Temporal Insights into Microbial Ecology
TIME is a web application which enables microbiome researchers to visually explore, make logical inferences, and gather insights from time series microbiome datasets. TIME has been designed with a user friendly graphical interface. The intuitive and interactive mouse operations allow the end users to visually explore the datasets and discern the underlying biological interactions of the habitat. In addition, the generated plots as well as the tables can be easily downloaded for publication or further analysis.
The TIME web application is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples defined by a series of longitudinal time points along with their metadata information can be analyzed. The web server implements several popular methods as well as introduces a novel method to cluster time series data and interactively visualize the same. Such clustering information pertaining to the inherent taxonomic groups augmented with their stationary information are used to further predict the competition and other community statistics. Variations within a sample can also be interactively visualized and analyzed across a timeline. Additionally, we introduce a ‘causality graph analysis’ module which allow predicting taxa that might have a higher influence on community structure in different perturbed states. TIME allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis from a selected range of time points (defined in the metadata) for the chosen samples. You can explore the utility of various available features in TIME using the provided three published time series microbiome datasets.
"TIME" software application is free for academic, non-profit use. In case you are interested to use "TIME" for commercial use, please contact the authors of the manuscript.
Within any publication that uses any methods or results inspired by "TIME", please cite:
Baksi KD, Kuntal BK, Mande SS. “"TIME"”: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data. Frontiers in Microbiology. 2018;9:36. doi:10.3389/fmicb.2018.00036.
"TIME" SOFTWARE TOOL IS NOT INTENDED TO BE USED FOR TREATING OR DIAGNOSING HUMAN SUBJECTS.
"TIME" or any documents available from this server ARE PROVIDED AS IS WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESS, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND FREEDOM FROM INFRINGEMENT, OR THAT "TIME" or any documents available from this server WILL BE ERROR FREE.
In no event will the authors, their employers or any of the lab/office members be liable for any damages, including but not limited to direct, indirect, special or consequential damages, arising out of, resulting from, or in any way connected with the use of "TIME" or documents available from this server.
The authors will try their best to maintain the privacy and confidentiality of the uploaded user data and will not use the data for any work directly or indirectly except for software debugging purpose.
| Library | Language | License |
|---|---|---|
| Numpy 1.13 | Python 2.7 | Link |
| Scipy 0.19.1 | Python 2.7 | Link |
| Pandas 0.19.1 | Python 2.7 | Link |
| Statsmodels 0.8.0 | Python 2.7 | Link |
| Scikit-learn 0.17.1 | Python 2.7 | Link |
| Matplotlib 1.3.1 | Python 2.7 | Link |
| Seaborn 0.8.1 | Python 2.7 | Link |
| Dygraphs | JavaScript | Link |
| D3 | JavaScript | Link |
| Responsive Heatmap | JavaScript | Link |
| phylotree | JavaScript | Link |