Congratulations!! ChemChains is now installed and ready for your first simulation!

-ispecs inFiles/CChain/specs/sampleSpecs.txt

-ispecs inFiles/CChain/specs/sampleSpecs.txt -patterns -isettings inFiles/exts/Patterns/settings.txt

-itables inFiles/exts/FileConverter/sampleNet -o outputFileName.txt@]

-inodelist inFiles/exts/FileConverter/sampleNodeList.txt -itables inFiles/exts/FileConverter/sampleNet@ -o outputFileName.txt]

ChemChains can be run with randomly generated conditions for every simulation. To run ChemChains with random initial conditions enabled, use the '-randInit' flag.

-ispecs inFiles/exts/CChain/specs/sampleSpecs.txt

-ispecs inFiles/exts/CChain/specs/sampleSpecs.txt

-ispecs inFiles/exts/CChain/specs/sampleSpecs.txt

1. Unpack ChemChains onto your Desktop and copy/move the ChemChains directory into the Cygwin\home\username\ directory (the cygwin directory should be on your Desktop as the instructions above suggested). This is also where your simulation results will be stored.
2. Start Cygwin by clicking on the Cygwin shortcut on your Desktop. When Cygwin is launched you will begin in the default directory, /home/yourUsername/.

1. Select the root directory. For this tutorial, select a directory on your Desktop as the root directory. E.g., "C:\Documents and Settings\yourUsername\Desktop\cygwin" (A message will pop up, saying that you should not choose a path that contains spaces. Proceed anyway. Once you're familiar with Cygwin, you can reinstall Cygwin in a different directory)

1. Select the location to download packages from (you can use ftp://ftp/gtlib/gatech.edu which has been faster than others in our case).

1. Unpack ChemChains onto your Desktop and copy/move the ChemChains directory into the Cygwin\home\username\ directory (the cygwin directory should be on your Desktop as the instructions above suggested)

1. Type in 'cd ChemChains1.0_clean' and press ENTER to get to the ChemChains directory
2. Compile ChemChains by typing 'make' and pressing ENTER.

Comgratulations!!ChemChains is now installed and ready for your first simulation!

1. Select the root directory. For this tutorial, select your Desktop as the root directory. (A message will pop up, saying that you should not choose a path that contains spaces. Proceed anyway. Once you're familiar with Cygwin, you can reinstall Cygwin in a different directory)

1. Select the root directory. For this tutorial, select your Desktop as the root directory.

1. Click Finish once the installation is completed. This will create a shortcut on your Desktop.

1. Unpack ChemChains onto your Desktop
2. Start Cygwin by clicking on the Cygwin shortcut on your Desktop.

1. Hit next. The installer will download and install the selected packages. This may take a while, depending on your Internet connection speed. (If anytime in the future a new package needs to be added the Cygwin installer can be re-run and additional package(s) selected.)

1. The package list interface will come up to select packages to install. To compile and run ChemChains the following packages are necessary from the Developer package IN ADDITION TO the ones preselected by Cygwin: binutils, gcc-g++, and make packages

1. The package list interface will come up to select packages to install. To compile and run ChemChains the following packages are necessary from the Developer package IN ADDITION TO the ones preselected by Cygwin: binutils, gcc-c++, and make packages

1. Select your connection type (Direct connection should suffice). Hit next.
2. Select the location to download packages from (try to select one closer to your location to reach faster download speed).

1. Select the package directory (this is where it the installation files are kept); for this tutorial, use your Desktop location (which should be selected by default). Click next.

1. Select the package directory (this is where it the installation files are kept); for this tutorial, select your Desktop location. Click next.

1. File download manager will pop up. Select Run.

1. Go to here and click on "Install or update now!" link. (The Cygwin installation wizard will come up)

Running Cygwin & Setting up ChemChains

1. Download ChemChains package from here and save it to your desktop.

1. Download ChemChains package from here and save it to your desktop.

You can use a freely available Cygwin (see below).

1. You will need to copy the ChemChains sourcefiles into a subdirectory within cygwin
2. To enter the ChemChains directory, type cd followed by the directory you put ChemChains in and press ENTER

Flag to Specify the Simulation Specification File

Flag to Specify the Network Descriptor File

Once finished, save the file as inFiles/CChain/logic/myNetwork.txt or just use the sample network descriptor provided in the current release as mentioned above.

\\

Flag to Specify the Network Descriptor File

(:cell:)Simulation specification file name

(:cell:)Network descriptor file name

\\

These activation mechanisms can be expressed as individual truth tables (Figure 2).

