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Automating the PathLinker app for Cytoscape
PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since Decemb...
| Autores principales: | , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
F1000 Research Limited
2018
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051191/ https://www.ncbi.nlm.nih.gov/pubmed/30057757 http://dx.doi.org/10.12688/f1000research.14616.1 |
| _version_ | 1783340477323411456 |
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| author | Huang, Li Jun Law, Jeffrey N. Murali, T. M. |
| author_facet | Huang, Li Jun Law, Jeffrey N. Murali, T. M. |
| author_sort | Huang, Li Jun |
| collection | PubMed |
| description | PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since December 2015, PathLinker has been available as an app for Cytoscape. This paper describes how we automated the app to use the CyRest infrastructure and how users can incorporate PathLinker into their software pipelines. |
| format | Online Article Text |
| id | pubmed-6051191 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2018 |
| publisher | F1000 Research Limited |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-60511912018-07-27 Automating the PathLinker app for Cytoscape Huang, Li Jun Law, Jeffrey N. Murali, T. M. F1000Res Software Tool Article PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since December 2015, PathLinker has been available as an app for Cytoscape. This paper describes how we automated the app to use the CyRest infrastructure and how users can incorporate PathLinker into their software pipelines. F1000 Research Limited 2018-06-12 /pmc/articles/PMC6051191/ /pubmed/30057757 http://dx.doi.org/10.12688/f1000research.14616.1 Text en Copyright: © 2018 Huang LJ et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| spellingShingle | Software Tool Article Huang, Li Jun Law, Jeffrey N. Murali, T. M. Automating the PathLinker app for Cytoscape |
| title | Automating the PathLinker app for Cytoscape |
| title_full | Automating the PathLinker app for Cytoscape |
| title_fullStr | Automating the PathLinker app for Cytoscape |
| title_full_unstemmed | Automating the PathLinker app for Cytoscape |
| title_short | Automating the PathLinker app for Cytoscape |
| title_sort | automating the pathlinker app for cytoscape |
| topic | Software Tool Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051191/ https://www.ncbi.nlm.nih.gov/pubmed/30057757 http://dx.doi.org/10.12688/f1000research.14616.1 |
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