the Oracle OpenJDK distribution merely lacks the long-term support provided under the subscription. Oracle might add proprietary enhancements (e.g., advanced garbage collection algorithms, just-in-time compilation, profilers, and other tools) to future commercial runtimes, but at the moment, these distributions should be interchangeable.

In response to these changes and our clients’ requests, LabKey has shifted our development, testing, and hosting to focus on Oracle OpenJDK 11. We will continue limited testing on the commercial Oracle Java SE releases, but the vast majority of our attention will be focused on OpenJDK. We plan to support future OpenJDK releases at or shortly after they’re released. Where possible, we’ll hotfix the current production release of LabKey Server to ensure it’s compatible with newly released versions of OpenJDK. (For example, even though it won’t be released until March 2019, we’re already testing OpenJDK 12 early-access builds against our 18.3 and pre-19.1 builds.)

Since older OpenJDK releases will not receive public support from Oracle (i.e., no security patches), LabKey will stop supporting them shortly after they’re end-of-lifed. To ensure you have all the latest Java security patches and bug fixes, you must regularly upgrade to the latest Java runtime release. You’ll need to upgrade to each six-month feature release plus the intervening security releases (two or three per feature release… roughly every two months).

Based on the published Java release schedule, Java support in LabKey Server for the next year will likely roll-out as follows (where “Java X” means “OpenJDK X and Oracle Java SE X”):

LabKey ReleaseJava Versions SupportedChanges
18.3 – Nov 2018Java 11, Oracle Java SE 8Add Java 11
19.1 – Mar 2019Java 11 & 12Add Java 12, Remove Java 8
19.2 – Jul 2019Java 12Remove Java 11
19.3 – Nov 2019Java 12 & 13Add Java 13

You can always visit our Supported Technologies page to review the latest plan.

Since OpenJDK is a true open-source project, many organizations other than Oracle are now building, distributing, and supporting it. A few of the most prominent examples:

  • AdoptOpenJDK has promised community-driven LTS builds of OpenJDK
  • Red Hat and other Linux distributions provide and support OpenJDK
  • Azul Zulu, IBM, SAP, et al offer free and commercial options
  • Amazon recently announced Corretto, a no-cost distribution of OpenJDK that includes long-term support

All of these implementations derive from the same OpenJDK source, so, in theory, they should be interchangeable. However, it’s important to understand that LabKey has not yet tested any of the non-Oracle distributions and, therefore, we do not support them. We plan to test more of these distributions over the next year. But for now, you will need to utilize one of the two Oracle distributions.

Recommendations for Your Team

It’s time to take action on these changes. Java 11 is here and Java 12 is coming soon. Java 8 will reach “End of Public Updates” for commercial users in January 2019, and will stop being a viable option for most deployments. Our recommendations:

  • Discuss Java licensing with your legal, licensing, and IT teams. They may have already put in place a runtime subscription or developed a policy around Java. If not, they need to understand these changes and create a plan.
  • Based on your organization’s policies, choose the runtime that’s appropriate for your deployments going forward: Oracle OpenJDK 11 or Oracle Java SE 11.
  • Upgrade to LabKey 18.3 and then switch to that Java 11 runtime.
  • Keep upgrading your runtime… every two months to stay secure.
  • If you’re building Java modules, switch your development and testing to JDK 11. IntelliJ makes it easy to configure multiple JDKs and switch between them, if you still need to build with JDK 8 for other work.

Comments? Suggestions? Questions? Please share them on the LabKey support forum

06 Nov 2018
Data sharing platform for infectious disease collaboration

Built for Science: Data Sharing in Emerging Infectious Disease Research

Emerging infectious diseases rapidly rise to prevalence and spread quickly across a population. In order to minimize their impact on public health, scientists must reach across geographical and organizational boundaries to share data that will help the global research community understand, contain, and ultimately cure aggressive infectious diseases. This type of large scale collaboration requires a robust research platform to centralize data and facilitate the shared generation of insight.

