Author: Arafat

Python for Bioinformatics: An Online Course from Me!

I teach an on-line course ‘Python/Biopython for Bioinformatics’ in cBLAST. This is three month’s course, I use biological examples showing how we use Python to handle and analyze biological data. The video lectures are in Bangla, and video’s are both slides and scree-casts of coding.

CBA13

Center for Bioinformatics Learning Advancement and Systematic Training, or cBLAST, is part of University of Dhaka, Bangladesh. One will get certificate after successfully completing this 3-month course for University of Dhaka.

Python, is an easy-to learn, high-level computer language that is used in many of the computational analysis in Bioinformatics.  This course will start developing initial skills of interactive programming and script writing in Python. Then we’ll cover Biopython, Matplotlib and NumPy. Finally, some algorithmic aspects of programming will be discussed in this course. Read more

A note on learning computational biology

Many asks me about learning Bioinformatics. So, I’m going to put some good learning resources in this note.

 

Complete Beginner

If you are a complete beginner, don’t aim to ‘understand’ everything discussed in a course or lecture or book. It’s okay to be partially ignorant but still moving forward. Try to go through 60-70% content of following source within one-two months. The objective in this stage is to get some good understanding of core Bioinformatics concepts and terminology.

1. Bioinformatics Methods I and II, offered by Toronto University in massive-open-online-couse (MOOC) Coursera.org has pretty good materials (video+tutorial). One can download the course materials from this Google drive folder.

2. On Shikkhok.com, a MOOC platform in Bengali language, there is a very short course on Bioinformatics, বায়োইনফরমেটিক্স পরিচিতি, offered by Bio-Bio-1 Foundation.

3. Reading books is the best way. I’ve found ‘Essential Bioinformatics’ by Jin Xiong an easy to understand book.

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Optical Density Hack: Use Visual Comparator in Antibiogram

Say you have a bacterial isolate and you need to check its antibiotic resistance profile. In this case, you need to do an antibiogram study. Ideally, you’ll need to make bacterial lawn on Mueller-Hinton agar medium for doing antibiogram. For that purpose, you prepare bacterial culture from stock in nutrient broth and place it in shaking-incubator. When the culture is young enough, that means when the bacteria on the beginning of its growth phase, you use the culture to make lawn on Mueller-Hinton agar plate. How do you know the culture is young? The common practice is to measure its spectrophotometric absorbance at 600nm. If the culture’s optical density or OD is near to 0.1, then it is perfect for making a lawn. Very simple procedure.

But this can be a cumbersome job when you have to handle many bacterial cultures rather than one. If bacterial samples you are working with are of different species, then their binary fission time will vary. For some bacteria cell division rate is higher and it’s culture will approach to 0.1 OD fast. For other, the rate will be slow and thereby their culture will take time to get that point. Read more