move old lab pages imported from forums to old/

-

-# Lab Support

-

-Support Information for SBGrid Core Supported Labs:

-

-* [Bradner Lab DFCI](howto-bradner-lab-dfci)

-* [D'Souza Lab Harvard University](howto-d-souza-lab-harvard-university)

-* Shared Resources for Labs at [Longwood Center labs DFCI](howto-eck-lab-dfci) including:

- * Dhe-Paganon Lab

- * Eck Lab

- * Fischer Lab

- * Wang Lab

-

-* [Gaudet Lab Harvard University](./howto-gaudet-lab-harvard-university)

-* [Heldwein Lab Tufts Univertsity](./howto-heldwein-lab-tufts)

-* [Kahne Lab Harvard University](./howto-kahne-lab-harvard-university)

-* [kirchhausen Lab, BCH](./howto-kirchhausen-lab-bch)

-* [Leschziner Lab Harvard University](./howto-leschziner-lab-harvard-university)

-* [Miller Lab MGH](./howto-miller-lab-mgh)

-* [Sliz Lab Harvard Medical School](./howto-sliz-lab)

-* [Springer Lab BCH](./howto-springer-lab-bch)

-* [Dhe-Paganon Lab](./howto-structural-biol-core-dhe-paganon-lab-dfci)

-* [Wei Lab Genzyme](./howto-wei-lab)

-* [Wucherpfennig Lab DFCI](./howto-wucherpfennig-lab-dfci)

-These files are for historical purposes and verisons of the content we

-had on our old forums at forums.sbgrid.org.

- **[Core Wiki](../Home)**

-

-##### Help

-* [How To Get Help & Support](../boston-cmcd-faqs-and-discussion/getting-help)

-* [Lab Support](Home)

-* [FAQ](boston-cmcd-faqs-and-discussion/Home)

-# HOWTO, Bradner Lab, DFCI

-

-#Site Overview:

-Members of the Bradner Lab at the Dana Farber Cancer Institute have access to

-a Linux workstation in the wet lab,  running a large collection of structural

-biology software. It shares authentication and data directories and can be

-only accessed locally from within the lab.

-

-Research Computing support is provided by SBGrid.  Pl ease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Workstations:

-

-Name|OS|Hardware Configuration|Location|Notes

----|---|---|---|---

-jbl1|Sci Linux 5|Intel Core i7 at 3.20GHz. 4 cores. 6GB of RAM. Nvidia Quadro 600.| |Last checked: 11/17/2014

-

-##Data Backups:

-

-Backups on the linux workstations are performed on a regular basis by the

-research computing group at DFCI. If you have any questions about backups,

-need files restored, or have any general issue regarding backups, contact the

-Research Computing group via this web page: [Help Me - DFCI Reseach

-Computing](http://research4.dfci.harvard.edu/content/helpme) .

-

-## 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.

-

-HKL2000 can be accessed and run on Plum, Aqua, and MJEL12.

-

-Please contact Mike Eck to obtain guest privileges.

-

-## Networking and General IT Support:

-

-To report problems regarding the network at DFCI, or general computing

-support, contact the Partners Healthcare Help desk at:

-[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only

-works from a Partners network connection)

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-

-

-# HOWTO, D'Souza Lab, Harvard University

-

-## Site Overview:

-Members of the D’Souza Lab at Harvard University have access to five Linux

-workstations running a large collection of structural biology software. These

-workstations share authentication and data directories.

-

-Research Computing support is provided by SBGrid. P lease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Workstations:

-

-

-| Name | Operating System | Hardware Configuration|Location|Notes|

-|---|---|---|---|---|

-|chef|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014|

-|clyde|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro 4000|NW 311|09/25/2014|

-|jack|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GH. 4 Cores. 16G of RAM. Nvidia GeForce 9600GT. |NW 311 |09/25/2014|

-|kenny|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro FX 380.| NW 311 |09/25/2014

-|rufus|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014|HKL2000 licensed system.

