Difference between revisions of "Template:Article of the week"

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(Updated article of the week text.)
(Updated article of the week text.)
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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Reisman EBioinformatics2016 12.jpg|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Guo JofPathInformatics2016 7.jpg|240px]]</div>
'''"[[Journal:A polyglot approach to bioinformatics data integration: A phylogenetic analysis of HIV-1|A polyglot approach to bioinformatics data integration: A phylogenetic analysis of HIV-1]]"'''
'''"[[Journal:Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out|Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out]]"'''


As [[sequencing]] technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 sequences. Phylogenetic analyses were conducted for >6,000 HIV-1 sequences revealing spatial and temporal factors influence the evolution of the individual genes uniquely. Nevertheless, signatures of origin can be extrapolated even despite increased globalization. The approach developed here can easily be customized for any species of interest. ('''[[Journal:A polyglot approach to bioinformatics data integration: A phylogenetic analysis of HIV-1|Full article...]]''')<br />
The adoption of digital pathology offers benefits over labor-intensive, time-consuming, and error-prone manual processes. However, because most workflow and [[laboratory]] transactions are centered around the anatomical pathology laboratory information system (APLIS), adoption of digital pathology ideally requires integration with the APLIS. A digital pathology system (DPS) integrated with the APLIS was recently implemented at our institution for diagnostic use. We demonstrate how such integration supports digital workflow to sign-out anatomical pathology cases.
 
Workflow begins when pathology cases get accessioned into the APLIS ([[Cerner Corporation|CoPathPlus]]). Glass slides from these cases are then digitized (Omnyx VL120 scanner) and automatically uploaded into the DPS (Omnyx; Integrated Digital Pathology (IDP) software v.1.3). The APLIS transmits case data to the DPS via a publishing web service. The DPS associates scanned images with the correct case using barcode labels on slides and information received from the APLIS. When pathologists remotely open a case in the DPS, additional information (e.g. gross pathology details, prior cases) gets retrieved from the APLIS through a query web service. ('''[[Journal:Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out|Full article...]]''')<br />
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''Recently featured'':  
''Recently featured'':  
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Revision as of 14:55, 11 July 2016

Fig1 Guo JofPathInformatics2016 7.jpg

"Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out"

The adoption of digital pathology offers benefits over labor-intensive, time-consuming, and error-prone manual processes. However, because most workflow and laboratory transactions are centered around the anatomical pathology laboratory information system (APLIS), adoption of digital pathology ideally requires integration with the APLIS. A digital pathology system (DPS) integrated with the APLIS was recently implemented at our institution for diagnostic use. We demonstrate how such integration supports digital workflow to sign-out anatomical pathology cases.

Workflow begins when pathology cases get accessioned into the APLIS (CoPathPlus). Glass slides from these cases are then digitized (Omnyx VL120 scanner) and automatically uploaded into the DPS (Omnyx; Integrated Digital Pathology (IDP) software v.1.3). The APLIS transmits case data to the DPS via a publishing web service. The DPS associates scanned images with the correct case using barcode labels on slides and information received from the APLIS. When pathologists remotely open a case in the DPS, additional information (e.g. gross pathology details, prior cases) gets retrieved from the APLIS through a query web service. (Full article...)

Recently featured:

A polyglot approach to bioinformatics data integration: A phylogenetic analysis of HIV-1
The systems biology format converter
Chemozart: A web-based 3D molecular structure editor and visualizer platform