Some observations as a trainee — Rule 1: Triangle of bioinformatics Taking at least an introductory course for the topics listed below will help you understand what and why you are doing certain things and better come up with innovative ideas. Otherwise, you are just performing tasks that you’ve been told instead of practicing science. Rule 2: Reading more papers I remember there was once a…

Bayesian modeling and related — Compared to deep learning topics and techniques, I found very few tutorials focusing on probabilistic modeling. Strictly speaking, deep learning is also part of probabilistic modeling, depending on how you view this problem. Probabilistic modeling can be a very powerful tool to model complex dependencies, integrate prior knowledge, and account…

I would like to share two approaches to generating the most essential parts of a Sankey plot in pure Python — Sankey plot is a very nice and neat way to visualize how the values flow from its source category to the target category. In the left panel shown above, I used the Sankey plot to demonstrate how each hematopoietic population (stem cell, erythroid progenitors) can be further divided into more…

Some thoughts after experiencing both sides — So we all heard “The grass is always greener on the other side”, I think the same concept applies to the the career path between academia and industry. A bit of introduction of myself, I am a rising 4th year bioinformatics PhD student, and I am conducting a summer internship…

Although static plot is the default option for scientific presentation, interactivity has its own power — Although the interactive plot has been widely used in fields like finance, the static plot is still the mainstream of scientific visualization. The reasons are simple, science emphasizes truth, not appearance. …

Differences, usages, Python versus NumPy versus Pandas? — “String” in Python? Sounds like the most basic topics that every Python programmer should have already mastered in their first Python tutorial. However, do you know there are at least four types of strings in primitive Python? Do you know how your strings are actually represented in Numpy or Pandas…

Creating any colormap at your wills — Imagine you find a pretty colormap that other people used in their publications, and you want to use that in your results as well. However, unfortunately, it is not a built-in colormap in matplotlib. Is there a solution around? So today I am going to show you how I usually…

All you need to know to begin your Matlab journey — Matlab has arguably the most comprehensive documentation compared to other open-source programming languages. …

The concept of “Module” in Python — In the simplest case, we write codes in a single Python file (the file name ends with .py). We run it and everything works as expected, and we are happy. However, things can get a bit complicated when you have to split up your codes into multiple Python files, usually…