Tutorials – 2. Getting Started

2. Getting Started
This Chapter covers the following:

  • What types of files are required to run BiologicalNetworks
  • How to modify computer’s configurations to run BiologicalNetworks
  • Java WEB START intsructions
  • How to download and install BiologicalNetworks
  • How to download additional Data files

2.1 System Requirements

In order to run BiologicalNetworks successfully, your computer must meet the following minimum system requirements.

Windows
1GHz Intel Pentium CPU
Microsoft Windows 95, 98, 2000 and XP
256MB RAM
25MB Free Disk Space

Linux
Linux 2.2.* Kernel on i686 processors
256MB RAM
25MB Free Disk Space

Macintosh
800MHz PowerPC G3 or G4
Mac OS X 10.1 and above
256MB RAM
25MB Free Disk Space

2.2 Java WEB START Instructions

Begin by clicking WEB START version of the BiologicalNetworks (download size: ~20 MB; download time: depending on your internet connection ~ 2 minutes first download and ~10 seconds all subsequent runs). This starts BiologicalNetworks on your own computer, after downloading the program and annotation from our website. (On subsequent runs, the program or annotation will not be downloaded again unless we have new versions or new annotation for you to use.) If BiologicalNetworks does not start, you may need to install last version of JAVA with Java Web Start inside. It is highly recommended to read the Tutorials section, before starting to use the program.

2.3 Download Additional Data Files.

  1. For making Microarray, 3D protein structure, Functional Data analysis you can download example data files.
    Download the ExampleData.ZIP file containing Stanford (tab delimited), Affymetrix, TIGR, GenePix microarray data, GeneOnology data files and PDB 3D structures of proteins from the BiologicalNetworks website (http://BiologicalNetworks.net/ExampleData.zip). Before you download a file, notice that its byte size is provided on the download page. Once the download has completed, check that you have downloaded the full, uncorrupted data file.
  2. Zip file also contains GO annotation files, to make GeneOntology annotation analysis.
  3. Unzip the file anywhere into your hard drive. Now you can load these data files into BiologicalNetworks analysis environment.

2.4 Troubleshooting.

If you have problems running BiologicalNetworks try to disable you firewall program and launch BiologicalNetworks again. If it helps you need to change firewall settings to allow Sun Java to connect to Internet.

For example to enable Sun Java access to Internet in Norton Internet Security you may follow these steps:

  1. Open NIS.
  2. Click on Status & Setting menu item on the left.
  3. Click on Personal Firewall.
  4. Press Configure button.
  5. Select Programs tab.
  6. Find java item in list.
  7. Select Permit All option in Internet Access column.
  8. Click OK.

For other firewall program please refer to it’s manual for more details.

If it doesn’t help try to restart your computer.

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