Changes in 40e9fd3: dfci-eck-fischer-wang-dhepaganon-arthanari.md overall edits

				dfci-eck-fischer-wang-dhepaganon-arthanari.md
			
          @@ -1,66 +1,76 @@

           <!-- ---title: DFCI: Eck, Dhe-Paganon, Wang, Fischer, & Arthanari Labs -->

           # Overview

          -At DFCI SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers. 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. 

          +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**.

          -To reach this network from an external location please ssh to **crystal.harvard.edu**, and access your local resources from there.

           # Get Help

          -Email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and please include the name of your Lab. For support with software installation please email [bugs@sbgrid.org](mailto:bugs@sbgrid.org). 

          +For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) nd include your name and the name of your lab. Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org). 

          +

          +New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.

          -New members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.

           # Email Access

          -Lab members have access to a Crystal email through Google Apps. If one is not already setup for you, please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request one and CC your PI in the request. 

          +Lab members have access to a Crystal email account through Google Apps. If you do not have an account, email [help@sbgrid.org](mailto: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](mailto:help@sbgrid.org).

          -SBGrid maintains a google mailing list for the labs on the Crystal Google domain. If your lab actively uses it and you need to be added to it, please contact [help@sbgrid.org](mailto:help@sbgrid.org).

           #Lab Wiki

          -An instance of standalone Confluence server is running on a virtual machine on a SBGrid hosted VM cluster. The current version is Confluence 5.8. 

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

          -Access is available to users at the PI’s request. Users must have a crystal email account to be able to use the wiki.

          +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

          -Setup on Linux Computers: Linux computers share authentication and data directories and can be only accessed locally from within the lab. Home directories are located at /nfs/<lab initials>/<username> (example: /nfs/mje/eck). A comprehensive collections of SBGrid applications is located at the /programs directory. All systems are configured with Stereo 3D. In addition, ivory which is a 48 cores workstation 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 questions. PI’s should discuss file permissions with SBGrid to suit their needs.

          -# Mac OS X

          -Setup on OS X Computers: The Mac computers all have local administrative accounts and are specific to the lab members. Your home directory is located at /Users/<username> (example /Users/eck). This 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. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account. 

          +### Linux

          +Linux computers share authentication and data directories and can  only beaccessed 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 at 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 questions. 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. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account. 

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

          -# Windows

          -Windows Computers: Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, except for making 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 are also on the same network are used for instrument control and data collection. These include the RockImager and FPLC systems.

          +### 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. You can access your linux network home directory using Samba (SMB) as follows:

          +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 server address: `smb://blacker.in.hwlab`

          +* Open Finder, click Go, then click 'Go to Server'

          +* Type in the server address: `smb://blacker.in.hwlab`

           	* Click ‘Connect’.

          -* Enter your Samba username and password. (contact SBGrid for SMB account issues)

          +* Enter your Samba username and password (contact SBGrid for SMB account issues).

          +

           # Data Backups

          -Hourly and daily snapshots are taken on the file server Z file system. Data is replicated to another server at the C buildings on the HMS Quad. For supported Mac, local home directories are backed up to a Crashplan server, located at the SGM building also on the HMS Quad.

          +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 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, or need it installed, please email [help@sbgrid.org](mailto:help@sbgrid.org).

          +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](mailto:help@sbgrid.org) with any printing problems.

          +

           # RockImager Setup

           There are two types of data generated by the imager:

          -* Images: These are regular “jpg” image files and are stored directly in the file system on the main file server.

          +* Images: Regular “jpg” image files that are stored directly in the file system on the main file server.

           * Experiment 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 on the instrument and has remote access for troubleshooting purposes. SBGrid maintains the servers configuration.

          +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.

           # Networking and General IT Support

          -There are HMS network switches on each floor (3rd and 4th), that connect the labs to the SBGrid infrastructure. For new SBGrid systems, new port must be activated before using the computers. SBGrid can work with DFCI/LC IT support to get them activated. Please provide the port number you need activated. 

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

          +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](mailto: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/>

...	...	@@ -1,66 +1,76 @@
1	1	<!-- ---title: DFCI: Eck, Dhe-Paganon, Wang, Fischer, & Arthanari Labs -->
2	2
3	3	# Overview
4		-At DFCI SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers. 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.
	4	+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.
	5	+
	6	+To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
5	7
6		-To reach this network from an external location please ssh to crystal.harvard.edu, and access your local resources from there.
7	8
8	9	# Get Help
9		-Email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and please include the name of your Lab. For support with software installation please email [bugs@sbgrid.org](mailto:bugs@sbgrid.org).
	10	+For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) nd include your name and the name of your lab. Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org).
	11	+
	12	+New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
10	13
11		-New members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
12	14
13	15	# Email Access
14		-Lab members have access to a Crystal email through Google Apps. If one is not already setup for you, please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request one and CC your PI in the request.
	16	+Lab members have access to a Crystal email account through Google Apps. If you do not have an account, email [help@sbgrid.org](mailto:help@sbgrid.org) and cc your PI in the request.
	17	+
	18	+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](mailto:help@sbgrid.org).
15	19
16		-SBGrid maintains a google mailing list for the labs on the Crystal Google domain. If your lab actively uses it and you need to be added to it, please contact [help@sbgrid.org](mailto:help@sbgrid.org).
17	20
18	21	#Lab Wiki
19		-An instance of standalone Confluence server is running on a virtual machine on a SBGrid hosted VM cluster. The current version is Confluence 5.8.
	22	+A standalone Confluence server instance (version 5.8) is running on a virtual machine on an SBGrid-hosted VM cluster.
20	23
21		-Access is available to users at the PI’s request. Users must have a crystal email account to be able to use the wiki.
	24	+Users with a crystal email account can access the wiki at the PI’s request.
22	25
23	26	To access the lab wiki go to <http://wiki.sbgrid.org> and login with your crystal email.
24	27
25	28	# Computers
26		-## Linux
27		-Setup on Linux Computers: Linux computers share authentication and data directories and can be only accessed locally from within the lab. Home directories are located at /nfs/<lab initials>/<username> (example: /nfs/mje/eck). A comprehensive collections of SBGrid applications is located at the /programs directory. All systems are configured with Stereo 3D. In addition, ivory which is a 48 cores workstation can be accessed remotely and is typically used for docking computations and data processing.
28		-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 questions. PI’s should discuss file permissions with SBGrid to suit their needs.
29		-# Mac OS X
30		-Setup on OS X Computers: The Mac computers all have local administrative accounts and are specific to the lab members. Your home directory is located at /Users/<username> (example /Users/eck). This allows users to install and update software without requesting help from SBGrid. Every local account is backed up to CrashPlan.
31		-Any network share, including home directories, are mounted via Samba, and require user authentication. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account.
	29	+### Linux
	30	+Linux computers share authentication and data directories and can only beaccessed 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 at 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.
	31	+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 questions. PIs can request modifications to file permissions to suit the lab's needs.
	32	+
	33	+### Mac OS X
	34	+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.
	35	+Any network share, including home directories, are mounted via Samba and require user authentication. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account.
32	36	These computers are also connected to the lab printers on the 3rd and 4th floors of Longwood Center.
33		-# Windows
34		-Windows Computers: Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, except for making them available on the network.
35	37
36		-#Data collection and Instrument Control Computers
37		-The scanner room has two linux systems (aqua and plum) that control the x-ray scanner. Windows computers are also on the same network are used for instrument control and data collection. These include the RockImager and FPLC systems.
	38	+### Windows
	39	+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.
	40	+
	41	+
	42	+###Data collection and Instrument Control Computers
	43	+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.
	44	+
38	45
39	46	## Accessing your Samba shares
40		-Macs have local accounts with local home directories. You can access your linux network home directory using Samba (SMB) as follows:
	47	+Macs have local accounts with local home directories. To access your Linux network home directory using Samba (SMB):
41	48
42		-* Open Finder, click Go then click 'Go to Server'
43		-* Type in server address: `smb://blacker.in.hwlab`
	49	+* Open Finder, click Go, then click 'Go to Server'
	50	+* Type in the server address: `smb://blacker.in.hwlab`
44	51	* Click ‘Connect’.
45		-* Enter your Samba username and password. (contact SBGrid for SMB account issues)
	52	+* Enter your Samba username and password (contact SBGrid for SMB account issues).
	53	+
46	54
47	55	# Data Backups
48		-Hourly and daily snapshots are taken on the file server Z file system. Data is replicated to another server at the C buildings on the HMS Quad. For supported Mac, local home directories are backed up to a Crashplan server, located at the SGM building also on the HMS Quad.
	56	+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.
	57	+
49	58
50	59	# Printing
51		-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, or need it installed, please email [help@sbgrid.org](mailto:help@sbgrid.org).
	60	+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](mailto:help@sbgrid.org) with any printing problems.
	61	+
52	62
53	63	# RockImager Setup
54	64	There are two types of data generated by the imager:
55	65
56		-* Images: These are regular “jpg” image files and are stored directly in the file system on the main file server.
	66	+* Images: Regular “jpg” image files that are stored directly in the file system on the main file server.
57	67	* Experiment data: As experiments are created, the data is stored on a “Microsoft SQL Server 2014” database, currently running on a Windows 2012 server.
58	68
59		-The data is accessible on the RockImager PCs and also through the RockMaker software. Formulatrix provides technical support on the instrument and has remote access for troubleshooting purposes. SBGrid maintains the servers configuration.
	69	+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.
60	70
61	71	# Networking and General IT Support
62		-There are HMS network switches on each floor (3rd and 4th), that connect the labs to the SBGrid infrastructure. For new SBGrid systems, new port must be activated before using the computers. SBGrid can work with DFCI/LC IT support to get them activated. Please provide the port number you need activated.
63		-To report problems regarding the network at DFCI, or general computing support, contact the Partners Healthcare Help desk at:
	72	+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](mailto:help@sbgrid.org) with the computer information and port number and SBGrid will work with DFCI/LC IT support to activate the port.
	73	+To report DFCI network problems, or for general computing support, contact the Partners Healthcare Help desk at:
64	74
65	75	* <http://helpdesk.partners.org/>
66	76