[Nov 23, 2009 14:09] Web access to Microsoft Live@edu accounts now works.
Franklin.achs is Academic Computing Health Sciences' main server for molecular biology analyses. Franklin is a Dell PowerEdge R710 server (two 2.26GHz, quad-core, Intel Core i7 CPUs) with 32 GB RAM, connected to a Promise VTrak E-class ~13TB RAID.
Software available on Franklin
web interfaces
- mirror of the UCSC Genome Browser
- documentation for the Genome Borwser is available from within the web application, or the UCSC Genome Browser home site
- GenePattern (current temporary URL is
http://opus.achs.virginia.edu:8080/gp/pages/login.jsf)
- documentation is available by web links within the application, or at the Broad Institute's Gene Pattern home page
command line tools
- R (v. 2.9.1) and Bioconductor
- EMBOSS (v. 6.0.1) and the Embassy suite of programs
- ClustalW
- MUSCLE
- T-Coffee
- PHYLIP (v. 3.68)
Connecting to franklin for command line tools
You must use a secure shell connection (SSH) to franklin. Windows users - use secureCRT or eXceed.
Apple OS X users - use ssh in terminal, or Apple's X11 application
Franklin mounts your home directory space, so you can access your franklin files at any time from your ITC home directory.
You can move files to and from your home directory on watson using ITC's home directory login application to mount your home directory to your local machine's desktop (this ITC application is available for both Windows and Apple OS X).
You may also use secure FTP to move files to and from your local machine and watson. Windows users may download and use SecureFX for SFTP transfers. Apple OS X users may use sftp from the command line in the terminal application, or use the graphic application Fugu (also available from ITC software downloads). CyberDuck is another free application for OS X users, and supports directory as well as file transfers.