Team:Edinburgh/Notebook/Modelling

From 2010.igem.org

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== Modelling ==
== Modelling ==
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First meeting regarding modelling capabilities, decisions of what software to use and other priorities.
First meeting regarding modelling capabilities, decisions of what software to use and other priorities.
 +
 +
 +
'''17/6/10'''
 +
 +
Presentation of basic ideas to advisors. Given the green light to proceed using tools and languages discussed.
 +
 +
 +
'''18/6/10'''
 +
 +
Commencement of detailed research regarding proposed pathways and their actions.
 +
 +
 +
'''21/6/10'''
 +
 +
Setting up the various tools required to use Kappa throughout the project. Collaboration with Donal's Masters project, and the simulation package he's developing for it. Debugging and testing of said package to continue throughout project timeline.
 +
 +
 +
'''22/6/10'''
 +
 +
Commencement of analysis and understanding of Ty Thomson's repressilator model, as well as the underlying framework proposed for BioBricks. BioBricks are not characterised to the level of detail necessary for full accuracy, so apparent even at this stage that the initial model will focus on design and prototyping of the system rather than precise interactions. Presentation of framework as a possible future standard of characterisation?
 +
 +
Also talked to biologists regarding the model itself and what assumptions can be safely made, i.e. levels of light linked to expression levels of light-producing protein, in turn indirectly linked to the characteristics (such as transcription rates) of promoters. The ultimate modelling question could thus be: how to calibrate production of protein (and thus light) such that the sensor is able to react to it appropriately? Will we be able to characterise the parts to the correct extent such that we're able to do this accurately?
 +
 +
... we hope so.
 +
'''24/6/10'''
'''24/6/10'''
-
Subcultured transformants from ampicillin plates to new plates
+
Plan of action drawn up for the next two weeks, including the proposed milestones for the modelling side of the project. Aim is to get preliminary model done (and debugged, very important this) by 10/7.
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Lorem ipsum dolor sit amet, consectetur adipiscing elit. Mauris auctor dolor quis diam fringilla non malesuada sapien volutpat. Proin purus arcu, tristique ut ultricies eget, elementum ac odio. Nam gravida blandit nisl, in vestibulum nunc malesuada id. Cras sit amet mi a massa aliquet auctor. Morbi lorem magna, ultrices vitae iaculis id, malesuada vitae nibh. Fusce elementum euismod vehicula. Maecenas mattis bibendum elit, sed semper diam scelerisque eget. Vivamus enim arcu, consequat non volutpat nec, hendrerit id quam. Quisque dapibus, augue non scelerisque tincidunt, ipsum magna posuere nunc, consectetur blandit elit odio non orci. Morbi congue molestie ipsum non ultricies. Pellentesque sed nisl nunc, id facilisis magna. Sed sit amet est ut magna tempor eleifend. Duis pulvinar lobortis rutrum.
+
Repressilator model tweaked slightly for our purposes. Preliminary modelling of red and blue light pathways (both based on pre-existing parts, unlike the proposed green pathway) begun.
 +
 
 +
 
 +
'''3/7/10'''
 +
 
 +
Base pathways in place. Debugging phase commenced. Bring out the sledgehammers!
 +
 
 +
 
 +
'''6/7/10'''
 +
 
 +
Two pages worth of process of elimination later, critical 'no oscillation' bug found to be caused by software issue rather than modelling error. Now resolved. Take that, Murphy!
 +
 
 +
 
 +
'''7/7/10'''
 +
 
 +
Balancing of rate parameters in order to elicit desired behaviour. A very delicate process, especially given that mostly working blind without much wet-lab characterisation / quantification data. Rates are mostly guesstimates (and restricted such that they don't crash either the lab computer or the laptop through the presence of Far Too Many Agents).
 +
 
 +
Issues involve copy number assumption, the action of the OmpF and OmpC promoters, the promoter mechanism of the repressilator, choice between indirect action (i.e. RED light on Cph8) vs. direct action (phosphorylation of OmpR), and so forth. Hopefully I've actually managed to document all the assumptions and decisions that I've made!
 +
 
 +
 
 +
'''12/7/10'''
 +
 
 +
Preliminary model complete. All modelling work now put on hold while wiki design and implementation takes centre stage, also to try to allow wet-work to catch up.
 +
 
 +
 
 +
'''16/8/10'''
 +
 
 +
Have decided that Kappa is a lot less soul-destroying than CSS. At least the wiki looks fairly good for now.
 +
 
 +
Work on second (genomic) model commenced, codenamed 'BRIDGE', mainly to refresh my mind on perturbations and to test the capabilities of the simulator. All previous work now renamed 'Moodlighting', will be revisited soon.
 +
 
 +
 
 +
'''20/8/10'''
 +
 
 +
BRIDGE model complete, simulator has been thoroughly debugged and will now serve its purpose for more strenuous perturbation analysis. Have also begun write-up of modelling BRIDGEs on wiki, including an introduction to Kappa.
 +
 
