Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations
The affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper, we pre...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-02-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00288/full |
| _version_ | 1818573715405799424 |
|---|---|
| author | Bhusan K. Kuntal Bhusan K. Kuntal Bhusan K. Kuntal Chetan Gadgil Chetan Gadgil Chetan Gadgil Sharmila S. Mande |
| author_facet | Bhusan K. Kuntal Bhusan K. Kuntal Bhusan K. Kuntal Chetan Gadgil Chetan Gadgil Chetan Gadgil Sharmila S. Mande |
| author_sort | Bhusan K. Kuntal |
| collection | DOAJ |
| description | The affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper, we present Web-gLV—a GUI based interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations. We also demonstrate the utility of our tool on few publicly available datasets. The case studies demonstrate the ease with which the current tool can be used by biologists to model bacterial populations and simulate their dynamics to get biological insights. We expect Web-gLV to be a valuable contribution in the field of ecological modeling and metagenomic systems biology. |
| first_indexed | 2024-12-15T00:16:08Z |
| format | Article |
| id | doaj.art-37703be3794d449cb3d926fa4d4eb885 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-15T00:16:08Z |
| publishDate | 2019-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-37703be3794d449cb3d926fa4d4eb8852022-12-21T22:42:28ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-02-011010.3389/fmicb.2019.00288428845Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial PopulationsBhusan K. Kuntal0Bhusan K. Kuntal1Bhusan K. Kuntal2Chetan Gadgil3Chetan Gadgil4Chetan Gadgil5Sharmila S. Mande6Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, IndiaCSIR-National Chemical Laboratory, Chemical Engineering and Process Development Division, Pune, IndiaCSIR-National Chemical Laboratory, Academy of Scientific and Innovative Research, Pune, IndiaCSIR-National Chemical Laboratory, Chemical Engineering and Process Development Division, Pune, IndiaCSIR-National Chemical Laboratory, Academy of Scientific and Innovative Research, Pune, IndiaCSIR-Institute of Genomics and Integrative Biology, New Delhi, IndiaBio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, IndiaThe affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper, we present Web-gLV—a GUI based interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations. We also demonstrate the utility of our tool on few publicly available datasets. The case studies demonstrate the ease with which the current tool can be used by biologists to model bacterial populations and simulate their dynamics to get biological insights. We expect Web-gLV to be a valuable contribution in the field of ecological modeling and metagenomic systems biology.https://www.frontiersin.org/article/10.3389/fmicb.2019.00288/fullmicrobiomemodelingnumerical-simulationweb-servertime-seriesvisualization |
| spellingShingle | Bhusan K. Kuntal Bhusan K. Kuntal Bhusan K. Kuntal Chetan Gadgil Chetan Gadgil Chetan Gadgil Sharmila S. Mande Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations Frontiers in Microbiology microbiome modeling numerical-simulation web-server time-series visualization |
| title | Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations |
| title_full | Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations |
| title_fullStr | Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations |
| title_full_unstemmed | Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations |
| title_short | Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations |
| title_sort | web glv a web based platform for lotka volterra based modeling and simulation of microbial populations |
| topic | microbiome modeling numerical-simulation web-server time-series visualization |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.00288/full |
| work_keys_str_mv | AT bhusankkuntal webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT bhusankkuntal webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT bhusankkuntal webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT chetangadgil webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT chetangadgil webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT chetangadgil webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations AT sharmilasmande webglvawebbasedplatformforlotkavolterrabasedmodelingandsimulationofmicrobialpopulations |