(The following example of a simple simulation specification file is included with the current ChemChains release and can be found in "inFiles/CChain/specs/sampleSpecs.txt" file in the ChemChains directory)

\\(The following example of a simple simulation specification file is included with the current ChemChains release and can be found in "inFiles/CChain/specs/sampleSpecs.txt" file in the ChemChains directory)

(The following example of a simple toy network is included with the current ChemChains release and can be found in "inFiles/CChain/logic/sampleNet.txt" file in the ChemChains directory)

(The following example of a simple toy network is available with the current ChemChains release and can be found in "inFiles/CChain/logic/sampleNet.txt" file in the ChemChains directory)

(The following example of a simple toy network is available with the current ChemChains release and can be found in "inFiles/CChain/logic/sampleNet.txt" file in the ChemChains directory)

1. Type "make" to compile ChemChains (This should create an executable file called ChemChains)

1. Change to the unziped ChemChains directory on your desktop
2. make (This should create an executable file called ChemChains)

1. Download ChemChains package from here and save it to your desktop.

Download

1. Download ChemChains package from here and save it to your desktop.
2. Unzip the package to your desktop (you can unzip the package anywhere on your computer, but this tutorial assumes the location of the ChemChains directory on your desktop)

When Cygwin is launched you will begin in the default directory, C:\cygwin\~.

1. The package list interface will come up to select packages to install. To compile and run ChemChains the following packages are necessary from the Developer packages IN ADDITION TO the ones preselected by Cygwin: binutils, gcc-c++, and make packages

When Cygwin is started the default directory is C:\cygwin\~.

1. Type in 'cd ..' and press ENTER to get to the root directory 'C:\cygwin'
2. To enter the ChemChains directory, type 'cd xxx' and press ENTER
3. Compile ChemChains by typing 'make' and pressing ENTER

Some basic Unix commands
There are a couple useful commands for working in a Unix environment:

1. Go to here and download and run the file Install.exe (The Cygwin installation wizard will come up)
2. Select Install From Internet and hit next
3. Select the root directory (default = C:\cygwin)
4. Select the package directory (this is where it the installation files are kept); the same directory as used for root is acceptable. Click next.
5. Select your connection type. Hit next.
6. Select the location to download packages from.
7. The package list interface will come up to select packages to install. To compile and

run ChemChains the following packages are necessary from the Developer packages IN ADDITION TO the ones preselected by Cygwin: binutils, gcc-c++, and make packages

1. Hit next. The installer will download and install the selected packages. (If anytime in the future a new package needs to be added the Cygwin installer can be re-run and additional package(s) selected.)

1. cd [name] - changes directory to [name], if you use .., it will take you up a directory

Installing Cygwin

First go here and download the file Install.exe, when you run it it will open the Cygwin installation wizard. If you don't have any cygwin packages downloaded allready select Install From Internet and hit next. It will prompt you for a root directory with the default C:\cygwin. You can use another directory if you want but I would advise against using C:\. It will then prompt you for a package directory, this is where it will keep the installation files for  the packages you install, I usually use the same directory as I selected for root. Click next and it will prompt you for your connection type, select it and hit next, then select a mirror to download packages from. Then it will bring up a package list interface. To compile and run ChemChains you will need the binutils, gcc-c++, and make packages from the Developer packages in addition to all of the packages that Cygwin will automatically select. After you select the packages that you want hit next and the installer will download and install the packages you've selected. If anytime in the future you find that you need a new package installed you can re-run the Cygwin installer and select the package(s) you need and it will install them for you.

Running Cygwin

There are a couple useful commands for working in a Unix environment,

1. ls - shows the contents of the current directory
2. mkdir [name] - makes a new directory named [name]
3. cd [name] - changes directory to [name], if you use .., it will take
4. you up a directory

When you start Cygwin it will start you into C:\cygwin\~, you need to cd .. to get to C:\cygwin, when you get to the directory that you put the ChemChains binary into you can use the command make to compile it. When it finishes it creates the executable ChemChains, to run it it use the command ./ChemChains along with the flags you want to use. You can use ./ChemChains -h to view flag usage documentation.

To create a sustain node, use the following syntax:

(:cellnr:)-A (:cell:)Output all nodes

Table 1: List of currently available flags.

