Overview

SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at DFCI. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI.

To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.

Get Help

For general questions, email SBGrid at help@sbgrid.org and include your name and the name of your lab. Email questions about your software installation to bugs@sbgrid.org.

New lab members should contact help@sbgrid.org to complete their initial setup.

Email Access

Lab members have access to a Crystal email account through Google Apps. If you do not have an account, email help@sbgrid.org and cc your PI in the request.

SBGrid maintains a Google mailing list for labs on the Crystal Google domain upon request. If your lab actively uses the mailing list and you would like your name added to the list, please contact help@sbgrid.org.

Lab Wiki

A standalone Confluence server instance (version 5.8) is running on a virtual machine on an SBGrid-hosted VM cluster.

Users with a crystal email account can access the wiki at the PI’s request.

To access the lab wiki go to http://wiki.sbgrid.org and login with your crystal email.

Computers

Linux

Linux computers share authentication and data directories and can only be accessed locally from within the lab.

Home directories are located at

• /nfs/<lab initials>/<username> (example: /nfs/mje/eck)

SBGrid's comprehensive collections of structural biology applications is located in the /programs directory. All systems are configured with Stereo 3D.

The Ivory workstation, which has 48 cores, can be accessed remotely and is typically used for docking computations and data processing.

Please note that your home directories are only visible to your labmates and PI by default. Permissions vary depending on the nature of the directory or files in question. PIs can request modifications to file permissions to suit the lab's needs.

Mac OS X

All Mac computers have local administrative accounts that are specific to the lab members. Each user's home directory is located at

• /Users/<username> (example /Users/eck)

This setup allows users to install and update software without requesting help from SBGrid. Every local account is backed up to CrashPlan. Any network share, including home directories, are mounted via Samba and require user authentication.

These computers are also connected to the lab printers on the 3rd and 4th floors of Longwood Center.

Please contact help@sbgrid.org to request an account.

Windows

Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, however, SBGrid will make them available on the network.

Data collection and Instrument Control Computers

The scanner room has two Linux systems (aqua and plum) that control the x-ray scanner. Windows computers on this network are used for instrument control and data collection for the RockImager and FPLC systems.

Accessing your Samba shares

Macs have local accounts with local home directories. To access your Linux network home directory using Samba (SMB):

• Open Finder, click Go, then click 'Go to Server'
• Type in the server address: smb://blacker.in.hwlab
  • Click ‘Connect’.
• Enter your Samba username with @SBGRID.ORG prepended to your username
  • E.G. if my user name is jack, I would enter jack@SBGRID.ORG as my username.
• Enter your password (contact SBGrid for SMB account issues)

Data Backups

Hourly and daily snapshots are taken of the file server Z file system. Data is replicated to another server in building C on the HMS Quad. The local home directories of SBGrid-supported Macs are backed up to a Crashplan server located in the SGM Building on the HMS Quad.

Printing

A Xerox Phaser 8860 is located on the third floor near the kitchen area. Another inkjet printer is located directly above on the fourth floor. Email help@sbgrid.org with any printing problems.

RockImager Setup

There are two types of data generated by the imager:

• Images: Regular “jpg” image files that are stored directly in the file system on the main file server.
• Experimental data: As experiments are created, the data is stored on a “Microsoft SQL Server 2014” database, currently running on a Windows 2012 server.

The data is accessible on the RockImager PCs and also through the RockMaker software. Formulatrix provides technical support for the instrument and has remote access for troubleshooting. SBGrid maintains the server configuration.

Custom Software

HKL2000

Licenses for HKL2000 are limited to one specific system per lab. At DFCI you can use the following systems:

• mjel6
• mjel12

Networking and General IT Support

There are HMS network switches on the 3rd and 4th floors that connect the labs to SBGrid infrastructure. A new port must be activated for all new SBGrid-supported systems. Email help@sbgrid.org with the computer information and port number and SBGrid will work with DFCI/LC IT support to activate the port. To report DFCI network problems, or for general computing support, contact the Partners Healthcare Help desk at:

• http://helpdesk.partners.org/

Note: this link only works from within the Partners network.