= Workshop: Metabolic Modelling and its Applications = === 27 - 30 June 2016 === == Tribhuvan University, Kirtipur, Kathmandu, Nepal == . The workshop is organised by Tribhuvan University and the Society for Biological Applications Nepal (SBAN). . . {{http://mudsharkstatic.brookes.ac.uk/Graphics/Tribhuvan University.png|University logo|align="top",height="200",width="192"}} {{http://mudsharkstatic.brookes.ac.uk/Graphics/SBAN.png|SBAN logo|align="top",height="150",width="295"}} . A brief introduction to the workshop is available on the website for the [[http://sbanepal.com/events/|SBAN]]. ==== Tutors ==== . The course is presented by: * Dr Mark Poolman * Prof David Fell * Kailash Adhikari, and * Dipali Singh . all of Oxford Brookes University, Oxford, UK. Examples presented in the workshop will include results from their research, which has been funded by the EU via the !AccliPhot project and the BBSRC (UK). . {{http://mudsharkstatic.brookes.ac.uk/Graphics/brookes.jpg|brookes logo|align="bottom",height="100",width="243"}} {{http://mudsharkstatic.brookes.ac.uk/Graphics/accliphot-logo.png|accliphot logo|align="bottom",height="90",width="352"}} {{http://mudsharkstatic.brookes.ac.uk/Graphics/bbsrc_new.png|bbsrc logo|height="80",width="319"}} ==== Application ==== . To apply for the workshop, complete the registration form an the [[http://sbanepal.com/events/|SBAN website]]. If the workshop is over-subscribed, successful applicants will be selected and notified. ==== Instructions for workshop attendees ==== . You are required to bring a laptop to the workshop. The metabolic modelling package used in the course, [[http://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]], will be made available to you. The two options for installing !ScrumPy on your computer are to directly install the package on a suitable Linux operating system, or to run a virtual machine under other operating system. Instructions are [[Meetings/Nepal2016/ScrumPyInstall|here]]. ) ==== Timetable ==== . To help plan your attendance, the provisional workshop timetable is given below. The precise content and order of topics may be changed - even during the workshop itself! ||'''Day''' ||'''Time''' ||'''Room''' ||'''Activity''' ||'''Resources''' ||'''Who''' || ||Mon 27th, AM ||10:30 || ||Arrival and registration || ||SBAN || ||11:00 || ||Welcome talks || ||MP + TU || ||11:30 || ||'''Talk:''' Introductory theory ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L1/Slides.pdf|Slides]] ||MP || ||12:30 || ||Lunch || ||All || ||Mon 27th, PM ||14:00 || ||'''Talk:''' Python, object-orientation and models. ||[[http://mudsharkstatic.brookes.ac.uk/Pune2016/L2/Slides.pdf|Slides]] ||MP || ||15:00 || ||'''Practical 0:''' Checking !ScrumPy Installation and familiarisation with the Python language. ||[[Meetings/Nepal2016/P0|Instructions]] ||All || ||17:30 || ||Close || || || ||Tue 28th, AM ||09:30 || ||'''Talk:''' Structural analysis of small models. (+ break) ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L3/Slides.pdf|Slides]] ||DF || ||11:00 || ||'''Talk: '''Introduction to plant metabolism and its modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L4/Slides.pdf|Slides]] [[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L4a/Slides.pdf|Slides2]] ||DS, KA, MP || ||12:30 || ||Lunch || || || ||Tue 28th, PM ||14:00 || ||'''Practical 1''': Structural analysis of small models ||[[Meetings/Nepal2016/P1|Instructions]] ||All || ||17:00 || ||Close || || || ||Wed 29th, AM ||09:30 || ||'''Talk:''' Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L5/Slides.pdf|Slides]] ||DF || ||10:15 || ||'''Talk:''' Construction of Genome-Scale Models ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L6/Slides.pdf|Slides]] ||MP || ||11:15 || ||'''Talk:''' Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L7/Slides.pdf|Slides]] ||MP || ||12:30 || ||Lunch || || || ||Wed 29th, PM ||14:00 || ||'''Practical 2'''''':''' Construction of a working !ScrumPy model from databases ||[[Meetings/Nepal2016/P2|Instructions]] ||All || ||15:30 || ||'''Practical 3'''''':''' Flux Balance Analysis of a simple model ||[[Meetings/Nepal/P3|Instructions]] ||All || ||17:00 || ||'''Close''' || || || ||Thur 30^th^, AM ||09:30 || ||'''Talk:''' Biotechnological Applications of Metabolic Network Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L8/Slides.pdf|Slides]] ||DF || ||10:30 || ||'''Talk:''' Genome scale modelling of Arabidopsis ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L9/Slides.pdf|Slides]] ||KA || ||11:30 || ||'''Talk:''' Genome scale modelling of a diatom for oil production ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2016/L10/Slides.pdf|Slides]] ||DS || ||12:30 || ||Lunch || || || ||Thur 30^th^, PM ||14:00 || ||'''Practical 4: '''GSM of Arabidopsis – metabolic phenotypes of mutants – metabolic responses to light intensity ||[[Meetings/Nepal2016/P4|instructions]] ||All || ||16:30 || ||Concluding remarks and presentation of certificates || ||All || ||17:00 || ||'''Close of the Workshop''' || || ||