Computational Core for Plant Metabolomics: A Case for Interdisciplinary Research

摘要

Computational Core for Plant Metabolomics (CCPM) is a web-based collaborative platform for researchers in the field of metabolomics to store, analyze and share their data. Metabolomics is a newly emerging field of 'omics' research that is concerned with characterizing large numbers of metabolites using chromatography, mass spectrometry and NMR. There is abundant volume and variety in the data, with velocity being unpredictable. An interdisciplinary engagement such as this faces significant non-technical challenges solvable using a balanced approach to software management in a university setting to create an environment promoting collaborative contributions. In this paper we report on our experiences, challenges and methods in delivering a usable solution. CCPM provides a secure data repository with advanced tools for analysis including preprocessing, pretreatment, data filtration, statistical analysis, and pathway analysis functions; and also visualization, integration and sharing of data. As all users are not equally IT-savvy, it is essential that the user interface is robust, friendly and interactive where the user can submit and control various tasks running simultaneously without stopping/interfering with other tasks. In each stage of its pipeline architecture, users are also allowed to upload external data that has been partially processed till the previous stage in other platforms. Use of open source softwares for development makes the maintenance and development of our modules easier than the others which depend on proprietary softwares.