blocks|key|367479|text|如果你能把你的物种集中当作一个参数，这是最简单的解决方案:直接设定变化的速度。如果被要求计算物种的数量，将该浓度乘以间隔的大小。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|367480|但是，如果你的模拟器和大多数SBML模拟器一样，你的基本变化单位是物种数量。这使得这种情况特别尴尬，因为物种数量的变化速度必须从物种浓度的变化率以及舱室大小的变化率得出。|367481|然而，它仍然是可行的。如果我们使用"S1“作为物种数量，使用"S1”作为物种浓度，使用"C“作为间隔大小：|367482|​|367483|📷|atomic|offset|length|367484|367485|同样，这也适用于dC/dt和dS1/dt定义的场景，dS1/dt是未知的。|367486|这可以得出如下结论：|367487|367488|367489|367490|367491|367492|(通过链式规则)|367493|367494|367495|367496|367497|367498|367499|367500|367501|367502|367503|367504|367505|entityMap|0|IMAGE|mutability|IMMUTABLE|imageUrl|https://developer.qcloudimg.com/http-save/yehe-900000/c264a1d8b14f901d2b8e036d923f81db.gif|imageAlt|1|https://developer.qcloudimg.com/http-save/yehe-900000/4f0b806991bcd45f1dbf664d5eb49b72.gif|2|https://developer.qcloudimg.com/http-save/yehe-900000/7e9e10d539ff5cdf888187753efeac58.gif|3|https://developer.qcloudimg.com/http-save/yehe-900000/f126796e303e4e47c9948bee2124e558.gif|4|https://developer.qcloudimg.com/http-save/yehe-900000/a068395c713a20f1d9b87d53a3111b75.gif|5|https://developer.qcloudimg.com/http-save/yehe-900000/e2f391fbde98679a0e1ecbc2074a8143.gif|6^0|0|0|0|0|0|1|0|0|0|0|0|0|0|1|1|0|0|0|0|1|2|0|0|0|0|1|3|0|0|0|0|1|4|0|0|0|0|1|5|0|0|0|0|1|6|0|0^^$0|@$1|2|3|4|5|6|7|1U|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|1V|8|@]|9|@]|A|$]]|$1|D|3|E|5|6|7|1W|8|@]|9|@]|A|$]]|$1|F|3|G|5|6|7|1X|8|@]|9|@]|A|$]]|$1|H|3|I|5|J|7|1Y|8|@]|9|@$K|1Z|L|20|1|21]]|A|$]]|$1|M|3|G|5|6|7|22|8|@]|9|@]|A|$]]|$1|N|3|O|5|6|7|23|8|@]|9|@]|A|$]]|$1|P|3|Q|5|6|7|24|8|@]|9|@]|A|$]]|$1|R|3|G|5|6|7|25|8|@]|9|@]|A|$]]|$1|S|3|I|5|J|7|26|8|@]|9|@$K|27|L|28|1|29]]|A|$]]|$1|T|3|G|5|6|7|2A|8|@]|9|@]|A|$]]|$1|U|3|G|5|6|7|2B|8|@]|9|@]|A|$]]|$1|V|3|I|5|J|7|2C|8|@]|9|@$K|2D|L|2E|1|2F]]|A|$]]|$1|W|3|X|5|6|7|2G|8|@]|9|@]|A|$]]|$1|Y|3|G|5|6|7|2H|8|@]|9|@]|A|$]]|$1|Z|3|I|5|J|7|2I|8|@]|9|@$K|2J|L|2K|1|2L]]|A|$]]|$1|10|3|G|5|6|7|2M|8|@]|9|@]|A|$]]|$1|11|3|G|5|6|7|2N|8|@]|9|@]|A|$]]|$1|12|3|I|5|J|7|2O|8|@]|9|@$K|2P|L|2Q|1|2R]]|A|$]]|$1|13|3|G|5|6|7|2S|8|@]|9|@]|A|$]]|$1|14|3|G|5|6|7|2T|8|@]|9|@]|A|$]]|$1|15|3|I|5|J|7|2U|8|@]|9|@$K|2V|L|2W|1|2X]]|A|$]]|$1|16|3|G|5|6|7|2Y|8|@]|9|@]|A|$]]|$1|17|3|G|5|6|7|2Z|8|@]|9|@]|A|$]]|$1|18|3|I|5|J|7|30|8|@]|9|@$K|31|L|32|1|33]]|A|$]]|$1|19|3|G|5|6|7|34|8|@]|9|@]|A|$]]|$1|1A|3|-4|5|6|7|35|8|@]|9|@]|A|$]]]|1B|$1C|$5|1D|1E|1F|A|$1G|1H|1I|-4]]|1J|$5|1D|1E|1F|A|$1G|1K|1I|-4]]|1L|$5|1D|1E|1F|A|$1G|1M|1I|-4]]|1N|$5|1D|1E|1F|A|$1G|1O|1I|-4]]|1P|$5|1D|1E|1F|A|$1G|1Q|1I|-4]]|1R|$5|1D|1E|1F|A|$1G|1S|1I|-4]]|1T|$5|1D|1E|1F|A|$1G|1H|1I|-4]]]]

