What I use

Computing system/OS/Prgramming

Computing system

  • I handle several desktops, laptops, workstations as a system administrator and managing the user environment.
  • I work with different high-performance computing systems, clusters or supercomputing system.
  • I work with multi-threaded CPU-system as well as GPU-system.

OS

  • I started with Windows OS (Windows 98), but after graduation I switched to Linux distros. I used different linux distros starting with Fedora, moved to Linux Mint and at present mainly working with Ubuntu and Cent OS.
  • Besides Linux system, I use Macbook pro (x64 Intel chip) for office task. I do have a old Macbook air since 2007 that I use for old Apple apps, iBookAuthor.
  • To test a tools/softwares on Windows, sometime I borrow a Windows OS (10 or 11) from the University IT department and use it as an admin.
  • As a part of work, I use RedHat as well as amazon aws/google cloud solution.

Programming/Scripting

  • I use R as main scripting language with different CRAN and bioconductor packages. I use ploly, tidyverse, datatable, ggplot2 for data curation and visualization.
  • I also use python with pandas, numpy, scipy, matplotlib for data analysis and visualization.
  • During my doctoral degree, I worked with Perl, MATLAB but not any more.
  • I use different types of Shell (sh, tcsh, ksh, zsh, bash) for regular work.
  • I learned C/C++, database management system MySQL during my graduation.

Reporducible report

  • I use LaTex, pandoc, lua for writing. Typora to edit standalone Markdown files and hackmd.io for online share with others.
  • I use Rmarkdown for R script and documentation, Jupyter for python scripting and documentation and Quarto for using mixed scripting documentation. I use parameterized report using Rmarkdown.
  • I combine Quarto documentation with cutomized css for customized documentation generating HTML, PDF, docx or ePub.
  • I use Jupyter and Google CoLab for shared documentation.

Font-end

  • I use different tools for front-end development, HTML/CSS/JS, WordPress, Shiny, DASH, and Quarto.

Statistical Analysis

  • I use SPSS, MATLAB, GraphPad, STATA, OriginLab, R, RStudio for statistical data analysis
  • I use R and Bioconductor packages for several quatitative data analysis, t‐test, within‐/between‐subjects/Repeated Measures ANOVAs, Regressions, Clustering, HLM, Factor Analysis, Network Analysis, SEM, PCA, MDS, Unsupervised/Supervised Machine Learning, text mining, exploratory data analysis (EDA).

Graphics designing/Image Processing

  • I use Photoshop, Lightroom and Illustrator CC for long time but now I use Inkscape for graphics designing.
  • I use ImageJ, CellProfiler as image editing tools. I also use GIMP for photo editing.
  • I use MacOS preview for quick editing of images.

Virtual Machines/Containers

  • I use different virtual machines Oracle VM, VirtualBox, VMware to use different versions of OS.
  • I use several container system to make automated/semi-automated bioinformatics pipelines, Conda, Singularity/Apptainer, Docker, Podman.
  • I prefer docker to build containers for different OS architecture, intel x86, arm.

Workflow manager/shceduler

  • I mainly use Nextflow, and Snakemake for automated/semi-automated bioinformatics pipelines.
  • I use slurm job scheduler and cron for planned job submission.

Version control

  • Everything I script, I make git (pro version) repo. I use Github actions for automation through github.
  • I use zenodo for publishing github codes with version.
  • I use bitbucket for private code sharing (business models).

Editors

  • I use notepad++ in WindowsOS; textEdit, Atom in MacOS; and vi, vim, nano, gedit in LinuxOS. I am more comfortable with terminal editors.

Integrated Development Environment (IDE)

  • I use VS Code for script, documentation, compiling as well as testing versions. Combined with WakaTime, it calculates the time I spent on different projects. With git integration, I directly commit to GitHub. I use Prettier for document formatting.

  • I sometimes use VS codium and DataSpell as IDE.

Office tools

  • I use different office programs Open office, google docs, Microsoft office, pages, keynote, numbers.
  • Recently I start using Quarto with revealjs for slide presentation. I also use Prezi for online slide presentation.
  • I use Microsoft forms, Google forms for different surveys and menti for audience response.
  • I use MacOS Notes, Freeform; Microsoft OneNote and Goodnotes (licensed version) for note taking. I also use Obsidian for note-taking purpose.

UML

  • I use plantuml to generate UML files. I used Edrawmax but dropped due to high subscription fees.
  • I use SimpleMind Pro for flow-charts and mind-maps.