SpatioTemporalModellingNetwork - User contributions [en]

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2009-03-23T13:55:09Z

AndrewBangham:

=Spatio-temporal modeling network on plant systems ('''STEMN''')=
'''From observation to theory.'''

{| border="0" cellpadding="5" cellspacing="3" width="550"
|valign="top"|
''Imagine'' clicking on a plant and zooming in to any level of detail. Finding links to experimental observations, to theory and above all to computable models of any or all parts of the plant. Watch growth, differentiation, responses to parasites and much more. Well, it's not yet possible. Why do it? Quite apart from educational merits it would provide evidence that all these things are properly understood and that will help society. A worthwhile goal.

Try clicking on names: right (and add links to your work)
|valign="top"|
<imagemap> Image:Web_page_graphic.png|300px|right
rect 360 209 443 231 [[Clickon_leaves|Leaves]]
rect 352 88 443 115 [[Clickon_flowers|Flowers]]
desc bottom-right
</imagemap>
|}

[[Clickon leaves | Leaves]]
[[Clickon flowers| Flowers]]
[[Clickon reproduction| Reproduction]]
[[Clickon clocks| Clocks]]
[[Clickon growing meristem| Growing meristem]]
[[Clickon Seliques| Seliques]]
[[Clickon Energetics| Energetics]]
[[Clickon Regulation| Regulation]]
[[Clickon Control| Control]]
[[Clickon Signalling| Signalling]]
[[Clickon Differentiation| Differentiation]]
[[Clickon Branching| Branching]]
[[Clickon Root| Root]]
[[Clickon Defence| Defence]]

==Prize: learn a technique by visiting a laboratory==
[[Image:Happy idea.png|thumb|80px|right]]
[[Travel Prize | Travel Prize]] to be won by participants of any of the sponsored workshops. [[Travel Prize | Find out more]].

==[[Summary of STEMN | Summary of STEMN ]]==

==Links==

*[http://garnet.arabidopsis.org.uk/ GARNet] (Genomic Arabidopsis Resource Network)
*[http://www.cellsignet.org.uk/ Signet] Cell Signalling Network
*[http://www.cpib.info/ CPIB] Centre for Plant Integrative Biology
*[http://sites.google.com/a/stompnet.org/stompnet/ SToMP] network is a collaborative research network between mathematical modellers and microbiologists.
*[http://www.genesys.ac.uk/ GENESYS] Promote the required integration between genetics, bioinformatics and mathematics to facilitate the reverse-engineering of regulatory networks
*[http://www.amsta.leeds.ac.uk/Applied/I2M/ I2M] Immunology, Imaging and Modelling
*[http://iplantcollaborative.org/ iPlant] Tackling the 'Grand challenge' of creating a cyberinfrastructure that supports plant biology.
*[http://www.computableplant.org/ Computable Plant] An early start on the challenge.
*[http://algorithmicbotany.org/ L-systems] a classical work of beauty.
*[http://algorithmicbotany.org/virtual_laboratory/ Virtual Laboratory software] plant modelling software.
*[http://www-sop.inria.fr/virtualplants/wiki/doku.php?id=software:plantgl:roadmap Virtual Plants] OpenAlea for plant modelling and analysis. Software toolkit V-Plants, dedicated to the modeling and analysis of plant development at different scales.
*[http://sbml.org/Main_Page Systems Biology Markup Language] computer-readable format for representing models of biochemical reaction networks in software (note spatio-temporal aspects not yet developed).
*[http://fizz.cmp.uea.ac.uk/wiki/DArT_Toolshed/index.php/%22Visualising_Plant_Development_and_Gene_Expression_in_3D_using_Optical_Projection_Tomography%22 3D viewer that uses graphics card accelerator - good for OPT and confocal images] Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography
*[http://fizz.cmp.uea.ac.uk/wiki/DArT_Toolshed/index.php/Main_Page PCA analysis of shapes] Shape model toolbox for analysing 2D shapes (contact Andrew Bangham if you want 3D, stereo or haptics).

==Programme==
Year [[2008]]
[[2009]]
[[2010]]

==Using the Wiki==
Why not start by consulting the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Or consult the sites [[Wikisyntax|Wiki Syntax]] page for information on using the wiki syntax.