(:cellnr:)-itables xxx

(:table border=1 bgcolor=#b5dbff cellspacing=0 :) (:cellnr colspan=2:) Table 2: Contents of output generated during calculation mode. (:cellnr align=center:)File/Directory Name (:cell align=center:) Description (:cellnr:)all_avg.mtb (:cell:)Tab-delimited text file with activation levels of all nodes across all simulations (:cellnr:)all_dosage.mtb (:cell:)Activity levels of all inputs across all simulations (:cellnr:)outputNode_avg.csv (:cell:)Activity levels of nodes specified for pattern analysis. (:cellnr:)inputNames.csv (:cell:)List of input nodes. (:cellnr:)nodeNames.csv (:cell:)Names of all nodes in the network. (:cellnr:)specs.txt (:cell:)Specification file used for this experiment. (:cellnr:)logic/ (:cell:)Directory containing all logic files associated with this experiment (:cellnr:)nodesAvg/ (:cell:)Directory containing activity level information for each node. (:cellnr:)patterns/ (:cell:)Output directory for the patterns extension. (:cellnr:)bits/ (:cell:)Output directory holding ON/OFF sequences for all nodes in the network

(:cellnr colspan=2:)Flags used with Visual mode (:cellnr:)-vis xxx (:cell:)Instantiates the visual mode and sets the output file name

(:cellnr colspan=2:)Flags used for Pattern analysis extension

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag. All flags available in the most recent version of ChemChains are described in Table 1.

All flags available in the most recent version of ChemChains are described in Table 1. (:table border=1 bgcolor=#b5dbff cellspacing=0 :) (:cellnr colspan=2:) Table 1: List of flags available in the calculation mode. (:cellnr align=center:)Flag (:cell align=center:) Description (:cellnr colspan=2:)General flags used with all running modes (:cellnr:)-ispecs xxx (:cell:)Specification file name (:cellnr:)-ilogic xxx (:cell:)Network logic file name (:cellnr:)-v (:cell:)Verbose mode (:cellnr colspan=2:)Flags used with FileConversion mode (:cellnr:)-ND2TT (:cell:)Convert -ilogic file into a truth table (:cellnr:)-TT2ND (:cell:)Convert truth tables into a specs file (:cellnr:)itables xxx (:cell:)File path for list of truthtables, and the nodelist (:cellnr:)-inodelist xxx (:cell:)File for List of Nodes, Used with TT2ND (:cellnr:)-o xxx (:cell:)File Converter output path/file (:cellnr colspan=2:)Flags used with Calculation mode (:cellnr:)-calc xxx (:cell:)Calculation mode and experiment name (:cellnr:)-n xxx (:cell:)Number of consecutive simulations (:cellnr:)-noBits (:cell:)Suppress bitfile printing (:cellnr:)-randInit (:cell:)Generate random network initial conditions for each simulation (:cellnr colspan=2:)Flags used with Visual mode (:cellnr:)-vis xxx (:cell:)Instantiates the visual mode and sets the output file name (:cellnr colspan=2:)Flags used with Calculation mode (:cellnr:)-patterns (:cell:)Instatiate patterns analysis (:cellnr:)-isettings xxx (:cell:)Patterns file with node activity range settings (:cellnr:)-inodes xxx (:cell:)File with nodes to be analyzed (:tableend:)

To run ChemChains in the calculation mode, use the '-calc' flag.

You can run ChemChains (using our previously created network descriptor and simulation specification files) in the calculation mode in the most basic way (without the use of any extensions) as follows:

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt 
-ispecs inFiles/exts/CChain/logic/sampleNet.txt 
-n 5 -calc myFirstCalcSimulation 

This command will simulate our toy network five times and will save all output in CCOutput/stats/myFirstCalcSimulation folder.

The following table describes the structure and contents of the output folder.

Table 3: Contents of output generated during calculation mode.

Save the file as sampleNodelist.txt.

Note: All parameters are case sensitive.

Note: Each input needs to be declared on a new line.

Figure 1: Sample network.

As an example, let's assume a toy network (Figure 1) consisting of nodes A, B, C, and external input IN1, where green line (with an arrow) denotes positive regulation (e.g., activation) and red line (with a stop line) denotes negative regulation (e.g., inhibition). Because we're dealing with a boolean network, each node has an activation mechanism (represented by truth tables) associated with it. As an example, the activation mechanisms for the nodes of this network are as follows:

Figure 2: Truth tables for nodes A, B, and C, representing the sample network in Fig. 1

These activation mechanisms can be expressed as individual truth tables (Figure 2).

Once the network and truth tables are established, they can be used to create the network descriptor file. Use the following syntax to create the file:

For our example, we'll set the total time to 100 iterations and transient time to 70 as follows:

Note: Each input needs to be declared on a new line. Note: All parameters are case sensitive.

• Initial/Default value - True or False

Note: The name of the delay, sustain, and output nodes has to differ from the names of their inputs.

To create a delay node, use the following syntax:

To create a delay node, use the following syntax:

Output nodes are nodes that will be printed out via ChemChains' visual mode.

