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DFCI New User Orientation

System Administration


SBGrid provides system administration for the servers and individual workstations in your lab. We provide ongoing support and maintenance of these machines to ensure their reliability, security and performance, and to ensure that your data is safe and accessible.

We typically deploy Linux systems running CentOS, and Apple systems running Mac OS X. These machines include access to network accounts, so any user with an account in the lab can log in. We have carefully configured these systems to integrate with the SBGrid programs environment. Structural biology applications on both operating systems are located in the /programs directory (see below). General applications can be found in the /Applications folder (on OS X) or in the Applications menu (on CentOS).

In addition to hardware and operating system maintenance, we provide support for:
 

  • Network user accounts, so you can log in to machines in your lab.
  • Email mailing lists, so you can contact the members of your lab and receive information regarding SBGrid services.
  • Computational nodes, for analyzing data.
  • Assistance with scripting and configuration of specialized applications.

Lab Computers Overview

Eck, Wang, and Blacklow Labs

SBGrid provides support for several Linux and Apple scientific workstations. Computers can be found in three locations in the lab; In the Xray room, in the lab Computer room, and at lab members' desks in the wet lab.

Shared Linux workstations are located in the computer room at the end of the hall. All machines except for MJEL1 are configured for Strereo 3-D output.

Wucherpfennig Lab

SBGrid currenty supports a single linux workstation in the wet lab.

Bradner Lab

SBGrid maintains one linux workstation in the Bradner wet lab.

X-Ray Data Collection

Plum and Aqua are workstations designated for data collection, and are located in the X-Ray room. These machines have custom local software installs to interact with the Marresearch scanner.

HKL200 can be accessed and run on Plum, Aqua, and MJEL7.

Please contact Mike Eck (eck@dfci.harvard.edu) to obtain guest privileges.

Printing

A Xerox Phaser 8860 printer is located in the Computer room for use by the Eck, Wang, and Blacklow labs. If you need your workstation configured for printing, please send an email to help@sbgrid.org

Backups

SBGrid does not supply backups at DFCI. Backups are performed by the DFCI research computing group. See Getting Help for more information.

E-mail

  • Eck, Wang, and Blacklow lab members have an email address associated with your network account at <username>@red.dfci.harvard.edu
  • Webmail is accessible at http://red.dfci.harvard.edu/webmail
  • To configure a mail client, use these settings:
    • IMAP
    • Incoming Mail Server: red.dfci.harvard.edu
    • SSL Enabled at port 465
    • Outgoing Mail Server: red.dfci.harvard.edu NOTE: This will only work from a DFCI internet connection. Use the webmail interface or your internet service providers SMTP server when outside of the network.

Remote Access

External SSH access is available at red.dfci.harvard.edu to the Eck, Blacklow, and Wang lab computing resources.

Structural Biology applicatons


SBGrid also provides an extensive collection of scientific software. On each workstation, the programs are mounted at /programs. In most cases, you will easily be able to run any program in the collection by opening up a terminal shell, and typing the name of the program that you want to run. Linux applications are installed in the /programs/i386-linux subdirectory.  Mac applications are installed in the /programs/i386-mac subdirectory (for intel macs) or the /programs/powermac subdirectory (for PPC macs).

Most of the software titles installed in the SBGrid Suite have several versions available. Typically, we try to provide at least three versions of each software package, although very old or very new applications may have fewer versions. To override the default version, follow the instructions posted to the SBGrid Consortium website.



 

Commonly used applications


Aside from structural biology applications, the following system tools are commonly used by SBGrid members and are included in your workstation software installation:

Linux:

 

  • gedit (text editing)
  • gimp (image editing)
  • acroread -- "Adobe Reader" (reading PDFs)
  • firefox (Web-Browsing)
  • oowriter, ooimpress, oocalc -- "Open-Office" (Word processing, slideshows, spreadsheets)

OSX:

 

  • TextWrangler (text editing)   Adobe Photoshop (image editing)
  • Adobe Reader (reading PDFs)
  • Cyberduck (SFTP, FTP)
  • Firefox (Web Browsing)
  • Microsoft Office (Word processing, slideshows, spreadsheets)

 

Recommended UNIX tutorial

New to UNIX? You can read the first few chapters of this tutorial to understand the basics of the UNIX command line: http://www.ee.surrey.ac.uk/Teaching/Unix/

 

How to contact us

You may contact SBGrid by sending an email to help@sbgrid.org, or by using the contact form.