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Deterministic network simulation component of GNLab 

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Program Information

Name: Deterministic network simulation component of GNLab 
Domain: Bioinformatics
Functionality: A command-line tool for large-scale analysis and simulation of gene regulatory networks (GRNs) 
Input: A directed weighted graph G 
Output: R:The output of G 

Reference

An innovative approach for testing bioinformatics programs using metamorphic testing  10.1186/1471-2105-10-24 

MR Information

MR1------

Description:
Property: $R_{2}$=$R_{1}$+the output of P 
Source input:
Source output: $R_{1}$ 
Follow-up input: G’ 
Follow-up output: $R_{2}$ 
Input relation: G’:Addition of a disconnected node P to G 
Output relation: $R_{2}$=$R_{1}$+the output of P 
Pattern:

MR2------

Description:
Property: $R_{2}$=$R_{1}$+the output of P 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G’ 
Follow-up output: $R_{2}$ 
Input relation: G’: Addition of a non-regulator node P to G 
Output relation: $R_{2}$=$R_{1}$+the output of P 
Pattern:

MR3------

Description:
Property: the output of P would be increased, while output of the other nodes should remain unchanged 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G’ ,Non-regulator node P 
Follow-up output: $R_{2}$ 
Input relation: G’: Add an edge, which is directed to P with a positive weight 
Output relation: the output of P would be increased, while output of the other nodes should remain unchanged 
Pattern:

MR4------

Description:
Property: only the output of P would be decreased, while output of the other nodes should remain unchanged 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G’, Non-regulator node P 
Follow-up output:  $R_{2}$ 
Input relation: G’: Add an edge, which is directed to P with a negative weight 
Output relation: only the output of P would be decreased, while output of the other nodes should remain unchanged 
Pattern:

MR5------

Description:
Property: $R_{1}=R_{2}$ 
Source input:
Source output: $R_{1}$ 
Follow-up input: G’, Node P 
Follow-up output: $R_{2}$ 
Input relation:  G’:Add an edge, which is directed to P with zero weight
Output relation:  $R_{1}=R_{2}$
Pattern:

MR6------

Description:
Property: $R_{2}$=$R_{1}$-the output of P 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G’, Non-regulator node P 
Follow-up output: $R_{2}$ 
Input relation: G’: Delete P from G 
Output relation: $R_{2}$=$R_{1}$-the output of P 
Pattern:

MR7------

Description:
Property:  Such a deletion should affect the outputs related to all P's descendant nodes, while the outputs related to P's non-descendant nodes should remain unchanged
Source input: G
Source output: $R_{1}$ 
Follow-up input: G’, Node P 
Follow-up output: $R_{2}$ 
Input relation: G’: Delete P from G 
Output relation: Such a deletion should affect the outputs related to all P's descendant nodes, while the outputs related to P's non-descendant nodes should remain unchanged 
Pattern:

MR8------

Description:
Property: $R_{2}=R_{1}+R_{1}$ 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G'
Follow-up output:  $R_{2}$ 
Input relation: G’=G+G 
Output relation: $R_{2}=R_{1}+R_{1}$ 
Pattern:

MR9------

Description:
Property: Increase all the expression values associated with P 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G'
Follow-up output:  $R_{2}$ 
Input relation: G’: A node P in G and an edge E directed to P, increase the weight of E 
Output relation: Increase all the expression values associated with P 
Pattern:

MR10------

Description:
Property: Decrease all the expression values associated with P 
Source input: G
Source output: $R_{1}$ 
Follow-up input: G'
Follow-up output:  $R_{2}$ 
Input relation: G’: A node P in G and an edge E directed to P, decrease the weight of E 
Output relation: Decrease all the expression values associated with P 
Pattern:
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