PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible.[1][2][3]
PathVisio was created primarily at Maastricht University and Gladstone Institutes.[6] The software is developed in Java and it's also used as part of the WikiPathways framework as an applet.[7] Starting from version 3.0 (released in 2012) plugins are OSGi compliant and a plugin directory, describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PVJS) is being developed to replace the applet. From 2015 it also allows small edits and in the future it will be a full editor.
Integration with other programming languages via PathVisioRPC[11]
ReferencesEdit
^. Archived from the original on 23 September 2013. Retrieved 19 September 2013.
^van Iersel, Martijn P; Kelder, Thomas; Pico, Alexander R; Hanspers, Kristina; Coort, Susan; Conklin, Bruce R; Evelo, Chris (2008). "Presenting and exploring biological pathways with PathVisio". BMC Bioinformatics. 9 (1): 399. doi:10.1186/1471-2105-9-399. ISSN 1471-2105. PMC2569944. PMID 18817533.
^Kutmon, Martina; van Iersel, Martijn P.; Bohler, Anwesha; Kelder, Thomas; Nunes, Nuno; Pico, Alexander R.; Evelo, Chris T.; Murphy, Robert F. (23 February 2015). "PathVisio 3: An Extendable Pathway Analysis Toolbox". PLOS Computational Biology. 11 (2): e1004085. Bibcode:2015PLSCB..11E4085K. doi:10.1371/journal.pcbi.1004085. PMC4338111. PMID 25706687.
^Jaiswal, Pankaj; Usadel, Björn (2016). "Chapter 4: Plant Pathway Databases". Plant Bioinformatics. Springer. pp. 71–87. ISBN978-1-4939-3166-8.
^Habermann, Bianca; Villaveces, Jose; Koti, Prasanna (June 2015). "Tools for visualization and analysis of molecular networks, pathways, and -omics data". Advances and Applications in Bioinformatics and Chemistry. 8: 11–22. doi:10.2147/AABC.S63534. PMC4461095. PMID 26082651.
^. Archived from the original on 23 February 2014. Retrieved 10 February 2014.
^Pico, AR; Kelder T; van Iersel MP; Hanspers K; Conklin BR; et al. (22 July 2008). "WikiPathways: Pathway Editing for the People". PLOS Biology. 6 (7): e184. doi:10.1371/journal.pbio.0060184. PMC2475545. PMID 18651794.
^. Archived from the original on 2015-11-25. Retrieved 2015-11-24.
^. Archived from the original on 2015-11-25. Retrieved 2015-11-24.
^Kutmon, Martina; Lotia, Samad; Evelo, Chris T; Pico, Alexander R (2014). "WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization". F1000Research. 3: 152. doi:10.12688/f1000research.4254.1. ISSN 2046-1402. PMC4168754. PMID 25254103.
^Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T (2015). "Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment". BMC Bioinformatics. 16 (1): 267. doi:10.1186/s12859-015-0708-8. PMC4546821. PMID 26298294.
External linksEdit
Official website
PathVisio on Twitter
September 02, 2023
pathvisio, free, open, source, pathway, analysis, drawing, software, allows, drawing, editing, analyzing, biological, pathways, visualization, ones, experimental, data, pathways, finding, relevant, pathways, that, over, represented, your, data, possible, initi. PathVisio is a free open source pathway analysis and drawing software It allows drawing editing and analyzing biological pathways Visualization of ones experimental data on the pathways for finding relevant pathways that are over represented in your data set is possible 1 2 3 Initial release2008Stable release3 3 0 January 28 2018Repositorygithub wbr com wbr PathVisioWritten inJavaOperating systemAny Java based TypePathways editing analysis visualizationLicenseApache 2 0Websitewww wbr pathvisio wbr orgPathVisio provides a basic set of features for pathway drawing analysis and visualization 4 5 Additional features are available as plugins Contents 1 History 2 Features 3 References 4 External linksHistory EditPathVisio was created primarily at Maastricht University and Gladstone Institutes 6 The software is developed in Java and it s also used as part of the WikiPathways framework as an applet 7 Starting from version 3 0 released in 2012 plugins are OSGi compliant and a plugin directory describing them was developed In 2015 version 3 2 was released This was the first signed version with a certificate issued by a certification authority Many of the running issues introduced by java 1 7 and 1 8 with the new security rules were solved Since 2013 a javascript version PVJS is being developed to replace the applet From 2015 it also allows small edits and in the future it will be a full editor Features EditPathway drawing and annotation 8 Pathway analysis 9 Integration with WikiPathways for easy editing publishing Integration with Cytoscape 10 Integration with other programming languages via PathVisioRPC 11 References Edit What is PathVisio Archived from the original on 23 September 2013 Retrieved 19 September 2013 van Iersel Martijn P Kelder Thomas Pico Alexander R Hanspers Kristina Coort Susan Conklin Bruce R Evelo Chris 2008 Presenting and exploring biological pathways with PathVisio BMC Bioinformatics 9 1 399 doi 10 1186 1471 2105 9 399 ISSN 1471 2105 PMC 2569944 PMID 18817533 Kutmon Martina van Iersel Martijn P Bohler Anwesha Kelder Thomas Nunes Nuno Pico Alexander R Evelo Chris T Murphy Robert F 23 February 2015 PathVisio 3 An Extendable Pathway Analysis Toolbox PLOS Computational Biology 11 2 e1004085 Bibcode 2015PLSCB 11E4085K doi 10 1371 journal pcbi 1004085 PMC 4338111 PMID 25706687 Jaiswal Pankaj Usadel Bjorn 2016 Chapter 4 Plant Pathway Databases Plant Bioinformatics Springer pp 71 87 ISBN 978 1 4939 3166 8 Habermann Bianca Villaveces Jose Koti Prasanna June 2015 Tools for visualization and analysis of molecular networks pathways and omics data Advances and Applications in Bioinformatics and Chemistry 8 11 22 doi 10 2147 AABC S63534 PMC 4461095 PMID 26082651 About Core development team Archived from the original on 23 February 2014 Retrieved 10 February 2014 Pico AR Kelder T van Iersel MP Hanspers K Conklin BR et al 22 July 2008 WikiPathways Pathway Editing for the People PLOS Biology 6 7 e184 doi 10 1371 journal pbio 0060184 PMC 2475545 PMID 18651794 Tutorial 1 Drawing and annotating pathways in PathVisio Archived from the original on 2015 11 25 Retrieved 2015 11 24 Tutorial 2 Analyzing experimental data in PathVisio data import visualization and statistics Archived from the original on 2015 11 25 Retrieved 2015 11 24 Kutmon Martina Lotia Samad Evelo Chris T Pico Alexander R 2014 WikiPathways App for Cytoscape Making biological pathways amenable to network analysis and visualization F1000Research 3 152 doi 10 12688 f1000research 4254 1 ISSN 2046 1402 PMC 4168754 PMID 25254103 Bohler Anwesha Eijssen Lars M T van Iersel Martijn P Leemans Christ Willighagen Egon L Kutmon Martina Jaillard Magali Evelo Chris T 2015 Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment BMC Bioinformatics 16 1 267 doi 10 1186 s12859 015 0708 8 PMC 4546821 PMID 26298294 External links EditOfficial website PathVisio on Twitter Retrieved from https en wikipedia org w index php title PathVisio amp oldid 1173390958, wikipedia, wiki, book, books, library,
