Team:Newcastle/Modelling/RuleBender

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==== '''Getting started with RuleBender'''====
==== '''Getting started with RuleBender'''====
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Follow the link above and install RulBender2.0.320
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Follow the link above and install RulBender2.0.320.
 +
 
 +
If running on Windows, you may be asked to download Perl and the java development kit. These can be found
 +
 
 +
<html>
 +
<a href="http://www.perl.org/get.html">here</a>
 +
and
 +
<a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">here.</a>
 +
</html>
 +
 
Assuming RuleBender has been installed on the C: drive of your computer:
Assuming RuleBender has been installed on the C: drive of your computer:
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1. Open windows Explorer and click on the C: drive (under Computer
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<ol>
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2. Open the RuleBender 2.0.320 folder
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    <li> Open windows Explorer and click on the C: drive (under Computer)</li>
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3. Locate and execute RuleBender.exe
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    <li> Open the RuleBender 2.0.320 folder </li>
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4. If you are asked for a workspace:
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    <li> Locate and execute RuleBender.exe </li>
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  a. enter C:\BNGWorkspace
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    <li> If you are asked for a workspace:
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  b. Tick 'Remember workspace'
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        <ol> <li> enter C:\BNGWorkspace </li>
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  c. Click OK twice
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            <li> Tick 'Remember workspace' </li>
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5. Tell RuleBender where the simulation engines are. Go to Window -> Preferences -> Simulator  
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            <li> Click OK twice </li> </ol> </li>
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  a. Click on browse
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    <li> Tell RuleBender where the simulation engines are. Go to Window -> Preferences -> Simulator </li>
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  b. Select the folder C:\RuleBender-2.0.320-win64\BioNetGen-2.2.4
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        <ol> <li> Click on browse </li>
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  c. Click OK
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            <li> Select the folder C:\RuleBender-2.0.320-win64\BioNetGen-2.2.4 </li>
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  d. Click apply
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            <li> Click OK </li>
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  e. Click OK
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            <li> Click apply </li>
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6. We need to create a project. Go to File -> New -> Project
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            <li> Click OK </li> </ol> </li>
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  a. Click next
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    <li> We need to create a project. Go to File -> New -> Project </li>
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  b. Enter the name of your project
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        <ol> <li> Click next </li>
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  c. Click OK
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            <li> Enter the name of your project </li>
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7. Either write or import a BioNetGen model into RuleBender. If importing:
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            <li> Click OK </li> </ol> </li>
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  a. Locate the file of interest
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    <li> Either write or import a BioNetGen model into RuleBender. If importing: </li>
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  b. Right click in the Navigation tab
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        <ol> <li> Locate the file of interest </li>
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  c. Click import
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              <li> Right click in the Navigation tab </li>
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  d. Select file system  
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              <li> Click import </li>
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  e. Click Next
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              <li> Select file system </li>
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  f. Click on browse  
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              <li> Click Next </li>
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  g. Select the folder where the file is saved
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              <li> Click on browse </li>
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  h. Tick  
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              <li> Select the folder where the file is saved </li>
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  i. Click finish
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              <li> Tick </li>
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8. Open the project created in the navigation tab
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              <li> Click finish </li> </ol> </li>
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9. Double click on a 'filename'.bngl
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    <li> Open the project created in the navigation tab </li>
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10. To simulate the model click on Run (under the simulation tab)
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    <li> Double click on a 'filename'.bngl </li>
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11. Results should appear in the Navigation tab
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    <li> To simulate the model click on Run (under the simulation tab) </li>
 +
    <li> Results should appear in the Navigation tab </li> </ol>
 +
 
 +
====BioNetGen Manual====
 +
 
 +
We also recommend having a look at the BioNetGen Primer (BioNetGen manual). We found it really useful, the link to it is <html>
 +
<a href="http://dl.dropboxusercontent.com/u/9028382/Reprints/RuleBasedPrimer-2011.pdf">here.</a>
 +
</html>

Latest revision as of 12:17, 10 July 2013

 
X
 
IGEM Home Newcastle University

RuleBender

RuleBender download link

Getting started with RuleBender

Follow the link above and install RulBender2.0.320.

If running on Windows, you may be asked to download Perl and the java development kit. These can be found

here and here.


Assuming RuleBender has been installed on the C: drive of your computer:

  1. Open windows Explorer and click on the C: drive (under Computer)
  2. Open the RuleBender 2.0.320 folder
  3. Locate and execute RuleBender.exe
  4. If you are asked for a workspace:
    1. enter C:\BNGWorkspace
    2. Tick 'Remember workspace'
    3. Click OK twice
  5. Tell RuleBender where the simulation engines are. Go to Window -> Preferences -> Simulator
    1. Click on browse
    2. Select the folder C:\RuleBender-2.0.320-win64\BioNetGen-2.2.4
    3. Click OK
    4. Click apply
    5. Click OK
  6. We need to create a project. Go to File -> New -> Project
    1. Click next
    2. Enter the name of your project
    3. Click OK
  7. Either write or import a BioNetGen model into RuleBender. If importing:
    1. Locate the file of interest
    2. Right click in the Navigation tab
    3. Click import
    4. Select file system
    5. Click Next
    6. Click on browse
    7. Select the folder where the file is saved
    8. Tick
    9. Click finish
  8. Open the project created in the navigation tab
  9. Double click on a 'filename'.bngl
  10. To simulate the model click on Run (under the simulation tab)
  11. Results should appear in the Navigation tab

BioNetGen Manual

We also recommend having a look at the BioNetGen Primer (BioNetGen manual). We found it really useful, the link to it is here.

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