-

-##Printers:

-

-| Name | Model | Location | Notes |

-|---|---|---|---|

-|carmen|HP LaserJet 4700|Computer Lab|color printer|

-|vger|Ricoh Aficio C410|Wet Lab|color printer

-

-## Data Replication:

-

-Data is replicated to a secondary server. Snapshots are taken every hour and

-kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up

-to 12 months. If you need a file restored,  please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Remote access:

-

-SSH access is available through galactica.mcb.harvard.edu . Remote access is

-not enabled by default. If you need to access Galactica remotely,  please

-contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Networking and General IT Support:

-

-To report problems regarding the network at Harvard University, or general

-computing support, contact the Harvard University Help desk.

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-# HOWTO, Longwood Center labs, DFCI

-

-## Site Overview:

-

-###

-

-* Eck

-* Dhe-Paganon

-* Wang

-* Fischer

-

-

-Members of these labs at the Dana Farber Cancer Institute have access to

-several shared Linux and Mac computers running a large collection of

-structural biology software. The Linux computers share authentication and data

-directories and can be only accessed locally from within the lab.

-

-Linux computers are located in the graphics room (fish bowl) on the third

-floor and in cubicles on the fourth floor. The X-ray room has two workstations

-for data acquisition. Macs are located on lab member’s desks.

-

-All linux machines are configured for Stereo 3D output.

-

-Research Computing support is provided by SBGrid - contact them

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-

-## Shared Workstations: (see below)

-

-

-

-## Mac Workstations: (see below)

-

-

-

-## Home and Data Directories:

-

-### Linux systems:

-

-NFS mounted home directories: **/nfs/<PI initials>/<username>**

-

-NFS mounted synchrotron data:** /synchrotron**

-

-NFS read only mounted programs tree: **/programs**

-

-

-

-### On Mac systems:

-

-NFS read only mounted home directories: **/nfs/<PI

-initials>/<username>**

-

-NFS read only mounted synchrotron data: **/synchrotron**

-

-NFS read only mounted programs tree: **/programs**

-

-SMB read and write mounted home directory:

-

-To mount your home directory using Samba (SMB):

-

-\- In Finder, click **Go** then click **'Go to Server'**

-

-\- Type in server address: **smb://blacker.in.hwlab**

-

-\- Enter your SMB username and password. (contact SBGrid for SMB account

-issues)

-

-To change your SMB password, use this command on a **linux** system:

-

- 1. smbpasswd -R blacker.in.hwlab -U <username>

-

-

-

-## Data Backups:

-

-Fileserver data is snapshotted and also replicated to another server at HMS/C

-building. Local iMac accounts are backed up using crashplan.

-

-## Printing:

-

-A Xerox Phaser 8860 is located in the third floor near the kitchen area.

-Another inkJet printer is located directly above on the fourth floor. If you

-are having issues with printing, please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us).

-

-## X-Ray Data Collection:

-

-Plum and Aqua are workstations designated for data collection, and are located

-in the X-Ray room on the third floor. These machines have custom local

-software installs to interact with the Marresearch scanner.

-

-HKL2000 can be accessed and run on Plum, Aqua, mjel14 and sdp2.

-

-Please contact Mike Eck to obtain guest privileges.

-

-## Remote Access:

-

-External SSH access is available at crystal.harvard.edu.

-

-**Forwarding your red email to Crystal:**

-

-* Please contact SBGrid help if you have questions about forwarding.