LabKey is helping teams around the globe combat emerging infectious diseases by providing a web-based platform to help overcome key collaboration challenges, including:

how to integrate heterogeneous data in infectious disease researchIntegrating Heterogeneous Data

Scientists, public health officials, and medical professionals must be able to collect and integrate data from multiple sources (clinics, labs, etc.) in order to develop a comprehensive understanding of an emerging infectious disease. By housing data in one centralized location, researchers and collaborators can improve pathogen tracking and disease surveillance.

LabKey Server facilitates the collection and integration of data from a variety of sources by providing:

  • Specialized import tools to integrate data from a variety of immunoassay types, including ELISA/ELISpot, luminex and flow cytometry
  • Demographic datasets to capture metadata about individuals within a population
  • A study framework that connects demographic, clinical, and analytical data in order to monitor the disease and/or treatment status of individuals over time

adaptable database software for infectious disease researchCreating an Adaptable Database

During the early stages of a disease outbreak data is collected rapidly and abundantly. As the scientific community’s understanding of a disease increases, the data collection needs of researchers will shift as they determine which pieces of information are most valuable. The central data management system used by infectious disease researchers must provide both high levels of flexibility and structure in order to keep up with these broad and evolving data needs.

LabKey Server provides a highly flexible environment for data capture, allowing teams to evolve their research environment using:

  • A configurable and customizable user interface
  • Powerful query tools to merge and present data
  • APIs to import data from a wide variety of external sources and formats

Data sharing software infectious disease researchReal-Time Data Sharing

In recent years, researchers working in the field of emerging infectious disease have begun to forgo traditional data publishing processes during times of a public health crisis, in favor of real-time data sharing. Real-time sharing of research observations and analytical data is helping accelerate the pace of understanding and development of treatments for aggressive infectious diseases.

LabKey Server facilitates real-time data sharing by providing:

  • Study publication tools that allow research teams to curate and publish public-facing datasets without compromising the security of their original data
  • Dynamic or static reports and visualizations to quickly summarize data for collaborators
  • Easy export of data to common research formats for ancillary investigation

 

Explore LabKey Server

With the right tools, research teams have the ability to more rapidly understand and eradicate emerging infectious disease. Sign-up for a free trial to see how LabKey Server can help your team overcome these and other key research challenges.

Related Resource

User Presentation

Real-Time Open Data Sharing of Zika Virus Research Using LabKey

The laboratory of David O’Connor at the University of Wisconsin-Madison has been at the forefront of Zika virus research since the disease’s 2015-2016 outbreak in the Americas. The laboratory conducts studies with non-human primates to establish the natural history of infection and create a model that can be used to target future vaccine development. A key component of the lab’s work is the usage of the LabKey Server platform for real-time open data sharing of zika virus data with researchers worldwide and aggregation of diverse types of data that have been contributed by a large group of researchers into a central place.

In this presentation Michael Graham of the O’Connor lab shares how their team partnered with LabKey to provide open access to data during this public health emergency. Watch presentation >

23 Oct 2018
Templates for analytical assay data in LabKey Biologics.

Achieving Deeper Insight with a Consistent Analytical Data Structure

Teams conducting biotherapeutic research use analytical data derived from molecular biology assays to assess the performance of protein targets. These often include simple measurements such as titer and amino acid measurements, as well as more complicated signal data assays like chromatography or differential scanning calorimetry. In order to effectively assess the performance of a protein target, analytical scientists must be able to compare results across multiple assays.

Consistent structure of analytical data is essential for conducting this type of cross experiment analysis. LabKey Biologics provides essential software tools to help protein engineering teams collect and centralize laboratory data with a structure that allows them to ask complex questions and achieve a deeper level of insight.

