Extracting patterns of database and software usage from the bioinformatics literature

Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2014) Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics, 30(17), i601-i608. (doi: 10.1093/bioinformatics/btu471) (PMID:25161253) (PMCID:PMC4147923)

Abstract

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David
• Authors: Duck, G., Nenadic, G., Brass, A., Robertson, D. L., and Stevens, R.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Bioinformatics
• Publisher: Oxford University Press
• ISSN: 1367-4803
• ISSN (Online): 1460-2059
• Published Online: 22 August 2014
• Copyright Holders: Copyright © 2014 The Authors
• First Published: First published in Bioinformatics 30(17): i601-i608
• Publisher Policy: Reproduced under a Creative Commons License