Cancer as a Dynamic Network - Revision history

Monika: /* Model Parameters */

2007-06-18T23:44:26Z

Model Parameters

← Older revision		Revision as of 23:44, 18 June 2007
Line 96:		Line 96:

	==Model Parameters==		==Model Parameters==
	~~soon~~		Recent research data shows that '''glucose concentrations''' below 2,5mM seemed to be extreme difficult to most of the cancer cell lines. For comparison, normal (physiological) blood glucose levels are around 5 mM (normally before a meal) up to 10mM or slightly higher within two hours after a meal.

			The '''oxygen pressure''' varies in dependency where the tissue is located, in other words how far away is the next blood vessel. Oxygen pressure in arteries is 90mmHg and in veins it is around 40mmHg, so that physiological conditions are somewhere in between. Consumption of oxygen (by tumour cells) depends on the different mutations a tumour could have. Most surviving (in patients) tumours have developed the ability to induce angiogenesis, by secreting VEGF, (EGF) and FGF - which are known growth factors. Depending on the tumour ability to induce angiogenesis, tumours growth deprnds on oxygen levels between 40 and 90 mm Hg. '''But, there are reports about tumours growing totally without oxygen''' – the tumours contained the cells growing under anaerobe conditions forming lactate out of glucose.

			Hence, we have to look at each single condition for each single tumour or, to set of parameters describing the tumour environment.

	= Work Schedule =		= Work Schedule =

Sangus: /* Update */

2007-06-18T21:00:58Z

Update

← Older revision		Revision as of 21:00, 18 June 2007
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	[[User:Sangus\|Sangus]] 19:10, 17 June 2007 (MDT) ... oooops..! Sorry, ''addlib'' is a function I use to load Matlab libraries that I have written. The only function required is 'choose.m' and this is included. So just comment out the ''addlib'' line and all should (!) be fine...?		[[User:Sangus\|Sangus]] 19:10, 17 June 2007 (MDT) ... oooops..! Sorry, ''addlib'' is a function I use to load Matlab libraries that I have written. The only function required is 'choose.m' and this is included. So just comment out the ''addlib'' line and all should (!) be fine...?

			no.. won't be fine.. now you will need this: [http://149.171.208.159/lucinda/images/3/35/Choose.zip Choose.zip]

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Sangus: /* Group Org */

2007-06-18T01:18:22Z

Group Org

← Older revision		Revision as of 01:18, 18 June 2007
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	= Group Org =		= Group Org =
	;Next Meeting		;Next Meeting
	Monday, Week 3 (location ~~<tba>~~, time ~~<tba>~~)		Monday, Week 3 (location Student Centre Cafe, time 6:30pm)
	;Agenda		;Agenda
	:~~Feedback on pseudo~~-~~code generation~~		:Discuss model as it is, what needs to be added (and in what priority); current literature -- who has done similar to this before???

	== People ==		== People ==

Sangus: /* Update */

2007-06-18T01:10:39Z

Update

← Older revision		Revision as of 01:10, 18 June 2007
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	Are you sure that you used the matlab function?		Are you sure that you used the matlab function?
	Which matlab function (instead of addlib) can I use?		Which matlab function (instead of addlib) can I use?

			[[User:Sangus\|Sangus]] 19:10, 17 June 2007 (MDT) ... oooops..! Sorry, ''addlib'' is a function I use to load Matlab libraries that I have written. The only function required is 'choose.m' and this is included. So just comment out the ''addlib'' line and all should (!) be fine...?

	----		----

Monika: /* Nutrient supply */

2007-06-17T02:22:48Z

Nutrient supply

← Older revision		Revision as of 02:22, 17 June 2007
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	Growth: nutrients will be largely influenced by ''h''.		Growth: nutrients will be largely influenced by ''h''.
	Angiogenesis: nutrients will be influenced by the intrusion of vessels into the tumor, causing inner-cells to become 'leaf-nodes', hence dramatically reduces the value of ''h_min''. More than one path-way might be close to cell ''x_i'' in which case, the nutrients it is able to use will approach a limiting value (say) ''m_0'', the basal metabolic rate for a cell.		Angiogenesis: nutrients will be influenced by the intrusion of vessels into the tumor, causing inner-cells to become 'leaf-nodes', hence dramatically reduces the value of ''h_min''. More than one path-way might be close to cell ''x_i'' in which case, the nutrients it is able to use will approach a limiting value (say) ''m_0'', the basal metabolic rate for a cell.


