Date Topic Readings Things to do before next class Due
20 January 2012 Introduction to class
Background Readings
Project Readings
  1. Login to the Google Group and request access.
  2. Begin skimming the papers under Project Readings to the left, once your group has a decision as to which you would like to present on Wednesday (25 January 2012), please e-mail with your selection. If another group has already selected the article I'll let you know as soon as possible. Also, if you find another selection along the same ilk you believe to be relevant to the short read assembly/alignment problem please send me or Dr. Chamberlain the link and we'll see about including it.
25 January 2012, in class
25 January 2012 Presentations, Auto-pipe, SEAS and Mercury Group logins After the presentations Jonathan will give a brief introduction to Auto-pipe. Before or after class you'll need to read the API documentation for the Auto-pipe version 2 port interface link. Part 1
Follow up with a post to the Google groups message board. Each group presenting will post a quick summary of what they presented (either before or shortly after the presentation), a few short sentences will do. After that we'll require at least one comment per person for everyones presentation (the ones that your group did not give), at least two constructive sentences. This will be weekly requirement. Since we're only meeting for one hour per week as a class this is your chance to give real detailed criticism (I use that word for positive and negative remarks) of each others projects. BE RESPECTFUL!! This is also a great opportunity to help each other out, (i.e. ask for help or simply present alternative methods to what was presented).
Part 2
Listen to the posted lecture (will be posted shortly) and then build the basic averaging application that will be added to your SVN repositories. This is a simple project to help you gain experience with the build system before we start adding in things that might be a bit more complex to get working.
1 February 2012, by the time class starts.
1 February 2012 Auto-pipe, interface and QA The only additional reading for this presentation is the Auto-pipe version 2 port interface link. Your assignment this week is to create a merge sort software block and test it. The software block should be functionally equivalent to the hardware merge sort described in the this paper. I've created a brief diagram on how to map and test the software merge sort which can be found here. Feel free to use the perl script included in the repositories to create the block shell, remember you'll have to make the script executable by using chmod +x Please use the Google group for help as you need it, it's probably the fastest way for everyone to get answers. 8 February 2012, by the time class starts.
8 February 2012 Short read assembly, biological significance. Required
Auto-pipe Simulation Guide
Quick video on how to add HDL to your existing C blocks
Chapter 21, Data Structures for Disjoint Sets, Introduction to Algorithms (Cormen et al., editions >=2)
Your assignment this week is to begin work on your hardware merge sort block and simulate it. I've placed a simulation guide under the assigned readings (you can also get to it from shell by typing 'apsim_doc' on the shell comamnd line), if you have any problems while working through it please send an e-mail to the Google Group soon so we can work through it. 15 February 2012, by the time class starts.
15 February 2012 Short read assembly, biological significance...and the algorithms. Required
Dr. Buhler's notes from the last two sessions
Chapter 21, Data Structures for Disjoint Sets, Introduction to Algorithms (Cormen et al., editions >=2)
You have two assignments this week and one due week after next (29 February 2012). As a group, finish up your hardware merge sort blocks and submit the code to your svn repositories. Individually discuss section 5 of the notes on the message board (I want to see reasoning, references, math...prove what you say). Lastly as a group I'm assigning project proposals (the part due 29 February 2012). There are guidelines on what to turn in are here. This is the project you'll be working on for most of the semester so put some thought into it.
22 February 2012, by the time class starts.
22 February 2012 Scala-pipe Required
Scala-pipe documentation
Programming in Scala, 1st Edition (free from Proquest Books)
Finish project proposal, finish up google group comments on Section 5 of Dr. Buhler's notes (see link from last weeks assignment). 29 February 2012, by the time class starts.
7 March 2012 Review of sorting projects NONE!! Make your merge sorts functional!! YOU will be presenting your projects, no power points....just code and chalk. You may use my laptop. This isn't to expose flaws in your design, this is to make your future designs better....and functional. You should also be working on your projects at this point. NONE!!
14 March through 18 April 2012 Student presentations and active discussion of projects. NONE!! Participate in discussions. NONE!!
24 April 2012 Final Project Presentations Grading criteria can be found here: Prepare presentation with the following: results, conclusions and final thoughts on your project. You don't need to present your entire projects over again, at this point we're all very familiar. What we want to know know is how does your project perform, what would you do differently and lastly what should follow this work? TODO: Project write-up Tuesday, 8 May 2012 by 5:00 p.m. Central Standard Time.

Let me know if there are any typos or things you don't understand (class related of course)