SimFluVar Simulation tool for influenza virus variation

1. Program Introduction
SimFluVar is a program in the SimFlu (Simulation tool for influenza virus) series; its modification parameters, in 61x61 formations, are calculated based on year-to-year modification patterns extracted from empirically discovered influenza virus gene information. This programs output is codon-level computation of the modification patterns with time on influenza A virus classified by year; the program also provides analysis results on change in base creation within Wobble base position of each codon. Read More

2. Setup
Setup can be done automatically by simply executing the distributed setup program. First, ensure that Java Runtime Environment (JRE) is already installed on the computer; if it is not, please visit the JAVA distribution page (http://www.oracle.com/technetwork/java/javase/downloads/index.html) to install the latest JRE. After downloading it on the PC, run the program by double-clicking on the 'SimFluVar2013_xxxx.setupexe' file. Upon entering all required information about the setup, you will be taken to the next screen, where the final setup will take place. Read More

3. Project Creation and Execution
When selecting 'Project-Crete Project' from the menu, Project Creation Wizard shown below gets executed. In the above form, enter project name, author, and description and press the Next button to generate output similar to below; it should be noted that having a gap within the project name or leaving any of the slots for author and description blank, the project creation does not get processed at the final stage. Read More

4. Checking Results
Upon creation of a new project, a node is generated on the tree on the left hand side that indicates input files and output files, where the Input Data folder stores input files. Double-clicking on the DNA-shaped icon will produce a window illustrating input sequence as follows. Read More

5. ClustalW Convert Tool
Within the SimFluVar program, there is a conversion tool that changes ClustalW's result files to its own input file. Selecting 'Tool-ClustalW to SimFluvar' in the menu produces a window as shown below. Next, press the Search button to select the folder containing ClustalW's output file; then, generate all output files created in ClustalW as shown below. From there, select the desired file and press the 'OK' button to convert the selected file to SimFluVar's input file. Read More

6. Saving/Reading Projects
Click on the project name from the project tree of SimFluVar program and select 'File>Save Project' menu to save the selected project as the designated file, which gets stored in '*.svf' format. This file can be read in project format when you select File-Load Project menu. Read More