If you can treat your species concentration like a parameter, this is the easiest solution: simply set the rate of change directly. If asked to compute the amount of the species, multiply that concentration by the compartment size.
If, however, your simulator is like most SBML simulators, your fundamental unit of change is the species amount. This makes this scenario particularly awkward, because the rate of change of the species amount must be derived from the rate of change of the species concentration as well as the rate of change of the compartment size.
However, it's still doable. If we use &quot;S1&quot; as the species amount, &quot;[S1]&quot; as the species concentration, and &quot;C&quot; as the compartment size:
<img src="https://latex.codecogs.com/gif.latex?%5Cfrac%7BdS1%7D%7Bdt%7D&space;=&space;[S1]%5Cfrac%7BdC%7D%7Bdt%7D&space;&plus;&space;C%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="\frac{dS1}{dt} = [S1]\frac{dC}{dt} + C\frac{d[S1]}{dt}" />
Again, this applies in the scenario where dC/dt and d[S1]/dt are defined, and dS1/dt is unknown.
This can be derived as follows:
<img src="https://latex.codecogs.com/gif.latex?%5Cfrac%7Bd(S1/C)%7D%7Bdt%7D&space;=&space;%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="\frac{d(S1/C)}{dt} = \frac{d[S1]}{dt}" />
<img src="https://latex.codecogs.com/gif.latex?%5Cfrac%7B(C%5Cfrac%7BdS1%7D%7Bdt%7D&space;-&space;S1%5Cfrac%7BdC%7D%7Bdt%7D)%7D%7BC%5E2%7D&space;=&space;%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="\frac{(C\frac{dS1}{dt} - S1\frac{dC}{dt})}{C^2} = \frac{d[S1]}{dt}" /> (via the chain rule)
<img src="https://latex.codecogs.com/gif.latex?C%5Cfrac%7BdS1%7D%7Bdt%7D&space;-&space;S1%5Cfrac%7BdC%7D%7Bdt%7D&space;=&space;C%5E2%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="C\frac{dS1}{dt} - S1\frac{dC}{dt} = C^2\frac{d[S1]}{dt}" />
<img src="https://latex.codecogs.com/gif.latex?C%5Cfrac%7BdS1%7D%7Bdt%7D&space;=&space;S1%5Cfrac%7BdC%7D%7Bdt%7D&space;&plus;&space;C%5E2%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="C\frac{dS1}{dt} = S1\frac{dC}{dt} + C^2\frac{d[S1]}{dt}" />
<img src="https://latex.codecogs.com/gif.latex?%5Cfrac%7BdS1%7D%7Bdt%7D&space;=&space;%5Cfrac%7BS1%7D%7BC%7D%5Cfrac%7BdC%7D%7Bdt%7D&space;&plus;&space;C%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="\frac{dS1}{dt} = \frac{S1}{C}\frac{dC}{dt} + C\frac{d[S1]}{dt}" />
<img src="https://latex.codecogs.com/gif.latex?%5Cfrac%7BdS1%7D%7Bdt%7D&space;=&space;[S1]%5Cfrac%7BdC%7D%7Bdt%7D&space;&plus;&space;C%5Cfrac%7Bd[S1]%7D%7Bdt%7D" title="\frac{dS1}{dt} = [S1]\frac{dC}{dt} + C\frac{d[S1]}{dt}" />

I am working on the Simulation Biology Simulation Core Library (<a href="https://github.com/draeger-lab/SBSCL" rel="nofollow noreferrer">SBSCL</a>) where we are currently simulating the SBML models from the <a href="https://github.com/sbmlteam/sbml-test-suite" rel="nofollow noreferrer">SBML Test Suite</a>. But I am having issues in simulating the SBML models where there are coupled compartment and species rate rules and the species are in concentration units (i.e. the species depends on the values of the compartment). The models with this property can be found in the SBML Test Suite with one of them being the test case <a href="https://github.com/sbmlteam/sbml-test-suite/blob/master/cases/semantic/01198/01198-sbml-l3v2.xml" rel="nofollow noreferrer">1198</a>.
The series of discussions on this issue can also be found at the sbml-discuss google group <a href="https://groups.google.com/forum/#!msg/sbml-discuss/jbAFdCkM-fA/l-PANnpmWAgJ" rel="nofollow noreferrer">[Link]</a>. Even I have created an <a href="https://github.com/draeger-lab/SBSCL/issues/50" rel="nofollow noreferrer">issue</a> for this in SBSCL.
Can I get the best way of simulating this type of SBML models?

Simulating the SBML models with coupled compartment and species rate rules

翻译质量差，导致语言生硬或混乱。

没有提供实际的解决方法或示例。

解答不清晰，无法理解或解决问题。

页面排版不美观，阅读体验差。

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我正在从事模拟生物学模拟核心库()的工作，我们目前正在从中模拟SBML模型。但是，我在模拟SBML模型时遇到了问题，在这种模型中有耦合的间隔和物种速率规则，并且物种在浓度单位中(即物种取决于该区域的值)。具有此属性的模型可以在Suite中找到，其中一个是测试用例。关于这个问题的一系列讨论也可以在sbml讨论google小组上找到。甚至我也在SBSCL中为此创建了一个。我能得到最好的方法来模拟这类S

问用耦合室和物种率规则模拟SBML模型
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