-

-## Networking and General IT Support:

-

-To report problems regarding the network at DFCI, or general computing

-support, contact the Partners Healthcare Help desk at:

-[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only

-works from a Partners network connection)

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-## Shared Linux Workstations:

-

-| Name | OS | Hardware Configuration|Location|Notes|

-|---|---|---|---|---|

-|aqua|Sci Linux 6|Intel Core 2 Duo at 3.33GHz. 2 cores. 1GB or RAM. Nvidia Quadro FX 3700.|X-Ray room(Longwood Center) |Last checked: 13/09/2015, HKL2000 licensed, Works with Marresearch scanner |

-|plum|Sci Linux 6 |AMD Athlon 64 Dual Core Processor 4800+. 2 cores. 1GB of RAM.|X-Ray room (Longwood Center)|Last checked: 03/09/2015, HKL2000 licensed, Works with Marresearch scanner |

-|mjel11|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015|

-|mjel12|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015, HKL2000 licensed|

-|mjel13|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM.| Wet lab|Last checked: 03/03/2015|

-|mjel14|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 32 GB of RAM. Nvidia Quadro 4000.| Graphics room ((Longwood Center)|Last checked: 03/09/2015 \

-|mjel15|Sci Linux 6|Intel Core i7 at 3.60GHz. 4 cores. 16 GB of RAM. Nvidia Quadro 4000.| Computer lab|Last checked: 03/04/2015 \

-|xrc1|Sci Linux 6|Intel Core Quad at 2.66GHz. 4 cores. 4GB of RAM. Nvidia Quadro FX 1400| Graphics room (Longwood Center)|Last checked: 03/02/2015 \

-

-## Mac Workstations:

-

-| Name | OS | Hardware Configuration|Account Backed up| Administrator |

-|---|---|---|---|---|

-|wood-imac|OSX 10.10.5|iMac10,1, Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes|David Wood |

-|mje-dwood-imac|OSX 10.5.8|iMac8,1, Intel Core 2 Duo 2.66 GHz 2 Cores, Memory: 2 GB, ATI Radeon HD 2600 Pro, |No|

-|jwh-macpro|OSX 10.8.5|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 10 GB, NVIDIA Quadro FX 5600, |Yes|Jia-Huai |

-|yiquns-imac|OSX 10.8.5|iMac11,2, Intel Core i3 3.06 GHz 2 Cores Memory: 4 GB ATI Radeon HD 4670|Yes|SBGrid, (user: hjeon) |

-|randalls-imac (broken)|OSX 10.8.5|iMac10,1 Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes| Randall McNally |

-|mike_eck_macpro|OSX 10.9.4|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 8GB, NVIDIA Quadro FX 5600|Yes|Mike Eck |

-|humayuns-imac|OSX 10.10.1|iMac14,2 Intel Core i5 4 Cores, Memory 16GB, NVIDIA GeForce GT 755M| Yes|Humayun Sharif |

-|asher-page-imac|OSX 10.8.5|iMac13,1 Intel Core i5 2.7 GHz 4 Cores, Memory: 8GB,NVIDIA GeForce GT 640M|Yes|Randall McNally |

-|li-imac|tbd|tbd|Yes|Qing Li |

-|dhcp-155-52-53-43|tbd|tbd| |common iMac (gel reader)|

-

-

-

-# HOWTO, Gaudet Lab, Harvard University

-

-## Site Overview:

-Members of the Gaudet Lab at Harvard University have access to two graphical

-workstations , Pioneer and Cobincho, and a regular workstation ‘Curry’, all

-running a large collection of structural biology software. The linux

-workstations share authentication and data directories. Pioneer contains a

-license for running HKL2000.

-

-Research Computing support is provided by SBGrid. P lease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Workstations:

-

-|Name|Operating System|Hardware Configuration|Location|Last Checked|Notes|

-|---|---|---|---|---|---

-|cobincho|CentOS 6.5, |Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014

-| curry|CentOS 6.5|Intel Core i7 CPU at 2.8GHz, 4 Cores. 2GB of RAM. Nvidia Quadro FX 380. |NW 305|10/27/2014

-| pioneer|CentOS 6.4|Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014|HKL2000 licensed system.

