Blog of Andrés Aravena
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Bioinformatics 2022

Genomics and DNA analysis

10 October 2022

Things to do

In this course we teach how to interpret and understand the results of bioinformatic analyses. Most molecular biologists will work in team with (or hire, or be hired by) bioinformatic teams, so even if they do not use the tools, all molecular biologists need to understand what is the meaning of the results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment’s success or failure.

Classes

This year’s slides are different to previous years, in content and organization. Sometimes we use copyrighted material that is ok to show in classes, but not ok for putting on the web. In those cases the slides are not here. We recommend you to take notes during classes, since many important things are written in the whiteboard but not in the slides. We recommend taking notes with pen and paper using the Cornell Method.

You can find the slides and videos of previous years at Bioinfo 2021 and Bioinfo 2020. Here you will find this year’s slides.

Homework

Homework is an integral part of this course, since we want to match theory and practice. Besides, without practice we tend to forget more often. All homework should be sent to andres.aravena+bioinfo@istanbul.edu.tr before the deadline to get a grade. Please be careful, otherwise you will get a grade zero.

Attendance

By regulation from the Rectory, students need to attend at least 70% of the classes. If you cannot attend, you must deliver all homework on time. Late submissions will not be accepted.

The attendance book is updated every week and can be seen in Google Sheets.

Prerequisites

This course does not require knowledge of coding or programming, but it will always be a strong advantage —in this course and in professional life— to know how to code a program.

You will need:

We recommend (but not require):

Syllabus

We follow partially the plan proposed by Sayres (2018)Sayres, et al. “Bioinformatics Core Competencies for Undergraduate Life Sciences Education.” PLoS ONE 13, no. 6 (2018): 1–20. https://doi.org/10.1371/journal.pone.0196878.

. At the end of the course students should be able to:

Online supplementary material

Bibliography

The list of recommended and mandatory papers is in a separate page.

Web references

NCBI Videos: Sequences

These videos are complementary to our classes. They cover the same topics with more detail. Please watch them to understand better this course.

NCBI Genome Visualization

Searching

BLAST

General Literature