Difference between revisions of "Phylogenetics: Bioinformatics Cluster"
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|<span style="font-size: x-large">[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Syllabus EEB 349: Phylogenetics]</span> | |<span style="font-size: x-large">[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Syllabus EEB 349: Phylogenetics]</span> | ||
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| − | |The goal of this lab exercise is to show you how to | + | |The goal of this lab exercise is to show you how to use the [http://www.biotech.uconn.edu/bf/ Bioinformatics Facility] computer cluster to run PAUP* and GARLI. |
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== Part A: Using the UConn Bioinformatics Facility cluster == | == Part A: Using the UConn Bioinformatics Facility cluster == | ||
| + | The Bioinformatics Facility is part of the UConn Biotechnology Center, which is located behind the Up-N-Atom Cafe in the lower level of the Biology/Physics building. Jeff Lary maintains a 17-node Apple Xserve G5 Cluster that can be used by UConn graduate students and faculty to conduct bioinformatics-related research (sequence analysis, biological database searches, phylogenetics, molecular evolution). You have each been given accounts on the cluster, and today you will learn how to start analyses remotely (i.e. from this computer lab), check on their status, and download the results when your analysis is finished. | ||
| + | |||
| + | === Obtaining the necessary communications software === | ||
| + | You will be using a couple of simple (and free) programs to communicate with the head node of the cluster. Visit the [http://www.putty.nl/download.html PuTTY web site], scroll down to the section labeled "Binaries" and download two of the files listed: <tt>putty.exe</tt> and <tt>pscp.exe</tt>. | ||
| + | |||
| + | === Logging in for the first time === | ||
| + | On the whiteboard you will find your login id (user name) and password. The first step is to change your password. Be sure to remember your username and password for future labs. | ||
== Part B: Starting a PAUP* run on the cluster == | == Part B: Starting a PAUP* run on the cluster == | ||
Revision as of 00:04, 18 February 2007
|
EEB 349: Phylogenetics |
| The goal of this lab exercise is to show you how to use the Bioinformatics Facility computer cluster to run PAUP* and GARLI. |
Contents
Part A: Using the UConn Bioinformatics Facility cluster
The Bioinformatics Facility is part of the UConn Biotechnology Center, which is located behind the Up-N-Atom Cafe in the lower level of the Biology/Physics building. Jeff Lary maintains a 17-node Apple Xserve G5 Cluster that can be used by UConn graduate students and faculty to conduct bioinformatics-related research (sequence analysis, biological database searches, phylogenetics, molecular evolution). You have each been given accounts on the cluster, and today you will learn how to start analyses remotely (i.e. from this computer lab), check on their status, and download the results when your analysis is finished.
Obtaining the necessary communications software
You will be using a couple of simple (and free) programs to communicate with the head node of the cluster. Visit the PuTTY web site, scroll down to the section labeled "Binaries" and download two of the files listed: putty.exe and pscp.exe.
Logging in for the first time
On the whiteboard you will find your login id (user name) and password. The first step is to change your password. Be sure to remember your username and password for future labs.