==Contacts and acknowledgements==

* [[ContactsList|Contacts]]

* Sponsored by the BBSRC, UK

* The logo (top left) is a reference to [http://www-gap.dcs.st-and.ac.uk/~history/Mathematicians/Thompson_D%27Arcy.html D'Arcy Thompson 'On Growth and Form' 1917]

Clickon leaves

2009-03-23T13:53:24Z

AndrewBangham:

Add your links here. With just four seed points (below) it will start out anarchic, however, a better job will be possible once there are examples.

*Web pages
*Software
*Comment
*Research papers

Clickon flowers

2009-03-23T13:52:56Z

AndrewBangham:

Add your links here. With just four seed points (below) it will start out anarchic, however, a better job will be possible once there are examples.

*Web pages
*Software
*Comment
*Research papers

File:Logo.png

2009-03-23T12:54:57Z

AndrewBangham: uploaded a new version of "Image:Logo.png"

Travel Prize

2009-03-23T12:27:37Z

AndrewBangham: /* Travel Prize */

==Travel Prize==

If you are a participant in any of the workshops or meeting sponsored by STEMN you can enter a competition for a travel prize.

The prize is travel and subsistance for a one or two week laboratory visit that you have arranged as result of the meeting with a view to learning about a new mathematical or computing technique or software. To enter, politely get yourself invited to the host laboratory, write a one page explanation of your work and how it will benefit from the visit (including Figures) and send your entry within two months of the end of the meeting (participants in meetings held before April in 2009 are eligible up to July 2009) to Sue Koria, UEA (sue.koria@uea.ac.uk) PLEASE INCLUDE STEMN in the title

ContactsList

2009-03-22T18:45:20Z

AndrewBangham: New page: Secretary: Sue Koria (suek@cmp.uea.ac.uk) [[http://www.uea.ac.uk/cmp/People/Faculty/J.+Andrew+Bangham?selectedTab=Research Prof. J. Andrew Bangham] [[http://www.maths.nott.ac.uk/director...

Secretary: Sue Koria (suek@cmp.uea.ac.uk)

[[http://www.uea.ac.uk/cmp/People/Faculty/J.+Andrew+Bangham?selectedTab=Research Prof. J. Andrew Bangham]

[[http://www.maths.nott.ac.uk/directory/homepage.php?initials=jrk Prof. John King]]

File:Happy idea.png

2009-03-22T18:36:12Z

AndrewBangham:

2010

2009-03-22T18:21:38Z

AndrewBangham: New page: Provisional programme {| border="1" cellpadding="2" |- |width="120pt" valign="top"| July |width="200pt" valign="top"| Two week workshop on spatio-temporal modelling at UEA and John Innes ...

Provisional programme

{| border="1" cellpadding="2"
|-
|width="120pt" valign="top"| July
|width="200pt" valign="top"| Two week workshop on spatio-temporal modelling at UEA and John Innes Centre, Norwich.
|width="200pt" valign="top"| STEMN,
|width="200pt" valign="top"| This workshop aims to introduce some of the concepts and software used for modelling plant growth and development.
|-
|width="120pt" valign="top"| December
|width="200pt" valign="top"| 4th Mathematics in the Plant Sciences Study Group. University of Nottingham
|width="200pt" valign="top"| CPIB GARNet STEMN
|width="200pt" valign="top"| Introduce mathematics into plant science, form collaborations across the life – theoretical science interface to graduate students, post-docs and other researchers.
|-
}

2009

2009-03-22T18:19:29Z

AndrewBangham:

{| border="1" cellpadding="2"
|-
|width="120pt" valign="top"| January (COMPLETED)
|width="200pt" valign="top"| 2nd Mathematics in the Plant Sciences Study Group. University of Nottingham
|width="200pt" valign="top"| CPIB GARNet STEMN
|width="200pt" valign="top"| Introduce mathematics into plant science, form collaborations across the life – theoretical science interface to graduate students, post-docs and other researchers.
|-
|width="120pt" valign="top"| 23rd to 27th March
|width="200pt" valign="top"| Biomechanics of Growth in Plant Biology, Bristol
|width="200pt" valign="top"| STEMN
|width="200pt" valign="top"| This three-day meeting aims to promote interactions between experimental researchers and modellers from life science, engineering, computer science and mathematical backgrounds, with a focus on the biomechanics of plant growth.
|-
|width="120pt" valign="top"| 19th to 24th July
|width="200pt" valign="top"| Workshop on spatio-temporal modelling at UEA and John Innes Centre, Norwich.
|width="200pt" valign="top"| STEMN,
|width="200pt" valign="top"| This week long workshop aims to introduce some of the concepts and software used for modelling plant growth and development.
|-
|width="120pt" valign="top"| December
|width="200pt" valign="top"| 3rd Mathematics in the Plant Sciences Study Group. University of Nottingham
|width="200pt" valign="top"| CPIB GARNet STEMN
|width="200pt" valign="top"| Introduce mathematics into plant science, form collaborations across the life – theoretical science interface to graduate students, post-docs and other researchers.
|-
}

2008

2009-03-22T17:59:59Z

AndrewBangham:

{| border="1" cellpadding="2"
|-
|width="120pt" valign="top"|18th – 19th March (COMPLETED)
|width="200pt" valign="top"| BCS/UKCRC Grand Challenges in Computing Science 1: In Vivo In Silico a challenge to model a higher organism by 2020
|width="200pt" valign="top"| STEMN, Andrew Bangham
|width="200pt" valign="top"| BCS and Royal Society, Pre-meeting gathering to develop case for Grand Challenge status
|-
|width="120pt" valign="top"| May (COMPLETED)
|width="200pt" valign="top"| auxin workshop
|width="200pt" valign="top"| CPIB, SIGNET, GARNet, STEMN. John King and Malcolm Bennett
|width="200pt" valign="top"| Mini symposium at
|-
|width="120pt" valign="top"| June 30th - July 4th (COMPLETED)
|width="200pt" valign="top"| Modelling challenges in plant science
|width="200pt" valign="top"| STEMN. Andrew Millar
|width="200pt" valign="top"| Parallel session as part of the main conference designed to increase awareness of plant science as an area of interest for mathematicians.
|-
|width="120pt" valign="top"| July (COMPLETED)
|width="200pt" valign="top"| Participate in the Systems Biology Session at the Society for Experimental Biology Meeting.
|width="200pt" valign="top"| STEMN, SIGNET
|width="200pt" valign="top"| Contribution to workshop.
|-
|width="120pt" valign="top"| 15-18 September (COMPLETED)
|width="200pt" valign="top"| Plant Modelling Summer School. University of Nottingham
|width="200pt" valign="top"| CPIB GARNet CISBE STEMN SIGNET
|width="200pt" valign="top"| To introduce modelling and quantitative approaches to biology. To encourage experimental design which generates data suitable for modelling.
|-
}

File:Web page graphic.png

2009-03-22T16:23:37Z

AndrewBangham:

Summary of STEMN

2009-03-20T13:27:03Z

AndrewBangham: New page: Whilst it is essential to understand aspects of cells that are common within organisms and across species it is the spatiotemporal differences between cells that arise during development a...

Whilst it is essential to understand aspects of cells that are common within organisms and across species it is the spatiotemporal
differences between cells that arise during development and responses to the environment that are of particular
importance to higher organisms. What distinguishes man from the ape is the integrated system, likewise it is the
differences between cell types and their integration that distinguishes higher plants from algae. There is increasing
research activity on the spatio-temporal determinants of gene expression patterns, regulatory control systems,
mechanical properties, etc. that integrate to lead to growth and development and there is an increasing need to create
mathematical, models of the observations and, more importantly, the underlying mechanisms.

These can be quite complex because the relationships between the changes have to be understood in relation to each
other. In other words, although components can be studied in isolation a full understanding is only obtained when they
are treated as an integrated whole. This requires concise mathematical models that are usually translated into
computable models. Although focussed on plants, the work will have general application. The initial goal of the network is
to catalyse the rapid distribution of mathematical ideas, methods and the articulation of potential problems, a distant goal
is the creation of a Virtual Plant.