LabKey Biologics assay data templates ensure a consistent structure for analytical data.Configurable Assay Design Templates

Configurable assay design templates within LabKey Biologics provide a consistent structure for data being captured and ensure that each run of instrument data is stored in the same way. The use of a template for data capture prevents teams from accumulating data in independently designed spreadsheets when collected for different experiments or by different operators. Using an assay design template also allows you to indicate required fields, set data validation criteria, and normalize data as it is being brought into the central system.

Keep the same analytical data structure regardless of the upload method to import assay data.Easy Mechanisms for Importing Data

LabKey Biologics provides several straightforward methods for loading data into these consistent structures. These include:

  • Automated loading of data via LabKey Biologics API
  • Uploading data files (.xls, .csv., .tsv)
  • Copy/pasting tab separated values
  • Entering values directly into an assay grid

Importing data using any of these methods will populate the assay data structures discussed above, creating a structured catalog of analytical data for easy cross experiment analysis.

Using LabKey Biologics software tools to connect analytical data to sample details, cell culture media, and entity registration for protein therapeutic development.Powerful Querying of Sample Lineage

Consistently structured and centrally organized analytical data enables basic analysis and comparison of experiment results, but the real value of LabKey Biologics lies in the connection that the application makes between this data and the lineage of associated samples. Within LabKey Biologics users can view the lineage details of each sample; which bioreactor run a sample is derived from, what media recipe was used, or what molecule is was expressed. By connecting these details about a sample’s derivation and physical characteristics to structured data about it’s experimental performance, protein engineering teams can significantly reduce the amount of manual effort required to ask challenging questions of their data.

With the right tools, biologics R&D teams can significantly reduce time investment required to derive insight from their analytical data. Explore LabKey Biologics free for 30-days in our hosted trial environment, or contact us to request a demo.

17 Oct 2018
Using look ups to standardize laboratory nomenclature and clean data entry

Setting Yourself Up for Success: 3 Best Practices for Using Standard Nomenclature

A standard nomenclature is incredibly valuable for teams using LabKey Server to do collaborative biomedical research and becomes increasingly more important as they grow in size and data volume. Defining how data fields should be named is essential to the efficiency of teams, as it aids both those generating and/or capturing data as well as those conducting data analysis.

As you get started using LabKey Server, keep in mind the best practices below for defining and maintaining a standard nomenclature in your lab:

Define standard nomenclature for scientific research up front.Define Nomenclature Up Front

Standardizing nomenclature may seem like an unnecessary up-front investment, but ultimately your team will experience less confusion and more efficiency as they progress with their work. Empower your team by allowing them to have a voice as you define which terms will be used in your research. By including team members in the process, they will feel more invested and be more likely to adhere to standard naming conventions.

Use LabKey QC Features to Ensure Consistency

In an ideal world, all team members will consistently use the nomenclature agreed upon by the team when adding data to your LabKey Server. But in practical application, it is more likely that from time to time a team member will mistakenly enter “H20” instead of the lab standard name “Water” into their ingredient list, potentially breaking standard reports, grid views, etc.

Using lookups in LabKey helps standardize the nomenclature used in your research data.

Using LabKey quality control features like lookups, aliases, and validators in key fields can help combat this scenario. A LabKey lookup will allow you to to map several common variations of a term to a desired standard field value. For example, an administrator could configure a lookup so that “H20” and “Tap Water,” common deviations from the standard, would both map to “Water.” These types of lookups allow teams to maintain the integrity of their data, in spite of inevitable human error.

Administrators can also use to regex or range validators on new data being entered to ensure that users are entering valid data into the system. By placing these restrictions, teams can improve data entry and help analyses down the pipeline.

Regularly evaluate and refine the standard nomenclature you use in your scientific research.Evaluate and Adjust

It’s easy to enforce the use of standard nomenclature when your team is small and your research is in its early stages. But over time, as teams grow and become further removed from when nomenclature guidelines were established, they can develop a “laboratory shift” in how things are named. In order to stay on top of your terminology and keep your data clean, plan to regularly review and assess your standard nomenclature. Are there additional terms that need to be defined? Have any standard terms become outdated? Are certain terms consistently being used incorrectly? Making small adjustments as your research needs evolve will help maintain the integrity of your data.

