Third course: Applied Programming for Life Sciences

The third course at Karolinska Institute is the Programming course. As the programme of MTLS is heavy in computational biology, this course is of utmost importance. The course focuses on python programming. It is a short course of 1.5 credits on the basics of programming and gives an insight on how the same can be applied in handling biological data sets.

The main idea of this course is to familiarize students with the programming language- python and prepare for the next semester courses on Bioinformatics.

The course is designed such that students who have little or no prior knowledge of programming can start writing basic codes to perform simple tasks of generating the complementary strands of the DNA/RNA, search for a particular sequence in the given DNA sample, etc.

The first day of the course includes introduction to python and the instruction to install. In the further classes we learn to print strings, understand different data types and the type of data structures. Later in the course we also learn to handle data and perform statistical tests and generate graphs for representing various results.

The structure of the class is very flexible. In the mornings we had lectures where we were introduced to a new topic and post lunch we had exercises that were related to the topics. We had to solve the exercises in  the classroom to pass the course. However, it was made very was designed to encourage learning and applying. As beginners in python programming, we faced difficulties in applying what we had learned, so the TA’s helped us solve the problems and errors that we faced while solving the exercise. I have personally tired learning python from many online courses, but this was the best learning experience. The main reason was that the TA’s gave individual attention to each student and guided according to their problem at respective steps, unlike the tutorials or solutions that give only a single way to solve the problem. And many times it is not the approach that we use.

We also had a final exam at the end of the course, where we had few challenging questions. One such question was to convert the given DNA sequence to protein sequence. It was really fun and challenging to accomplish that as a beginner. Few days after the exam we had planned a secret Santa party in our class, where we wrote a python code to assign the secret Santa to everyone.

The course was really helpful to learn or refresh basics. It helped me feel more confident about programming and Bioinformatics courses in the next semester.

Application Check List

With the deadlines approaching for the application, I would like to inform you about the application requirements and provide with checklist for last minute reference.

The application for the master’s programme in Molecular Techniques in Life Sciences can be done through KTH Royal Institute of Technology, as it is the host Institute for our joint programme.  It is easy to find on the University admissions application website by searching the key words ‘Molecular Techniques’. Choose the programme that shows 120 credits and hosted by the KTH Royal Institute of Technology.

Further, as an applicant, having good grades in Bachelor studies and a complete summary sheet is very important. You can find the detailed list of all requirements and specifics on the programme website. I have also made a checklist to ensure that you do not miss any important  document that needs to be submitted for a complete application.

Checklist

  1. Passport
  2. English Proficiency test (Test scores should be sent to the Institute officially through the testing services)
  3. Degree Certificate (If you have not received the degree certificate, then alternatively a provisional certificate can be uploaded)
  4. Academic Transcripts
  5. Curriculum Vitae
  6. Letter of Recommendation (minimum: 1, maximum: 3)
  7. Summary sheet
  8. Documentation of relevant work experience (if any)

Please note that everything listen needs to be scanned and uploaded in the documents section. The scan should be of the original documents (Not from the xerox).

You can find more information on writing motivation letter in the summary sheet and English proficiency test in previous blogs.

If you have any specific questions regarding the application then feel free to contact me.

Second Course: Applied Communication

The course of applied communication is one of the best courses at KI. It is a course that focuses on the development of individual’s ability to communicate scientific knowledge. It can be often observed that a groundbreaking research when poorly presented makes it unappealing to the audience. Thus, presenting one’s research in an engaging way is of utmost importance. The course of applied communication targets to do the same.

The course is very well designed to cover various aspects of communication. The course starts with Poster presentation, Scientific writing, Rhetorics and ends with Bioethics. Each section is explored in an interactive manner over a period of a week.

In the first week we started with introduction to Poster Presentation. We were divided into groups and given a list of research paper to a select from. After few weeks of preparation, we presented to our peers in an interactive and constructive feedback session. We were able to see and understand the use of different styles of organizing the posters.

Here is an example: My group’s poster

Further, in the course we had lectures on Scientific communication. In these sessions we learned about practical details of screening papers for literature review, reading, writing and finally publishing papers. We gained practical experience of peer review during the course. Each of us had to write an abstract from an already published paper. Then we were assigned a peer reviewer (fellow classmate) to send it for a detailed review. The reviewer had to read the paper, assess the abstract and write a report on the same. This report was later discussed in a group as a constructive feedback.

An example of peer reviewed abstract.

Coming to the best part of the course; the Rhetorics session. Our first session was a body language class. A dramatics director and performer from Uppsala University was our instructor for the day. We started with freeing our body with small exercises, and actions in form of a game. Later, we performed an exercise to amplify our voice and feel more confident to speak. It was hilarious, as it was making funny, weird, loud noises that are of different tones and pitches.

After all the body and sound exercises, we explored the aspect of details and imagination. One week before the class we were asked to prepare two things. One of which was to recollect a memory that would include adventures or different experiences. We had to narrate our memory to our peers with maximum details like the description of the landscape, life style of people around, auditory cues, olfactory elements, etc. so that they can live and experience the same feeling sitting inside the room. At the end, the listeners were to describe the feeling they experienced during the narration.

