“CCPM4 November 2014” was one day workshop held at two places (IIIT Hyderabad and JNU New Delhi) on 17 November, 2014, both online and physical), was organized to demonstrate the functionalities which are available, in the latest release of the CCPM LIMS platform, to the potential users. Invitations, with link to the Information Brochure and the registration portal were sent to DBT experts and to DBT Plant Metabolomics network partners in India. Participants were given an option to choose a mode (online / physical) as well as place (Hyderabad/ N. Delhi) of their convenience for workshop participation.
Apart from a demonstration, the Agenda included a hands-on tutorial session to familiarize the potential users with the navigation and the workflow involved in accessing the functionalities, and to take their feedback. The workshop was concluded with a detailed discussion involving DBT experts and other participants. While highlighting the inherent potential and the importance of the CCPM portal, the discussions served as a critical review of the current release.
Several concrete suggestions emerged, regarding immediate steps that are needed to achieve the project objective of creating a fully functional, reliable and user friendly platform, adhering to international standards, which can induce confidence in the users to upload their experimental data for analysis.
Functionality of the current portal
As detailed in the SOP, the portal follows a modular workflow, involving three modules, to process a raw input data-set up to the identification of metabolites which can then be linked with the pathways they occur in. Module I includes the capture of raw (instrumental) data on samples along with associated metadata. Module II preprocesses the raw data for generating the peak list and facilitates the identification of metabolites by providing connectivity to different chemical prediction databases. Module III carries out data normalization and transformation for statistical analysis of metabolite data and is being developed to provide connectivity to Genomics, Transcriptomics, Proteomics and Pathway related resources. The following new functionalities were introduced in this workshop:
Versioning of the projects
Links to the GOLM database to identify metabolites
Different algorithms for Statistical analysis of the data
Enhanced protection of the uploaded data
Suggestions and feedback related to look feel and user friendliness of the portal
Transformation of GUI is needed to make the portal more user-friendly.
A permanent workshop/tutorial portal, to provide full instruction for easy analysis using CCPM portal, should soon be implemented, in addition to the tutorial, help and demo provided for in the current portal
Data security and assigning of quota/ space for repository on CCPM portal
Frequent data backup should be taken on daily, weekly and monthly basis.
Identification and allotment of PI list should be done with allotment of space to different PI. Defined quota will be given to every PI and upon request additional space will be provided.
Experts and other participants were happy with the data protection features that are currently incorporated in the portal.
Awareness of the CCPM portal
The PIs were urged to publish about the CCPM portal in some reputed journal so that it is acknowledged internationally and its standards are recognized. Researchers using the portal can thus cite it in their publications. This would also help to increase awareness of the CCPM portal among experimentalists.
Feedback on functional enhancement of the CCPM portal
Implementation of comparative metabolite identification, by two methods and integration of pathway networks, should be taken up urgently.
Plans are ready for connecting metabolomics data to other web servers and databases which provide connectivity to transcriptomics, proteomics and genomics databases. PlantCYC is one of the options which, however, does not take care of new repositories.
It was clarified that though mapping can only be done with the known pathways & metabolites, it is possible to make the provision for users to upload new data for archiving, if required.
Answering a request to experimentalists, Dr. Arun (experimentalist) from DU provided the feedback. They are expecting that the available web links to Genomics, Transcriptomics and Proteomics resources associated with Plants are to be integrated with the pathway information.
Discussions on the next workshop and beyond:
The next workshop CCPM5 was tentatively proposed to be held in February 2015, after addressing the following issues.
The portal needs to be made fully functional. Dr. Sanjay Singh & Dr. Munshi commented on several issues, related to the GUI and its user friendliness, which need to be addressed.
Implementation and testing of the remaining statistical methods need to be completed.
Identified metabolites need to be connected / linked to pathways and Omics resources like genomics, transcriptomics and proteomics.
It was suggested that the project should be revised after completion and it should continue working in future.
In this regards there was a suggestion to organize a Metabolomics Symposium/Workshop in June 2015, where researchers from metabolomics groups in India could be invited to discuss the future proposal regarding the project/portal.
Workshop Brochure: click here to view the brochure
Invitation: click here to view the invitation letter
Agenda: click here to view the Agenda
List of Attendees: click here to view the List of Attendees
The one day workshop at both the places was successful and provided value added suggestions. It was hoped that the rate of progress, in terms of implementation of the project, would improve further, and that the ACTUAL FUNCTIONAL CCPM would be launched in January 2015 for testing.