CGA-BNI is a promising and scalable tool to predict both the structure and the dynamics of a gene regulatory network when a highest accuracy is needed at the cost of sacrificing the execution time.
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Install Java SE Development Kit, recommended version is 8 (from https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html). We are using the java version "1.8.0_171"
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Install NetBeans IDE, recommeded version is above 7.3 (from https://www.oracle.com/technetwork/java/javase/downloads/jdk-netbeans-jsp-3413139-esa.html)
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Download this project into a folder, for example, "CGAProj"
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Extract all .zip files in the /data/Inference folder
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Open the project by NetBeans IDE, and open the file "InferBN.java":
- The main function, and also inference funtions is in this Java file
- Build and run the project with the default config:
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The config has three arguments: the path to data, type of data, number of trials
- path to data: the path to the data folder containing DREAM3, random networks, and the large-scale E.coli datasets. We could make another dataset by making another dataset folder and chaning the source codes a little similar to the way of the large-scale Ecoli dataset.
- type of data: "dream", "rbn", and "ecoli" correspond to DREAM3, random networks, and the large-scale Ecoli dataset, respectively
- number of trials: repeat the experiment a number of times to get avergage results
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Right-click in the project, choose menu Properties -> Run
- We could change the arguments as in the above figure
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Some examples of arguments:
- E:\CGA_BNI\data\ dream 1
- E:\CGA_BNI\data\ rbn 50
- E:\CGA_BNI\data\ ecoli 20
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Results are stored in the project folder and named as run1, run2, ...
Contact us: trinhhungcuong@tdtu.edu.vn
Thanks for your interests!