Appendix

Getting Started Guide

For a four page getting started guide, including shortcuts, keyboard controls and a diagram of the GenomeBrowse interface see the GenomeBrowse: Getting Started Guide.

Platform Notes

This section will contain notable information regarding the use of GenomeBrowse on specific platforms.

Under some platforms the behavior of GenomeBrowse could vary slightly in specific situations. Also, on some platforms certain system settings can be used to improve the performance of program.

Microsoft Windows

Memory Usage

Allow up to 3GB of memory usage under 32~bit Windows

By default, 32~bit Windows versions allow applications to run in a 2GB memory space. Applications that attempt to use more than this 2GB limit will crash. When working with very large datasets, it may no longer be possible to fit the required data into the default memory space supplied by Windows. Using the /3GB switch in boot.ini allows certain applications to access up to 3GB of virtual address space leaving 1GB for the windows kernel.

To allow GenomeBrowse to use more than 2GB of memory, you can edit your system’s boot.ini file.

To open the boot.ini file:

  1. Click Start, click Run
  2. Enter sysdm.cpl, and click OK

On the resulting window, select the Advanced tab, and click Settings under Startup and Recovery. Next, click the Edit button in the System startup group.

Now the boot.ini file should be open in a Notepad editor. Before you edit the file, it is recommended that you create a backup of the original. To do this: select File > Save As..., and choose a location to create the backup file. Close the Notepad editor, and click the Edit button again. Now you should be ready to edit the file.

To allow GenomeBrowse to use up to 3GB of memory add the entry /3GB to the end of the line under the [operating systems] section corresponding to your current configuration. Save the file to keep this option. A reboot is required before the change will take effect.

Memory Availability Under 64~bit Windows

Windows XP Professional x64 Edition (for PCs with x86~64 processors) is capable of running GenomeBrowse in its 32~bit emulation mode efficiently and allows the application to address up to 4 GB of virtual memory if available. Windows XP 64~bit Edition (built for Intel’s IA~64 Itanium processors) is discontinued as an operating system as of 2005, and is not supported by Golden Helix, Inc.