-

-## Printers:

-

-|Name|Model|Location|Notes|

-|---|---|---|--- |

-|carmen|HP LaserJet 4700|Computer Lab|color printer

-|vger|Ricoh Aficio C410|Wet Lab|color printer

-

-## Using SBGrid programs:

-

-All applications are located in ```/programs``` directory and are configured to run without additional settings. 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.

-

-## Data Replication:

-

-Data is replicated to a secondary server. Snapshots are taken every hour and

-kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up

-to 12 months. If you need a file restored,  please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Remote access:

-

-SSH access is available through galactica.mcb.harvard.edu . Remote access is

-not enabled by default. If you need to access Galactica remotely,  please

-contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Networking and General IT Support:

-

-To report problems regarding the network at Harvard University, or general

-computing support, contact the Harvard University Help desk.

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-# HOWTO, Heldwein Lab, Tufts

-

-## Site Overview:

-Members of the Heldwein lab at Tufts University have access to three Linux

-computers and a Mac workstation running a large collection of structural

-biology software. The Linux computers share authentication and data

-directories and can be only accessed locally from within the lab. Lab members

-also have access to an HP LaserJet printer. Research Computing support is

-provided by SBGrid.  Please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## WOrkstations

-

-Name|OS|Hardware Configuration|Location|Notes

----|---|---|---|---

-ruby|Sci Linux 6.5| Intel Core i7 at 3.20GHz. 6 cores. 16GB of RAM. Nvidia Quadro 400| |Last checked: 11/13/2014

-diamond|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014

-beryl|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014

-

-## Storage and Backup:

-

-Backup of /nfs/home, which is hosted via Tufts NAS, are performed by the IT

-group at Tufts University.

-

-## Using SBGrid programs:

-

-All applications are located in /programs directory and are configured to run

-without additional settings.

-

-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 these instructions.

-

-Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-

-programs) if you need information on how to run SBGrid programs remotely or

-locally on your machine.

-

-## General IT Support:

-

-Support for office computing is provided by Tufts IT.

-

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-# HOWTO, Kahne Lab, Harvard University

-

-# Site Overview:

-Members of the Kahne Lab at Harvard University have access to Linux and Mac

-workstations running a large collection of structural biology software.

-

-Research Computing support is provided by SBGrid. P lease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Workstations:

-

-Name|OS|Hardware Configuration|Location|Notes|

----|---|---|---|---|

-blain|Sci Linux, 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM.Nvida GeForce GTX 760. || Last checked: 11/03/2014

-billy|OS X 10.6.8, |Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770. | |Last checked: 10/27/2014. HKL2000 licensed machine.

-dutch|Sci Linux 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM. Nvida GeForce GTX 760.| |Last checked: 10/27/2014

-mac|OS X 10.6.8|Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770.| |Last checked: 10/27/2014

-

-## Data Backups:

-

-TBD

-

-## Networking and General IT Support:

-

-To report problems regarding the network at Harvard University, or general

-computing support, contact the Harvard University Help desk.

-

-## Remote access:

-

-SSH access is available through 128.103.94.191. This accesses the primary

-Linux workstation.

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-# HOWTO, Kirchhausen Lab, BCH

-

-## Site Overview:

-Members of the Kirchhausen Lab at the Children’s Hospital Boston have access

-to a large collection of structural biology software. Research Computing

-support is provided by SBGrid. Please contact them [here

-](https://sbgrid.org/help/?tab=contact-us) .

-

-# Data 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 contact SBGrid  [here

-](https://sbgrid.org/help/?tab=contact-us) .

-

-## Networking and General IT Support:

-

-Contact Children’s help desk at (617) 919 4357 or at [

-](mailto:help.desk@childrens.harvard.edu) [

-](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu)

-.

