SU course: Bioinformatics (Part-1)

The first course at Stockholm University is Bioinformatics. I will talk about this course in two parts. The reason being that the course is divided into two parts in the study structure.

 1. Sequence based Bioinformatics

 2. Structure Prediction

Today I will be talking about the first part of the course which is associated with the sequence based Bioinformatics.

The course in general has two components in both the parts of the course.

A) Theory lectures

B) Lab

1) Sequence based Bioinformatics

This part of the course deals with the basics tools used for the initial analysis of all kinds of sequences found in biological organisms. The focus is on the algorithms and the specific details  related to each algorithm.

A) Theory lectures

I have mentioned the list of topics covered in the first half of the course below. It is interesting to see how all the topics have a very good flow and connectivity to each other as if all of them are coming together to tell us a biological (magical) story.

We start with various databases that contains different types of sequences, from there we learn to search and align sequences in database using various methods and their specific algorithms. From pairwise alignment we go to Multiple Sequence Alignment (MSA) and various algorithms associated with it. Based on MSA we go on to different methods used to generate phylogenetic relationships among various sequences and see their evolutionary pattern.

Practical demonstration using knots in rope to calculate evolutionary distance of 3 organisms.

As we know some patterns are very obvious and can be observed directly, but nature many times has these hidden patterns that cannot be detected easily based on the direct observation of the data  we have. So in order to unfold and reveal these hidden patterns, we resort to the aid of Machine Learning by the use of Artificial Neural Networks.

(The words in the Italics are the names of the chapters)

Ribose molecule – Use of models to understand various conformations of RNA

The grading for the course is done in multiple ways. This is done in order to ensure that the grades do not depend on one exam which has very high stakes. So, we have a pre-lecture quiz based on the assigned relevant reading for the upcoming lecture. The course has two partial exams, the first one covers the Sequence based Bioinformatics, the second covers the Structural aspects of Bioinformatics. The Lab component is also graded. And last but not the least we have a individual project that also contributes to the final grade.

A plus point of the course is that all the lectures are recorded and accessible. So one can go back and look at specific parts of the lecture again for complete understanding.

B) Lab

As I mentioned earlier, we have a Lab component to this course. All the labs go hand in hand with the topics in theory courses. For example, we have a lab on phylogeny on the same day as that of the lecture on phylogeny. This helps to apply the knowledge learnt about a particular tools on the same day.

In the lab we are generally given tool(s)/software(s) and a sample data set along with a specific set of questions. Answering these questions enables us to play around with various parameters of the software and see how and what exact effect does changing the parameters have.

The lab component is really helpful to visualize the theory, which otherwise seems to be pretty bland and incomprehensible.

In the second part of the blog I will be telling about the second half of the course and the individual project, so stay tuned!