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Data Analysis

Desktop Computers

The CGC computer lab has three Dell Optiplex PC's running Windows XP Professional, needed for the ABI software, and two Apple G5 1.8 GHz dual processor PowerMacs running OS X 10.5. Users can work with the ABI software like Sequence Analysis 5.2/3 and GeneMapper v3.7/4.0 in "offline" mode on the Windows XP PC's. All the computers have the standard MS Office applications and the ability to back up data on CD's (ROM and RW) and DVD's, and are networked. Sequencher from the UW license pool, MacVector, and Photoshop CS are installed on the Macs. You can also run UNIX processes, do graphics, etc., on the G5's.   There is also a Quad core HP xw8600 workstation with Ubuntu-based BioLinux installed for running open source Bio/Molecular Unix/Linux software, running CLCBio GenomicsWorkbench, and transferring large files onto and off of the Linux server.

Hard at work analyzing data

The ABI sequencers and the BioRobot, and most of the other instruments are connected to their own PC's, running Windows XP. Some of these computers are not networked. Data can be moved back and forth between these instrument-dedicated computers and the networked computers in the computer lab using USB flash memory drives or on CD's.

Next Generation Sequencing Data Analysis

NGS data analysis is provided by a Linux server which hosts CLCBio Genomics Server software and PacBio SMRT Analysis software. Genomics Server is accessed through the desktop application Genomics Workbench, for which the CGC has 2 network licenses. SMRT Analysis software is accessed through a web interface portal. There is a quad CPU HP xw8600 Workstation running Ubuntu Linux for running Genomics Workbench locally in the CGC which also serves as a high-speed data upload/download port for the server. External hard drives with USB 2.0 or 3.0, Firewire, or eSATA interfaces can be connected to the HP Workstation for import and export of NGS data via Genomics Workbench or the Linux shell. Use of the Linux server has a recharge rate based on cpu seconds. Use of the CLCBio Genomics Server software and the Genomics Workbench licenses can be arranged for researchers outside of the Department on a cpu seconds based rate.

Data backup

Computer lab users are responsible for backing up their own data. Blank CD's are available (free of charge) in the Biology stock room in the basement of Kincaid Hall.   If a user would like to be able to keep project files on a computer in the CGC computer lab, an account can easily be created on either or both the Mac's and PC's.  Occasional computer use can be accommodated by the guest (PC) or visitor (Mac) logins.

Color printing

The CGC has a Lexmark C544 color laser printer for printing output from sequence analysis, fragment analysis, and other experiments where the data is displayed in color.

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Date last changed Sep 29th, 2016 @ 09:21:31 PDT