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Articles 1 - 7 of 7
Full-Text Articles in Physical Sciences and Mathematics
Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi
Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi
John David N. Dionisio
GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of …
Teleradiology As A Foundation For An Enterprise-Wide Health Care Delivery System, John David N. Dionisio, Ricky K. Taira, Usha Sinha, David B. Johnson, Benjamin Y. Dai, Gregory H. Tashima, Stephen Blythe, Richard Johnson, Hooshang Kangarloo
Teleradiology As A Foundation For An Enterprise-Wide Health Care Delivery System, John David N. Dionisio, Ricky K. Taira, Usha Sinha, David B. Johnson, Benjamin Y. Dai, Gregory H. Tashima, Stephen Blythe, Richard Johnson, Hooshang Kangarloo
John David N. Dionisio
An effective, integrated telemedicine system has been developed that allows (a) teleconsultation between local primary health care providers (primary care physicians and general radiologists) and remote imaging subspecialists and (b) active patient participation related to his or her medical condition and patient education. The initial stage of system development was a traditional teleradiology consultation service between general radiologists and specialists; this established system was expanded to include primary care physicians and patients. The system was developed by using a well-defined process model, resulting in three integrated modules: a patient module, a primary health care provider module, and a specialist module. …
3d Virtual Worlds And The Metaverse: Current Status And Future Possibilities, John David N. Dionisio, William G. Burns Iii, Richard Gilbert
3d Virtual Worlds And The Metaverse: Current Status And Future Possibilities, John David N. Dionisio, William G. Burns Iii, Richard Gilbert
John David N. Dionisio
Moving from a set of independent virtual worlds to an integrated network of 3D virtual worlds or Metaverse rests on progress in four areas: immersive realism, ubiquity of access and identity, interoperability, and scalability. For each area, the current status and needed developments in order to achieve a functional Metaverse are described. Factors that support the formation of a viable Metaverse, such as institutional and popular interest and ongoing improvements in hardware performance, and factors that constrain the achievement of this goal, including limits in computational methods and unrealized collaboration among virtual world stakeholders and developers, are also considered.
The Next Step, Benjamin Y. Dai, Lynn Thompson, John David N. Dionisio, Hooshang Kangarloo, Ricky K. Taira
The Next Step, Benjamin Y. Dai, Lynn Thompson, John David N. Dionisio, Hooshang Kangarloo, Ricky K. Taira
John David N. Dionisio
In traditional radiology practice, reports are typically dictated and then transcribed.? While the free-text reports represent the semantic knowledge interpreted and conveyed by a physician, the information can be hard to access. The advantages of representing medical data in a structured format using standard terminology are clearly recognized. These include the ability to implement a standardized electronic medical record, automatically invoke medical guidelines when appropriate, and conduct outcomes research. Standard structured reports facilitate intelligent indexing, searching, and retrieval of documents from clinical databases. Recent attempts have been made in the industry to enable structured data entry using preformatted templates, but …
Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist
Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist
John David N. Dionisio
Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total "incubation time" of six months.
Integrated Multimedia Timeline Of Medical Images And Data For Thoracic Oncology Patients, Denise R. Aberle, John David N. Dionisio, Michael F. Mcnitt-Gray, Ricky K. Taira, Alfonso F. Cárdenas, Jonathan G. Goldin, Kathleen Brown, Robert A. Figlin, Wesley W. Chu
Integrated Multimedia Timeline Of Medical Images And Data For Thoracic Oncology Patients, Denise R. Aberle, John David N. Dionisio, Michael F. Mcnitt-Gray, Ricky K. Taira, Alfonso F. Cárdenas, Jonathan G. Goldin, Kathleen Brown, Robert A. Figlin, Wesley W. Chu
John David N. Dionisio
A prototype multimedia medical database has been developed to provide image and textual data for thoracic oncology patients undergoing treatment of advanced malignancies. The database integrates image data from the hospital pieture archiving and communication system with textual reports from the radiology information system, alphanumeric data contained in the hospital information system, and other electronic medical data. The database presents information in a timeline format and also contains visualization programs that permit the user to view and annotate radiographic measurements in tabular or graphic form. The database provides an efficient and intuitive display of the changing status of oncology patients. …
An Open Source Software Culture In The Undergraduate Computer Science Curriculum, John David N. Dionisio, Caskey L. Dickson, Stephanie E. August, Philip M. Dorin, Ray Toal
An Open Source Software Culture In The Undergraduate Computer Science Curriculum, John David N. Dionisio, Caskey L. Dickson, Stephanie E. August, Philip M. Dorin, Ray Toal
John David N. Dionisio
Open source software has made inroads into mainstream computing where it was once the territory of software altruists, and the open source culture of technological collegiality and accountability may benefit education as well as industry. This paper describes the Recourse project, which seeks to transform the computer science undergraduate curriculum through teaching methods based on open source principles, values, ethics, and tools. Recourse differs from similar projects by bringing the open source culture into the curriculum comprehensively, systematically, and institutionally. The current state of the project is described, and initial results from a pilot exercise are presented.