A self-updating road map of The Cancer Genome Atlas.

Motivation: Since 2011, The Cancer Genome Atlas' (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required.

A meta-composite software development approach for translational research.

Translational researchers conduct research in a highly data-intensive and continuously changing environment and need to use multiple, disparate tools to achieve their goals. These researchers would greatly benefit from meta-composite software development or the ability to continuously compose and recompose tools together in response to their ever-changing needs. However, the available tools are largely disconnected, and current software approaches are inefficient and ineffective in their support for meta-composite software development.

Enhancing medical research efficiency by using concept maps.

Even with today's advances in technology, the processes involved in medical research continue to be both time consuming and labor intensive. We have built an experimental integrated tool to convert the textual information available to the researchers into a concept map using the Web Ontology Language as an intermediate source of information. This tool is based on building semantic models using concept maps.

Development of a point-of-care HIV/AIDS medication dosing support system using the Android mobile platform.

Medication dosing errors can greatly reduce HIV treatment effectiveness as incorrect dosing leads to drug resistance and non-adherence. In order to dose correctly, HIV therapy providers must balance several patient characteristics such as renal functions and weight. In developing countries and other resource-limited settings, dosing errors are more likely because treatment is provided by mid-level providers with only basic training in HIV therapy.

A system for building clinical research applications using semantic web-based approach.

In this paper we present a system using Semantic Web by which applications can be effectively constructed for clinical research purposes. We are aware of the immense difficulties and variations involved in clinical research applications. With a purpose of mitigating some of these difficulties in the process of developing clinical research applications we are presenting an approach for building information systems based on Semantic Web.

Genetic region characterization (Gene RECQuest) - software to assist in identification and selection of candidate genes from genomic regions.

Background: The availability of research platforms like the web tools of the National Center for Biotechnology Information (NCBI) has transformed the time-consuming task of identifying candidate genes from genetic studies to an interactive process where data from a variety of sources are obtained to select likely genes for follow-up. This process presents its own set of challenges, as the genetic researcher has to interact with several tools in a time-intensive, manual, and cumbersome manner. We developed a method and implemented an effective software system to address these challenges by multidisciplinary efforts of professional software developers with domain experts.

Sharing information and data across heterogeneous e-health systems.

Information and data sharing across heterogeneous e-health systems, focusing on the management of patient care, have become the backbone of modern delivery of sustainable telemedicine services. Information and data available to healthcare practitioners in such environments range from patient's medical records, stored in repositories at places where patients have been treated, to a variety of information related to medical research, pharmaceutical products, or information stored within social networks of healthcare interest groups. This study sought to demonstrate two different approaches enabling the sharing of information/data across heterogeneous e-health systems: (1) Context-Aware Data Retrieval Architecture (CADRA), which secures the extraction and presentation of e-health information to users in requested format, and (2) Generic Ontology for Context Aware, Interoperable, and Data Sharing (Go-CID) software applications, which secure semantic interoperation across heterogeneous e-health data sources.

An overview of statistical decomposition techniques applied to complex systems.

The current state of the art in applied decomposition techniques is summarized within a comparative uniform framework. These techniques are classified by the parametric or information theoretic approaches they adopt. An underlying structural model common to all parametric approaches is outlined.

Towards sound epistemological foundations of statistical methods for high-dimensional biology.

A sound epistemological foundation for biological inquiry comes, in part, from application of valid statistical procedures. This tenet is widely appreciated by scientists studying the new realm of high-dimensional biology, or 'omic' research, which involves multiplicity at unprecedented scales. Many papers aimed at the high-dimensional biology community describe the development or application of statistical techniques.