Lab Matters Fall 2020 - Page 48

The viewer will be able to examine layers within the framework as well as develop an understanding of the competencies needed to excel in a lab informatics role , and how this fits into an overall public health curriculum .
Presenter : Rachel Shepherd , Association of Public Health Laboratories , Silver Spring , MD , rachel . shepherd @ aphl . org
Smooth Sailing on the Data Lake
D . Shirazi , D . Sanderson , R . Merrick and M . Sibley , Association of Public Health Laboratories , Silver Spring , MD
This poster will examine one of the more recent innovations on the AIMS Platform--the data lake . The data lake is a new technological capability that will revolutionize the ways we can store , access , and utilize data . As opposed to the traditional data warehouse that stores data categorically according to purpose , a data lake serves as a single repository for enterprise-wide raw data , meaning that all structured and unstructured data from a variety of sources is dumped in a single pool ( or lake ). When raw data is accessible from a variety of sources and it can be repurposed to meet multiple data needs and can be more easily used for reporting , visualization , analytics and machine learning .
Benefits of this solution include :
• Ability to import different formats ( As long as you can validate the upload content , the data lake will accept the data format ( HL7 , CSV , excel file … etc .)
• Access to the original / raw data
• Validation ( structure and content )
• Data field Error handling
• Lake is searchable
• Fast data loads
• Supports updating of tests / value sets without the assistance of a developer
• Reduced cost , liability and maintenance ( Product ≈70 % done ; 30 % to get ARLN data linked )
• Will be able to bring new programs on much faster
This poster will look at the process and implications of the data lake for several of the programs beginning to utilize the data lake solution , such as ARLN .
Presenter : Dari Shirazi , Association of Public Health Laboratories , Silver Spring , MD , dari . shirazi @ aphl . org
Supporting Instrument Interfaces for Public Health Laboratories
J . Park , J . Kondamuri , M . K . Yost-Daljev and T . Hardin , J Michael Consulting , LLC , Atlanta , GA
Public health laboratories ( PHLs ) use instruments with a diverse set of capabilities and complexity that integrate with LIMS applications . Existing instrument interfaces are rigid , often proprietary , and tightly coupled . Development and maintenance of such interfaces is complex , time consuming , and dependent on third-party software , as well as unnecessarily expensive . These factors can deter PHLs from implementing instrument interfacing . An architecture that is loosely coupled , reusable , and able to support agile implementations can be a cost-effective and sustainable alternative for any laboratory . J Michael consulting ( JMC ) is collaborating with the South Carolina Department of Health and Environmental Control ( DHEC ) and the OpenELIS Foundation to integrate DHEC ’ s laboratory instruments with its OpenELIS application using Rhapsody , a highperformance interoperability engine that is capable of electronic transfer , conversion , storage , or display of data from devices / applications . Rhapsody has built-in standard communication adaptors to connect with instruments . The Rhapsody components are portable , modular , and reusable . These features give the flexibility of a plug-and-play model to integrate different instruments with minimal development effort . The JMC team will implement DHEC interfaces in phases . In Phase I , JMC will develop a prototype of the bi-directional interface with OpenELIS and Abbott Architect . The interface will import run setup information from OpenELIS , validate , transform , and convert the data to an instrument-readable format . Once the instrument completes its test run , the interface will read the results , validate , transform , and process the results data into the OpenELIS backend . In Phase II , JMC will decrease the development effort for the remaining 20 instrument interfaces by using the portable and reusable components developed during Phase I . Notably , the integration will be the same for each instrument type ; for example if there are 5 GC / MS instruments , JMC will develop only one Rhapsody route . The interfacing for all the instruments at the DHEC laboratory with OpenELIS can be achieved by leveraging the existing Rhapsody engine , a software that DHEC already utilizes for electronic messaging with various partners . This approach will not only eliminate the upfront cost of third-party software , it will also allow DHEC to flexibly use existing communication adaptors and functions in a cost-effective manner . Moreover , it provides ownership of the interfaces to the laboratory , rather than to a vendor , and with improved performance and reliability . DHEC will be able to customize , maintain , and adapt reusable Rhapsody instrument interface templates to instruments and LIMS applications throughout the enterprise .
Presenter : Mary-Kate Yost-Daljev , J . Michael Consulting , LLC , Atlanta , GA , myostdaljev @ jmichael-consulting . com
Expanding Bioinformatics Capabilities at a State Public Health Lab Through Partnership with a University
A . Kampoowale , W . Hottel , F . Delin , M . Nelson , W . Aldous , M . Pentella and V . Reeb , State Hygienic Laboratory at The University of Iowa , Iowa City , IA
Increased public health applications of next-generation sequencing has created new laboratory challenges including additional demands for bioinformatics expertise and computing power . During the past year , the State Hygienic Laboratory ( SHL ) greatly expanded its bioinformatics capability . An SHL IT application developer started pursuing a bioinformatics certificate and SHL became a host lab for an APHL Bioinformatics Fellow . Additionally , SHL is housed within the University of Iowa ( UI ), and as such , has access to the UI high performance computing ( HPC ) Argon cluster and other analytic resources . The Argon cluster consists of over 15,000 processor cores with access to more than 200 software packages . SHL was able to obtain a group account on Argon , allowing our bioinformaticians to install pipelines necessary for sequence data QC , sequence typing , antibiotic resistance and virulence profiling , and outbreak investigations . Lab analysts can access the group account via an individual login system and execute one or more pipeline ( s ) in parallel . Available pipelines include modified versions of the Type pipeline ( Colorado Department of Public Health and Environment ),