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.
X-Ray Data Collection
To request access:
1. Please contact Stephen Harrison (schadmin@crystal.harvard.edu) to obtain guest privileges.
2. All users must view the HHMI X-ray safety video and sign a statement that they have done so. Please contact Karen Lee for more information.
3. All external users will need to have the assistance or collaboration of a sponsor colleague from the CMCD laboratory. Your sponsor will provide initial orientation, make ongoing equipment bookings and supervise your experiments. Please contact Gary Frey, John Genova or Piotr Sliz.
During your experiment:
1. Make sure your experiment is scheduled on the CMCD Calendar. Ask your sponsor to create an entry.
2. Login account names are mar006 and mar157 for two scanner respectively. Your sponsor will provide you with the account password.
3. Remove ALL your data within 3 days of data collection. Data left behind will be deleted on the 1st and 15th of every month. There is no remote access to your data. Be sure to take it with you.
Storage Quotas
Your storage quota is the amount of space that you are allowed on SBGrid file servers.
- You will have a 'soft' quota. If the amount of space that your files consume exceeds this quota, you will be sent a warning email, and will be given 7 days to reduce your space usage to below the soft quota. If you do not get back under the quota during this grace period, you will be enable to log into your network account without administrative assistance. By default, this quota is set to 5GBs on Crystal, and 100GBs on /nfs/xray.
- You will also have a 'hard' quota. If you exceed the hard quota at any time, your access to your network account will suspended immediately, and regaining access will require administrative assistance. By default, this quota is set to 7GBs on crystal, and 120GBs on /nfs/xray.
Backups
Full and incremental backups of SBGrid file servers are conducted. This includes your home and data directories. In general, backups are kept for three months, and then are stored on physical media for archival purposes. If you need a file restored, please send an email to help@sbgrid.org or use the contact form.
There is an email account associated with your CMCD network account at <username>@crystal.harvard.edu. You may access the webmail client at http://cmcd.med.harvard.edu/mail
To use a mail client, you can use the following credentials:
- IMAP
- Incoming Mail Server: crystal.harvard.edu, SSL enabled using port 465
- Outgoing Mail Server: crystal.harvard.edu, SSL enabled using port 993
You can set a vacation responder in the webmail client by clicking 'Personal Settings' and then clicking the 'Vacation' tab.
SBGrid also maintains a mailing list for the CMCD labs. You can maintain your subscription settings by visiting http://cmcd.med.harvard.edu/sympa
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.