Biomedical subjects

Christopher Dubay

Publications and source records attributed to Christopher Dubay.

3 recordsLinked to original sources

PubMed2004

Applying task analysis to describe and facilitate bioinformatics tasks.

OBJECTIVE: To document bioinformatics tasks currently per-formed by researchers in genomics and proteomics in an effort to recognize unmet informatics needs and challenges, identify system features that would enhance the performance of those tasks, and inform the development of new bioinformatics tools. DESIGN: A cross-sectional study of bioinformatics tasks performed by OHSU investigators involved in genomics and proteomics research was conducted using task analysis techniques. RESULTS: Four major categories emerged from 22 bioinformatics tasks reported by 6 research laboratories. These were: 1) gene analysis, 2) protein analysis, 3) biostatistical analysis, and 4) literature searching. Analysis of the data also raised the following challenging issues: 1) lack of procedural documentation, 2) use of home-grown strategies to accomplish goals, 3) individual needs and preferences, and 4) lack of awareness of existing bioinformatics tools. CONCLUSION: Task analysis was effective at documenting bioinformatics tasks performed by researchers in the fields of genomics and proteomics, at identifying potentially desirable system features and useful bioinformatics tools, and at providing a better understanding of some of the unmet needs and challenges faced by these researchers.

Computational Biology↗

PubMed2003

BioQuery: an object framework for building queries to biomedical databases.

SUMMARY: BioQuery is an application that helps scientists automate database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. The application is implemented on a portable object framework that can provide database-searching capability to other applications. This framework is easily extensible, allowing users to develop plug-ins that provide access to new databases. BioQuery thus provides end-users with a complete database searching interface and updating service, and gives developers a toolkit to provide database-searching capability to their applications. AVAILABILITY: Free to all users: http://www.bioquery.org.

Biomedical Research↗

PubMed2002

Delivering bioinformatics training: bridging the gaps between computer science and biomedicine.

Biomedical researchers have always sought innovative methodologies to elucidate the underlying biology in their experimental models. As the pace of research has increased with new technologies that 'scale-up' these experiments, researchers have developed acute needs for the information technologies which assist them in managing and processing their experiments and results into useful data analyses that support scientific discovery. The application of information technology to support this discovery process is often called bioinformatics. We have observed a 'gap' in the training of those individuals who traditionally aid in the delivery of information technology at the level of the end-user (e.g. a systems analyst working with a biomedical researcher) which can negatively impact the successful application of technological solutions to biomedical research problems. In this paper we describe the roots and branches of bioinformatics to illustrate a range of applications and technologies that it encompasses. We then propose a taxonomy of bioinformatics as a framework for the identification of skills employed in the field. The taxonomy can be used to assess a set of skills required by a student to traverse this hierarchy from one area to another. We then describe a curriculum that attempts to deliver the identified skills to a broad audience of participants, and describe our experiences with the curriculum to show how it can help bridge the 'gap'.

Computational Biology↗