macOS

In genomic data analysis, we often use a pipeline function to process data stored in a dataframe by calling several mini-functions. Each mini-function may modify the dataframe by adding a new column with new values and then filter out the rows that do not meet certain criteria. However, this may result in an empty dataframe if none of the rows satisfy the filters and can lead to errors or unexpected results when the pipeline function tries to perform more operations on the empty dataframe....

Debugging, an essential process for identifying and rectifying errors in a computer program, is particularly crucial for computational biologists dealing with complex codebases that often involve intricate mathematical models, data analysis, and simulations. Merely reading the code may not suffice to grasp the logic and functionality of the project. To gain a deeper understanding, you may need to run the code, examine the variables, and observe the outputs. Towards this end, the integrated debuggers in PyCharm and VSCode prove invaluable....

When it comes to Python development on macOS, I rely on a combination of two tools that have served me exceptionally well over the past few years: Pyenv and Poetry. Pyenv provides an elegant solution for managing different Python versions on my system, while Poetry simplifies dependency management and the creation of virtual environments for my projects. In this article, I will guide you through the process of setting up Pyenv to install a specific Python version and then using Poetry to create a virtual environment for your project....

NetMHCPan, a widely used tool for predicting peptide binding to major histocompatibility complex (MHC) molecules, is essential for understanding immune responses. However, the tool’s binaries are currently available only for the x86_64 architecture, whether on Darwin (macOS) or Linux. As I intended to conduct test runs on my Apple Silicon device (arm64), I encountered the following error: 1netMHCpan: no binaries found for Darwin_arm64 /net/sund-nas.win.dtu.dk/storage/services/www/packages/netMHCpan/4.1/netMHCpan-4.1/Darwin_arm64/bin/netMHCpan To address this, one option is to run NetMHCPan using Rosetta, a dynamic binary translator that translates executable code on-the-fly....

Using renv is an excellent choice for maintaining a clean and reproducible R environment on macOS. Here, I will share my experiences and provide a guide on setting up R on macOS. The post is divided into the following sections: Installing system dependencies required for R libraries using Homebrew. Installing R libraries using renv. Saving and restoring R environments using renv. Installing R libraries hosted on private repositories. Building R libraries from source using Makevars....

If you are facing difficulties with large data sets in R, using data.table could provide a performance boost. However, when loading data.table, especially on macOS, you might encounter a warning indicating the absence of OpenMP support, causing data.table to operate in a single-threaded mode. This limitation prevents you from fully utilizing the potential benefits of using data.table and taking advantage of the underlying hardware. 1library(data.table) 2data.table 1.14.0 using 1 threads (see ?...

Here, I summarise how I setup my macOS for the purpose of Data Science. Ultimately, I should invest some time into automating the process. Install Command Line Developer Tools 1xcode-select --install Install HomeBrew 1/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" Turn off analytic (optional) 1brew analytics off Install iTerm 1brew install iterm Configure iTerm To download different colour schemes, visit iTerm Themes Install Go2Sehll Download and install from Go2Shell, then configure it to work with iTerm:...

To mount a network drive as a local one, you can use sshfs. Generate SSH key 1$ mkdir ~/.ssh #if it does not already exist 2$ chmod 700 ~/.ssh 3$ cd ~/.ssh 4$ ssh-keygen -t rsa 5$ enter a keyname 6$ enter a passphrase 7$ ssh-copy-id -i [path to rsa file] USER@SERVER Where -i indicates where the rsa file is located. The .pub key is the one needed to be copied....