Overview

SBGrid provides comprehensive system administration support for Linux, Mac, and Windows systems for the Harrison and Chou labs at HMS.

All SBGrid-supported systems are located on an integrated, private network segment.

To reach this network for access to local resources from an external location, please SSH to xtal200.harvard.edu. Please review our instructions the following, as you will need to request external SSH access:

If you are a member of the Harrison Lab at CLS, please see the BCH Harrison & Chen page.

Table of Contents

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 & CC their PI, their Lab Admin, or a senior member of their lab to complete their initial setup.

Email Access

Lab members have a Crystal Google Account with access to email and other Google services, including Google Calendar, Drive, Docs, Sheets, and more.

Access mail from the following address (you will be redirected to Gmail):

Access the Google Calendar from this address:

If you encounter problems, go to:

Login using your Crystal Google account: username@crystal.harvard.edu.

If you do not have an account, email help@sbgrid.org and cc your PI in the request.

Using your @crystal.harvard.edu email address

Using webmail

There is an email associated with your Linux account at <username>@crystal.harvard.edu. You may access the webmail at:

You can set a vacation responder in the webmail client by clicking Personal Settings and then clicking the Vacation tab.

Crystal email is currently hosted through Google's GSuite

Configuring a Mail Client for IMAP

To configure your address in a client such as Apple's Mail Application or Thunderbird, Select mail type GMail

  • Username: yourusername@crystal.harvard.edu
  • Password:
  • Your GSuite username@crystal.harvard.edu is different from your Linux account ##
  • Set up 2FA for Crystal GSuite

See faq-using-crystal-google-apps for more detailed information on how to use Email, Calendaring.

Email Lists

Harrison Lab

The Harrison lab at SGM has a private Google group for internal communications and communications with SBGrid:

To view the Harrison lab Google group go to:

To post to the Harrison lab Google group send your email to:

Contact Karen Lee if you are not currently a member of this list and wish to be added.

Chou Lab

The Chou lab has a private Google group for internal communications and for communications with SBGrid.

To view the Chou lab Google group go to:

To post to the Chou lab Google group send your email to:

If you are not currently a member of this list and wish to be added, contact Professor Chou for approval.

Accounts

SBGrid manages two different types of Crystal accounts. For simplicity, we use the same username for both accounts, but each has a different password. The first gives you access to Linux systems in your lab. The second is used to access your Crystal Gmail and other Google services.

Computers

SBGrid supports Linux, Mac, and Windows computers in the Harrison & Chou labs.

Linux

Most Linux computers use network accounts, which means that your home directory is on a network storage server and is backed up. If you accidentally delete important files, please let us know as soon as possible and we may be able to restore the file for you. Please note that your home directory has limited disk space and should not be used to store large data sets such as EM data, neither should you run Relion in your home directory.

Linux systems have network home directories and access to the SBGrid programs tree (via /programs). See this link for information on how to access the software.

Mac

Mac computers rely on either network accounts or local accounts. As of May 2017 we are in the process of transitioning all Harrison Mac computers to local accounts. Chou Lab systems will stay as they are for the immediate future as many of these Macs are too old to upgrade.

For Macs with local accounts, users will have administrative access with permission to install and update software. The SBGrid Installer will be used to access the SBGrid software tree and will allow users to install and update the software independently. These computers are backed up via Crashplan, hosted by HMS. If your Mac is not backed up, or you receive warning messages about Crashplan backup failures, please contact us immediately to ensure that no data is lost.

If you need to install or configure Crashplan see this page:

Windows

Windows computers used to run instruments in the labs should not be used for browsing the Web. If you encounter any problems with these machines, please contact SBGrid as soon as possible. If SBGrid is unavailable, please contact HMS-IT with details about your problem and the buiding and floor where the machine is located. Be sure to notify SBGrid that you have contacted HMS-IT so we can liaise with them.

Data Collection Machine

There is a Mac Mini named bcmp-remotedata-macmini for use when collecting data from beamlines.

Harrison lab members can share data via this network directory:

/nfs/userdocs/sch/COMMON

Chou lab members can share data via this network directory:

/nfs/userdocs/jc/COMMON

EM Suite

To access the EM Suite in the basement of SGM, please contact Zongli Li or Sarah Sterling.

If you need a data directory created on the EM systems, please email SBGrid and cc Zongi Li. Please remember that data directories on the EM systems are not backed up. It is essential that you store your data elsewhere.

Custom Software

Harrison Lab

CryoSPARC

CryoSPARC is installed on one of the Harrison Lab GPU nodes for use by Harrison Lab Members. Contact the SBGrid for more info.

HKL2000

We have a limited number of HKL2000 Licenses. Harrison Lab members can use the following systems to run HKL2000:

  • schel1

EndNote

Karen can order licenses via:

SBGrid SBGrid Wiki

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