Difference between revisions of "Open lab"

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(Additional optional labs)
(Accessing the cluster outside MBL)
 
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==Life after Woods Hole==
 
==Life after Woods Hole==
 +
[[Media:Life_After_Woods_Hole.pdf|Life_After_Woods_Hole.pdf]]
  
 +
===Accessing the cluster outside MBL===
 +
You can access your files on the class clusters until the end of August form outside MBL. To do this you need to first login to the mbl network. The command to do so is
 +
<pre>
 +
username@class.mbl.edu
 +
</pre>
 +
From here you ssh to the class cluster node. E.g.
 +
<pre>
 +
ssh class01
 +
</pre>
  
==Additional Links==
+
In order to put files up/get files down from the cluster you can do this through the class.mbl.edu interface. All files you put on here will appear in your class home directory. E.g. if I want to scp a file from my computer to evol5 I use the command
Links to information shared in the open lab:
+
<pre>
 +
scp test.txt cmeehan@class.mbl.edu:~/
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</pre>
 +
This file will also be accessible on the class cluster where you can run it. <br />
 +
Cyberduck can be used to connect to class.mbl.edu (use the same process as we did for connecting to a class cluster but use class.mbl.edu instead of class-01.mbl.edu). Any files you copy here will appear in the class home directory. Also, any files created on the class cluster will appear here as well.
  
 +
==Cluster resources==
 
[https://molevol.mbl.edu/wiki/index.php/iplant Using the *FREE* iPlant cluster]
 
[https://molevol.mbl.edu/wiki/index.php/iplant Using the *FREE* iPlant cluster]
 +
 +
Compute time grants for researchers on Amazon AWS
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[http://aws.amazon.com/grants/]
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Xsede (US only)
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[https://www.xsede.org/]
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 +
CIPRES (browser interface)
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[http://www.phylo.org/]
 +
 +
==Data Repositories==
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Dryad
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[http://datadryad.org/]
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TreeBASE
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[http://treebase.org/treebase-web/home.html]
 +
 +
==Learning how to program==
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[http://www.codecademy.com Code Academy - An incredible sandbox for learning how to program in many different programming languages.]
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[http://biopython.org/wiki/Main_Page BioPython]
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[http://pythonhosted.org/DendroPy/ Dendropy]
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Books
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    [http://practicalcomputing.org/ Practical Computing for Biologists - Haddock and Dunn]
 +
    [http://www.greenteapress.com/thinkpython/ Think Python (Free)]
 +
Online tutorials and resources
 +
    [http://software-carpentry.org/ Software Carpentry (online tutorials)]
 +
    [http://www.codecademy.com/ Code Academy interactive lessons)]
 +
 +
==MCMC Implementation with [http://cteg.berkeley.edu/huelsenbeck.html John Huelsenbeck]==
 +
This will be a live demonstration of MCMC programming in C++
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* C++ programming resources
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** for MacOS X, you will need to install the [https://developer.apple.com/technologies/tools/ Apple Developer Tools] -- this includes the Xcode IDE demonstrated in the lab
 +
** for any platform, you can use [http://www.eclipse.org/ Eclipse], which is a multi-language IDE (languages include: C++, Fortran, Haskell, JavaScript, Perl, Python, R, Ruby, etc.)
 +
** C++ reference: http://www.cplusplus.com/
  
  
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* Applying [http://treethinkers.org/tutorials/continuous-trait-evolution/ independent contrasts], a tutorial on continuous-trait evolution by [http://lukemahler.com/ Luke Mahler]
 
* Applying [http://treethinkers.org/tutorials/continuous-trait-evolution/ independent contrasts], a tutorial on continuous-trait evolution by [http://lukemahler.com/ Luke Mahler]
 
* [http://nucleus.biology.duke.edu/~bredelings/bali-phy-www/Tutorial2.html Tutorial on alignment] using [http://faculty.biomath.ucla.edu/msuchard/htdocs/bali-phy/ Bali-Phy] by [http://people.duke.edu/~br51/ Ben Redelings]
 
* [http://nucleus.biology.duke.edu/~bredelings/bali-phy-www/Tutorial2.html Tutorial on alignment] using [http://faculty.biomath.ucla.edu/msuchard/htdocs/bali-phy/ Bali-Phy] by [http://people.duke.edu/~br51/ Ben Redelings]
 +
* [http://biopython.org/wiki/Concatenate_nexus Concatenating NEXUS]
 +
  
 
== Miscellany ==
 
== Miscellany ==

Latest revision as of 12:04, 23 July 2015

Life after Woods Hole

Life_After_Woods_Hole.pdf

Accessing the cluster outside MBL

You can access your files on the class clusters until the end of August form outside MBL. To do this you need to first login to the mbl network. The command to do so is

username@class.mbl.edu

From here you ssh to the class cluster node. E.g.

ssh class01

In order to put files up/get files down from the cluster you can do this through the class.mbl.edu interface. All files you put on here will appear in your class home directory. E.g. if I want to scp a file from my computer to evol5 I use the command

scp test.txt cmeehan@class.mbl.edu:~/

This file will also be accessible on the class cluster where you can run it.
Cyberduck can be used to connect to class.mbl.edu (use the same process as we did for connecting to a class cluster but use class.mbl.edu instead of class-01.mbl.edu). Any files you copy here will appear in the class home directory. Also, any files created on the class cluster will appear here as well.

Cluster resources

Using the *FREE* iPlant cluster

Compute time grants for researchers on Amazon AWS [1]

Xsede (US only) [2]

CIPRES (browser interface) [3]

Data Repositories

Dryad [4]

TreeBASE [5]

Learning how to program

Code Academy - An incredible sandbox for learning how to program in many different programming languages.

BioPython

Dendropy

Books

   Practical Computing for Biologists - Haddock and Dunn
   Think Python (Free)

Online tutorials and resources

   Software Carpentry (online tutorials)
   Code Academy interactive lessons)

MCMC Implementation with John Huelsenbeck

This will be a live demonstration of MCMC programming in C++

  • C++ programming resources
    • for MacOS X, you will need to install the Apple Developer Tools -- this includes the Xcode IDE demonstrated in the lab
    • for any platform, you can use Eclipse, which is a multi-language IDE (languages include: C++, Fortran, Haskell, JavaScript, Perl, Python, R, Ruby, etc.)
    • C++ reference: http://www.cplusplus.com/


Additional optional labs


Miscellany

Links to (somewhat off-topic) things that came up in discussions at the Captain Kidd (or elsewhere)

  • Sim Daltonism: a program that simulates how colors are perceived by people with different types of color blindness
  • PhyloPic: a repository for silhouette images of living organisms