GCG

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Contents

Introduction

Suspended service
We've suspended this service indefinitely till further notices.

The Wisconsin Package, or more commonly referred to as GCG, is a suite of over 130 programs for sequence analysis. Just a few of the things you can do with GCG:

  • pattern, motif and reference database searches
  • sequence editing, analysis, annotation and comparison
  • RNA secondary structure prediction
  • restriction mapping
  • fragment assembly

The programs in the Wisconsin Package can be used via a command-line and/or via the graphical interface SeqLab.

If you have any other questions regarding our GCG server that isn't covered by this wiki page, please contact us.

Remote access

Our GCG server is available on the Internet at:

gcg.rrc.uic.edu

For security reasons, we no longer offer telnet and FTP services on our GCG server.

Now you may be wondering, “If I can't use telnet and FTP, how do I access the server and transfer files?”. There's a good chance that your telnet and FTP clients already support SSH/SFTP. If that is the case, all you need to do is tell your client program to use the SSH/SFTP protocol instead of telnet/FTP.

SSH

To keep this help page short, we've skipped the technical details. For information about SSH, please see our SSH wiki page.

X Server

In order to use the graphical interface SeqLab, you'll need some X Server software. If you're running Linux or a recent version of Mac OS X, you already have everything you need. For Windows users, we highly recommend Xming which is easy to use and also free (More about Xming on Wikipedia: http://en.wikipedia.org/wiki/Xming).

Installing Xming

For your convenience, we've made a copy of Xming available on our GCG server in the folder /usr/people/FREEWARE/Xming. For the most basic installation, only the main setup package is needed:

Xming-6-9-0-31-setup.exe

Though optional, installing the fonts package is recommended:

Xming-fonts-7-3-0-11-setup.exe

Transferring files

SFTP

Many SSH clients also support SFTP, so you may not need a separate program. But if you'd still like one, here are a few that we recommend:

Linux
GNOME's Nautilus file manager includes SFTP support. Once connected, you can drag-n-drop files just like other folders.
Mac OS X
http://rsug.itd.umich.edu/software/fugu/
Microsoft Windows
http://filezilla.sourceforge.net/

Network drive

This option is more difficult to understand, but it is by far the most convenient way to access your files on any server that offers SSH which includes our GCG and ACCC's “tigger”.

It really is much more difficult to describe it than it is to use. In a nutshell, it's an easy way to connect to a folder on a server as though it were a local folder on your computer. Once connected, you can open, copy, delete and work directly with your files without having to transfer them to and from the server.

The system requirements are FUSE and SSHFS being available for the operating system you are using.

For more information about FUSE: http://en.wikipedia.org/wiki/Filesystem_in_Userspace

Linux
FUSE was originally created for Linux, so unless the distribution you're running is more than 2 or 3 years old, it's mostly likely already installed and/or readily available via the package repositories: http://fuse.sourceforge.net/
Mac OS X
http://code.google.com/p/macfuse/
Microsoft Windows
We're currently not aware of a FUSE/SSHFS implementation for Windows. SftpDrive is the closest alternative we've found so far.

External links



Scientific Computing Support (SCS) provides solutions to research problems and scientific endeavors that require advanced computing tools. Our staff has experience with a variety of computing architectures, commercial/open-source software and programming languages.

Facility Homepage: http://www.rrc.uic.edu/scs


Return to the SCS wiki home page

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