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Project/Presentation guidelines

November 30, 2012 in Administrivia

Reports: One report per team. 3-4 pages. Should have the following items/sections: title page (Title, names and IDs of the team members), Introduction, Data and Method, Results. Describe the question(s) that you are trying to address, the data that you used to address the question(s), analysis pipeline or workflow, and the main findings from their analysis (results, summarized in table or graphical form as appropriate).  Provide a link to the code that you developed for this project as github repository or an archive of your source code. You should provide references to any tools, datasets, or background concepts you refer to with the use of literature references.

Presentations: 10-15 mins. One presentation per team. Present the same material as paper, but summarize for audience what you were trying to address and what results you were able to find. Discuss your methods and code you needed to develop to solve the problems in your project. Each team needs to prepare a set of power point slides as they would do for a lab meeting or conference. One member can represent the team and do the whole presentation, or several members can talk about different parts of the presentation.

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by stajich

Homework instructions

October 8, 2012 in Administrivia, Problem Sets

Homework is due at 11:59PM on Tuesday unless specified at a different time.

It will be graded for completeness (did you get the right answer).
The best way to turn in the homework is to upload your code as a gist at – send to Dr Stajich the link to each of your solutions.  If you cannot use the gist system for this homework you can also email the two scripts to me – however, it will be harder to show you how to fix your code if you do not upload it to a system like github.
Make sure it is public or we cannot see it.
Please write GEN220 homework 2 in your message or subject.
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Lecture notes and examples in github repository

October 5, 2012 in Administrivia

Github is a repository for source code we will attempt to use for the class as a way to turn in homework so that if changes need to be made, we can more easily show you what is needed.

You can upload code at this site:  and get a tracked “gist” repository for your answers.  This can then be shared with the instructors by emailing us the link.  The best scenario, so you can track all of your gists, is to create a github account, this will allow you keep track of your assignments. I will go over this in class too, but this is something you will want to check out.

All the example code and lectures are available on github in this repository. For example, there are many sample bits of code pulled out from the lectures already available as scripts you can run.

I’m working to get the lecture notes rendered as PDF so you can download them, but having a little bit of trouble. For the time being you can read them in the web rendered form at gitub, just ignore the lines that have !perl on them. For example, here is a link to lecture 1 and is rendered by the github markup.



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Week 2 announcements

October 2, 2012 in Administrivia

This week’s lectures will be Wednesday 2-4PM and 2-3PM on Friday (but we will stick around to answer questions) and will cover an introduction to Perl. There are many tutorials out there on the web, many linked at the Resources page. Feel free to browse there in addition to the material that will be covered in class.

Homework problem sets

No problemsets were required to be turned in from last week’s UNIX problems and we will have problemsets for you to work for this week’s lectures on Wednesday and Friday.

Cluster accounts

Accounts are now ready. If you can come to class early on Wednesday we can get you setup. Or you are welcome to stop by Jason’s office on Wednesday and get your account information ahead of time.

Mailing list for the course

To accomodate those not registered but following along in the class, and encourage discussions among all of us, I have started a mailing list you can try out for asking questions. I will also use it to announce information in addition to what goes on iLearn. Please go there to read the list or subscribe if you want to get the regular emails (you can also just read the list via the web if you don’t want to get more emails – just don’t forget to check it or subscribe to the RSS feed).

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The lectures and problems from Week 1 are posted

September 28, 2012 in Administrivia

The problem sets and lectures have been updated to present the material on UNIX and command line usage on this site. The same material has been posted on iLearn.

Accounts for biocluster will be issued on Monday Oct 1 and will be able to provide these to you before class so you can practice.