Alberta Sepsis Network
www.albertasepsisnetwork.ca
Overview
The Alberta Sepsis Network (ASN) is a multi-disciplinary research project focused on the epidemiology and biology of severe sepsis and septic shock. A data management and analytic framework was designed and implemented to support this project. The system known as SepsisNet incorporates several open source and custom applications in a secure hosted server environment to facilitate research integrating clinical and biological data.
SepsiNet Computer Infrastructure
SepsisNet is hosted in a physically and virtually secure hosting environment. SepsisNet currently consists of five major software components. 1) WebReports: a custom web-based software application consisting of several analytic components including high-level charting and network diagrams, a Meta Data Repository (MDR) for documenting the content and structure of the various databases, and an R Code Repository that interfaces with the R Statistical Language (www.r-project.org); 2) RedCap1 a web-based system for supporting our clinical data entry forms; 3) LabKey2: a web-based system for supporting laboratory information, currently providing an interface for our Luminex and Metabolomics data; 4) RStudio(www.rstudio.org): an Integrated Development Environment (IDE) for the R statistical language; 5)FreezerWorks: an application supporting the data management of the Critical Care Epidemiologic and Biologic Tissue Resource tissue bank.
SepsisNet Applications
SepsisNet also uses 3 stand-alone applications. These applications are: 1) KnowledgeShare (KSv2) - an application for helping in systematic and scoping literature reviews; 2) Meta Data Respository (MDR) - an application for documentating the data contained in databases. The MDR is more powerful then a data dictionary as the MDR is dynamic and documents the schema, table, columns and content of several relational databases; 3) Patient-X - is a micro ETL (Extract/Transform/Load) application designed specifically for transfering data between multiple databases. Patient-X also provides one-way encoding and encryption. These applications can be used by any member of the Alberta Sepsis Network project.
SepsisNet Citation:
Yergens D, Doig CJ, Ray J, Winston BW, Research Framework for the Management and Analysis of Sepsis. American Medical Informatics Association (AMIA) 2012 Annual Symposium. November 2012.
References:
(1) Paul A. Harris et al. (2009). "Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support". Journal of Biomedical Informatics 42 (2): 377–381. doi:10.1016/j.jbi.2008.08.010
(2) Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory et al. (2011). "LabKey Server: An open source platform for scientific data integration, analysis and collaboration". BMC Bioinformatics 12: 71. doi:10.1186/1471-2105-12-71. PMC 3062597.PMID 21385461
Overview
The Alberta Sepsis Network (ASN) is a multi-disciplinary research project focused on the epidemiology and biology of severe sepsis and septic shock. A data management and analytic framework was designed and implemented to support this project. The system known as SepsisNet incorporates several open source and custom applications in a secure hosted server environment to facilitate research integrating clinical and biological data.
SepsiNet Computer Infrastructure
SepsisNet is hosted in a physically and virtually secure hosting environment. SepsisNet currently consists of five major software components. 1) WebReports: a custom web-based software application consisting of several analytic components including high-level charting and network diagrams, a Meta Data Repository (MDR) for documenting the content and structure of the various databases, and an R Code Repository that interfaces with the R Statistical Language (www.r-project.org); 2) RedCap1 a web-based system for supporting our clinical data entry forms; 3) LabKey2: a web-based system for supporting laboratory information, currently providing an interface for our Luminex and Metabolomics data; 4) RStudio(www.rstudio.org): an Integrated Development Environment (IDE) for the R statistical language; 5)FreezerWorks: an application supporting the data management of the Critical Care Epidemiologic and Biologic Tissue Resource tissue bank.
SepsisNet Applications
SepsisNet also uses 3 stand-alone applications. These applications are: 1) KnowledgeShare (KSv2) - an application for helping in systematic and scoping literature reviews; 2) Meta Data Respository (MDR) - an application for documentating the data contained in databases. The MDR is more powerful then a data dictionary as the MDR is dynamic and documents the schema, table, columns and content of several relational databases; 3) Patient-X - is a micro ETL (Extract/Transform/Load) application designed specifically for transfering data between multiple databases. Patient-X also provides one-way encoding and encryption. These applications can be used by any member of the Alberta Sepsis Network project.
SepsisNet Citation:
Yergens D, Doig CJ, Ray J, Winston BW, Research Framework for the Management and Analysis of Sepsis. American Medical Informatics Association (AMIA) 2012 Annual Symposium. November 2012.
References:
(1) Paul A. Harris et al. (2009). "Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support". Journal of Biomedical Informatics 42 (2): 377–381. doi:10.1016/j.jbi.2008.08.010
(2) Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory et al. (2011). "LabKey Server: An open source platform for scientific data integration, analysis and collaboration". BMC Bioinformatics 12: 71. doi:10.1186/1471-2105-12-71. PMC 3062597.PMID 21385461