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  • Review Article
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Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

Nature Reviews Genetics volume 9, pages 678–688 (2008)Cite this article

Key Points

  • A biological cyberinfrastructure facilitates online collaboration, data sharing and algorithm sharing in an increasingly information-driven field.

  • A fully developed cyberinfrastructure system consists of network-accessible data repositories, computational and analysis services, and an online communication and collaboration system.

  • The explosive growth of genomic information is forcing the field to move from traditional centralized databases and static paper publications to distributed information resources and interactive online publications.

  • Integration of diverse resources remains a challenge at the technical level owing to the competing demands of interoperability and the need for flexibility and diversity.

  • The most promising cyberinfrastructure systems combine a flexible, semantically driven framework for sharing information with a strong social and community-building component.

  • The emerging biology cyberinfrastructure has the potential to be a great leveller, giving all researchers equal access to data and compute facilities regardless of their geographical location or data-handling abilities.

Abstract

Wiki pages and commenting Biology is an information-driven science. Large-scale data sets from genomics, physiology, population genetics and imaging are driving research at a dizzying rate. Simultaneously, interdisciplinary collaborations among experimental biologists, theorists, statisticians and computer scientists have become the key to making effective use of these data sets. However, too many biologists have trouble accessing and using these electronic data sets and tools effectively. A 'cyberinfrastructure' is a combination of databases, network protocols and computational services that brings people, information and computational tools together to perform science in this information-driven world. This article reviews the components of a biological cyberinfrastructure, discusses current and pending implementations, and notes the many challenges that lie ahead.

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Figure 1: The components of a cyberinfrastructure.
Figure 2: The process of bioinformatics research now and in the future.
Figure 3: The Taverna workflow manager.
Figure 4: A mash-up mock-up.

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Acknowledgements

I wish to thank the staff of myGrid, BIRN, caBIG, iPlant, EcoliHub and nanoHub for their assistance during the research phase of this Review. I would also like to thank the three anonymous reviewers who took the time to review this article in manuscript stage and to make comments and suggestions. This work was supported in part by a grant from the National Science Foundation Division of Emerging Frontiers (0735191).

Author information

Authors and Affiliations

  1. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA

    Lincoln D. Stein

  2. Ontario Institute for Cancer Research, 101 College Street, Toronto, M5G 1L7, Ontario, Canada

    Lincoln D. Stein

Authors
  1. Lincoln D. Stein
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Competing interests

In the interests of full disclosure, the author has been directly or indirectly involved in the following projects discussed in this article: DAS, GMOD, BioMOBY, SSWAP, caBIG and iPC.

Related links

Related links

FURTHER INFORMATION

WIKI features and commenting

Lincoln Stein's homepage

BioMOBY

Biomedical Informatics Research Network (BIRN)

Cancer Bioinformatics Grid (caBIG)

EcoliWiki

Ensembl Genome Browser

EU Framework Programme 7 (FP7)

Generic Model Organism Database (GMOD) project

Globus Toolkit

iPlant Collaborative (iPC)

myExperiment

myGrid

NeuroNames

NCBI Taxonomy

Open Bioinformatics Ontologies (OBI)

Phenotype & Trait Ontology (PATO)

Simple Object Access Protocol (SOAP)

Simple Semantic Web Architecture and Protocol (SSWAP)

SSWAP protocol

UCSC Genome Browser

WikiPathways

Web Services Description Language (WSDL)

Virtual Plant Information Network (VPIN)

Glossary

WIKI

A popular web page authoring system that allows individuals to collaborate on large communal documents. Wikipedia is the best known example, but there are many tens of thousands of WIKIs in use. The name comes from the Hawaiian word for quick.

Ontology

An enumeration of the concepts used in a particular domain of knowledge, their definitions and the relationships between them.

Web service

A web-based resource that can be programmatically invoked to perform a database search or a computation, or to provide some other service.

Web Services Description Language

(WSDL). An XML-based language used to describe the nature of SOAP web services.

Simple Object Access Protocol

(SOAP). The dominant messaging protocol for defining and invoking web services.

OWL

A dyslexic acronym for Web Ontology Language. It is an XML-based language used to describe ontologies. A variant of OWL called OWL Description Logics (OWL DL) is particularly suited for creating semantic webs of ontologies that can be traversed by reasoning engines.

Representational State Transfer

(REST). An alternative web services protocol that is sometimes more suitable than SOAP for particular web services.

Semantic web

An interrelated network of ontologies that together describe resources available on the web.

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Stein, L. Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 9, 678–688 (2008). https://doi.org/10.1038/nrg2414

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