Overview

SBGrid provides comprehensive system administration support for all Linux & Mac computers at the Blacklow Lab at HMS, and for all Linux systems used by the Kruse and Rapoport Labs.

The Kruse & Rapoport Labs should contact HMS-IT for assistance with Mac and Windows systems.

New SBGrid-supported computers need to be registered to access the network.

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 crystal.harvard.edu. Please review our instructions the following, as you will need to request external SSH access:

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 SBGrid 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.

The Kruse and Rapoport labs should contact HMS-IT for assistance with Mac & Windows systems.

Email Access

Most Blacklow, Brown, Hogle, & Rapoport lab members use email provided by HMS, Harvard University, or other institutions. Lab members may choose to have a Crystal Google account with access to email and other Google services. If you wish to have an account, email help@sbgrid.org and CC your PI in the request.

Email Lists

Blacklow Lab

The Blacklow lab at HMS has a private Google group for internal communications and communications from the SBGrid.

To view the Blacklow Lab Google group go to:

To post to the Blacklow lab Google group, send your email to:

Archives can be viewed online, but you will need to have @crystal.harvard.edu email to view these archives. All members of each list will see all emails sent to their list.

Contact Professor Blacklow, Jill Dolan, or Tom Seegar if you are not currently a member of this list and wish to be added.

Brown Lab

The Brown lab at HMS has a private Google group for internal communications and communications from the SBGrid.

To view the Brown lab Google group go to:

To post to the Brown lab Google group, send your email to:

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

Kruse Lab

The Kruse lab at HMS has a private Google group for internal communications and communications from the SBGrid.

To view the Kruse lab Google group go to:

To post to the Kruse lab Google group, send your email to:

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

Rapoport Lab

The Rapoport lab at HMS has a private Google group for internal communications and communications from the SBGrid.

To view the Rapoport lab Google group go to:

To post to the Rapoport lab Google group, send your email to:

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

Computers

SBGrid supports Linux computers in the Blacklow, Kruse, and Rapoport labs and also provides the Blacklow lab with support for Mac systems. The Kruse and Rapoport labs should contact HMS-IT for Mac or Windows support.

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 be used to store large data sets such as EM data, neither should your process data using Relion on data in your home directory.

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

Mac

We can provide support for Mac systems for the Blacklow Lab. The Brown, Kruse & Rapoport Labs should contact HMS-IT for assistance.

All Lab members can get access to the SBGrid Software for their Mac using our Mac Installer. You need to request an account to use the installer, more information is available at:

You should install HMS Crashplan on any Mac or Windows workstations or Laptops that you. Please see the page below for more information:

If your Computer 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 Crashplan is not currently installed on your Mac, please contact SBGrid to determine if Crashplan should be installed. After you install HMS Crashplan, please email the SBGrid with your Ecommons ID so that we can monitor your Crashplan backups.

Blacklow Instruments Computers

Tom Seegar supports the Windows instruments systems. SBGrid is available to assist, but if you encounter problems on the weekend and SBGrid staff are unavailable, please contact HMS-IT.

HMS Crashplan should be used to backup all systems on the network. If you are setting up a new instrument, please let us know in advance so we can assist with setup and enable backups. Systems that are not on the network should have their hard drive cloned in the event of a hard drive failure.

Instrument systems should not be used for browsing the Web. If you encounter any problems with these machines, please contact SBGrid as soon as possible.

EM Facility

To access the EM Facility in the basement of SGM, please contact Zongi Li or Melissa Chambers.

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

HKL2000

Licenses for HKL2000 are limited to one specific system per lab.

Blacklow Lab

Blacklow Lab members can use the following system to run HKL2000:

  • scbl1
Kruse Lab

Kruse Lab members can use the following system to run HKL2000:

  • akl1
Rapoport Lab

Rapoport Lab members can use the following system to run HKL2000:

  • trl2

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