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!

Today’s lecture is all about the NCBI database and how to go about getting some data.  You can find the presentation here: MCB5472_Lecture_1_Jan-27-14 (pdf) MCB5472_Lecture_1_Jan-27-14 (pptx).

Remember that today we are in Kresge (TLS 263).

Jill Wegrzyn’s presentation about the UConn Biotechnology and Bioservices Center cluster and basic UNIX commands can be found here: Wegrzyn_BBC_Bioinformatics

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 can be found here: MCB5472_Assignment_1.  ALL 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 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!