Barry Demchak

Biological Network Exploration with Cytoscape 3

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, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump‐start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users. Curr. Protoc. Bioinform. 47:8.13.1‐8.13.24.

Validity of Palms Gps Scoring of Active and Passive Travel Compared with Sensecam

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, Taiwan) and SenseCam (camera worn around the neck capturing multiple images every minute) for a mean time of 4 d. PALMS used distance and speed between global positioning system (GPS) points to classify whether each minute was part of a trip (yes/no), and if so, the trip mode (walking/running, bicycling, or in vehicle). SenseCam images were annotated to create the same classifications (i.e., trip yes/no and mode). Contingency tables (2 × 2) and confusion matrices were calculated at the minute level for PALMS versus SenseCam classifications. Mixed-effects linear regression models estimated agreement (mean differences and intraclass correlation coefficients) between PALMS and SenseCam with regard to minutes/day in each mode. RESULTS Minute-level sensitivity, specificity, and negative predictive value were ≥88%, and positive predictive value was ≥75% for non-mode-specific trip detection. Seventy-two percent to 80% of outdoor walking/running minutes, 73% of bicycling minutes, and 74%-76% of in-vehicle minutes were correctly classified by PALMS. For minutes per day, PALMS had a mean bias (i.e., amount of over or under estimation) of 2.4-3.1 min (11%-15%) for walking/running, 2.3-2.9 min (7%-9%) for bicycling, and 4.3-5 min (15%-17%) for vehicle time. Intraclass correlation coefficients were ≥0.80 for all modes. CONCLUSIONS PALMS has validity for processing GPS data to objectively measure time spent walking/running, bicycling, and in vehicle in population studies. Assessing travel patterns is one of many valuable applications of GPS in physical activity research that can improve our understanding of the determinants and health outcomes of active transportation as well as its effect on physical activity.

Rich Services: The Integration Piece of the SOA Puzzle

One of the key challenges to successful systems-of- systems integration using Web services technologies is how to address crosscutting architectural concerns such as policy management, governance, and authentication, while still maintaining the lightweight implementation and deployment flavor that distinguishes Web services from earlier attempts at providing interoperable enterprise systems. To address this challenge, this article introduces the notion of a Rich Service, an extension of the standard service notion, based on an architectural pattern that allows hierarchical decomposition of system architecture according to separate concerns. Rich Services enable the capture of different system aspects and their interactions. By leveraging emerging Enterprise Service Bus technologies, Rich Services also enable a direct transition from a logical to a deployed service-oriented architecture (SOA). This results in immediate benefits not only in SOA design, implementation, deployment, and quality assurance, but also in the traceability of architectural requirements to an SOA implementation.

Cytoscape: the network visualization tool for GenomeSpace workflows.

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. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded it over 850 times since the release of its first version in September, 2013.

PALMS: A Modern Coevolution of Community and Computing Using Policy Driven Development

In 2007, the National Institutes of Health (NIH) funded the Physical Activity and Location Measurement System (PALMS) project at the University of California, San Diego. Its mission is to advance exposure biology research by developing new methods of physical activity data capture and analysis from a geospatial perspective. A key early insight was that while exposure biology investigators often employ their own data analysis frameworks, many frameworks are conceptually similar. Forming a community based on common requirements and research directions, and serving that community with a common computing framework would, itself, be a major contribution to the NIH mission. This paper describes the PALMS Cyber infrastructure (CI), which comprises both the PALMS computing services and the exposure biology community it serves. By leveraging state of the art software architecture techniques, the PALMS CI is well positioned to serve the co evolution of a thriving research community and the computing systems that support it.

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

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, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.

The Treasure Map for Rich Services

Large systems-of-systems often service large numbers of stakeholders - more stakeholders often means more concerns, many of which are crosscutting. The rich services architecture is a type of service-oriented architecture (SOA) that allows hierarchical decomposition of a system architecture into separate concerns, thereby capturing different system aspects and their interactions, and accounting for crosscutting concerns concisely and sensibly. By leveraging emerging enterprise service bus technology, rich services enable a simple and direct deployment mapping to a system-of-systems network. This paper describes a development process that leverages rich services and is compatible with agile development methodologies. It encompasses use cases, requirements decomposition, role identification, and service definition to produce a rich services logical architecture that can then be mapped to a virtual network topology, and finally a physical network topology. The process decouples development stages to improve flexibility and productivity of complex projects, promising reduced cost and risk.

The anatomy of successful computational biology software

Creators of software widely used in computational biology discuss the factors that contributed to their success

NeXO Web: the NeXO ontology database and visualization platform

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 cellular components and processes. Here, we describe the development of the NeXO Web platform (http://www.nexontology.org)—an online database and graphical user interface for visualizing, browsing and performing term enrichment analysis using NeXO and the gene ontology. The platform applies state-of-the-art web technology and visualization techniques to provide an intuitive framework for investigating biological machinery captured by both data-driven and manually curated ontologies.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.