[AgMIP] Online tutorials Tues 1700GMT, Fri 0900GMT on Arabidopsis Framework Model

[agmip at lists.agmip.org]

For plant modellers,

We are now using our whole-plant Framework Model to understand how the gene circuit of the circadian clock affects plant physiology. This is the work I presented at the Wheat modelling meeting in Clermont Ferrand, and Yin Hoon brought to the MACSUR meeting last February. 

So far as we know there is no other such model for Arabidopsis growth. One version of the model was created in a user-friendly simulation environment, specifically for non-modellers to simulate and test hypotheses. We're offering real-time tutorials online to help you to use this model - please see below and in the attached PDF.

The software grows an Arabidopsis plant 'live' on screen, so it also has some potential as a teaching tool. A lot of plant physiology is included (often in a very simplified form) in the four models that Yin Hoon Chew combined to make the Framework Model: 
-photosynthesis and starch/sugar partitioning, 
-source-sink partitioning at the organ level in the rosette, 
-control of development by ambient temperature, vernalisation and photoperiod,
-control of photoperiodism by the circadian clock (of course!).

All the instructions are already public in our PlaSMo resource, see below, but sometimes it's also helpful to have a 'live' demonstration with an opportunity to ask questions. Based on these sessions, we'll record a version that addresses the most common points and make it public.

Best wishes,
Andrew


From: News and Discussion from/for the UK Arabidopsis and wider plant community [mailto:ARABUK at JISCMAIL.AC.UK] On Behalf Of MILLAR Andrew
Sent: 14 November 2014 09:22
To: ARABUK at JISCMAIL.AC.UK
Subject: Online Tutorials on the Arabidopsis Framework Model

SynthSys Hands-on Tutorials on the Arabidopsis Framework Model 
for plant scientists, 2 and 5 December 2014.

What limits the size and mass of a growing plant? How would your experimental plants grow under different conditions? Simulate and see! 

Whether you are a plant scientist with no modelling experience or a mathematical modeller new to plant science, our simulation model has a user-friendly interface and an animation of the growing plant to get you started. Please see the attached PDF for all the details.

Aim: Our online tutorials are intended for plants scientists, systems biologists and modellers interested in running the Arabidopsis Framework Model (recently published as Chew et al., PNAS 2014; http://dx.doi.org/10.1073/pnas.1410238111). Participants will run the model on their own computers, in the free version of the graphical modelling software Simile.  You will learn protocols that alter environmental conditions such as light and temperature, and the genotype of the plant, together with some pointers on working with your results. 

Times: We are running two online sessions. Join us at ONE of the sessions below: 
Tuesday 2nd December 2014 (17:00 - 18.30 GMT): EU and Americas.
Friday 5th December 2014 (09:00 - 10.30 GMT): Europe, Africa and Asia.

Contacts
Ms. Julie Fyffe, J.Fyffe at ed.ac.uk; @CSBEd (for questions about the web conferencing)
Dr. Yin Hoon Chew, YinHoon.Chew at ed.ac.uk (for questions about the model details)
Prof. Andrew J. Millar, Andrew.Millar at ed.ac.uk; @A_J_Millar (for questions about the tutorial)

Prof. Andrew Millar FRS
SynthSys 
University of Edinburgh
C.H. Waddington Building
King's Buildings
Edinburgh EH9 3JD
UK

+44 131 651 3325
www.amillar.org; www.synthsys.ed.ac.uk



-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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