-

-* [ Using SBGrid programs ](http://forums.sbgrid.org/topic/using-sbgrid-

-programs)

-*[ Getting help from SBGrid ](http://forums.sbgrid.org/topic/getting-help)

-*[ Other Resources ](http://forums.sbgrid.org/topic/other-resources)

-

-

-##Synchronizing working directories between tklab and orchestra**

-

-### Overview

-

-The [ data synchronization ](http://forums.sbgrid.org/topic/tklab-data-

-synchronization-to-orchestra) process is a one-way synchronization, and files

-and directories transfered are no longer writable. For processing, there is a

-two-way synchronization of the ` ~/sync ` directory between the ` tklab `

-server and ` orchestra ` . Since the ` ~/sync ` directories are in the user's

-home directories, users have full ability to create, delete, rename, etc

-anything within them without effecting the raw images stored in `

-/groups/kirchhausen/datasync ` .

-

-**Anything outside the ` ~/sync ` directory, including ` .cshrc ` , ` .ssh ` will not be copied to orchestra.**

-

-### Suggested Working Directory Structure

-

-Symlinks can be used to keep the processing directories linked to the raw data

-directories, without requiring write/delete permissions for data directories.

-For example, instead of nstead of creating ` /datasync/Dataset001/process1 ` ,

-create a ` ~/sync/Dataset001 ` directory. Within ` ~/sync/Dataset001 ` ,

-create a symlink pointing to the images ( ` cd ~/sync/Dataset001 ; ln -s

-/groups/kirchhausen/datasync/Dataset001 images ` ).

-

-### Step by Step

-

-Setup [ passwordless ssh logins ](http://forums.sbgrid.org/topic/setting-up-

-passwordless-ssh) between ` tklab ` and ` orchestra ` before using two-way

-sync.

-

- 1. Process within the ` ~/sync ` directory, on ` orchestra ` or ` tklab ` .

- 2. When done, or at a checkpoint, initiate synchronization from ` tklab ` : ` unison -auto ` (interactive) or ` unison -batch ` (non-interactive).

-

-### More details

-

-Nightly non-interactive synchronization runs will be run from cron.

-

-If you're curious about unison, more detail is available from the [ project

-website ](http://www.cis.upenn.edu/~bcpierce/unison/download.html) .

-

-# HOWTO, Leschziner Lab, Harvard University

-Lab Moved and is no longer at HU.

-

-## Site Overview

-Members of the Leschziner Lab at Harvard University have access to 10 Linux

-and 2 Mac workstations running a large collection of structural biology

-software. The linux workstations share authentication and data directories and

-can be only accessed locally from within the computer room.

-

-Research Computing support is provided by SBGrid - contact them

-[here](https://sbgrid.org/help/?tab=contact-us)   .

-

-

-## Workstation** (see comment below)

-##Printers** (see comment below)

-

-

-

-## Data Replication

-

-Data is replicated to a secondary server. Snapshots are taken every hour and

-kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up

-to 12 months. If you need a file restored,  please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Remote access:

-

-SSH access is available through galactica.mcb.harvard.edu . Remote access is

-not enabled by default. If you need to access Galactica remotely,  please

-contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .

-

-##Networking and General IT Support:

-

-To report problems regarding the network at Harvard University, or general

-computing support, contact the Harvard University Help desk.

-

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-*[Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-## Workstations:

-

-Name|Operating System|Hardware Configuration|Location|Notes

----|---|---|---|---

-aida|Sci Linux, 6.5|Intel Core i7 CPU at 3.07GHz, 4 cores. 12GB of RAM. Nvidia Quadro 4000.|NW 305|Last checked 10/20/2014

-dutchman|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz, 4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW311|Last checked 10/20/2014

-fidelio|OSX, 10.6.4|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW305|Last checked 10/20/2014

-figaro|OSX, 10.7.5|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW 305|Last checked 10/20/2014

-giovanni|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014

-isolde|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM.Nvidia NVS 290.|NW305|Last checked 10/20/2014

-leginon|tbd|tbd|tbd|

-leonora|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014

-otello|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz,4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW 305|Last checked 10/20/2014

-tristan|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014

-lothario|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz.6 cores. 32GB of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014

-mignon|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz. 6 cores. 32G of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014

-

-## Printers:

-

-Name|Model|Location|Notes

----|---|---|---

-carmen|HP LaserJet 4700|Computer Lab|color printer

-vger|Ricoh Aficio C410|Wet Lab|color printer

-

-# HOWTO, Miller Lab, MGH

-

-## Site Overview:

-Members of the Miller Lab at MGH have remote access to the SBGrid software

-tree and can run jobs on Zorin.

