Our team is building something amazing. The Centers for Disease Control and Prevention (CDC) and its partners need better, faster tools to stay ahead of disease and other public health threats. Those tools must allow laboratory teams to use the best technology available. JMC will build some of those tools and make them available to everyone. We will work with multiple partners within the US public health system to build a suite of flexible, standardized, and centralized public health laboratory support tools. Laboratorians and epidemiologists will leverage these tools to more effectively identify and respond to public health threats. These tools include:
- a workflow management tool to capture and leverage the increasingly complex and growing laboratory data streams, making it easier for laboratorians to track samples;
- an accessible accessioning tool to meet the key business needs that drive the division’s requirements, allowing laboratories to process samples more quickly and to collaborate with other laboratories on testing services;
- and hooks for bioinformatics pipeline support and visualization tool services, which means more testing and more detailed analysis.
Modern laboratories are large, complicated places with a lot of moving parts. Most laboratories today have specialized software, called laboratory information management systems or LIMS, that they use to manage the intricate dance of receiving samples to test, tracking the testing process, and recording and sending results. One of the largest laboratory systems in the world is the US Public Health Laboratory network that spans from small facilities serving a single community, to state public health laboratories up to and including the many laboratories of the Centers for Disease Control and Prevention (CDC). It can be challenging for this laboratory network to incorporate new disruptive technologies into their workflows. For example, LIMS capabilities have not kept pace with the rapid advances of next-generation sequencing or NGS. Many laboratories use LIMS adjacent software tools that have been built and grown largely outside of the traditional laboratory software development environment and integrating these custom-built bioinformatics software tools with the rigor of a LIMS system has not been easy. The expansive coverage and critical data sharing needs of the public health laboratory network adds complexity to this integration. Public health laboratory testing is performed in a system that is distributed across the country and indeed the world. Moreover, laboratories must be able to share standard information with various partners in a format that will enable analysts to tie laboratory data to clinical outbreak investigational data, yet with adjustable access to sensitive identifying information. When data management and exchange are seamless, public health professionals can concentrate on public health, not system integration.
It is in this environment that small business, J Michael Consulting has been awarded a contract of over $4.6 million from the CDC to design, develop, and maintain a cloud-based system that will enable management and analysis of next-generation sequencing (NGS) data for public health. Over the next three (3) years the talented JMC team that includes members from JMC as well as from General Dynamics Information Technology (GDIT), Yahara Software, and Blackhawk Genomics, will work with CDC to build, deploy, and support an inherently flexible technology platform that will provide for the same software deployment across all environments including on-premises, in the cloud, or on a laptop. Plus, the containerized Linux architecture will allow module use across environments. For example, data could flow from tools run on a laptop to an on-premises LIMS, then pass to a bioinformatics pipeline in the cloud as raw sequencing output files.
JMC is helping CDC leverage existing and emerging technologies to enhance the capabilities and capacity of the nation’s public health laboratory network. This work will have an immediate impact on public health monitoring and response. This is going to be amazing.