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Registration and other information about ACC's Bioinformatics course for instructors
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ACC Bioinformatics course for instructors 

Registration is now open for our on-line Bioinformatics course for instructors, offered through Austin Community College.

This email contains information about:
1.  Registration and cost
2.  How will the course work? 
3.  How many hours a week will this take?
4.  Technology requirements
5.  What does the course cover?
6.  What if the course fills up? And what about next year?
 

1.  Registration and cost

The course costs $551 and is offered through the continuing education group at Austin Community College.  At the end of the course, you will get a certificate of completion.

To register:

Go to http://continue.austincc.edu/schedule/view?id=64107 

1. Click Add to your Schedule.
2. Click a button to choose whether you'll register on campus or Online.
3.  If you click register online and do not have an ACCeID, click New Student Registration.
4.  Click "Click Here to Open a Secure Registration Window"
5.  Select the Course Prefix, enter the course number, and section number.

Course Prefix: BITX
Course number:  3000
Section number:  200

When you're done the form should look like this:


6. Click the Submit button.

You should see the name of the course.  If you see a message about No classes, make you've entered the correct information.  

7.   Check the Check box in front of the course name and click Submit.

8. Complete the form.  

****Note:  you must pick one of the counties in the list, even you don't live in Texas.

9.  Click submit.  The directions are pretty clear after this point.

10.  If you have any problems, please contact Sonia Castillo in registration.  Her email is sonia.castillo@austincc.edu and her phone number is  512-223-7542.  She is very nice and very helpful.
 

2.  How will the course work?
This course will be on-line.  It starts Jan. 18th, 2018 and ends May 13th.  

Early in January, I'll email everyone and set up a poll to pick 2-3 times during the week for video chats.  You don't have to attend twice a week, I just want to make sure that everyone can attend at least one meeting. Each week, we will meet through video chat (Zoom) for 1-1.5 hours. We'll discuss the topic for the week and approaches to teaching that topic.  

We will use the Spring 2018 section of the ACC Bioinformatics course as kind of teaching laboratory. The instructor course will run in parallel to our student course.  Students get new assignments each week and spend at least 10-15 hours completing them.  Participants in the instructor course will have the option of completing the same assignments as the students.  

I will set up accounts for all of you in our teaching web site so you can see examples of student work and assignments.  I'll demonstrate the assignments and we'll talk about different approaches and how you might set up different kinds of investigations. Your work will not be graded, but we will discuss the results.

We will also discuss examples of student work and how to address some of the common questions and challenges that students have.
 

3.  How many hours a week will this take?

This depends on what you want to get out of the course and your background.  At the very least, you should need plan on 3-5 hours a week in order to attend a 1-1.5 hr discussion and read through the weekly assignments.  I know many of you are teaching at the same time, so I'm trying to set realistic expectations.
 

 

 

What kinds of technology do we need?

We will use Zoom for our meetings so you will definitely need an internet connection and a computer that supports video and audio.  

As far as computers, it would be ideal if you have an iPad and a Mac laptop.  But, much of the work can also be done on a laptop with Windows 10.  

The textbook(s) we are using is available as an iBook. iBooks work on iPhones, iPods, iPads, and Macs.  If you can use this, I will send you promo codes so you can get a copy for free.  I will also make PDF versions of the text available.  Unfortunately, there isn't a Windows equivalent of iBooks so PDF versions will not have all the features available in iBooks, like study cards, glossary, videos, interactive features, etc.  I will make Kindle versions at some point, but it take a bit of time.

The molecular modeling program we'll use (Molecule World) only works on the iPad, right now.  We plan to put it on Macs and Windows eventually, but it may be a couple of years.  In the meantime, you can get Cn3D from the NCBI and it will run on Macs and Windows 10.   Cn3D is missing many of the features in Molecule World, but it works okay.  You just have to work a bit harder.  

What does the course cover?
Students who take the ACC Bioinformatics course vary greatly in reading ability and pre-existing knowledge of biology and chemistry.  To accommodate our students' wide range of abilities, and make sure students develop the skills described above, the course has been designed to address bioinformatics skills and concepts in biochemistry & biology at the same time. 

We start with databases, since knowing how to use a database is fundamental.  Then, we learn about molecular structures, covering nucleic acids and proteins, and their building blocks, properties, and they kinds of bonds they form.

After molecular structures, students work with molecular sequences and learn how to use the core blast programs:  blastn, blastp, blastx, and primer blast. They do a multiple alignment, make a phylogenetic tree, and identify conserved amino acid residues and their function.

Students also do some experiments with drug discovery, learn how to use databases, and compare mutant and normal structures to explain changes in structure and function.

In the final section, we pull everything together and look at genetic variation.  Students translate sequences and use blastp to identify different types of mutations, then use modeling to assess their impact on protein activity.  They also compare mutant and normal proteins to explain different phenotypes.

In the ACC student course final project, every student is expected to be able to:

1.  Identify the gene that codes for an unknown sequence of mRNA.

2.  Identify a mutation in that mRNA, the type of mutation (missense, nonsense, frameshift), the exon where it's located, the original codon, new codon, original amino acid, and the new amino acid.

3.  For nonsense and frameshift mutations, a student should be able to model the affect on a protein structure (i.e. hide all the missing residues).

4.  For missense mutations, a student should be able to show where the mutation would map in protein structure, identify a type of bond formed by that residue (disulfide, ionic, hydrogen, hydrophobic), and explain how the mutation will affect that bond along with the activity or function of the protein.

Since you're taking the instructor course, we will spend time on the kinds of research that needs to be done to put investigations like this together and construct data sets.

I thought it might also be fun, if everyone has their own research project that they work on during the course.  This could lead to new curriculum that you can use in your class or contribute to a data set that we can all use.

6.  What if the course fills up?  What about next year?
If you try to register and find that the course is full, let me know and I'll start a waiting list.  If we have enough interest, we might be able to have a second section.  We do plan to offer this next year, depending on interest.

Feel free to send me questions and I hope to see you all in the new year!  

Sandra

Sandra Porter, PhD
Austin Community College
Digital World Biology LLC
Bio-Link
AC2 Bio-Link




 

 

Copyright © 2017 Digital World Biology, All rights reserved.


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