Interactive display of molecular pathways and dynamics
As research progression of bioinformatics study expands, there is a growing demand to create platforms which can undertake roles to assist research analysis and network visualization. Interaction networks and biological data are getting more sophisticated in the gene expression profiles and expressi...
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| Format: | Final Year Project (FYP) |
| Language: | English |
| Published: |
2012
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| Online Access: | http://hdl.handle.net/10356/48529 |
| _version_ | 1826109781659615232 |
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| author | Lee, Tat Loon. |
| author2 | Rajapakse Jagath Chandana |
| author_facet | Rajapakse Jagath Chandana Lee, Tat Loon. |
| author_sort | Lee, Tat Loon. |
| collection | NTU |
| description | As research progression of bioinformatics study expands, there is a growing demand to create platforms which can undertake roles to assist research analysis and network visualization. Interaction networks and biological data are getting more sophisticated in the gene expression profiles and expression data, thus it will be fruitful to have a software system that is able to query networks and visually integrate networks.
In this project, an interactive display of molecular pathways is proposed to further aid biological network research through the design of a plugin using open-source software: Cytoscape.
The software plugin for Cytoscape is designed to handle merging of networks from file. Manipulation and simulation of the network dynamics of signaling transduction is made possible using Boolean networks. Baynesian network analysis is allowed for user to choose as choice of prior node prediction or basic baynesian analysis results. In this project, to understand and have a better idea of the immune system gene functions, fusing networks of the responsible genes will be used to display relevant activity especially with options to remove certain genes from the set of given genes. These immune system cells consist of genes and with this it will be able to give an overall view of how the remaining genes would link up in a gene network.
Removal of nodes in a given network is part of the scope of work and estimating the dynamics, network strength according to the network interaction is important.
The report concludes by suggesting improvements and features which can be enhanced better for future versions of the software plugin. |
| first_indexed | 2024-10-01T02:23:56Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/48529 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:23:56Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | ntu-10356/485292023-03-03T20:48:55Z Interactive display of molecular pathways and dynamics Lee, Tat Loon. Rajapakse Jagath Chandana School of Computer Engineering DRNTU::Engineering::Computer science and engineering::Information systems::Information interfaces and presentation DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences As research progression of bioinformatics study expands, there is a growing demand to create platforms which can undertake roles to assist research analysis and network visualization. Interaction networks and biological data are getting more sophisticated in the gene expression profiles and expression data, thus it will be fruitful to have a software system that is able to query networks and visually integrate networks. In this project, an interactive display of molecular pathways is proposed to further aid biological network research through the design of a plugin using open-source software: Cytoscape. The software plugin for Cytoscape is designed to handle merging of networks from file. Manipulation and simulation of the network dynamics of signaling transduction is made possible using Boolean networks. Baynesian network analysis is allowed for user to choose as choice of prior node prediction or basic baynesian analysis results. In this project, to understand and have a better idea of the immune system gene functions, fusing networks of the responsible genes will be used to display relevant activity especially with options to remove certain genes from the set of given genes. These immune system cells consist of genes and with this it will be able to give an overall view of how the remaining genes would link up in a gene network. Removal of nodes in a given network is part of the scope of work and estimating the dynamics, network strength according to the network interaction is important. The report concludes by suggesting improvements and features which can be enhanced better for future versions of the software plugin. Bachelor of Engineering (Computer Science) 2012-04-25T09:04:39Z 2012-04-25T09:04:39Z 2012 2012 Final Year Project (FYP) http://hdl.handle.net/10356/48529 en Nanyang Technological University 51 p. application/pdf |
| spellingShingle | DRNTU::Engineering::Computer science and engineering::Information systems::Information interfaces and presentation DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences Lee, Tat Loon. Interactive display of molecular pathways and dynamics |
| title | Interactive display of molecular pathways and dynamics |
| title_full | Interactive display of molecular pathways and dynamics |
| title_fullStr | Interactive display of molecular pathways and dynamics |
| title_full_unstemmed | Interactive display of molecular pathways and dynamics |
| title_short | Interactive display of molecular pathways and dynamics |
| title_sort | interactive display of molecular pathways and dynamics |
| topic | DRNTU::Engineering::Computer science and engineering::Information systems::Information interfaces and presentation DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences |
| url | http://hdl.handle.net/10356/48529 |
| work_keys_str_mv | AT leetatloon interactivedisplayofmolecularpathwaysanddynamics |