1. Co-ordination & Harmonisation of Advanced e-Infrastructures for Research and Education Data Sharing Research Infrastructures – Proposal n. 306819 Plant Tissue Culture Simulation (Plantisc) CHAIN-REDS School on SGs – 11 June 2014 Roberto Barbera – University of Catania and INFN - Italy (roberto.barbera@ct.infn.it)roberto.barbera@ct.infn.it

2. Introduction  Plant Tissue culture is a method for plant propagation under in vitro conditions  Different types and parts of plants (known as explants) may be cultivated in vitro. These may be organs (roots, stems, shoot tips, leaves and fruits); tissues; cells (suspension cultures) and special tissues and organs such as embryos, canthers, pollen and protoplasts  Plant tissue culture is time and material intensive, running into several months of laboratory efforts in trying to build hormonal combinations that will be best for mass propagation of a particular species CHAIN-REDS School on Science Gateways - 11 June 2014 2

3. Introduction  Potentially, modeling or computer simulation can provide a useful method for gaining insight into these complex processes by reducing the time needed to screen numerous hormonal combinations.  Plantisc is a simulation application based on multiple regression models deployed on a grid computing infrastructure  The application simulates the plant tissue culture experiments and predicts the amount and combinations of auxins and cytokinins needed to yield optimal growth of propagules  The results obtained from the simulation show over 67% prediction accuracy as compared to the laboratory experiments CHAIN-REDS School on Science Gateways - 11 June 2014 3

4. Partners and context  University of Nigeria Nsukka (Nigeria)  Faculty of Biological Sciences, Plant Science and Biotechnology Dept.  Faculty of Physical of Physical Sciences, Computer Science Dept,  Plant Tissue Culture laboratory of National Root Crops Research Institute, Umudike, Umuahia, Abia State  New York State University (USA)  Department of Technical Vocational Education  Application developed within the UNESCO – HP Brain Gain Project  Contact:  Dr Collins Udanor, University of Nigeria Nsukka, collins.udanor@unn.edu.ng 4

5. Software design  Matrix formulation of a linear regression model used to estimate the yields of the propagules CHAIN-REDS School on Science Gateways - 11 June 2014 5

6. Software implementation  In the implementation Python has been used as programming language because of its ability to handle the manipulation of data, even at large scale  This provides the ability efficiently perform the matrix operations required in less time  With the help of python libraries such as NumPy and SciPy, matrix operations were handled and results confirmed to be accurate CHAIN-REDS School on Science Gateways - 11 June 2014 6

7. Software implementation  From the model equation (v) in slide 5, existing data obtained from real case experiment were used to obtain β values and assuming ε to be 0 at all times in equation (vi), one can easily predict the outcome of the yield of propagules (  ) with a given combination of growth hormones ( χ 1 and χ 2)  750 test cases were used for the estimation of the β values CHAIN-REDS School on Science Gateways - 11 June 2014 7

8. Example of results CHAIN-REDS School on Science Gateways - 11 June 2014 8 More at: Florence I. Akaneme et al., A Grid-enabled Application for the Simulation of Plant Tissue Culture Experiments, International Journal of Advanced Computer Science and Information Technology (IJACSIT), Vol. 3, No. 3, 2014, Page: 227-242, ISSN: 2296-1739 - © Helvetic Editions LTD, Switzerland - www.elvedit.com

9. Some screenshots (the home page) CHAIN-REDS School on Science Gateways - 11 June 2014 9

10. Some screenshots (file upload) CHAIN-REDS School on Science Gateways - 11 June 2014 10

11. Some screenshots (file listing) CHAIN-REDS School on Science Gateways - 11 June 2014 11

12. Some screenshots (input page) CHAIN-REDS School on Science Gateways - 11 June 2014 12

13. Some screenshots (output page) CHAIN-REDS School on Science Gateways - 11 June 2014 13

14. Co-ordination & Harmonisation of Advanced e-Infrastructures for Research and Education Data Sharing Research Infrastructures – Proposal n. 306819 Questions ?