To create a new output node, use the following syntax:

Depending on which mode ChemChains is run in, different output will be generated. In general, both the visual and calculation modes will create and save their output in a directory called 'CCOutput' that will be created (if it already doesn't exist) in a directory directly above the directory with ChemChains software. Refer to the Running Modes section on detailed description of output generated by ChemChains.

Thus, for the toy network (Figure 1) with truth tables as shown in Figure 2, create a new directory called "sampleNet" in "inFiles/exts/FileConverter", and three text files (A.csv, B.csv, and C.csv) with the truth tables in tab-delimited format and save them in the "inFiles/exts/FileConverter/sampleNet" directory.

To simulate logical networks with ChemChains, two input files are required: the network descriptor file and simulation specification file (additional input files may be required for individual running modes.

ChemChains Output

Running Modes

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag.

Input Files

To simulate logical networks with ChemChains, two input files are required: the network descriptor file and simulation specification file.

Network Descriptor

Simulation Specification file

(:toc:)(:num 1.1.1.1. :)(:indent:)

font-size=smaller bgcolor=#e0e0ff%

%

Advanced Example: For each simulation, to set IN1 between 0-10% for the first 30 iterations, 11-50% for iterations 31-70, and 51-100% for the remaining simulation time, add the following:

-n 5 -calc myFirstCalcSimulation @]

Random Initial Conditions

ChemChains can be run with randomly generated conditions for every simulation. To run ChemChains with random initial conditions enabled, use the '-rand_init' flag.

• Runtime - specifies the overall length of each simulation, as well as the number of iterations (transient time) before any analysis is conducted.

• Inputs - external inputs (IN1 in the above toy network)

• Noise

• Mutation

• Delay Nodes

• Sustain Nodes

• Output Nodes

To simulate logical networks with ChemChains, two input files are required: the network descriptor file and simulation specification file.

Note: The declaration of each node is on a new line.

Syntax to declare an input:

Note: Each input needs to be declared on a new line

Note: If the initial value is False (i.e., 0 ) we can leave the third column empty.

Note: Make sure that you have created at least one output node in the simulation specification file!

Note: When running in the visual mode, ChemChains can run only one simulation at a time. To run multiple simulations in an automated fashion, run ChemChains in calculation mode.

Note: that the declaration of each node is on a new line.

(:toc:)(:num 1.1.1.1. :)(:indent:)

(:toc:)(:num 1.1.1.1:)(:indent:)

• List of nodes to be analyzed

List of nodes to be analyzed'''

(:toc:)(:num 1.1.1.1.1:)(:indent:)

(:toc:)(:num 1.1.1.1:)(:indent:)

• Settings File

• List of nodes to be analyzed

• Settings File

• List of nodes to be analyzed

List of nodes to be analyzed

(:toc:)(:num 1.1.1:)(:indent:)

(:num:)

Settings File

(:toc:)

(:num:)

(:nonum:)

• Settings File

• List of nodes to be analyzed

ChemChains Output

Installation

Linux

Windows

Basic How-to

Introduction

Input Files

Network Descriptor

Simulation Specification file

ChemChains Output

Running Modes

File Conversion Mode

Visual Mode

Calculation Mode

Patterns Analysis

Settings File

List of nodes to be analyzed

(:num:)

(:num;)

Requirements

1. Requirements

1. How-to
   • Introduction
   • Input Files
   • Simulation Modes

1. Requirements

1. Requirements

1. Requirements
2. Installation
3. Basic How-to
   1. Introduction
   2. Input Files
   3. Simulation Modes
4. Advanced How-to

As an example, let's assume a toy network (Figure 1) consisting of nodes A, B, C, and external input IN1, where green line (with an arrow) denotes positive regulation (i.e., activation) and red line (with a stop line) denotes negative regulation. Because this is a boolean network, each node has a an activation mechanism associated with it. Let's assume the activation mechanisms for the nodes of this network as follows:

• Node A: Node A is activated by node C.

• Node C: Node C is activated by input node IN1 and node B.
• Input node IN1: this node is an input node and hence has no input.

Once finished, save the file as inFiles/CChain/logic/myNetwork.txt.

The next section describes how to create the simulation specification file.

Once finished, save the file as myNetwork.txtin inFiles/CChain/logic/ and move on to the simulation specification file.

