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CytoASP: A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks

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CytoASP : A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. / Kittas, Aristotelis; Barozet, Amélie; Sereshti, Jekaterina; Grabe, Niels; Tsoka, Sophia.

In: Bmc Systems Biology, 11.07.2015.

Research output: Contribution to journalArticle

Harvard

Kittas, A, Barozet, A, Sereshti, J, Grabe, N & Tsoka, S 2015, 'CytoASP: A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks', Bmc Systems Biology. https://doi.org/10.1186/s12918-015-0179-6

APA

Kittas, A., Barozet, A., Sereshti, J., Grabe, N., & Tsoka, S. (2015). CytoASP: A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. Bmc Systems Biology. https://doi.org/10.1186/s12918-015-0179-6

Vancouver

Kittas A, Barozet A, Sereshti J, Grabe N, Tsoka S. CytoASP: A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. Bmc Systems Biology. 2015 Jul 11. https://doi.org/10.1186/s12918-015-0179-6

Author

Kittas, Aristotelis ; Barozet, Amélie ; Sereshti, Jekaterina ; Grabe, Niels ; Tsoka, Sophia. / CytoASP : A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. In: Bmc Systems Biology. 2015.

Bibtex Download

@article{8d5ba2593d9a4ef89c1d8f3a63cd40ce,
title = "CytoASP: A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks",
abstract = "Background: Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted. The BioASP software collection offers ideal tools for such analyses. Additionally, the Cytoscape platform can offer extensive functionality and visualisation capabilities. However, specialist programming knowledge is required to use BioASP and no methods exist to integrate both of these software platforms effectively. Results: We report the implementation of CytoASP, an app that allows the use of BioASP for influence graph consistency checking, prediction and repair operations through Cytoscape. While offering inherent benefits over traditional approaches using BioASP, it provides additional advantages such as customised visualisation of predictions and repairs, as well as the ability to analyse multiple networks in parallel, exploiting multi-core architecture. We demonstrate its usage in a case study of a yeast genetic network, and highlight its capabilities in reasoning over regulatory networks. Conclusion: We have presented a user-friendly Cytoscape app for the analysis of regulatory networks using BioASP. It allows easy integration of qualitative modelling, combining the functionality of BioASP with the visualisation and processing capability in Cytoscape, and thereby greatly simplifying qualitative network modelling, promoting its use in relevant projects.",
keywords = "BioASP, Biological networks, Qualitative modelling, Regulatory networks",
author = "Aristotelis Kittas and Am{\'e}lie Barozet and Jekaterina Sereshti and Niels Grabe and Sophia Tsoka",
year = "2015",
month = jul,
day = "11",
doi = "10.1186/s12918-015-0179-6",
language = "English",
journal = "Bmc Systems Biology",
issn = "1752-0509",
publisher = "BioMed Central",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - CytoASP

T2 - A Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks

AU - Kittas, Aristotelis

AU - Barozet, Amélie

AU - Sereshti, Jekaterina

AU - Grabe, Niels

AU - Tsoka, Sophia

PY - 2015/7/11

Y1 - 2015/7/11

N2 - Background: Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted. The BioASP software collection offers ideal tools for such analyses. Additionally, the Cytoscape platform can offer extensive functionality and visualisation capabilities. However, specialist programming knowledge is required to use BioASP and no methods exist to integrate both of these software platforms effectively. Results: We report the implementation of CytoASP, an app that allows the use of BioASP for influence graph consistency checking, prediction and repair operations through Cytoscape. While offering inherent benefits over traditional approaches using BioASP, it provides additional advantages such as customised visualisation of predictions and repairs, as well as the ability to analyse multiple networks in parallel, exploiting multi-core architecture. We demonstrate its usage in a case study of a yeast genetic network, and highlight its capabilities in reasoning over regulatory networks. Conclusion: We have presented a user-friendly Cytoscape app for the analysis of regulatory networks using BioASP. It allows easy integration of qualitative modelling, combining the functionality of BioASP with the visualisation and processing capability in Cytoscape, and thereby greatly simplifying qualitative network modelling, promoting its use in relevant projects.

AB - Background: Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted. The BioASP software collection offers ideal tools for such analyses. Additionally, the Cytoscape platform can offer extensive functionality and visualisation capabilities. However, specialist programming knowledge is required to use BioASP and no methods exist to integrate both of these software platforms effectively. Results: We report the implementation of CytoASP, an app that allows the use of BioASP for influence graph consistency checking, prediction and repair operations through Cytoscape. While offering inherent benefits over traditional approaches using BioASP, it provides additional advantages such as customised visualisation of predictions and repairs, as well as the ability to analyse multiple networks in parallel, exploiting multi-core architecture. We demonstrate its usage in a case study of a yeast genetic network, and highlight its capabilities in reasoning over regulatory networks. Conclusion: We have presented a user-friendly Cytoscape app for the analysis of regulatory networks using BioASP. It allows easy integration of qualitative modelling, combining the functionality of BioASP with the visualisation and processing capability in Cytoscape, and thereby greatly simplifying qualitative network modelling, promoting its use in relevant projects.

KW - BioASP

KW - Biological networks

KW - Qualitative modelling

KW - Regulatory networks

UR - http://www.scopus.com/inward/record.url?scp=84936855480&partnerID=8YFLogxK

U2 - 10.1186/s12918-015-0179-6

DO - 10.1186/s12918-015-0179-6

M3 - Article

AN - SCOPUS:84936855480

JO - Bmc Systems Biology

JF - Bmc Systems Biology

SN - 1752-0509

ER -

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