Team:USTC-Software/model

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            <h1><img src="https://static.igem.org/mediawiki/2011/b/b8/USTC_Software_iGEM_logo.jpg" alt="iGEM" width="173" height="150" /> </br> </br> USTC-Software </h1>
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<p> Contents:
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  <ul type="circle">
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          <li><a href="#Assembly View"> Assembly View </a></li>
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            <ul type="disc">
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              <li><a href="#Biological Components Browser">Biological Components Browser</a></li>
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              <li><a href="#Editing Component">Editing Component</a></li>
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              <li><a href="#Solving the MoDeL">Solving the MoDeL</a></li>
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<h2>MoDeL</h2>
 +
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<p>The Perl language is a powerful tool for dealing with regular expressions, and it manages to process complex problems in a timely way. For example, for a hash array with a few elements in the buckets almost get the same manipulating time with a big hash with millions of elements. This feature improves the speed of rule based modeling remarkably.</p>
 +
 +
<p>Dealing with regular expressions is also Perl's cup of tea. So the software can spend more running time saved by perl on providing a better user's interface, making it more convenient for users.</p>
 +
 +
<p>Our approach first realized by Liaochen and 2010igemers emphasize on the structure of the species.</p>
 +
 +
<p>Here is a detailed explanation to the input file of the rule based modeling approach There are four blocks, respectively lists the definition of parameters, the definition of compartments, seed species and events.</p>
 +
 +
<p>The definition of parameters consists of two items. The left side term is the name of the variable, to the right is the expression of that parameter. Note that variables in that expression must be defined by the user. But it makes no difference whether they are defined before the expression. This is to avoid redundant definition and no definition.</p>
 +
 +
<h3>SYNTAX</h3>
 +
 +
<p>The compartments definition is in this way: <br/>
 +
[name ][outside][ruletable]{volume}{population}, where terms in the square brackets are mandatory, while terms in the curly braces are optional.<br/>
 +
The default value of the volume is 1. The outside term means the compartment outside the compartment, which is usually the medium that held the compartment like the ecoli. <br/>
 +
Ruletable is used to associate a rule in the data base with the compartment.</p>
 +
 +
<P>The third block, reads [compartment][name][structure][init_concentration]{const}, structure is the definition of the complex structure, const is optional since it's in the curly brace. If the substance has a const property, then after the substance, write a const. if not, leave it blank.</p>
 +
 +
<p>The last block is the events definition. The formats are [name][trigger_condition][event_assignments...] The name of the event is usr defined, trigger_condition is a bool expression, all the variables inside this bool expression must have been defined in one of the above three blocks. Event_assignments is a list of assignments, something like assignment1 assignment2 assignment3, with white space separated. There is no constraint on the number of assignments. Each assignment must be the format [variable]=[expression]</p>
 +
 +
<p>A general rule in the algorithm is that the name of the variable must be started by A-Z –z and other characters can be A-Z-a-z-0-9.</p>
 +
 +
<h3>Technology</h3>
 +
 +
<p>Detailed technology used by the re-build version of MoDeL is not available for now. Please refer to our previous year's website here(https://2010.igem.org/Team:USTC_Software/MoDeL). The basic ideas are the same, but the algorithms are re-designed to run hundreds times faster.</p>
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Revision as of 09:04, 5 October 2011


Team:USTC-Software - 2011.igem.org/views

MoDeL

The Perl language is a powerful tool for dealing with regular expressions, and it manages to process complex problems in a timely way. For example, for a hash array with a few elements in the buckets almost get the same manipulating time with a big hash with millions of elements. This feature improves the speed of rule based modeling remarkably.

Dealing with regular expressions is also Perl's cup of tea. So the software can spend more running time saved by perl on providing a better user's interface, making it more convenient for users.

Our approach first realized by Liaochen and 2010igemers emphasize on the structure of the species.

Here is a detailed explanation to the input file of the rule based modeling approach There are four blocks, respectively lists the definition of parameters, the definition of compartments, seed species and events.

The definition of parameters consists of two items. The left side term is the name of the variable, to the right is the expression of that parameter. Note that variables in that expression must be defined by the user. But it makes no difference whether they are defined before the expression. This is to avoid redundant definition and no definition.

SYNTAX

The compartments definition is in this way:
[name ][outside][ruletable]{volume}{population}, where terms in the square brackets are mandatory, while terms in the curly braces are optional.
The default value of the volume is 1. The outside term means the compartment outside the compartment, which is usually the medium that held the compartment like the ecoli.
Ruletable is used to associate a rule in the data base with the compartment.

The third block, reads [compartment][name][structure][init_concentration]{const}, structure is the definition of the complex structure, const is optional since it's in the curly brace. If the substance has a const property, then after the substance, write a const. if not, leave it blank.

The last block is the events definition. The formats are [name][trigger_condition][event_assignments...] The name of the event is usr defined, trigger_condition is a bool expression, all the variables inside this bool expression must have been defined in one of the above three blocks. Event_assignments is a list of assignments, something like assignment1 assignment2 assignment3, with white space separated. There is no constraint on the number of assignments. Each assignment must be the format [variable]=[expression]

A general rule in the algorithm is that the name of the variable must be started by A-Z –z and other characters can be A-Z-a-z-0-9.

Technology

Detailed technology used by the re-build version of MoDeL is not available for now. Please refer to our previous year's website here(https://2010.igem.org/Team:USTC_Software/MoDeL). The basic ideas are the same, but the algorithms are re-designed to run hundreds times faster.

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