LabKey helps enforce nomenclature standards, leading to cleaner data and more efficient research. Sign-up for a free trial to see these and other core LabKey Server features in action. 

 

Related Documentation

25 Sep 2018
LabKey and Linguamtics partner to speed Natural Language Processing of Clinical and Unstructured Documents

LabKey and Linguamatics Partner to Extract Clinical Insights from Big Data in Healthcare

Integrated NLP data management solution speeds clinical data abstraction and curation for disease registries, clinical research and quality reporting

Cambridge, England and Seattle, WA, USA — September 25, 2018 — Linguamatics, the leading natural language processing (NLP) text analytics provider, and LabKey, a provider of bioinformatics data management solutions, today announced an integrated solution designed to streamline the extraction and curation of valuable insights from large volumes of unstructured clinical notes and reports.

With Linguamatics NLP engine I2E, healthcare and life sciences teams can significantly reduce the manual processes involved in information analysis and extraction. When integrated with LabKey Server’s document processing pipeline and curation user interface (UI), the combined solution provides an end-to-end pathway for unstructured data from acquisition to analysis.

“Our partnership with LabKey empowers healthcare teams to achieve high accuracy data extraction in a wide variety of use cases” said Simon Beaulah, senior director, healthcare at Linguamatics. “Customers can speed extraction of EHR data into cancer registries and clinical data warehouses; reduce the manual burden associated with clinical study review; and rapidly extract relevant population health data and quality metrics to improve business critical HEDIS quality metrics reporting and patient outcomes.”

The LabKey and Linguamatics relationship is based on collaborative work with the NCI’s Surveillance, Epidemiology, and End Results (SEER) Program. This project has resulted in an NLP pipeline that automates the annotation and review of pathology reports, to build a large gold standard for machine learning training.

“Combining LabKey’s processing pipeline, workflow, and curation UI with Linguamatics’ NLP capabilities provides a complete solution for organizations that need to extract valuable information from large volumes of unstructured clinical data,” explained Adam Rauch, vice president of product management at LabKey. “This integrated system empowers abstractors and reviewers with the technologies they need to accelerate the extraction process from end-to-end.”

About Linguamatics

Linguamatics Natural Language Processing NLP Solutions for Healthcare and Life Sciences

Linguamatics transforms unstructured big data into big insights to advance human health and wellbeing. A world leader in deploying innovative natural language processing (NLP)-based text mining for high-value knowledge discovery and decision support, Linguamatics’ solutions are used by top commercial, academic and government organizations, including 18 of the top 20 global pharmaceutical companies, the US Food and Drug Administration (FDA) and leading US healthcare organizations.

Linguamatics I2E is used to mine a wide variety of text resources, such as scientific literature, patents, Electronic Health Records (EHRs), clinical trials data, news feeds, social media and proprietary content. I2E can be deployed as an in-house enterprise system, or as Software-as-a-Service (SaaS) on the cloud.

About LabKey

LabKey provides software solutions to help teams overcome the data management and workflow challenges faced in today’s biomedical research environment. LabKey works hand-in-hand with clients to understand the complex needs of modern labs and develop flexible, scalable, extensible systems to address them.

LabKey Server is an open source software platform for integrating biomedical research data and managing laboratory workflows. LabKey Server is highly configurable and is used by research organizations across the globe to provide reliable, scalable environment for research data. 

LabKey Media Contact

Kelsey Gibson, Marketing Manager
LabKey

+ 1 425.308.7033
kelseyg@labkey.com

Linguamatics Media Contact

Michelle Ronan Noteboom, Sr. Account Director
Amendola Communications

+ 1 512.426.2870
mnoteboom@acmarketingpr.com

24 Sep 2018
LabKey Biologics Cell Culture Media Development Software Tools

Data-Driven Tools for Optimizing Cell Culture Media

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:

Capture the steps, ingredients, concentrations, and other details of cell culture media recipes in the LabKey Biologics software

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.

