Computational Core for Plant Metabolomics (CCPM)
Welcome to CCPM!
CCPM provides a secure repository and analysis pipeline for metabolomics data and associated information. Separate modules have been designed for preprocessing, Pre-treatment and statistical analysis integrated with visualization tools. To access this database, one must register and get an account & password. There are published projects for registered users to view, analyze and download.
To create a new project and deposit data (unpublished) one needs to get access as Principal Investigator (PI). For this direct request to be sent to system Owner/PI of CCPM. Please note that only PI has the right to create new project, delete/modify and publish existing projects. Please check “User Manual” to learn how to use CCPM. We regularly organize workshops to familiarize users with CCPM.
Please check “Events” for upcoming workshops.
If CCPM was useful to you, please acknowledge by directly citing the web address: http://metabolomics.iiit.ac.in/
Our team is working on integration of other omics-based datasets (genomics, transcriptomics and proteomics) with CCPM to facilitate biological interpretation of the data and pathway analysis. Stay tuned for the updates!
Computational Core for Plant Metabolomics (CCPM) is a multi – institutional collaborative project, funded by the Department of Biotechnology, Govt. of India, being carried out at two institutes: IIIT Hyderabad and JNU, New Delhi. The objectives are the following:
- Develop a data repository which can capture, secure and serve metabolomic data
- Provide tools and metabolomics web resources for analysis of the data
- Provide connectivity for integration of metabolomics data with genomic, transcriptomic and proteomic databases
The functionalities of this portal are organized using a modular architecture.
- Module I is for data uploading. This module enables capture of raw instrumental data and associated metadata about the sample source, handling, about the instruments used along with their specifications, and parameter settings. Multiple raw files can also be uploaded simultaneously using 'Bulk upload' option.
Module II has two functionalities viz. data preprocessing and filtering and metabolite identification, with separate sub modeules for handling hyphenated MS and NMR data respectively:
- Preprocessing of raw instrumental data to remove noise and redundancies and to extract relevant information to enable visualization of the preprocessed data in terms of quantitative multiple group wise comparison, generation of peak list, filtering of peak list, identification of significant peaks, and linking peak list data to metabolite databases.
- Identification of metabolites from peak list data. This includes connectivity to GOLM and METLIN can be used directly by the user from their website (due to licensing issue) for MS data.
- Preprocessing (Binning) of untreated raw NMR spectral data in text format using binning feature.
- Metabolite identification interface searching two major publicly available NMR database (HMDB: Human Metabolome Database and MMCD: Madison Metabolomics Consortium Database) in background to display the result output from the selected database based on user input parameters.
Module III is for data analysis. The functionalities may be summarized as follows:
- Data pre-treatment and transformation
- Statistical analysis of metabolite data
- Generation of metabolites correlation edge list for network visualization.
- Comparisons of multiple groups during statistical analysis.
Module IV is for KEGG pathways visualization. The module deals with uploading a list of metabolites along with fold-change/p values (optional) to retrieve the associated KEGG pathways. The fold-change/p values can be used for rendering the visualization of pathway maps.
Privileges for Registered Users
- A registered user may browse data and analysis results reported in projects that have been published in this portal. Currently the published projects mainly contain data from published papers available in the net.
- Registered users, after appropriate approval, may also create their own projects and carry out operations corresponding to the currently completed and functional modules. Such projects will be stored as ‘Unpublished’ projects and will be visible only to the ‘Owner’ of the project, or to those who have been explicitly permitted by the ‘Owner’. Please register and browse ‘Help’ for further details.