-

-Research Computing support is provided by SBGrid. Pl ease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Networking and General IT Support:

-

-To report problems regarding the network at MGH, or general computing support, contact the Partners Healthcare Help desk at:

-[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only

-works from a Partners network connection)

-

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-# HOWTO, Sliz Lab

-

-

-## Computing Accounts:

-

-Members of Sliz lab will generally have six computing accounts:

-

- * an HKL account for email, calendar and shared documents

- * a local (administrator) account for Mac OS X workstations

- * a CMCD account for login to the Linux workstation, to crystal.harvard.edu and to other Linux workstations at HMS.

- * an HMS account for login to eCommons and to HMS email system.

- * SBGrid account (optional) for software update.

- * DropBox account - this is a business account with unlimited backups and unlimited storage space.

-

-##Network:

-All computers in the lab should be connected to the SBGrid network.

-For connecting a personal computer, you will need to email the [MAC

-address](http://forums.sbgrid.org/topic/how-to-find-mac-address-on-os-x-gui)

-of the ethernet card or adaptor to [help@sbgrid.org](mailto:help@sbgrid.org)

-. In order to access SBGrid wi-fi network you will need to email your MAC

-address to [help@sbgrid.org](mailto:help@sbgrid.org) and request activation

-on the SBGrid wifi network; to connect, authenticate with your CMCD username

-and password.

-

-

-

-##Printing:

-We have two printers in the lab, which are both available from the

-SBGrid network. ps-laserjet3000dn is located in the wet lab area, ps-

-brother2270 is located in the SBGrid computing room. Printing will not work if

-your computer is connected to the HMS Wifi access point (HMS Private or

-Public).

-

-

-

-##Personal Desktop Computers:

-Personal (OS X / Windows?) systems (sch-jlchoi-

-imac, ps-wang-macmini, ps-sophia-imac, sb-liz-imac, ps-nozhat-macmini) are

-administered by the primary user, with support from SBGrid and HMS/BCMP IT.

-

- * SBGrid software will be installed in /programs.

-

- * All research data should be backed-up . This is an NIH and HMS regulation.

-

- * Visiting Students should use HMS [CrashPlan](http://it.hms.harvard.edu/pg.asp?pn=cpp_backup) for backing up their work directories. (use registration code JJRR-RHW7-UHJW-H7JM).

-

- * Postdocs and Graduate Students should always work from a DropBox folder.

-

-##Software:

-

- * personal computers and laptops running OS X can have [SBGrid software installed](http://forums.sbgrid.org/topic/updating-sbgrid-software-on-your-mac-from-sbgrid-central-server)

- * [HMS licensed software](https://rc.hms.harvard.edu/#downloads) (such as ChemOffice or MATLAB)

- * MS office is available on request from [](mailto:bcmpit@hms.harvard.edu)[bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu)

- * Geneious: Geneious is preinstalled with SBGrid software collection and Sliz lab has access to a shared database. Please email Piotr for the database login credentials.

- * Please use ReadCube for managing your references and we will purchase a Pro version for your use (Pro supports syncing files between multiple computers).

-

-#Linux Workstations

-Two linux workstations ([schl12][1] and psl2) are fully

-administered by SBGrid. ps2 (in the 3rd bay) can dual-boot to Windows 7. To

-login to linux systems, use your CMCD credentials. To login to the windows

-partition, use the credentials posted over the machine.

