Overview

Below is a tentative schedule of laboratory assignments for the course.  Note that each laboratory will generally consist of (1) a set of background readings on the biological and computational theory behind the assignment; (2) a set of 'warm-up' preparatory exercises to gain familiarity with the software and the assignment domain, perhaps including some non-computer problems; and (3) the main assignment itself, which will be computer-based. Instructions for using the software for each laboratory will be provided. Most of the programs and all the data will be available for download to PCs, Macs, and Linux-based systems. Alternatively, you may use Athena computational resources.

• Goals.  The aim of the lab work is to make sure that you get a chance to apply the theory to real data.  We can talk and talk about evolutionary models, but in our experience, getting your hands dirty may be the best way to learn.
• Mechanics. In general, the labs will involve computer work with modeling and application to ‘live’ data sets.  The computational models and data will always be available to either download to your own computer (either pc, macintosh, or linux box), with the data available on the course website.  Software not available for public download will be made available on Athena, under the course directory /web.mit.edu/6.891.  I’ll give a separate, brief intro for folks not familiar with Athena, but otherwise the instructions should be self-contained.  We will arrange for a separate laboratory section in the Athena cluster in the basement of the Stata building that will serve as a question-answer time in general and for lab questions in particular.  During the latter part of the course, we can use this time to talk about projects.
• Format. Each lab will be divided into three parts: first, a ‘warmup’ section to get familiar with the computational tools; second, brief questions that review and extend the lecture material; and third, a substantive application to a real data set drawn from the literature.  We anticipate that each laboratory will take about two weeks, unless otherwise noted. In general, you won’t need to do your own programming in C++, Perl, Java, etc. – rather, we will use off-the-shelf tools.  However, some questions and projects later on may require some elementary skills with manipulating data, that you should be able to do via Perl, or Matlab – almost any such set of tools.  If you find that challenging, do not despair.  Please just talk to me: we can team up people that have complementary skill sets, or substitute alternative questions, etc. 
• Lab reports.  We will strive to make this a ‘paperless’ class.  Lab reports should be written up as web pages, with the final URL sent to me, berwick@csail.mit.edu. 
• Policy on cooperative work.  We strongly encourage cooperation. You are free to work in groups, but please do write up your lab yourself (however, the Final Project is a team effort and requires only one write-up).