Team:USTC-Software/Project/Method

From 2013.igem.org

(Difference between revisions)
Line 34: Line 34:
                                
                                
           <li><a href="#Alignment_Analyze" class="button">Operon Theory and Regulatory Model</a></br>
           <li><a href="#Alignment_Analyze" class="button">Operon Theory and Regulatory Model</a></br>
-
                 <a href="#dbabstract" class="button" id="subbutton">Abstract</a></br>
+
                 <a href="#ui" class="button" id="subbutton">User Input</a></br>
                 <a href="#fetch" class="button" id="subbutton">Fetch Regulation</a></br>
                 <a href="#fetch" class="button" id="subbutton">Fetch Regulation</a></br>
                 <a href="#fgi" class="button" id="subbutton">Fetch Gene Info</a></br>
                 <a href="#fgi" class="button" id="subbutton">Fetch Gene Info</a></br>
Line 256: Line 256:
<div class="jobs_trigger" id="cng"><strong>Construct New GRN</strong></div>
<div class="jobs_trigger" id="cng"><strong>Construct New GRN</strong></div>
   <div class="jobs_item" style="display: none;">
   <div class="jobs_item" style="display: none;">
-
     <h3>1 User Input</h3>
+
     <h3 id="ui">1 User Input</h3>
     <p align="justify">
     <p align="justify">
       Some genes' regulation could be get from experiment. So, if users could get the unknow regulation between new gene and old ones, they could manually set the interactions which do not need model. Those regulations will be used in later simulation.
       Some genes' regulation could be get from experiment. So, if users could get the unknow regulation between new gene and old ones, they could manually set the interactions which do not need model. Those regulations will be used in later simulation.

Revision as of 00:40, 28 October 2013

Header2


Methodologies

Methodologies

In order to simulate the GRN's working and analyze the changing after exogenous gene imported, some advanced algorithms and classical methods are employed in the software. These algorithms and methods include Binary Tree method, Needle-Wunsch Algorithm, Decision Tree method, Hill Equation and PSO Algorithm.

There are four parts of methodologies: Database, Operon Theory and Regulatory Model, Forward Analysis and Reverse Analysis.

Database

Abstract
Fetch Regulation
Fetch Gene Info
Fetch Promoter Info
Integration

Our software integrates all information we picked out about genes and generates a file named “all_info” —— all information about genes —— for the output graphical interface's reading. In the meanwhile, the array of objects containing all information has been stored in computer memory which greatly improve the computing speed of our software.

  The format of all_info database:
    No.    promoter_sequence    gene_sequence    gene_name    ID    left_position    right_position    promoter_name     description
The fetching module generates three files: old_GRN, all_info and uncertain_database.

Operon Theory and Regulatory Model

Operon Theory
Regulatory Model
Similarity and Homology

Forward Analysis

Construct New GRN
Network Model
Evaluate Network

Reverse Analysis

Virtual Gene
Expression Range
Particle Swarm Optimaztion
Locate Optimal Target