 +
 
 +
'''23/8/10'''
 +
 
 +
Perturbation analysis of individual light sensing pathways begun. Basically, this involves controlled perturbations on the isolated pathways - what does the pathway do when unresponsive, and how does it respond to a burst of light from the correct spectrum? Ultimately, it is hoped that we would be able to calibrate the reaction of the pathway to actual experimental results, but with the problems that have been experienced with parts from previous years, it's unlikely that we'll be able to get that far within the project lifespan. Bother.
 +
 
 +
 
 +
'''24/8/10'''
 +
 
 +
Found one or two minor bugs that somehow slipped the net earlier, mostly involving transcription factors that deactivate when they're not supposed to. Now fixed.
 +
 
 +
 
 +
'''27/8/10'''
 +
 
 +
Perturbation analysis of red and blue light pathways complete. Pleased to say that they work as intended, although how accurately they reflect the real biology is still up for debate.
 +
 
 +
 
 +
'''30/8/10'''
 +
 
 +
Discussed plans regarding the creation of an intercellular model detailing how the bacteria will hopefully react to one another or to a mechanical light source, as opposed to the intracellular model which we've been concentrating on so far. This may or may not involve a composite model consisting of individual agents (cellular automata or Kappa model) each reacting as dictated by the intercellular model... mindboggling. Decided to start out simple and work our way upwards.
 +
 
 +
Also discussed plan of action for further perturbation analysis of the intracellular model. This will be conducted and written up within the next month.
 +
 
 +
 
 +
'''1/9/10'''
 +
 
 +
Began running preliminary tests on the system as a whole. The results look promising!
 +
 
 +
 
 +
'''6/9/10'''
-
Etiam pretium mattis enim, ac pellentesque quam congue at. Ut interdum, velit sed aliquam dapibus, lacus turpis gravida nibh, sed iaculis sem ligula ut mi. Maecenas facilisis volutpat elit, sit amet pharetra dolor porta ac. Proin posuere, ante ac pretium luctus, ante nunc luctus orci, at mattis mi sem sit amet nisi. Sed venenatis auctor mi, ac porttitor quam ultricies quis. Suspendisse at orci elit. Praesent egestas metus at sem lacinia eu hendrerit est convallis. Praesent cursus mauris purus, id blandit nibh. Nulla consectetur, nunc in ornare mattis, ligula massa gravida magna, a pellentesque metus lacus id nunc. Donec eget ipsum eu turpis placerat semper. Donec ligula turpis, lobortis id sodales eget, fermentum vel turpis. Aenean at convallis eros. Cras cursus ligula id arcu venenatis accumsan sit amet volutpat nulla. Donec id ante id nisi porta volutpat sit amet quis quam. Vivamus tincidunt ligula id ante mollis non auctor sem porta. Etiam eleifend laoreet nunc vel laoreet. Cras quis nunc ac mi pulvinar imperdiet. Nam nec arcu non tortor tincidunt commodo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.
+
Began integration of hypothetical green light producing / sensing pathways into model.
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In hac habitasse platea dictumst. Praesent at dolor arcu, non cursus justo. Fusce non nibh felis. Nulla pharetra eleifend egestas. Sed semper ligula ac mi tincidunt mollis. Ut elementum justo sed urna luctus sed consectetur mauris euismod. Suspendisse potenti. Phasellus quam sem, ultrices et vulputate eu, egestas vitae nisi. Morbi non tellus sapien, faucibus sagittis diam. In hac habitasse platea dictumst. Aliquam tempor ipsum at sapien lobortis viverra. Sed volutpat nunc in justo vehicula egestas. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Nullam sed nisi velit. Praesent at quam nec metus imperdiet tincidunt vitae eget mi. Phasellus laoreet tincidunt tempus. Fusce nisl enim, hendrerit quis consequat quis, vestibulum pharetra lectus. Morbi cursus gravida sem, interdum sollicitudin mi aliquam id. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Morbi eleifend hendrerit leo, nec aliquet elit adipiscing vitae.
 
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Ut commodo vehicula erat eget laoreet. Duis elit quam, malesuada id semper sit amet, bibendum pellentesque risus. Nam non lacus nunc. Fusce mi arcu, fermentum eu tempus in, ornare sit amet sapien. Donec fringilla sem vel nunc hendrerit sit amet mollis urna pharetra. Duis eu arcu nec eros tempus interdum. Mauris tempus ultrices sapien ut malesuada. Fusce erat turpis, bibendum nec rutrum ac, dapibus id erat. In pretium malesuada libero, eu commodo purus sagittis in. Mauris est nibh, pulvinar in vulputate sed, porttitor sit amet nisl. Sed mattis fermentum erat, vitae molestie dui bibendum sit amet. Donec mattis mollis nisl, nec mattis ipsum cursus nec. Cras interdum vehicula turpis ut congue. Vestibulum consequat sem ut dui vulputate sed scelerisque justo pulvinar. Praesent ut congue tortor. Suspendisse euismod feugiat fermentum. Sed non magna ut odio egestas molestie ut a velit. Duis interdum auctor mi, a ornare justo malesuada a.
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'''8/9/10'''
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Nunc laoreet eleifend ultricies. Aenean vestibulum nisi vel justo blandit id commodo nunc luctus. Pellentesque vitae nunc lorem. Sed vehicula consectetur neque ac convallis. Fusce mattis ligula sit amet sem vehicula aliquet. Duis pulvinar laoreet neque eget egestas. Integer eu justo sapien. Vivamus purus lacus, vehicula id ullamcorper at, tempus nec velit. Curabitur vel odio turpis. Donec iaculis rhoncus porttitor. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Nunc magna lectus, ornare nec venenatis nec, interdum at nunc.
+
Completed integration of green light producing / sensing pathways into model. Now perturbation analysis of the intracellular model can begin in earnest.

