NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
Summary: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2017
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| Online Access: | https://hdl.handle.net/10356/85842 http://hdl.handle.net/10220/43851 |
| _version_ | 1811684565857599488 |
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| author | Guo, Jing Lin, Feng Zhang, Xiaomeng Tanavde, Vivek Zheng, Jie |
| author2 | School of Computer Science and Engineering |
| author_facet | School of Computer Science and Engineering Guo, Jing Lin, Feng Zhang, Xiaomeng Tanavde, Vivek Zheng, Jie |
| author_sort | Guo, Jing |
| collection | NTU |
| description | Summary: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming).
Availability and Implementation: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/. |
| first_indexed | 2024-10-01T04:30:39Z |
| format | Journal Article |
| id | ntu-10356/85842 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:30:39Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | ntu-10356/858422021-01-18T04:50:19Z NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential Guo, Jing Lin, Feng Zhang, Xiaomeng Tanavde, Vivek Zheng, Jie School of Computer Science and Engineering Complexity Institute Summary: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming). Availability and Implementation: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/. Published version 2017-10-09T02:22:23Z 2019-12-06T16:11:10Z 2017-10-09T02:22:23Z 2019-12-06T16:11:10Z 2017 Journal Article Guo, J., Lin, F., Zhang, X., Tanavde, V.,& Zheng, J. NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential. Bioinformatics, btx022-. 1367-4803 https://hdl.handle.net/10356/85842 http://hdl.handle.net/10220/43851 10.1093/bioinformatics/btx022 en Bioinformatics https://doi.org/10.21979/N9/IP6DBD © The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com 3 pg. application/pdf |
| spellingShingle | Guo, Jing Lin, Feng Zhang, Xiaomeng Tanavde, Vivek Zheng, Jie NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title | NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title_full | NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title_fullStr | NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title_full_unstemmed | NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title_short | NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
| title_sort | netland quantitative modeling and visualization of waddington s epigenetic landscape using probabilistic potential |
| url | https://hdl.handle.net/10356/85842 http://hdl.handle.net/10220/43851 |
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