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)

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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 > Institute of Infection Immunity and Inflammation
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

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