			==Model Parameters==
			soon

	= Work Schedule =		= Work Schedule =

Monika: /* Update */

2007-06-17T02:06:43Z

Update

@@ Line 1: / Line 1: @@
 ----
 = Update =
 Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.
 * [http://149.171.208.159/lucinda/images/e/e5/Tumor.zip Download zip here]
@@ Line 8: / Line 24: @@
 * One possible thing to do, would be to go back to NetLogo and try to code the physics stuff in a similar way to here (now that we know what works) .. since NL has better (faster) visualizations for spheres in 3D ...?
 * See you Sunday (or today?!)
 ----

Sangus: /* Update */

2007-06-16T13:24:45Z

Update

← Older revision		Revision as of 13:24, 16 June 2007
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	= Update =		= Update =
	Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.		Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.
	* [~~[Download zip here~~ http://149.171.208.159/lucinda/images/e/e5/Tumor.zip]]		* [http://149.171.208.159/lucinda/images/e/e5/Tumor.zip Download zip here]
	* As you will see, I have added the fact that the cells grow before differentiating -- this is to overcome 'explosive' events when a new cell is born, pushing others far away		* As you will see, I have added the fact that the cells grow before differentiating -- this is to overcome 'explosive' events when a new cell is born, pushing others far away
	* As you can also see, this visualization is in 2D, but it will be easy to convert to 3D now - I had to get this growth process working though		* As you can also see, this visualization is in 2D, but it will be easy to convert to 3D now - I had to get this growth process working though

Sangus: /* Update */

2007-06-16T13:23:45Z

Update

← Older revision		Revision as of 13:23, 16 June 2007
Line 2:		Line 2:
	= Update =		= Update =
	Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.		Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.
	* [Download zip here http://149.171.208.159/lucinda/images/e/e5/Tumor.zip]		* [[Download zip here http://149.171.208.159/lucinda/images/e/e5/Tumor.zip]]
	* As you will see, I have added the fact that the cells grow before differentiating -- this is to overcome 'explosive' events when a new cell is born, pushing others far away		* As you will see, I have added the fact that the cells grow before differentiating -- this is to overcome 'explosive' events when a new cell is born, pushing others far away
	* As you can also see, this visualization is in 2D, but it will be easy to convert to 3D now - I had to get this growth process working though		* As you can also see, this visualization is in 2D, but it will be easy to convert to 3D now - I had to get this growth process working though
Line 10:		Line 10:

	----		----

	= Group Org =		= Group Org =
	;Next Meeting		;Next Meeting

Sangus at 13:23, 16 June 2007

2007-06-16T13:23:05Z

← Older revision		Revision as of 13:23, 16 June 2007
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			----
			= Update =
			Monika -- here is the current work, in case you would like to do something on it today (Sat). I will be back Sunday.
			* [Download zip here http://149.171.208.159/lucinda/images/e/e5/Tumor.zip]
			* As you will see, I have added the fact that the cells grow before differentiating -- this is to overcome 'explosive' events when a new cell is born, pushing others far away
			* As you can also see, this visualization is in 2D, but it will be easy to convert to 3D now - I had to get this growth process working though
			* There are very nice visualizations in Matlab for drawing spheres, or even elliptical objects, which I have it set up to do (but commented out), though this takes some time
			* One possible thing to do, would be to go back to NetLogo and try to code the physics stuff in a similar way to here (now that we know what works) .. since NL has better (faster) visualizations for spheres in 3D ...?
			* See you Sunday (or today?!)

			----
	= Group Org =		= Group Org =
	;Next Meeting		;Next Meeting
Line 65:		Line 76:
	= Work Schedule =		= Work Schedule =
	'''Current'''		'''Current'''
	* develop pseudo-code for modelling approach (due Wk2-Friday)		* --develop pseudo-code for modelling approach (due Wk2-Friday)--

	'''Future'''		'''Future'''
	* build basic NetLogo model, check:		* build basic NetLogo model, check:
	** growth (!)		** --growth (!)--
	** network structure realistic ?		** network structure realistic ?
	** necrotic core ?		** necrotic core ?

Monika: /* Past Group Meetings */

2007-06-16T06:27:36Z

Past Group Meetings

← Older revision		Revision as of 06:27, 16 June 2007
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	; Week 1(Sun)		; Week 1(Sun)
	: Meeting at 8:30pm in cafe to organise model		: Meeting at 8:30pm in cafe to organise model
			; Week 2(Thu)
			: Meeting at 6:30pm in cafe
			; Week 2(Fri)
			: Meeting at 1:00pm in cafe

	= Refs =		= Refs =
	* [[Media:folkman-nature-cancer.pdf\|Quick overview of Cancer from recent Nature article]]		* [[Media:folkman-nature-cancer.pdf\|Quick overview of Cancer from recent Nature article]]
	* Cancer modelling database clearing house: http://calvino.polito.it/~mcrtn/index.html		* Cancer modelling database clearing house: http://calvino.polito.it/~mcrtn/index.html