KTH course: Applied Programming for Life Sciences III

The second mandatory course from the KTH semester is the Applied Programming in Life Sciences III. This aim of this part of the programming course is to impart knowledge in using Git-hub and managing various shared projects on Git-hub. This course is conducted by Olav Vahtras.

The course consists of 2 main parts , just like previous two parts of APLS (Applied Programming for Life Sciences).

1. Theory

There are 3 theory classes, each class covers one module i.e. Introduction to Git-hub, testing of user built functions, and usage of various scientific libraries.

We explored each of the modules in detail during the lab exercises.

Theory class on function testing

2. Lab exercises

The lab exercises are very detailed and complement the theory courses very well. In the first exercise we created our own Git-hub accounts and learned to move, download and copy folders from local system to the server, as well as the other way round. As a part of the exercise we forked the given directory and cloned it to our local system. Then we completed the incomplete code in the file, added and committed changes to the local system and pushed it to the individual accounts on git-hub and then submitted a pull request to allow the changes in the provided original directory as a user.

Git-hub accounts with different projects

In the second lab exercise we wrote new functions along with new set of codes that can test for the accuracy of the function i.e. if the function does what is expected or if it gives an incorrect output. If the function gives an incorrect output then the testing part of the function will give an error and an indication.

The third lab was an optional lab, were the main idea was to learn to implement various forms of python interface such as Jupyter, Anaconda, etc and usage of scientific libraries.

KTH course: Applied Gene Technology and large-scale data analysis part-2

2. Papers and discussion

The 2nd aspect of the course is based on self learning. The techniques we learned can be divided into 4 main sub-fields:

  1. Hybridization technologies for genotyping and sequencing
  2. Long-read sequencing applied in epigenetics and haplotyping
  3. Single-cell strategies for transcriptomics, proteomics and open chromatin
  4. Spatially resolved transcriptomics by in situ and high-throughput sequencing

Post lectures, we had few lectures for discussing the gist of the papers from each sub-field and connecting them to the application of basic molecular tools that we learned throughout the lectures.

3. Projects

We formed groups of 4 students and selected sub-field of our interest. Each sub-field was selected by 2 groups. The aim of the project was to understand the papers in depth and present them to the class. The papers part of each sub-field were the proof of concept papers for various advanced technologies. For example, my group selected the 4th sub-field that had papers on spatial transcriptomics, in-situ sequencing and MER-FISH.

Spatial Transcriptomics workflow
Source:https://spatialtranscriptomics.com/

The best part of the project was the discussions, these discussions were not just among the group members but between groups. First the groups with same sub-field met to discuss doubts about the paper. This helped us understand and explain concepts thoroughly. Then in the next round of discussions, we read papers from all, the other groups and discussed it within the group as well as with the faculty. We also prepared a set of questions for each project.

My classmate Amparo presenting Barcoded Linked read sequencing technology

Finally, we presented the papers to fellow classmates by discussing the pros and cons of each method, its appropriate applications based on the information gathered and the technical and financial considerations of using the technique. This was followed by the question answer session, where the presenting group was questioned about the technique based on the pre-prepared questions.

The repetitive nature of the course helped understand and discuss various aspects of each technology. Further, the discussions enabled us to question the findings of a research paper as well as the technical details of any new technology in depth.

KTH course: Applied Gene Technology and large-scale data analysis part-1

Welcome to the KTH semester! This course was the best course throughout the Masters.

The main aim of the course is to familiarize us to the advanced technologies in the field of transcriptomics while understanding the advantages and disadvantages of one over the other; thus, allowing us to make the decisions to use these advanced methods in the correct context of research questions. Further, it acclimatizes us to handle and perform basic analysis on various forms of RNA-seq datasets and make biological interpretations.

Image result for advanced sequencing technologies cartoon"
Image source: https://www.genengnews.com

The course is handled by 3 professors.

Patrik Ståhl, Stefania Giacomello, and Olof Emanuelsson. Patrik was the main course responsible and took most of the classes on different technologies. Stefania covered the topics related to single cell sequencing technologies and Olof introduced to the theory behind the large-scale data analysis and the practical aspects of the same.

The part of course taught by Patrik can be separated into 3 sections:

  1. Theory lectures
  2. Papers and discussions
  3. Projects

 

  1. Theory lectures

The theory lectures covered the various technologies right from molecular inversion probe, microarray, variations of bead array, various forms RNA FISH, conventional Sanger and Illumina sequencing to the various forms of advanced sequencing methods based on Illumina platform and last but not the least an introduction to the field of Spatial transcriptomics.

