First Time Guide

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.

A UNIX & Perl Primer

Go through this course if you haven't taken any programming courses

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. 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):

• darwin.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.

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)

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:

ssh <username>@<hostname>

where username is your username and hostname is the machine you want to connect to.

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)
• A shared directory is available to all users under

  /home/shared

  . 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

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