First Time Guide - Revision history

imported>Weigang at 16:02, 23 March 2016

2016-03-23T16:02:43Z

← Older revision		Revision as of 16:02, 23 March 2016
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	The following is a short guide to the lab, primarily intended for newcomers. Lab members are welcome to submit changes to this document.		The following is a short guide to the lab, primarily intended for newcomers. Lab members are welcome to submit changes to this document.
			=A UNIX & Perl Primer=
			[http://korflab.ucdavis.edu/Unix_and_Perl/current.html Go through this course if you haven't taken any programming courses]

	= Software Availablility =		= Software Availablility =

imported>Yozen: Updated instructions for new lab location/setup, fixed formatting

2015-02-02T19:42:42Z

Updated instructions for new lab location/setup, fixed formatting

← Older revision		Revision as of 19:42, 2 February 2015
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	= Working Remotely =		= Working Remotely =
	Lab members are able to work on their own computers at home, or on a laptop, or by logging in to a lab machine from home. To log into a machine remotely, you will use software called ssh.		Lab members are able to work on their own computers at home, or on a laptop, or by logging in to a lab machine from home. To log into a machine remotely, you will use software called <code>ssh</code>.

	ssh allows you to connect to a machine remotely and have a shell (command line interface) just as you would if you opened a terminal in a machine in the lab. ~~Only about 3 machines~~ can be connected to in this way from outside of Hunter. Like most machines exposed to the internet, the machines in the lab have names (hostnames) and you will use these names to connect to them with the appropriate software.		<code>ssh</code> allows you to connect to a machine remotely and have a shell (command line interface) just as you would if you opened a terminal in a machine in the lab. At the moment, only one machine can be connected to in this way from outside of Hunter. Like most machines exposed to the internet, the machines in the lab have names (hostnames) and you will use these names to connect to them with the appropriate software.

	Machines open to remote connection (ssh):		Machines open to remote connection (ssh):
	~~homology.hunter.cuny.edu~~		* darwin.hunter.cuny.edu
	~~linkage.hunter.cuny.edu~~
	~~synteny.hunter.cuny.edu~~
	~~allele~~.hunter.cuny.edu

	(wallace.hunter.cuny.edu is not available outside of Hunter...yet).		(wallace.hunter.cuny.edu is not available outside of Hunter...yet).
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	All of the machines can be logged into from any other machine when you are inside of Hunter.		All of the machines can be logged into from any other machine when you are inside of Hunter.

	Logging in remotely using Windows:		Please note that repeated failed password attempts may result in a BAN of your IP address. If this happens to you, please email the system administrator and Dr. Qiu.

			== Logging in remotely using Windows ==
	Download PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (putty.exe)		Download PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (putty.exe)

	~~Logging in remotely using Linux~~, ~~Mac OS X~~, ~~BSD~~,.~~..UNIX:~~		For PuTTY, simply provide the hostname of the machine you wish to use, your lab username, and your password. The port is the default.
	~~You already have ssh installed, just open a terminal and follow~~ the ~~instructions below~~.

	~~For PuTTY~~, ~~simply provide the hostname of the machine you wish to use~~, ~~your lab username~~, and ~~your password. The port is~~ the ~~default.~~		== Logging in remotely using Linux, Mac OS X, BSD,...UNIX ==
			You already have ssh installed, just open a terminal and use the command:

	~~For UNIX-like OS's, use the command:~~
	<pre>		<pre>
	ssh <username>@<hostname>		ssh <username>@<hostname>
	</pre>		</pre>
	where <username> is your username and <hostname> is the machine you want to connect to. ~~Remove the '<' and '>' from the command before executing.~~		where <code>username</code> is your username and <code>hostname</code> is the machine you want to connect to.


	= Group Resources =		= Group Resources =

imported>Yozen: Added shared directory info

2011-09-23T22:59:44Z

Added shared directory info

← Older revision		Revision as of 22:59, 23 September 2011
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	* The Calendar, which is automatically available to all lab members, lists important dates, and lab meetings. In particular, changes to lab meetings by the PI can be made here in the event something unexpected happens.		* The Calendar, which is automatically available to all lab members, lists important dates, and lab meetings. In particular, changes to lab meetings by the PI can be made here in the event something unexpected happens.
	* The Issue Tracker (Google Code) is an issue reporting and tracking system. You can submit issues here that you may be having with machines, software, or feature requests. If the software in question is being developed in-house, you can assign the issue to the developer who created it or maintains it. If there is a system error, or a software installation request, this should be assigned to the system administrator. The issue tracker can also be used by the PI to keep track of a project given to a lab member. '''(The issue tracker is currently in disuse)'''		* The Issue Tracker (Google Code) is an issue reporting and tracking system. You can submit issues here that you may be having with machines, software, or feature requests. If the software in question is being developed in-house, you can assign the issue to the developer who created it or maintains it. If there is a system error, or a software installation request, this should be assigned to the system administrator. The issue tracker can also be used by the PI to keep track of a project given to a lab member. '''(The issue tracker is currently in disuse)'''
			* A shared directory is available to all users under <pre>/home/shared</pre>. You must first type out the whole name of the directory before it becomes visible. Work or other files which are to be shared with others go into a subdirectory in this directory. Typically, you would create a subdirectory with the same name as your username.

	=WIP=		=WIP=
	'''-This document is still under construction. Please email me at yzhernand at gmail dot com if you have any questions/suggestions-'''		'''-This document is still under construction. Please email me at yzhernand at gmail dot com if you have any questions/suggestions-'''

imported>Yozen: Page creation

2011-09-23T22:54:33Z

Page creation

New page

'''Welcome to Dr. Qiu's Evolutionary Bioinformatics Lab!'''

The following is a short guide to the lab, primarily intended for newcomers. Lab members are welcome to submit changes to this document.

= Software Availablility =
In this lab, we use the GNU/Linux (Linux) operating system. All user workstations in the lab use the latest version of the Ubuntu Linux distribution. These workstations all make use of a centralized user account and file system so that a user can sit at any station, log in, and have all their files available. The only difference would be some difference in hardware such as video card, keyboard, mouse, etc.

While there is a graphical user interface (gui) presented to the user (in the form of "environments" such as GNOME or KDE)*, you'll find yourself using the command line interface for the majority of your work. The web browser and one text editor might make up the bulk of your GUI use.

Our centralized system also allows us to make certain widely used software available to all machines, including:
phylip, PAML, clustalw, clustalw-mpi (only runs on wallace), mrbayes (only runs on wallace), BEAST (gui), Dendroscope (gui)

Programs labeled (gui) are programs with a user interface, so they may not have a command line interface. Programs marked as running only on wallace are programs which will refuse to work unless you are logged into the machine called "wallace" (see below). Those programs will be doing some more intense work for longer runs, so you are made to run them only on wallace. Other software may also be available, and new software can be added upon request.

= Working Remotely =
Lab members are able to work on their own computers at home, or on a laptop, or by logging in to a lab machine from home. To log into a machine remotely, you will use software called ssh.

ssh allows you to connect to a machine remotely and have a shell (command line interface) just as you would if you opened a terminal in a machine in the lab. Only about 3 machines can be connected to in this way from outside of Hunter. Like most machines exposed to the internet, the machines in the lab have names (hostnames) and you will use these names to connect to them with the appropriate software.

Machines open to remote connection (ssh):
homology.hunter.cuny.edu
linkage.hunter.cuny.edu
synteny.hunter.cuny.edu
allele.hunter.cuny.edu

(wallace.hunter.cuny.edu is not available outside of Hunter...yet).

All of the machines can be logged into from any other machine when you are inside of Hunter.

Logging in remotely using Windows:
Download PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (putty.exe)

Logging in remotely using Linux, Mac OS X, BSD,...UNIX:
You already have ssh installed, just open a terminal and follow the instructions below.

For PuTTY, simply provide the hostname of the machine you wish to use, your lab username, and your password. The port is the default.

For UNIX-like OS's, use the command:
<pre>
ssh <username>@<hostname>
</pre>
where <username> is your username and <hostname> is the machine you want to connect to. Remove the '<' and '>' from the command before executing.

= Group Resources =
We provide some digital resources that are available to all lab members outside of the machines themselves. All lab members are automatically added to a mailing list provided by Google Groups, as well as access to the corresponding Groups page. The mailing list can be used for anything from alerting all users to some news, to asking help from the group.

The Lab Links page on the Groups page lists three more resources.
* The Lab Readings Spreadsheet (mostly deprecated) allows members to reserve lab meetings where they would like to present a paper to the group.
* The Calendar, which is automatically available to all lab members, lists important dates, and lab meetings. In particular, changes to lab meetings by the PI can be made here in the event something unexpected happens.
* The Issue Tracker (Google Code) is an issue reporting and tracking system. You can submit issues here that you may be having with machines, software, or feature requests. If the software in question is being developed in-house, you can assign the issue to the developer who created it or maintains it. If there is a system error, or a software installation request, this should be assigned to the system administrator. The issue tracker can also be used by the PI to keep track of a project given to a lab member. '''(The issue tracker is currently in disuse)'''

=WIP=
'''-This document is still under construction. Please email me at yzhernand at gmail dot com if you have any questions/suggestions-'''