Input:name:initial/default value:random(R)/fixed(F):noise(N)/fixed/(F):time to be
 introduced:dose (in percentage):duration of the dosage

(explanation of each option below)

[@./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt

[@./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt

[@./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt -patterns -isettings inFiles/exts/exts/Patterns/settings.txt -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt 
-vis myFirstSimulation.txt 

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt 
-n 5 -calc myFirstCalcSimulation 

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt
-patterns -isettings inFiles/exts/exts/Patterns/settings.txt -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt
-n 5 -calc myFirstCalcSimulation 

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt [[<<]]
-patterns -isettings inFiles/exts/exts/Patterns/settings.txt -n 5 -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt -calc myFirstCalcSimulation 

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt [[<<]]-patterns -isettings inFiles/exts/exts/Patterns/settings.txt -n 5 -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt -calc myFirstCalcSimulation

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt [<<]-patterns -isettings inFiles/exts/exts/Patterns/settings.txt -n 5 -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt -calc myFirstCalcSimulation

ChemChains Output

Depending on which mode ChemChains is run in, different output will be generated. In general, both the visual and calculation modes will create and save their output in a directory called 'CCOutput' that will be created (if it already doesn't exist) in a directory directly above the directory with ChemChains software. Refer to the Running Modes section on detailed description of output generated by ChemChains.

Although, ChemChains is a command-line program, it can output visual simulation results via its visual mode. To run ChemChains in visual mode, use the “-vis” flag. To simulate the toy network using the simulation specification file both created in the previous sections run ChemChains as follows:

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt -vis myFirstSimulation.txt

Note: Make sure that you have created at least one output node in the simulation specification file!

Once the simulation finishes, a new file will be created in the ChemChains output folder, in a text file called “myFirstSimulation.txt”.

Open the text file and we should see output similar to the Figure 3. ('*' denotes the active state of the node, while '.' represents the OFF state)

Note: When running in the visual mode, ChemChains can run only one simulation at a time. To run multiple simulations in an automated fashion, run ChemChains in calculation mode.

Calculation mode provide ChemChains users the ability to run thousands of automated simulations and subsequently use the generated data to analyze the dynamics of the simulated model.

To run ChemChains in the calculation mode, use the '-calc' flag. Other flags available within the calculation mode are listed in Table 2.

(:table border=1 width=40% align=center bgcolor=grey cellspacing=0 :) (:cellnr:) Table 2: List of flags available in the calculation mode. (:cellnr:)

• Requirements
• Installation
• Basic How-to
  • Introduction
  • Input Files
  • Simulation Modes
• Advanced How-to

(:tableend:)

You can run ChemChains (using our previously created network descriptor and simulation specification files) in the calculation mode in the most basic way (without the use of any extensions) as follows:

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt -n 5 -calc myFirstCalcSimulation

This command will simulate our toy network five times and will save all output in CCOutput/stats/myFirstCalcSimulation folder.

The following table describes the structure and contents of the output folder.

(:table border=1 width=40% align=center bgcolor=grey cellspacing=0 :) (:cellnr:) Table 3: Contents of output generated during calculation mode. (:cellnr:)

• Requirements
• Installation
• Basic How-to
  • Introduction
  • Input Files
  • Simulation Modes
• Advanced How-to

(:tableend:)

Patterns Analysis

To perform patterns analysis, ChemChains must be initiated in the calculation mode (as described above), and using '-patterns' flag. When using patterns to perform analysis, two additional input files are required: i) the settings file and ii) a text file with a list of nodes that will undergo the pattern analysis.

Settings File

The patterns settings file defines activity ranges that will form patterns.

For your convenience, a sample settings files has already been created. You can find it and edit it in inFiles/exts/Patterns/settings.txt. The file contains two groups of settings: i) default settings that are applied on all nodes subjected to patterns analysis and ii) node specific settings that apply to only one node at a time. The syntax is as follows:

Default settings:

The sample settings provided should have the following:

which means the activity of all nodes being analyzed will be categorized into three ranges: 0-9% (all nodes in this range will be coded “0”), 10-29% (all nodes in this range will be coded “1”), and 30-100% (all nodes in this range will be coded “2”)

Node specific settings:

List of nodes to be analyzed

An example of this file is also supplied with the latest ChemChains release, and is located in inFiles/exts/Patterns/sampleOutNodes.txt. In this file, each node to be analyzed with the patterns extension is entered on a new line.

To run ChemChains using these input files, type in the following command:

./ChemChains -ilogic inFiles/exts/CChain/logic/sampleNet.txt -ispecs inFiles/exts/CChain/logic/sampleNet.txt -patterns -isettings inFiles/exts/exts/Patterns/settings.txt -n 5 -inodes nFiles/exts/exts/Patterns/sampleOutNodes.txt -calc myFirstCalcSimulation

(:table border=1 width=40% align=left bgcolor=#cccc99 cellspacing=0 :) (:cellnr:) Navigation Links (:cellnr:)

• Requirements
• Installation
• Basic How-to
  • Introduction
  • Input Files
  • Simulation Modes
• Advanced How-to

(:tableend:)

Requirements

ChemChains is a platform independent command-line software written in C++, that has been tested on Linux and Windows platforms.

