BG 506: Bioinformatics

For those interested in Bioinformatics (esp. proteomics) or Medical Informatics and Artificial Intelligence/Machine Learning: we have established a Facebook page for the Biomedical Informatics Research Lab at Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad. To stay current of the latest activities, please like our page:

https://www.facebook.com/bmirlab/

You can find out your grades by downloading grading.pdf

Here is the final grading scheme for MPhil

Quiz 0: 2 %

Quiz 1: 4 %

Quiz 2: 4 %

Assignment 1: 30 %

Assignment 2: 10 %

Examination: 50%

Online participation bonus (based on questions/post/views etc.): 4%

Highest score: 86%

Median score: 79.5%

For PhD:

Quiz 0: 0 %

Quiz 1: 0 %

Quiz 2: 4 %

Assignment 1: 40 %

Assignment 2: 6 %

Examination: 50%

Online participation bonus (based on questions/post/views etc.): 4%

Median score: 61%

Maximum Score: 68%

I have forwarded the scores to the course coordinator. 

Enjoy!

-Fayyaz

Dear All

please download this folder. We will use these files for our DNA analyses

If you like to play computer games and like protein structures, design and engineering, I would recommend the FoldIt. It allows you to learn about how protein structures work. It has also been used to solve the structures of some proteins important in cancer studies.

You can download and play FoldIt at: https://fold.it/portal/

Also, if you would like to design artificial life and  nano machines, Nanocrafter is a pretty cool kit and game! You can access it at:

http://nanocrafter.org/landing

Enjoy!

If you haven't done so already, please use the course survey form to give me your feedback.

It is available at: http://goo.gl/forms/3GVpLT2jlc

This is mandatory for all students.

Dear Students,

You can submit your report as a .docx file to afsar@pieas.edu.pk. Please give the subject "BG 506 Assignment Submission".

-Fayyaz

It's great to see all of you working on the assignment and I hope you are enjoying learning about the given protein using a wide variety of tools. I would recommend that you keep exploring the tools I have mentioned as well as search for other tools on your own.

Here are a few things I thought I should let you know:

1. In the assignment, DO NOT simply copy paste the results / output of a program / webserver into your report without properly understanding it and describing it in your own words. As I had told you in the class, you will not get any scores for such attempts.

2. Feel free to read papers / wikipedia articles and other help and be sure to cite this in your report. You can use Zotero or EndNote or MS Word's builtin referencing feature for this purpose.

Lastly a note on using Piazza:

If you haven't received an answer to a question on Piazza, please do not mark the post as "resolved". "Unresolved" posts stand out and act as a indication that you need an answer to your question.

Good luck.

Dear Students,

We had some unexpected delays and technical problems in our connection today. However, I hope that you were able to learn to use PyMOL quite effectively. It is of utmost importance that you learn to use this as a tool to understand the structure of proteins. Our exercise in the class today focused not only on using PyMOL but also on understanding sequence-structure-function relationships for proteins. We discussed how motifs do actually allow Calmodulin to bind Calcium. You are most welcome to explore further. A good resource in this regard is the PDB-101. PyMOL can also be used to design proteins, make structural mutations, make movies of proteins, etc. You can explore these options too.

Other tools which we could not cover in the class that support such understanding include: