Beyond standardization: dynamic software infrastructures for systems biology

Morris A. Swertz; Ritsert C. Jansen

doi:10.1038/nrg2048

Beyond standardization: dynamic software infrastructures for systems biology

Morris A. Swertz, Ritsert C. Jansen^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

50 Citations (Scopus)

Abstract

Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.

Original language	English
Pages (from-to)	235-243
Number of pages	9
Journal	Nature Reviews Genetics
Volume	8
Issue number	3
DOIs	https://doi.org/10.1038/nrg2048
Publication status	Published - Mar-2007

Keywords

GENETIC GENOMICS
FUNCTIONAL GENOMICS
OBJECT MODEL
DATABASE
BIOINFORMATICS
INFORMATION
WILL
IMPLEMENTATION
WORKFLOWS
GENERATOR

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title = "Beyond standardization: dynamic software infrastructures for systems biology",

abstract = "Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.",

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note = "Relation: http://www.nature.com/reviews/genetics Rights: Nature Publishing Group",

year = "2007",

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T2 - dynamic software infrastructures for systems biology

AU - Swertz, Morris A.

AU - Jansen, Ritsert C.

N1 - Relation: http://www.nature.com/reviews/genetics Rights: Nature Publishing Group

PY - 2007/3

Y1 - 2007/3

N2 - Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.

AB - Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.

KW - GENETIC GENOMICS

KW - FUNCTIONAL GENOMICS

KW - OBJECT MODEL

KW - DATABASE

KW - BIOINFORMATICS

KW - INFORMATION

KW - WILL

KW - IMPLEMENTATION

KW - WORKFLOWS

KW - GENERATOR

U2 - 10.1038/nrg2048

DO - 10.1038/nrg2048

M3 - Review article

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VL - 8

SP - 235

EP - 243

JO - Nature Reviews Genetics

JF - Nature Reviews Genetics

IS - 3

ER -

Beyond standardization: dynamic software infrastructures for systems biology

Abstract

Keywords

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