-

-[1]:for consistency, schl12 will be renamed to psl1

-

-## Instrumentation Computers:

-Computers running our FPLCs (PS-FPLC1, PS-FPLC2, PS-FPLC3) are managed by HMS IT and backups are done on a daily basis using CrashPlan. They can print to the laboratory printer.

-

-Sliz lab also has access to crystallization-room computers (Gryphon

-controller, unknown system) Those computers are also managed by HMS IT and

-backed-up using CrashPlan.

-

-

-## Support:

-

-There are several options for support:

-

- 1. Please review SBGrid and CMCD support forums on the SBGrid website: forums.sbgrid.org

- 2. For assistance with Linux workstations and SBGrid network please contact SBGrid ( [help@sbgrid.org](mailto:help@sbgrid.org) ). In most cases Pete Meyer or Justin O’Connor will respond to your request.

- 3. For assistance with printing and your personal desktop please contact HMS IT at [bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu) . In most cases Peter Cobb will respond to your requests.

- 4. For assistance with the structural biology software please contact [bugs@sbgrid.org](mailto:bugs@sbgrid.org) (Rob and Jason).

-

-

-## Other Resources:

-

- * SBGrid.org website

-

- * rc.hms.harvard.edu - Harvard Medical School Research Computing Support

-

-## Communication:

-

- * All members of Sliz lab are signed up for the Sliz lab mailing lists and the BCMP mailing lists.

- * You will also receive a copy of SBGrid monthly newsletter.

- * e-mail: Goup members should use hkl.hms.harvard.edu account as the institutional/work email account. You should forward other accounts (e.g. hms.harvard.edu) to HKL.

-

-# HOWTO, Springer/Wu/Hur Lab, BCH

-

-## Site Overview:

-Members of the Springer, Wu and Hur Labs at the Children’s Hospital Boston

-have access to six Linux workstations; all running SBGrid Software Collection

-(see below). The Linux computers share authentication and data directories and

-can be accessed remotely by SSH (see

-[instructions](http://forums.sbgrid.org/topic/remote-access-to-linux-

-computers)).

-

-Research Computing support is provided by SBGrid - contact them

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Shared Workstations:

-

-Name|OS|Hardware Configuration|Location|Notes

----|---|---|---|---

-tsl1|Sci Linux 6.5|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer

-tsl2|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer

-tsl3|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer

-tsl4|Sci Linux 6.4|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer

-sun|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro FX 3700| CLS 03098|Last checked: 11/19/2014, Owned by Wu

-moon|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Wu

-

-## Data 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 contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us).

-

-#Printing:

-

-A Xerox Phaser 6700DN is located in the hallway outside CLS 03098. If you are

-having issues with printing,  please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-#Remote access:

-

-Please follow [this link](http://forums.sbgrid.org/topic/remote-access-to-

-linux-computers) for details on how to remotely connect to the workstations.

-

-##Networking and General IT Support:

-

-Contact Children’s help desk at (617) 919 4357 or at

-[](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu)

-.

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-

-

-

-

-# HOWTO, Dhe-Paganon Lab, DFCI

-

-## Site Overview:

-

-Members of the Dhe-Paganon Lab at the Dana Farber Cancer Institute have access

-to a Linux workstation running a large collection of structural biology

-software. It shares authentication and data directories.

-

-Lab members can use SBGrid machines in the Eck lab as well.

-

-The lab is located at the Longwood Center building.

-

-Research Computing support is provided by SBGrid.  Pl ease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us).

-

-

-## Workstations:

-

-Name|OS|Hardware Configuration|Location|Notes

----|---|---|---|---

-sdp1|Sci Linux 6.5|Intel Core i7 at 3.70GHz. 4 cores. 16 GB or RAM. Nvidia Quadro K4000. | Graphics room (Longwood Center)|Last checked: 03/01/2015

-

-## Data Backups:

-

-Backups on the linux workstations are performed on a regular basis by the

-research computing group at DFCI. If you have any questions about backups,

-need files restored, or have any general issue regarding backups, contact the

-Research Computing group via this web page: [Help Me - DFCI Reseach

-Computing](http://research4.dfci.harvard.edu/content/helpme) .

