(my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences

S Pettifer; K Wolstencroft; P Alper; T Attwood; A Coletta; C Goble; P Li; P McDermott; J Marsh; T Oinn; J Sinnott; D Thorne; S CohenBoulakia; V Yannen; Penn Genom Inst Microsoft Res Appl Sci

(my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences

S Pettifer
, K Wolstencroft
, P Alper
, T Attwood
, A Coletta
, C Goble
, P Li
, P McDermott
, J Marsh
, T Oinn
, J Sinnott
, D Thorne
, S CohenBoulakia (Editor)
, V Yannen (Editor)
, Penn Genom Inst Microsoft Res Appl Sci (Editor)

Research output: Chapter in Book/Conference proceeding › Conference contribution

Abstract

In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systems applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; (my)-Grid/Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.

Original language	English
Title of host publication	4th International Workshop on Data Integration in the Life Sciences
Editors	S CohenBoulakia, V Yannen, Penn Genom Inst Microsoft Res Appl Sci
Publisher	Springer Nature
Pages	59-70
Number of pages	12
Volume	4544
ISBN (Print)	0302-9743 978-3-540-73254-9
Publication status	Published - 2007
Event	4th International Workshop on Data Integration in the Life Sciences - Philadelphia, PA Duration: 27 Jun 2007 → 29 Jun 2007

Conference

Conference	4th International Workshop on Data Integration in the Life Sciences
City	Philadelphia, PA
Period	27/06/07 → 29/06/07

Keywords

workflows
visualisation
web services
in silico
experimentation
Biochemical Research Methods
Computer Science, Information Systems
Mathematical & Computational Biology

Cite this

Pettifer, S., Wolstencroft, K., Alper, P., Attwood, T., Coletta, A., Goble, C., Li, P., McDermott, P., Marsh, J., Oinn, T., Sinnott, J., Thorne, D., CohenBoulakia, S. (Ed.), Yannen, V. (Ed.), & Appl Sci, P. G. I. M. R. (Ed.) (2007). (my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences. In S. CohenBoulakia, V. Yannen, & P. G. I. M. R. Appl Sci (Eds.), 4th International Workshop on Data Integration in the Life Sciences (Vol. 4544, pp. 59-70). Springer Nature.

@inproceedings{a889c93dd06b48c7b3f36ba72bdffa54,

title = "(my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences",

abstract = "In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systems applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; (my)-Grid/Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.",

keywords = "workflows, visualisation, web services, in silico, experimentation, Biochemical Research Methods, Computer Science, Information Systems, Mathematical \& Computational Biology",

author = "S Pettifer and K Wolstencroft and P Alper and T Attwood and A Coletta and C Goble and P Li and P McDermott and J Marsh and T Oinn and J Sinnott and D Thorne and S CohenBoulakia and V Yannen and \{Appl Sci\}, \{Penn Genom Inst Microsoft Res\}",

note = "Univ Penn, Sch Engn Pettifer, Steve Wolstencroft, Katy Alper, Pinar Attwood, Teresa Coletta, Alain Goble, Carole Li, Peter McDermott, Philip Marsh, James Oinn, Tom Sinnott, James Thorne, David 15 BERLIN BGS72; 4th International Workshop on Data Integration in the Life Sciences ; Conference date: 27-06-2007 Through 29-06-2007",

year = "2007",

language = "English",

isbn = "0302-9743 978-3-540-73254-9",

volume = "4544",

pages = "59--70",

editor = "S CohenBoulakia and V Yannen and \{Appl Sci\}, \{Penn Genom Inst Microsoft Res\}",

booktitle = "4th International Workshop on Data Integration in the Life Sciences",

publisher = "Springer Nature",

address = "United States",

}

Pettifer, S, Wolstencroft, K, Alper, P, Attwood, T, Coletta, A, Goble, C, Li, P, McDermott, P, Marsh, J, Oinn, T, Sinnott, J, Thorne, D, CohenBoulakia, S (ed.), Yannen, V (ed.) & Appl Sci, PGIMR (ed.) 2007, (my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences. in S CohenBoulakia, V Yannen & PGIMR Appl Sci (eds), 4th International Workshop on Data Integration in the Life Sciences. vol. 4544, Springer Nature, pp. 59-70, 4th International Workshop on Data Integration in the Life Sciences, Philadelphia, PA, 27/06/07.

(my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences. / Pettifer, S; Wolstencroft, K; Alper, P et al.
4th International Workshop on Data Integration in the Life Sciences. ed. / S CohenBoulakia; V Yannen; Penn Genom Inst Microsoft Res Appl Sci. Vol. 4544 Springer Nature, 2007. p. 59-70.

Research output: Chapter in Book/Conference proceeding › Conference contribution

TY - GEN

T1 - (my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences

AU - Pettifer, S

AU - Wolstencroft, K

AU - Alper, P

AU - Attwood, T

AU - Coletta, A

AU - Goble, C

AU - Li, P

AU - McDermott, P

AU - Marsh, J

AU - Oinn, T

AU - Sinnott, J

AU - Thorne, D

A2 - CohenBoulakia, S

A2 - Yannen, V

A2 - Appl Sci, Penn Genom Inst Microsoft Res

A2 - CohenBoulakia, S

A2 - Yannen, V

A2 - Appl Sci, Penn Genom Inst Microsoft Res

N1 - Univ Penn, Sch Engn Pettifer, Steve Wolstencroft, Katy Alper, Pinar Attwood, Teresa Coletta, Alain Goble, Carole Li, Peter McDermott, Philip Marsh, James Oinn, Tom Sinnott, James Thorne, David 15 BERLIN BGS72

PY - 2007

Y1 - 2007

N2 - In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systems applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; (my)-Grid/Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.

AB - In silico experiments have hitherto required ad hoc collections of scripts and programs to process and visualise biological data, consuming substantial amounts of time and effort to build, and leading to tools that are difficult to use, are architecturally fragile and scale poorly. With examples of the systems applied to real biological problems, we describe two complimentary software frameworks that address this problem in a principled manner; (my)-Grid/Taverna, a workflow design and enactment environment enabling coherent experiments to be built, and UTOPIA, a flexible visualisation system to aid in examining experimental results.

KW - workflows

KW - visualisation

KW - web services

KW - in silico

KW - experimentation

KW - Biochemical Research Methods

KW - Computer Science, Information Systems

KW - Mathematical & Computational Biology

M3 - Conference contribution

SN - 0302-9743 978-3-540-73254-9

VL - 4544

SP - 59

EP - 70

BT - 4th International Workshop on Data Integration in the Life Sciences

PB - Springer Nature

T2 - 4th International Workshop on Data Integration in the Life Sciences

Y2 - 27 June 2007 through 29 June 2007

ER -

(my)Grid and UTOPIA: An integrated approach to enacting and visualising in silico experiments in the life sciences

Abstract

Conference

Keywords

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