Category: LabKey Custom Development

09 Jun 2017

Genomics England and LabKey: Creating and securing “a dialogue between the clinical context and researchers.”

Genomics England 100,000 Genomes ProjectIn late 2015, Genomics England began 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 100,000 Genomes Project, as characterized by Genomics England’s Chief Technology Officer, Jim Davies, is intended to promote “a dialogue between the clinical context and researchers.” This project, the largest national sequencing project of its kind in the world, will give both clinicians and researchers access to an unprecedented depth of data and information through the sequencing of 100,000 genomes from approximately 70,000 people including patients with a rare disease and their families, as well as patients with cancer. The mission of this dialogue is to ultimately bring benefit to patients and to enable new scientific discovery and medical insights in an ethical and transparent manner that will promote the development of a UK genomics industry.

The first phase of this collaboration centered around providing clinicians and researchers access to centralized phenotypic and sample information gathered from sites across the UK while ensuring security and privacy of patient information. The LabKey team focused development efforts during phase 1 on the aggregation, review, and integration of phenotype and genotype information from cancer and rare disease patient data.

This phase has provided:

  • Secure, extensible and reliable pipelines for data collection from 13 NHS Genomic Medicine Centres leading participant recruitment and partnering hospitals & clinics
  • Medical review workflow to assess data gathered of participants and families
  • Web portals for secure access of data
  • LabKey Server’s built-in reporting, querying, and visualization tools

LabKey and Genomics England are bringing the value of dialogue to the development process. LabKey is excited to continue its tradition of collaborating closely with its partners. With Genomics England, LabKey has developed a deep shared understanding of goals leading to a phased development roadmap of the LabKey Server platform. Close communication and collaboration will enable LabKey to flexibly accommodate new requirements and priority shifts to ensure a high-quality final product.

LabKey looks forward to the next phase of development of a “research” LabKey Server platform that will securely store and enable access to de-identified information that can be used by clinicians and researchers for advanced analysis. LabKey is proud to support Genomics England’s mission to promote a productive “dialogue” that will improve patient outcomes and scientific progress.

To learn more about the 100,000 Genomes Project, visit:

28 Nov 2016

Next Generation Clinical Trial Transparency: Providing Management and Analysis of RNA Sequencing Data

LabKey has begun work with long-time partner the Immune Tolerance Network (ITN) to further clinical trial transparency by extending the LabKey Server platform to support management of RNA sequencing (RNA-Seq) and Next Gen Sequencing data. The ITN will be providing access to sequencing data, connecting raw data to downstream sequence analysis and visualizations that incorporate clinical data and other assay data through ITN’s research web portal, ITN TrialShare.

ITN TrialShare is an application built on the LabKey Server platform that supports both operational data management and post-publication sharing of data from clinical trials. ITN TrialShare was the first application of its kind to allow direct linking from major clinical trial publications to de-identified participant-level data and analyses.

As part of this new project, the LabKey team will provide custom development and configuration services to extend ITN TrialShare to support integration of and enhanced access to sequencing data. Improvements being explored as part of this project include:

  • Support for big data downloads such as FAST-Q and BAM raw data files
  • Integration with sequencing data transfer tools such as Globus Genomics
  • The addition of assay data filtering for RNA-Seq data, T-cell Repertoire, and WGS data
  • Support for Shiny in LabKey’s reporting framework, allowing real-time visualization of big data

Interested in using LabKey Server to manage your research and help promote data transparency at your organization?  Contact the LabKey team for more information!

About the Immune Tolerance Network

The Immune Tolerance Network (ITN) is a collaborative network for clinical research focused on the development of therapeutic approaches for asthma and allergy, autoimmune diseases, type 1 diabetes and solid organ transplantation that lead to immune tolerance. The ITN encompasses over 250 clinical sites and investigators and 14 core labs supporting 95 clinical trials (23 Allergy trials; 43 Autoimmunity trials; 29 Transplant trials). Read about LabKey and ITN’s partnership to develop ITN TrialShare >

25 Oct 2016

LabKey to Provide Back End Data Storage and Analysis Portal for ResearchKit- and ResearchStack-based Apps

We are very excited to share that LabKey was recently selected to deliver a HIPAA and FISMA compliant data storage environment to support the collection of patient-provided data through a set of mobile device applications being developed by Boston Technology Corporation.

LabKey Server will serve as a centralized repository for data collected via the ResearchKit- and ResearchStack-based mobile applications and will integrate this data with related clinical information. The platform will also provide a portal for clinical partners to access and explore integrated data, conduct analysis, and share information with collaborators, using LabKey Server’s robust role-based permissions model and advanced security features to ensure HIPAA- and FISMA-compliant treatment of protected data.

The LabKey team is excited about this new project and the functionality it will bring to the LabKey Server platform, paving the way for future integrations with mobile research applications. This project will introduce the use of the LabKey Server platform as an enterprise-level back end service for applications developed with ResearchKit® and ResearchStack, and will allow us to offer this powerful technology to cutting-edge researchers who require rapid integration of patient-reported data with clinical data.

Interested in using LabKey Server as a data management and analysis platform for your mobile app?
Contact the LabKey team to learn more!

About Boston Technology Corporation

Boston Technology Corporation (BTC), a Boston-based digital health technology services company, provides mobile and web solution development for secure patient experience and engagement, medical and clinical research and IoT Human Interface applications. Please visit their case studies page for more information on applications developed by BTC for provider organizations, biotech and medical device companies, and major universities.

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About ResearchStack

ResearchStack is an SDK and UX framework for building research study apps on Android. It is designed from the ground up to meet the requirements of most scientific research, including capturing participant consent, extensible input tasks, and the security and privacy needs necessary for IRB approval.

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About ResearchKit

ResearchKit is an open source framework introduced by Apple that allows researchers and developers to create powerful apps for medical research.

30 Aug 2016

LabKey Kicks Off Abstraction and NLP Pipeline Project for NCI SEER

In support of the National Cancer Institute (NCI) and the Department of Energy (DoE) initiative to use large-scale computing to influence cancer science, NCI’s Surveillance, Epidemiology, and End Results (SEER) Program has partnered with LabKey to develop an abstraction workflow and Natural Language Processing (NLP) pipeline that will automate the annotation and review of free-text pathology reports.

The NCI SEER Program works to provide information on cancer statistics in an effort to reduce the burden of cancer among the U.S. Population. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 30 percent of the U.S. population. The registries receive at least one unstructured pathology report on the more than 450,000 cases reported annually that are used in conjunction with other sources to abstract relevant information on the cases.

The initial version of the application will allow SEER to identify and select pathology reports of interest using a Linguamatics-based text-mining tool and make them available in a LabKey Server portal for manual annotation and abstraction of key elements. An annotation and task management pipeline will manage the stages of the abstraction, annotation, and review process, ensuring consistency by standardizing tasks and automating the workflow. To ensure the security of data being processed and generated, the application will utilize LabKey Server’s role-based security model and facilities that ensure regulatory compliance.

Future phases of development will introduce the use of Natural Language Processing engines to further accelerate the annotation process. Manually abstracted data from the initial phase of the project will be used by DoE laboratories to help develop and train NLP algorithms that will then be used to automate the abstraction of large numbers of pathology reports.

LabKey Server for Your Research

Interested in exploring LabKey Server as a bioinformatics solution for your organization? Contact us and the LabKey team will work with you to understand your needs and help determine if LabKey is the right fit for your research.

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