Life after Woods Hole
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
From here you ssh to the class cluster node. E.g.
Your username for evol5 and the class clusters are the same.
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 firstname.lastname@example.org:~/
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.
Compute time grants for researchers on Amazon AWS 
Xsede (US only) 
CIPRES (browser interface) 
Learning how to program
Online tutorials and resources
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
- C++ reference: http://www.cplusplus.com/
Additional optional labs
- Tutorial on Blast+ (Question can be directed to Conor Meehan)
- Alexei Drummand & Remco Bouckaert's BEAST2 tutorial on: Measurably evolving populations, estimating rates, and Bayesian skyline plots
- Trevor Bedford's tutorial on (using BEAST1): Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data
- Information about analyzing MCMC output (convergence diagnostics, prior sensitivity, etc.) by Brian Moore
- Tutorial on model selection using PartitionFinder
- Tutorial on the evolution of morphological characters using R by Samantha Price
- Alternative MrBayes tutorial with exercise on assessing convergence and output quality using Tracer (exercise 2) by Conor Meehan and Tracy Heath
- Applying independent contrasts, a tutorial on continuous-trait evolution by Luke Mahler
- Tutorial on alignment using Bali-Phy by Ben Redelings
- Concatenating NEXUS
Links to (somewhat off-topic) things that came up in discussions at the Captain Kidd (or elsewhere)