The lectures were mainly short introduction to the concepts behind these and other basic tools in molecular biology to enable us to understand the advanced technical details upcoming in the next section of the course i.e. from the original papers of these technologies.

This is mostly covered in the first 2 weeks of the course, and forms important base for the rest of the course. Since, I was doing my internship, I was not able to attend this part of the course, I have written based on the information from my classmates.

Advice: I strongly recommend to attend all classes right from the beginning and not be late when returning from summer vacation, it can get very difficult to cope up with many things that run in parallel.

KTH semester course pattern

My last post about KTH was mainly describing the different campuses and locations of the classes for the MTLS courses. Here I am going to explain the general organization of the semester and the mandatory courses and electives for MTLS students at KTH.

Semester at KTH

KTH has a different system of organization of semester as compared to the previous semesters at KI and SU. It is partially overlap of both systems to some extent. Coming from KI and SU, it can seem a bit confusing (as Dexter seems to be below) at the beginning, but here’s a short guide to it.

Image result for kth period system cartoons"
Source: KTH blogs

Introduction to the period system

The semester is divided into 2 periods or two halves. Each period is independent of the other and so are the courses in each semester. One can take multiple courses in each period, and the examinations for those courses are at the end of that period. Typically the autumn semester’s (Hösttermin = HT) first period spans from the last week of August to mid of October including exams. After a weeks break the second period starts from the end of October to mid December followed by exams in January post the Christmas break. The schedules for the year with official dates are posted at the beginning of each academic year on the KTH website.

The courses run in parallel to each other similar to that at KI and the exams are at the end of the course like in SU and KI. Although, the courses can have different number of credits, all are of equal length in terms of time from the start of the course to the final exams. However, the work load depends on the number of credits.

Image result for work load cartoons"
Balanced work load for each course                                                                      Image source: https://blog.teamwork.com

Teaching pattern at KTH

Since KTH is a technical university, the general pattern of teaching and work load is significantly different as compared to KI and SU. The courses demand longer hours of work and the teaching pattern is such that the content of the course is repeated in greater detail over multiple iterations through different ways for Eg. by the professor in the class, followed by assignments and a small projects or lab exercises. The repetition enables us to not just cover most part of the studies in the class and during the semester but also ensures detailed understanding of the material by sequentially increasing the depth of the subject matter over each iteration.

MTLS courses at KTH

MTLS students have 3 mandatory courses in the 1st period and and option to take up 2 electives in the 2nd period.

1st period courses (all 3 mandatory courses) :

  1. Clinical applications of biotechnology
  2. Applied gene technology and large-scale data analysis
  3. Applied programming for life science 3

2nd period courses (2 out of 3) :

  1. Systems biology
  2. Project in molecular life science
  3. Drug Development

I will be talking about each of the courses in detail in my following posts. Stay tuned!

Nobel Prize 2019

One of the most awaited events within various fields of science is the Nobel Prize ceremony which take place every year in the city of Stockholm. The Nobel Forum announces the Nobel Laureates every year in the fields of Physics, Chemistry, Physiology or Medicine, Economics and Literature. The Nobel Peace Prize is announced and awarded in Oslo, Norway.

The second week of December every year is the Nobel Week where the laureates give public lectures for their discoveries in their respective fields. These lectures are open for all and are live streamed and recorded for the international audience to witness the much waited event. The Physiology or Medicine laureates are selected by the Nobel Assembly at Karolinska Institute and the Nobel lectures are conducted in Aula Medica at KI.

Nobel lecture in Physiology or Medicine

The laureates in Physics, Chemistry and Economics are selected by Royal Swedish Academy of Sciences. The Nobel lectures are conducted in the Aula Magna at Stockholm University. Literature and Peace prize laureates are selected by Swedish Academy and Norwegian Nobel Committee respectively.

Nobel lecture in Physics

The prize awarding ceremony is takes place on 10th December every year in the Stockholm Concert Hall. This ceremony is not open to public but is live streamed. The laureates are awarded a diploma, a medal and a statement of the prize amount by the King of Sweden. Following this the laureates proceed to the Blue Hall of the Stockholm City Hall for a formal dinner and celebration.