Workshop-2

“CCPM-2013”  was one day workshop held at two places (IIIT Hyderabad on November 15 and JNU Delhi on November 20, 2013), was organized to introduce a prototype of the LIMS platform to its potential users. Invitations were sent well in advance to most of the Plant Metabolomics network partners in India. Each potential participant was contacted and given an option to choose a place (Hyderabad/ New Delhi) of their convenience for workshop participation.

About 40 representatives from various laboratories such as, Prof. R. P. Sharma’s lab and Department of Plant Sciences - HCU, Division of Biochemistry & Physiology - Indian Institute of Horticultural Research and Vittal Mallya Scientific Research Foundation (VMSRF) - Bangalore, BASF – Kolkata, SC&IS, SLS and Stress Physiology & Molecular Biology Laboratory - JNU, National Institute of Plant Genome Research – New Delhi, Bioinformatics Centre and Plant Genomics Lab – University of Jammu, Department of Plant Pathology, TNAU – Coimbatore, CSIR IHBT – Palampur participated actively and enthusiastically.

Workshop Agenda/Activities:


  1. Inauguration speech by the Director of IIIT

  1. Presentation regarding the prototype

  • Current platform, database model and software architecture was detailed.

  • Emphasis on the features such as access rights, security layers & authentication etc., highlighted.

  • Framework and basis for data preprocessing algorithms used, and the advantages of using R scripts have been shown and explained.

  • Additional features and functionalities developed (Bulk upload of metadata for a group of samples using a pre-populated .csv template. Data preprocessing and comparative analysis of LC-MS data, Link provided to METLIN for metabolite identification) since the last workshop CCPM 2012, were also emphasized.

  • Flexibility and customization capabilities of the prototype was described.

  • Run through the important pages of the portal bringing out some of the important field level information.

  1. Demonstration of the prototype


(A)with already uploaded (Arabidopsis Thaliana data set) as example data

  • Meta data single sample upload.

  • Automatic bulk upload of Meta data to populate into samples under groups and Project.

  • Pre-processing of raw LC-MS data and visualization of output files and plots thus generated.


(B)How to populate the meta (single & bulk) and raw data and also to preprocess raw LC-MS data as an example.

  • Meta data single sample upload.

  • Automatic bulk upload of Meta data to populate into samples by filling an empty template file.

  • Pre-processing of raw LC-MS data and visualization of output files and plots thus generated.

  1. Hands on training for all the participants.

  • User documents were provided.

  • All the participants were given systems to upload their data.

  • Individual attention was given to each and every participant and doubts were clarified by all the volunteers regarding.

  1. Feed Back / Discussion session.

  • Apart from online feedback form on each and every page on the prototype, questions were raised and deliberated more in detail.



Workshop Brochure: click here to view the brochure.



Invitation: click here to view the invitation letter



Feedback: click here to view the feedback by participants



List of participants:

  1. Dr. Keshava Rao

  2. Mr. Prateek Gupta

  3. Dr. Rameshwaram Sharma

  4. Ms. Kilambi Himabindu Vasuki

  5. Mr. Kamal Tyagi

  6. Dr. Vajir Tamboli

  7. Ms. Supriya Sarma

  8. Mr. Reddaiah Bonanapu

  9. Ms. Pallawi Upadhyaya

  10. Dr. Abhijit Mitra

  11. Dr. Nita Parekh

  12. Dr. Vikram Pudi

  13. Dr. Geeta Y

  14. Dr. Narendra Babu K

  15. Mrs. Suvarna Shenvi

  16. Mr. Raghava T.

  17. Ms. Veena Shinde

  18. Ms. Prashanti Dharanipragada

  19. Ms. Hymavathi

  20. Ms. Sapna Devi

  21. Mr. Rakesh Kumar

  22. Mr. Kapil Sharma

  23. Ms. Hanjabam Mickey

  24. Ms. Preeti Pandey

  25. Dr. Darba Ghoshal

  26. Ms. Nidhi Sharma

  27. Ms. Soumya Smita

  28. Dr. Jeremy Dkhar

  29. Dr. Ashwni Pareek

  30. Mr. Mohit Sharma

  31. Mr. Vikramjit Mandal

  32. Mr. Nishant Gupta

  33. Dr. Paranidharan

  34. Ms. Kanika Narula

  35. Mr. Khalid Anwar

  36. Mr. Roshan Kumar

  37. Dr. Nita Lakra

  38. Prof. Indira Ghosh

  39. Mr. Amit Kumar



Follow up action plan to contribute further to the project’s objectives:

The suggestions and feedback from the participants at both the places were formulated and categorized. Incorporation of these suggestions is in the completion phase.



Conclusions:

The one day workshops at both the places were successful. The value added suggestions had enabled us to improve the prototype development.