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Team:HUST-China/Modeling/CAL/manual
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| - | <h2>Get a copy of CAL(for Windows users)</h2> | + | <h2>Get a copy of CAL(for Windows users)</h2><br /> |
| - | < | + | 1.Download a .exe file from <a href="https://code.google.com/p/caliteral/">https://code.google.com/p/caliteral/</a>.<br /> |
| - | + | 2.Download source codes from <a href="https://code.google.com/p/caliteral/">https://code.google.com/p/caliteral/</a>.<br /> | |
| - | < | + | |
</ol> | </ol> | ||
Qt SDK and Qt add-in is needed. It's all free and available on the Internet. We recommend you to compile with VS2010 since that's the only environment we use to build CAL. But we heard that Qt can also work with GCC.<br /> | Qt SDK and Qt add-in is needed. It's all free and available on the Internet. We recommend you to compile with VS2010 since that's the only environment we use to build CAL. But we heard that Qt can also work with GCC.<br /> | ||
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<h2>How to use it</h2> | <h2>How to use it</h2> | ||
| - | First | + | First, let's meet the interface of CAL. |
<img src="https://static.igem.org/mediawiki/2012/thumb/7/76/Interface.png/736px-Interface.png" alt="GUI of CAL" title="GUI of CAL"> | <img src="https://static.igem.org/mediawiki/2012/thumb/7/76/Interface.png/736px-Interface.png" alt="GUI of CAL" title="GUI of CAL"> | ||
<h3>Initializing states of cells</h3> | <h3>Initializing states of cells</h3> | ||
In the "Options" combobox shown in red box, there are two options concerning initializing states of cells.<br /> | In the "Options" combobox shown in red box, there are two options concerning initializing states of cells.<br /> | ||
"<dfn>Random</dfn>" together with "<dfn>Density</dfn>" will initialize the states of cells randomly, creating a given cell density. Density ranges from 0 to 1, with a precision of 1/2500 <br /> | "<dfn>Random</dfn>" together with "<dfn>Density</dfn>" will initialize the states of cells randomly, creating a given cell density. Density ranges from 0 to 1, with a precision of 1/2500 <br /> | ||
| - | "<dfn>From File</dfn>" options will initialize with a .txt file, in which there's a 50X50 matrix with "0" indicating a dead cell and "1" indicating a living cell. An example of such a .txt file is given in the source code pack, "data.txt"/<br /> | + | "<dfn>From File</dfn>" options will initialize with a .txt file, in which there's a 50X50 matrix with "0" indicating a dead cell and "1" indicating a living cell. An example of such a .txt file is given in the source code pack, "data.txt".<br /> |
| + | |||
| + | <h3>Parameters</h3> | ||
| + | Shown in pink box.<br /> | ||
| + | "Density" works with "Random" mode.<br /> | ||
| + | "<dfn>AHLThreshold</dfn>" define the AHL Threshold.Once the intracellular AHL reach such a threshold, the CcdB concentrations will be high enough to kill a cell.<br /> | ||
| + | "<dfn>HThreshold</dfn>" define the Proton Threshold. Once such threshold is reached, the cell will automatically moving towards the place with higher proton concentration. | ||
| + | <h3>Sensitivity correction</h3> | ||
| + | "<dfn>Sensitivity Correction</dfn>" option shown in blue box decides whether CcdB sensitivity correction is applied or not.Once applied, a $X \sim N(1.0,0.1^2)$ coefficient will be added. This option only works in "Combined Rules" and "Quorum Sensing" mode. | ||
| + | <h3>NSGs Setting</h3> | ||
| + | "<dfn>NSGs</dfn>" are acronym for Next-State Generators, which is equivalent to rules of CA.<br /> | ||
| + | "<dfn>Quorum Sensing</dfn>" is equivalent to AHL-CcdB, Sensitivity Correction and Production rules.<br /> | ||
| + | "<dfn>Aggregation</dfn>" is equivalent to Proton Concentrations-driven Chemotaxis rules.<br /> | ||
| + | "<dfn>Combines Rules</dfn>" are all rules stated above. | ||
| + | <h3>Print a file</h3> | ||
| + | Print a report when "<dfn>Stop</dfn>" button is pressed or CAL reach a steady state. The report file includes initial cell states, final cell states and parameters and settings.<br /> | ||
| + | <h3>Runtime information</h3> | ||
| + | "<dfn>Init.Cell(s)</dfn>" shows the initial number of cells.<br /> | ||
| + | "<dfn>Current Cell(s)</dfn>" shows the current number of cells.<br /> | ||
| + | "<dfn>Generations(s)</dfn>" shows the current generations of simulation.<br /> | ||
| + | <h2>FAQ</h2> | ||
| + | If you have any problem concerning the compiling or using CAL, please contact Li Chen<a href="mailto:LaiSum.Sid@Gmail.com?subject=CAL!">.Email Li Chen</a>. | ||
</div> | </div> | ||
</body> | </body> | ||
</html> | </html> | ||
Latest revision as of 03:01, 27 September 2012
HUST CHINA
Get a copy of CAL(for Windows users)
1.Download a .exe file from https://code.google.com/p/caliteral/.
2.Download source codes from https://code.google.com/p/caliteral/.
Qt SDK and Qt add-in is needed. It's all free and available on the Internet. We recommend you to compile with VS2010 since that's the only environment we use to build CAL. But we heard that Qt can also work with GCC.
We have to say sorry to Linux users and Mac users, for we didn't provide a Linux or Mac version. Nevertheless, you can get CAL running by compiling it using Qt SDK and addin. You will need to make a few adjustments on the source code in order to get CAL running under Linux and Mac environment.
For more information, please visit project on Google Code.
How to use it
First, let's meet the interface of CAL.
Initializing states of cells
In the "Options" combobox shown in red box, there are two options concerning initializing states of cells."Random" together with "Density" will initialize the states of cells randomly, creating a given cell density. Density ranges from 0 to 1, with a precision of 1/2500
"From File" options will initialize with a .txt file, in which there's a 50X50 matrix with "0" indicating a dead cell and "1" indicating a living cell. An example of such a .txt file is given in the source code pack, "data.txt".
Parameters
Shown in pink box."Density" works with "Random" mode.
"AHLThreshold" define the AHL Threshold.Once the intracellular AHL reach such a threshold, the CcdB concentrations will be high enough to kill a cell.
"HThreshold" define the Proton Threshold. Once such threshold is reached, the cell will automatically moving towards the place with higher proton concentration.
Sensitivity correction
"Sensitivity Correction" option shown in blue box decides whether CcdB sensitivity correction is applied or not.Once applied, a $X \sim N(1.0,0.1^2)$ coefficient will be added. This option only works in "Combined Rules" and "Quorum Sensing" mode.NSGs Setting
"NSGs" are acronym for Next-State Generators, which is equivalent to rules of CA."Quorum Sensing" is equivalent to AHL-CcdB, Sensitivity Correction and Production rules.
"Aggregation" is equivalent to Proton Concentrations-driven Chemotaxis rules.
"Combines Rules" are all rules stated above.
Print a file
Print a report when "Stop" button is pressed or CAL reach a steady state. The report file includes initial cell states, final cell states and parameters and settings.Runtime information
"Init.Cell(s)" shows the initial number of cells."Current Cell(s)" shows the current number of cells.
"Generations(s)" shows the current generations of simulation.
