Barry Demchak

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Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks.(More)
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data,(More)
Mobile information technology can help first responders assist patients more quickly, reliably, and safely, while focusing resources on those most in need. Yet the disaster setting complicates reliable networked computing. The WIISARD client-server architecture provides mobile IT support for medical response in disasters. Cached remote objects (CROs) are(More)
In existing Incident Command systems, situational awareness is achieved manually through paper tracking systems. Such systems often produce high latencies and incomplete data, resulting in inefficient and ineffective resource deployment. The WIISARD system collects much more data than a paper-based system, dramatically reducing latency while increasing the(More)
PURPOSE The objective of this study is to assess validity of the personal activity location measurement system (PALMS) for deriving time spent walking/running, bicycling, and in vehicle, using SenseCam (Microsoft, Redmond, WA) as the comparison. METHODS Forty adult cyclists wore a Qstarz BT-Q1000XT GPS data logger (Qstarz International Co., Taipei,(More)
In this work we present CitiSense, a new kind of “citizen infrastructure” for the monitoring of pollution and environmental conditions that users are exposed to. By utilizing mobile phones and affordable, small sensors placed in the environment and carried by users, data about pollutants such as ozone and carbon monoxide is collected and used to provide(More)
As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently,(More)
Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (, a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To(More)
Networks are a powerful and flexible methodology for expressing biological knowledge for computation and communication. Network-encoded information can include systematic screens for molecular interactions, biological relationships curated from literature, and outputs from analysis of Big Data. NDEx, the Network Data Exchange (, is an online(More)
The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hierarchy of(More)