Software tools for creating consistent cell culture media batches.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.

Data driven cell culture media optimization using LabKey Biologics softwareFollowing 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.

14 Sep 2018
LabKey Server software tools for immunology trial data management

Built for Science: Data Management Tools for Immunotherapy

CAR T and other cellular immunotherapy trials are rapidly expanding worldwide due to their high success rates and continued scientific advancements that are helping generate new therapeutic targets. The development of these advanced immunotherapies requires extensive data collection and collaboration between research scientists, clinical teams, and trial subjects. In order to manage this data efficiently and improve the feedback loop from current and ongoing trials many immunotherapy focused research teams are seeking out secure, web-based data management solutions in lieu of traditional paper based systems to manage their trial data.

LabKey is actively partnering with teams conducting immunotherapy trials to provide LabKey Server-based solutions to overcome a wide variety of challenges and accelerate their research, including:

Connect data from heterogeneous data sourcesIntegrating Heterogeneous Data

Cutting edge cellular immunotherapy trials rely on data generated at multiple sources often including the cellular manufacturing facility, the clinic gathering subject data, and research labs exploring the cellular profile of the therapy. Teams conducting CAR T and other immunotherapy trials need reliable software tools to integrate this heterogeneous data and provide a comprehensive view of the therapy’s efficacy and safety to clinicians and researchers.

LabKey Server helps immunotherapy research teams efficiently integrate heterogeneous data by providing:

  • A data-aware study module that can recognize and integrate disparate vendor datasets, alias subjects and track visits by name or by date
  • Built-in and customizable integration with electronic data capture systems and case report forms

Longitudinal Data Capture

Lengthy follow-up periods are typically required for subjects undergoing therapy involving genetically modified cells. Managing trial data over time in a secure and scalable manner quickly becomes very challenging for paper-based systems.

LabKey Server helps support the consistent collection and storage of longitudinal study data throughout the lifetime of a trial by providing:

  • A configurable study progress report that allows trial staff to manage samples and tests, ensuring that every result is accounted for.
  • The flexibility to customize and modify the system as the needs of the database grow and change, without compromising historic data.
  • Professional support and services to ensure that the system is maintained throughout the life of the trial.

Compliant Collaboration

LabKey software tools for sharing scientific data onlineSharing reports and data with collaborators improves research, innovation, and ultimately subject care. Maintaining compliance and having the ability to quickly share data and reports is an important topic to tackle in immunotherapy research where subject safety and care is the top priority.

LabKey Server improves reporting and collaboration amongst collaborators conducting immunotherapy trials by providing:

  • Dynamic and static reporting tables and visualizations that can be shared as-needed
  • Web-based access to a central platform for data sharing
  • The ability to remove PHI fields or provide randomized IDs when sharing
    information with collaborators

Explore LabKey Server

With the right tools, immunotherapy research teams can push the pace of this cutting edge research even further, increasing trial efficiency to bring life saving therapies to more patients faster. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common immunotherapy research challenges.

Related Resource

User Presentation

Using Existing LabKey Modules to Build a Platform for Immunotherapy Clinical Trials

The Correlative Studies Laboratory (CSL), part of the Immunotherapy Integration Hub at Seattle Children’s, focuses on understanding how reprogrammed T cells react in each patient in terms of their persistence, functionality and efficiency at reducing tumor burden. This data, combined with manufacturing and clinical data generated during clinical trials, enable researchers to answer pressing questions with minimal time and resource investment.

In this presentation Olivia Finney, shares how the CSL is working with LabKey to integrate, analyze and securely share data in order to create a truly translational research model. Watch presentation >

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