-

-Backups on Macs are managed by SBGrid.  Pl ease contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) for more information.

-Instructions on how to setup your Mac computer can be found

-[here](http://here) .

-

-##Printing:

-

-A Xerox Phaser 8860 is available for printing near the admin office. If you

-need your workstation configured for printing,  Please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## 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.

-

-HKL2000 can be accessed and run on Plum and Aqua, and mjel12.

-

-Please contact Mike Eck to obtain guest privileges.

-

-## Remote Access:

-

-External SSH access is available at red.dfci.harvard.edu.

-

-## Networking and General IT Support:

-

-To report problems regarding the network at DFCI, or general computing

-support, contact the Partners Healthcare Help desk at:

-[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only

-works from a Partners network connection)

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-# HOWTO, Wei Lab, Genzyme Corp

-

-## Site Overview:

-

-Members of the Wei lab at Genzyme Corporation have access to two Linux

-computers running a large collection of structural biology software. Both

-computers share authentication and data directories and can be only accessed

-locally from within the lab. Research Computing support is provided by

-[SBGrid](https://sbgrid.org/) .  Please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Backups

-

-Data backup is performed by the Genzyme IT department.

-

-## Workstations:

-Name|OS|Hardware Configuration|Location|Notes

----|---|---|---|---

-montana|CentOS 6.6| | Wei's office |Last checked: 03/02/2015

-colorado|Sci Linux 6.6| | Yanfeng's office|Last checked: 03/02/2015

-gpenguin|Sci Linux 6.6| | Dana's desk|Last checked: 03/02/2015

-

-##User Accounts:

-To create or delete your account, please refer to this

-[page](http://forums.sbgrid.org/topic/new-accounts) . To change your password

-please use the yppasswd command on one of the workstations.

-

-##Using SBGrid programs:

-

-All applications are located in /programs directory and are configured to run

-without additional settings.

-

-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 these instructions.

-

-Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-

-programs) if you need additional information on how to run SBGrid programs

-locally or remotely on your machine.

-

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-# HOWTO, Wucherpfennig Lab, DFCI

-## Site Overview:

-Members of the Wucherpfennig Lab at the Dana Farber Cancer Institute have

-access to a Linux workstation in the wet lab,  running a large collection of

-structural biology software. It shares authentication and data directories and

-can be only accessed locally from within the lab.

-

-Research Computing support is provided by SBGrid.  Please contact SBGrid

-[here](https://sbgrid.org/help/?tab=contact-us) .

-

-## Using SBGrid programs:

-

-All applications are located in /programs directory and are configured to run

-without additional settings. 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.

-

-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 [these

-instructions](http://forums.sbgrid.org/topic/overriding-software-versions) .

-

-Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-

-programs) if you need information on how to run SBGrid programs remotely or

-locally on your machine.

-

-## Data Backups:

-

-Backups on the linux workstations are performed on a regular basis by the

-research computing group at DFCI. If you have any questions about backups,

-need files restored, or have any general issue regarding backups, contact the

-Research Computing group via this web page: [Help Me - DFCI Reseach

-Computing](http://research4.dfci.harvard.edu/content/helpme) .

-

-## 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.

-

-HKL2000 can be accessed and run on Plum, Aqua and mjel12.

-

-Please contact Mike Eck to obtain guest privileges.

-

-

-

-## Networking and General IT Support:

-

-To report problems regarding the network at DFCI, or general computing

-support, contact the Partners Healthcare Help desk at:

-[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only

-works from a Partners network connection)

-

-* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)

-* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)

-* [Other Resources](http://forums.sbgrid.org/topic/other-resources)

-

-

-

-

-