To run ChemChains in Windows, a Linux-like environment is necessary. For example, you can download and install the freely available cygwin from here.

Installation

Linux

1. Open a new terminal window
2. Type: make (This should create an executable file called ChemChains)

Windows

1. Start Cygwin
2. In the Cygwin terminal window, type: make (This should create an executable file called ChemChains)

Basic How-to

Introduction

This section will provide you with the most basic ways of simulating your first network model using ChemChains.

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag.

Input Files

To simulate logical networks with ChemChains, two input files are required: the network descriptor and a simulation specification file.

Network Descriptor

Network descriptor is a syntax-specific text file that stores the network, and logic for each node.

Figure 1: Sample network.

As an example, let's assume a toy network (Figure 1) consisting of nodes A, B, and C, where green line (with an arrow) denotes positive regulation (i.e., activation) and red line (with a stop line) denotes negative regulation. Because this is a boolean network, each node has a an activation mechanism associated with it. Let's assume the activation mechanisms for the nodes of this network as follows:

• Node A: Node A is activated by node C
• Node B: Node B is inhibited by node A and activated by node C. In addition, node C is a required positive regulator. The negative regulation is dominant over the positive one.
• Node C: Node C is activated by node B

Figure 2: Truth tables for nodes A, B, and C.

These activation mechanisms can be expressed as individual truth tables (Figure 2).

Once we have the network and truth tables established, we can create our network descriptor file using these tables. To create the file, the following syntax needs to be used:

Thus, the network descriptor for our toy network can look like:

Note that the declaration of each node is on a new line. Once finished we can save the file as myNetwork.txtand move on to the simulation specification file.

Simulation Specification file

ChemChains is a feature-rich logic network simulation software, which offers users many advanced simulation options. These options are specified by users in the specification file, the second of the required input files, that is loaded into the program before each simulation experiment.

The following describes the various options contained within this file:

• Runtime - specifies the overall length of each simulation, as well as the number of iterations (transient time) before any analysis is conducted.

Syntax: RunTime:TransientTime:TotalTime

For our example, we'll set the total time to 20 iterations and transient time to 10 as follows:

• Inputs - external inputs (IN1 in the above toy network)

Syntax to declare an input (note that each input needs to be declared on a new line:

• Name -self-explanatory
• Initial/Default value - self-explanatory
• Random(R)/Fixed(F) - this parameter specifies whether the percentage ON should be as specified by the user or generated randomly
• Noise(N)/Fixed(F) - specifies whether the input will be set on a periodic cycle or randomly bounce around within a given range (see Noise below)
• Time to be introduced - time when a given percentage ON will come into an effect
• Dosage - specified percent ON for a given input (integer from 0 to 100)
• Duration of the dosage - the number of iterations the dosage amount will be exerted on the input (note that if the duration is shorter than the total runtime, the input will be set to 0% ON once the duration period is achieved)

To declare input IN1, with True as the initial condition, fixed percentage activity on a periodic cycle set to 10%, and effective for the entire simulation length add the following line in the specification file:

• Noise

To measure the current level of activity for each input during a simulation, ChemChains uses a sliding window (user pre-defined length) approach which allows the program to know whether the activity is within the desired percentage ON. In this example we'll set the sliding window to 5. Syntax: Noise:Window size:noise level To set the noise level as specified above, add the following line to the specification file:

• Mutation

The mutation parameter enables users to turn ON/OFF any node in the network to perform mutagenesis studies. When the node(s) is mutated, the corresponding truth table is ignored by the simulation engine and the activity of the node becomes fixed for the entire course of the simulation. For example, to turn off node A, you would add the following line to the specification file:

To mutate node A to be constitutively active, replace 'OFF' with 'ON'.

• Delay Nodes

• Sustain Nodes

• Output Nodes

Running Modes

The most recent version of ChemChains can be ran in three modes, one of which is a network construction mode (or File Conversion) and the remaining two are simulation modes.

File Conversion Mode

As mentioned above, to run ChemChains, a file with the network description is required. This file can be created manually as described in the previous section, or automatically from a provided set of truth tables for individual nodes.

These truth tables need to be in the form of a tab-delimited text file. Each table must be in a separate file which should be named the same as the name of the node of interest.