Revision as of 11:28, 8 September 2010





Modelling

14/6/10

First meeting regarding modelling capabilities, decisions of what software to use and other priorities.


17/6/10

Presentation of basic ideas to advisors. Given the green light to proceed using tools and languages discussed.


18/6/10

Commencement of detailed research regarding proposed pathways and their actions.


21/6/10

Setting up the various tools required to use Kappa throughout the project. Collaboration with Donal's Masters project, and the simulation package he's developing for it. Debugging and testing of said package to continue throughout project timeline.


22/6/10

Commencement of analysis and understanding of Ty Thomson's repressilator model, as well as the underlying framework proposed for BioBricks. BioBricks are not characterised to the level of detail necessary for full accuracy, so apparent even at this stage that the initial model will focus on design and prototyping of the system rather than precise interactions. Presentation of framework as a possible future standard of characterisation?

Also talked to biologists regarding the model itself and what assumptions can be safely made, i.e. levels of light linked to expression levels of light-producing protein, in turn indirectly linked to the characteristics (such as transcription rates) of promoters. The ultimate modelling question could thus be: how to calibrate production of protein (and thus light) such that the sensor is able to react to it appropriately? Will we be able to characterise the parts to the correct extent such that we're able to do this accurately?

... we hope so.


24/6/10

Plan of action drawn up for the next two weeks, including the proposed milestones for the modelling side of the project. Aim is to get preliminary model done (and debugged, very important this) by 10/7.

Repressilator model tweaked slightly for our purposes. Preliminary modelling of red and blue light pathways (both based on pre-existing parts, unlike the proposed green pathway) begun.


3/7/10

Base pathways in place. Debugging phase commenced. Bring out the sledgehammers!


6/7/10

Two pages worth of process of elimination later, critical 'no oscillation' bug found to be caused by software issue rather than modelling error. Now resolved. Take that, Murphy!


7/7/10

Balancing of rate parameters in order to elicit desired behaviour. A very delicate process, especially given that mostly working blind without much wet-lab characterisation / quantification data. Rates are mostly guesstimates (and restricted such that they don't crash either the lab computer or the laptop through the presence of Far Too Many Agents).

Issues involve copy number assumption, the action of the OmpF and OmpC promoters, the promoter mechanism of the repressilator, choice between indirect action (i.e. RED light on Cph8) vs. direct action (phosphorylation of OmpR), and so forth. Hopefully I've actually managed to document all the assumptions and decisions that I've made!


12/7/10

Preliminary model complete. All modelling work now put on hold while wiki design and implementation takes centre stage, also to try to allow wet-work to catch up.


16/8/10

Have decided that Kappa is a lot less soul-destroying than CSS. At least the wiki looks fairly good for now.

Work on second (genomic) model commenced, codenamed 'BRIDGE', mainly to refresh my mind on perturbations and to test the capabilities of the simulator. All previous work now renamed 'Moodlighting', will be revisited soon.


20/8/10

BRIDGE model complete, simulator has been thoroughly debugged and will now serve its purpose for more strenuous perturbation analysis. Have also begun write-up of modelling BRIDGEs on wiki, including an introduction to Kappa.


23/8/10

Perturbation analysis of individual light sensing pathways begun. Basically, this involves controlled perturbations on the isolated pathways - what does the pathway do when unresponsive, and how does it respond to a burst of light from the correct spectrum? Ultimately, it is hoped that we would be able to calibrate the reaction of the pathway to actual experimental results, but with the problems that have been experienced with parts from previous years, it's unlikely that we'll be able to get that far within the project lifespan. Bother.


24/8/10

Found one or two minor bugs that somehow slipped the net earlier, mostly involving transcription factors that deactivate when they're not supposed to. Now fixed.


27/8/10

Perturbation analysis of red and blue light pathways complete. Pleased to say that they work as intended, although how accurately they reflect the real biology is still up for debate.


30/8/10

Discussed plans regarding the creation of an intercellular model detailing how the bacteria will hopefully react to one another or to a mechanical light source, as opposed to the intracellular model which we've been concentrating on so far. This may or may not involve a composite model consisting of individual agents (cellular automata or Kappa model) each reacting as dictated by the intercellular model... mindboggling. Decided to start out simple and work our way upwards.

Also discussed plan of action for further perturbation analysis of the intracellular model. This will be conducted and written up within the next month.


1/9/10

Began running preliminary tests on the system as a whole. The results look promising!


6/9/10

Began integration of hypothetical green light producing / sensing pathways into model.


8/9/10

Completed integration of green light producing / sensing pathways into model. Now perturbation analysis of the intracellular model can begin in earnest.