Assignment #3

Hello all,

As you have likely heard, UConn is closed tomorrow and so we will not be having class.  There will be no make up lecture, however I am posting a new assignment building on the perl techniques you have already learned and applying them to think about some of the genome quality issues that we discussed on Monday.  The new assignment will be due before class on Wednesday Feb 12/14 and can be found here: MCB_5472_Assignment_3

Questions #1 and #2 from Assignment #2 will be due at 1pm on Thursday Feb 6/14 to accommodate UConn’s closure tomorrow.  Question #3 from this assignment has been moved to Assignment #3.

As always, please post your questions here or email myself or Peter directly.  Please note that if you question has been answered on the website already we will just refer you there, so you may as well make it your first stop!

Lecture #2 Feb 3/14

Hello all – Please find attached today’s lecture.  We will be covering a bit more about GenBank, and then taking a whirlwind tour of DNA sequencing and assembly.  The goal of this latter section is to understand how the methods used to sequence and assemble a particular genome can affect the quality of the input data used for any evolutionary analysis and how to deal with this problem.

Lecture #2 pdf: MCB5472_Lecture_2_Feb-3-14

Lecture #2 ppt: MCB5472_Lecture_2_Feb-3-14

Assignment #2 and Jan 29/14 Lecture

Hello all – Congratulations on making it through assignment #1!  Lest you be bored, please find Assignment #2 here: MCB_5472_Assignment_2 (Note: updated to correct error discovered in class)

Today’s lecture can be found here: MCB5472_Assignment_2_lecture_Jan-29-14.  There are no specifically assigned text readings, but as always you are encouraged to use any resource that you have to do the assignment.  As we are starting into more complicated code this week, I especially encourage you to post specific questions here.  When you do so, please include an exact copy of your code so that your colleagues in class, Peter and Jonathan can help you troubleshoot.

Happy coding!

Course Text and Alternative Resources

The text for MCB 5472 is “Unix and Perl Primer for Biologists” and can be found here: unix_and_perl_v3.1.1 (Alternatively, the web link is http://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v3.1.1.pdf)

Some other optional texts that we have found useful are:

“The Linux Command Line – A Complete Introduction” – http://www.amazon.com/The-Linux-Command-Line-Introduction/dp/1593273894  (Hat tip to K. Lee)

“Beginning Perl for Bioinformatics” http://www.amazon.com/Beginning-Perl-Bioinformatics-James-Tisdall/dp/0596000804/ref=sr_1_1?s=books&ie=UTF8&qid=1390329794&sr=1-1&keywords=Perl+for+Bioinformatics

Have you found other books or websites you’ve found useful?  Post a comment!

Assignment #1 and Jan 22/14 Lecture

Assignment #1 can be found here: MCB5472_Assignment_1ALL assignment files need to be emailed to Jonathan before the start of next Wednesday’s class (Jan 29/14) to be eligible for credit. jonathan.klassen@uconn.edu; please remember to add “MCB 5472” to your email title.

The accompanying lecture can be found here: Assignment_1_lecture (pptx) Assignment_1_lecture (pdf)

Specific questions can be posed and discussed in the comments section for this post.

Welcome to MCB 5472 and Course Outline

Welcome everyone to the Spring 2014 version of MCB 5472!

We will be posting course lectures and assignments on this website, so be sure to have it bookmarked and check it frequently.  This will be the primary means by which we disseminate documents pertaining to the course.  Commenting has also been enabled for each post.  PLEASE POST SPECIFIC QUESTIONS ABOUT THE MATERIAL HERE FIRST before emailing Jonathan or Peter directly.  You are also encouraged to answer questions if you can.  Posting and answering comments will be count towards your participation grade.

You can find the preliminary course outline here: Outline MCB5472 Computer Methods in Molecular Evolution.  Jonathan will primarily teach the material before the midterm and Peter will primarily teach the material after.  However, both of us are available to help with your questions regarding any of it.  The best method is to contact us via email: jonathan.klassen@uconn.edu and jpetergogarten@gmail.com.  Please include the text “MCB 5472” in the subject line of your email.

Philosophically, we expect that you will be in charge of understanding the course material, including finding the resources that you need wherever you can.  Truthfully, computational biology is a very open community and there are many resources and communities freely accessible on the internet.  Seqanswers (http://seqanswers.com/) and Biostar (http://www.biostars.org/) are two of the most popular.  Linux and perl have similarly open communities and there are many accessible resources available – if you don’t know, google!  Your peers are also an excellent resource, and peer-peer learning is a critical component of bioinformatics culture.  However, respect University regulations on plagerism and copying other’s work directly.  Jonathan and Peter comprise part of this community for you, and we will certainly work to keep you on track – if you need help, BE SURE TO ASK!  However, we will not explicitly give you step by step instructions to get your answer.  Your acquiring independent computational fluency is a critical learning goal of this course.

Good luck!