The post lunch session we integrated everything we learned in the morning to our acts. We had to present a poem or a song of our choice that we were asked to prepare in advance as the second task. Except it had to be expressed with all the emotions to make the audience give a feeling of actually living the experience. There were various suggestions and improvements made to this by the audience and or instructor.

The poem I choose depicted struggle, and in order to show that, we did something out of the box. I was being held back by two friends and I had to try moving: depicting the struggle. In the second round I did it without anyone holding me back. This enabled me how simple things can be done to improve one’s expression on stage.

Me, acting in the Rhetorics class                                                                PC: Vijay

Later in the week we also had a chance to practice the same with scientific presentations and try innovative things. We learned the difference styles of presenting specific to the type of audience.

 

This course helped us learn about the importance of presenting in correct style to the respective audience. It was not only a chance to learn, but also to develop one’s confidence on stage and in daily life. It filled us with new energy for the new courses.

First course at Karolinska Institute: Genetics

In the first semester at Karolinska we have 4 main courses:

1.  Genetics

2.  Applied Communications

3.  Applied Programming for Life Sciences- 1st part

4.  Frontiers in Translational Medicine

Today I am going to tell you about our first day as the master’s student and the first course of Genetics. The courses at Karolinska are full time courses that run in parallel to other courses.

Our semester started on the 3rd of September, 2018 at the Scilife Labs with an introduction to the programme. Programme directors from all the institutions spoke a few words about the course at the respective institute and then the Director of the Scilife Labs gave an introduction to the Scilife Labs and the intention behind this programme and its close association with the Scilife Labs.  After which we had lunch break, where we met all our new classmates for the first time.

Post Lunch we had our first lecture on Genetics.

The course of Genetics was a fast paced course. It was designed such that different students from different backgrounds of Biology, Biochemistry, Biotechnology and Chemistry can understand the general concepts. This course enabled everyone to be on the same page and have the same understanding of the basics concepts required in future courses.

The subject covered the basics concepts such as Fundamentals of the Genome, Core DNA technologies such as different types of Sequencing, Gene Regulation, Epigenetics, variation in the Genome and its association to monogenic and complex rare diseases.

In parallel to the theoretical knowledge, the course was made more practical and self-learning using the virtual lab simulator called the Labster.

Screenshot of the Labster simulations

Labster has various modules that allowed us to learn the flow of the big complex experiments.  Further, the simulator showed short animations of various biological processes that are complex and difficult to visualize based on description or images.

To give you a better understanding, here is a video of Labster simulation: https://www.youtube.com/watch?v=wUtdZ8A18fw&t=22s

Furthermore, along with this we were suggested a few research papers for further reading on specific topics.

The course was graded based on two parts. A final written exam and a research paper presentation. Our first final written exam as a master’s student was four after the start of the course on 28th of September. Two weeks later we had the second part of the exam, which was organized as a symposium on rare genetic diseases. We were divided in different groups and assigned a paper. Each group was given about 20 minutes to present and 5 minutes of question answer session.

Our first class photo after the Genetics presentation.                                                                   PC:David

MTLS Christmas Party!

 

Happy New Year to all the readers! Hope you are enjoying the Christmas holidays. Today, I would like to share how we celebrated Christmas here in Sweden.

Our class of MTLS, had decided to play Secret Santa before the Christmas break. Let me tell you briefly, how secret Santa works. Everyone participating is assigned a name secretly. That person becomes the secret Santa for the name he is assigned to. The Santa has to buy or make a gift for the person. Everyone gets together on the day of the party. All the gifts are collected and each person gets their gift. Based on the gift the receiver has to guess who would be their secret Santa.

One person has to take the responsibility to assign secret Santa to each person. Alternatively it can also be done using online programmes. Now here it gets interesting. As I have mentioned before, one of the course at Karolinska is the programming course in python. You must be wondering why am I talking about courses all of sudden in the secret Santa? In the spirit of programming one of our classmate, Luca decided to write a code to generate the list of names for secret Santa using python – ‘The secret Santa generator’. He successfully wrote it, or we would have ended with one person having two and the other one none. Thankfully, that didn’t happen.

We had our Christmas party in one of our classmate, Vijay’s place. It was well decorated, with lights and Christmas decorations.

Pre-party preparations                                                                                                                            PC:Akshay

We had some Christmas snacks and Christmas drinks i.e. Glogg and Julmust.

Finally, it was time to open presents and guess the Santa’s name. One by one gifts were given and three chances to guess the Santa’s name.

An example of the gifts                                                                                                                          PC:Akshay

This was one of the gifts prepared by a secret Santa. The Last supper by MTLS (Can you guess where I am?)

Later we danced, and played games and had photo sessions with various props. It was really fun experience. It was the first time, that I really celebrated Christmas by doing all the traditional things.  It was a evening well spent with friends that is now my new family here in Sweden.

 

PC:Vijay