Thus, for the toy network (Figure 1) with truth tables as shown in Figure 2, create a new directory called "sampleNet" in "inFiles/exts/FileConverter", and three text files (A.csv, B.csv, and C.csv) with the truth tables in tab-delimited format and save them in the "inFiles/exts/FileConverter/sampleNet" directory.

In addition, we need to create another file with the list of nodes comprising our network. In this file, each node has two properties, nodeID and initial value, associated with it. Each node and its properties need to be on a new line. The mentioned node properties need to be tab-separated.

The syntax is as follows:

Sample node list for our network will look like:

Save the file as sampleNodelist.txtc.

To create the Network Descriptor file from existing truth tables, run ChemChains with the following parameters:

Visual Mode

Although, ChemChains is a command-line program, it can output visual simulation results via its visual mode. To run ChemChains in visual mode, use the “-vis” flag.

Calculation Mode

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Advanced How-to

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• Noise

• Name -self-explanatory
• Initial/Default value - self-explanatory
• Random(R)/Fixed(F) - this parameter specifies whether the percentage ON should be as specified by the user or generated randomly
• Noise(N)/Fixed(F) - specifies whether the input will be set on a periodic cycle or randomly bounce around within a given range (see Noise below)
• Time to be introduced - time when a given percentage ON will come into an effect
• Dosage - specified percent ON for a given input (integer from 0 to 100)
• Duration of the dosage - the number of iterations the dosage amount will be exerted on the input (note that if the duration is shorter than the total runtime, the input will be set to 0% ON once the duration period is achieved)

Syntax to declare an input (note that each input needs to be declared on a new line:

To declare input IN1, with True as the initial condition, fixed percentage activity on a periodic cycle set to 10%, and effective for the entire simulation length add the following line in the specification file:

• Runtime - specifies the overall length of each simulation, as well as the number of iterations (transient time) before any analysis is conducted.

Syntax: RunTime:TransientTime:TotalTime

For our example, we'll set the total time to 20 iterations and transient time to 10 as follows:

• Inputs - external inputs (IN1 in the above toy network)

Syntax to declare an input (note that each input needs to be declared on a new line)

The most recent version of ChemChains can be ran in three modes, one of which is a network construction mode (or File Conversion) and the remaining two are simulation modes.

Visual Mode

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Calculation Mode

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File Conversion Mode

Thus, for the toy network (Figure 1) with truth tables as shown in Figure 2, create a new directory called "sampleNet" in "inFiles/exts/FileConverter", and three text files (A.csv, B.csv, and C.csv) with the truth tables in tab-delimited format and save them in the "inFiles/exts/FileConverter/sampleNet" directory.

Save the file as sampleNodelist.txtc.

To create the Network Descriptor file from existing truth tables, run ChemChains with the following parameters:

The syntax is as follows:

In addition, we need to create another file with the list of nodes comprising our network. In this file, each node has two properties, nodeID and initial value, associated with it. Each node and its properties need to be on a new line. The mentioned node properties need to be tab-separated.

Sample node list for our network will look like:

File Conversion

As mentioned above, to run ChemChains, a file with the network description is required. This file can be created manually as described in the previous section, or automatically from a provided set of truth tables for individual nodes.

• File Conversion

These truth tables need to be in the form of a tab-delimited text file. Each table must be in a separate file which should be named the same as the name of the node of interest.

Thus, for the toy network (Figure 1) with truth tables as shown in Figure 2, create three text files (A.csv, B.csv, and C.csv) with the truth tables in tab-delimited format.

To run ChemChains in Windows, a Linux-like environment is necessary. For example, you can download and install the freely available cygwin from here.

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Once finished we can save the file as myNetwork.txtand move on to the simulation specification file.

ChemChains is a feature-rich logic network simulation software, which offers users many advanced simulation options. These options are specified by users in the specification file, the second of the required input files, that is loaded into the program before each simulation experiment.

The following describes the various options contained within this file:

• Runtime
• Inputs
• Noise
• Mutation
• Delay Nodes
• Sustain Nodes
• Output Nodes

Thus, the network descriptor for our toy network can look like:

Note that the declaration of each node is on a new line. Once finished we can save the file as myNetwork.txt.

Thus, our toy network would look like:

Once we have the network and truth tables established, we can create our network descriptor file using these tables. To create the file, the following syntax needs to be used:

• Node B: Node B is inhibited by node A and activated by node C. In addition, node C is a required positive regulator. The negative regulation is dominant over the positive one.

• Node B: Node B is inhibited by node A and activated by node C. In addition, node C is a required positive regulator.

These activation mechanisms can be expressed as individual truth tables (Figure 2).

Attach:toynetwork_TT.jpg Δ | Figure 2.

Attach:toynetwork_TT.jpeg Δ | Figure 2.

These activation mechanisms can be expressed as a truth tables (Figure 2).

As an example, let's assume a toy network (Figure 1) consisting of nodes A, B, and C, where green line (with an arrow) denotes positive regulation (i.e., activation) and red line (with a stop line) denotes negative regulation. Because this is a boolean network, each node has a an activation mechanism associated with it. Let's assume the activation mechanisms for the nodes of this network as follows:

As an example, let's assume a toy network (Figure 1) consisting of nodes A, B, and C, where green line (with an arrow) denotes positive regulation (i.e., activation) and red line (with a stop line) denotes negative regulation. Because this is a boolean network, each node has a an activation mechanism associated with it. The activation mechanisms for the nodes of this network are as follows:

• Node A: Node A is activated by node C
• Node B: Node B is inhibited by node A
• Node C: Node C is activated by node B

This mechanism can be expressed as a truth table.

%lfloat text-align=center margin-top=5px margin-right=25px margin-bottom=5px margin-left=25px% |Figure 1.

Attach:toynet.jpeg]

toynet.jpeg"Sample toy network"

Attach:toynet1.jpeg Δ

http://example.com|

http://pmichaud.com/img/misc/pc.jpg | [- [[ (Wikipedia:Paper_clips | Paper clips ]] are fun to work with. -]

[[http://example.com|Attach:toynet1.jpg]]

Attach:Main.Tutorial/toynet1.jpg

Attach:Main/toynet1.jpg

Attach:toynet1.jpg

Attach:toynet11.png Δ

Network descriptor is a syntax-specific text file that stores the network, and logic for each node.

As an example, let's assume the following toy network consisting of nodes A, B, and C.

Network descriptor is a syntax-specific text file that stores the network and logic for each node.

Network Descriptor

Simulation Specification file

Requirements

1. !!Requirements

Introduction

Input Files

Simulation Modes

To simulate logical networks with ChemChains, two input files are required: the network descriptor and a simulation specification file.

Network Descriptor

Simulation Specification file

Simulation Modes

(:table border=1 width=40% align=left bgcolor=#cccc99 cellspacing=0 :)

• Simulation Modes

• Introduction
• Input Files

Input Files

Introduction

Input Files

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag.

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag.\\

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag.

./ChemChains -h

./ChemChains -h

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation. To see all available options and command-line parameters run ChemChains with the -h flag. (:markup:)

(:markupend:)

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation.

To run ChemChains, users must provide several input files. Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation.

This section will provide you with the most basic ways of simulating your first network model using ChemChains.\\

ChemChains is a platform independent command-line software written in C++, that has been tested on Linux and Windows platforms.\\

This section will provide you with the most basic ways of simulating your first network model using ChemChains.\\ \\

ChemChains is a platform independent command-line software written in C++, that has been tested on Linux and Windows platforms. \\

This section will provide you with the most basic ways of simulating your first network model using ChemChains.\\
To run ChemChains, users must provide several input files (described below). Once simulations and/or analysis are initiated, ChemChains will create several types of output file formats. Both the input files, as well as the desired output format and the output files must be specified by users in the form of command-line parameters provided to ChemChains at the time of program initiation.

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ChemChains is a platform independent software written in C++, that has been tested on Linux and Windows platforms. \\

Advanced How-to

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Linux

1. Open a new terminal window
2. Type: make (This should create an executable file called ChemChains)

Windows

1. Start Cygwin
2. In the Cygwin terminal window, type: make (This should create an executable file called ChemChains)

\\

To run ChemChains in Windows, a Linux-like environment is necessary. For example, you can download and install the freely available cygwin from here.

ChemChains is a platform independent software that has been tested on Linux and Windows platforms.
To run ChemChains in Windows, download cygwin

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• Installation
• Basic How-to
• Advanced How-to

Installation

Basic How-to

Advanced How-to

(:tableend:)

(:tableend:)

(:tableend:)//

Requirements

Requirements

• Requirements

• Installation
• Basic How-to
• Advanced How-to

(:table border=1 width=30% align=left bgcolor=#cccc99 cellspacing=0 :)

• Requirements

• Requirements?

• Main.Tutorial.Requirements?

• Requirements?
• Installation?
• Basic How-to?
• Advanced How-to?

(:table border=1 width=30% align=right bgcolor=#cccc99 cellspacing=0 :) (:cellnr:) Navigation Links (:cellnr:)

• Tables?
• Table directives?

(:tableend:)

• Advanced How-to

• Requirements
• Installation
• Basic How-to
• Advanced How-to

to be written...