Coding
Catalog entries using this tag (links open the entry card on its page):
- Claude Code — AI
- Cline — AI
- Codex — AI
- Cursor — AI
- Qoder — AI
- Trae — AI
- Windsurf — AI
- Anaconda — Coding
- Bioconda — Coding
- BioNumPy — Coding
- Biopython — Coding
- CODELF — Coding
- Conda cheatsheet (PDF) — Coding
- Conda user guide — getting started — Coding
- conda-forge — Coding
- Docker — Coding
- Docker Hub — Coding
- GitHub Pages — Coding
- hit-counter (GitHub) — Coding
- Keras — Coding
- Matplotlib — Coding
- MkDocs — Coding
- Nextflow — Coding
- nf-core — Coding
- NumPy — Coding
- pandas — Coding
- Plotly (Python) — Coding
- pyensembl — Coding
- pyliftover — Coding
- pysam — Coding
- Python packaging tutorial — Coding
- PyTorch — Coding
- Quick Reference (quickref.me) — Coding
- scikit-allel — Coding
- scikit-learn — Coding
- SciPy — Coding
- Seaborn — Coding
- Shields.io — Coding
- Singularity (GitHub) — Coding
- Singularity / Apptainer user guide — Coding
- Snakemake — Coding
- Snakemake (GitHub) — Coding
- statannotations — Coding
- statsmodels — Coding
- Sylabs Singularity — Coding
- TensorFlow — Coding
- The Bash Hackers Wiki — Coding
Entries
Claude Code
Company
Anthropic
DESCRIPTION
Anthropic’s terminal-based coding agent for large-scale refactors, test runs, and repo navigation using Claude models.
URL
Cline
Company
Open source
DESCRIPTION
Autonomous coding agent for VS Code (and compatible editors) that plans, edits files, runs commands, and uses browser tools with user approval.
URL
Codex
Company
OpenAI
DESCRIPTION
OpenAI’s cloud and local coding agent (CLI and integrations) for building, reviewing, and shipping code with GPT-based models.
URL
Cursor
Company
Anysphere
DESCRIPTION
AI-native code editor (VS Code fork) with inline chat, agent mode, and codebase-wide context for editing and refactoring.
URL
Qoder
Company
Alibaba
DESCRIPTION
Agentic coding platform with IDE, JetBrains plugin, and CLI—quest mode, repo-aware chat, and parallel expert-style agents.
URL
Trae
Company
ByteDance
DESCRIPTION
AI-native IDE (ByteDance) with builder mode, multi-model chat, and agent workflows for full-stack development.
URL
Windsurf
Company
Codeium
DESCRIPTION
Agentic IDE from Codeium with Cascade flow for multi-step edits, terminal integration, and deep workspace awareness.
URL
Anaconda
DESCRIPTION
Python/R data-science distribution and environment manager.
URL
Bioconda
DESCRIPTION
Conda channel for bioinformatics software.
URL
BioNumPy
DESCRIPTION
Biological data as NumPy-like arrays (see preprint in repo notes).
URL
Biopython
DESCRIPTION
Tools for biological computation in Python.
URL
CODELF
DESCRIPTION
Variable-name search from real open-source projects.
URL
Conda cheatsheet (PDF)
DESCRIPTION
Official Conda command reference (PDF).
URL
Conda user guide — getting started
DESCRIPTION
Official Conda tutorial.
URL
conda-forge
DESCRIPTION
Community-led Conda packages.
URL
Docker
DESCRIPTION
Container platform.
URL
Docker Hub
DESCRIPTION
Container image registry.
URL
GitHub Pages
DESCRIPTION
Static site hosting from GitHub repos.
URL
hit-counter (GitHub)
DESCRIPTION
GitHub visitor counter badge (referenced from original notes).
URL
Keras
DESCRIPTION
High-level neural network API.
URL
Matplotlib
DESCRIPTION
Plotting library.
URL
MkDocs
DESCRIPTION
Project documentation with Markdown.
URL
Nextflow
DESCRIPTION
Data-driven computational pipelines.
URL
nf-core
DESCRIPTION
Community Nextflow pipelines.
URL
NumPy
DESCRIPTION
Numerical arrays and routines.
URL
pandas
DESCRIPTION
Data analysis and manipulation.
URL
Plotly (Python)
DESCRIPTION
Interactive charts.
URL
pyensembl
DESCRIPTION
Python interface to Ensembl references.
URL
pyliftover
DESCRIPTION
Genomic coordinate liftover.
URL
pysam
DESCRIPTION
SAM/BAM/VCF interface for Python.
URL
Python packaging tutorial
DESCRIPTION
How to package and publish Python projects.
URL
PyTorch
DESCRIPTION
Deep learning framework.
URL
Quick Reference (quickref.me)
DESCRIPTION
Quick-reference cheat sheets.
URL
scikit-allel
DESCRIPTION
Large-scale genetic variation data utilities.
URL
scikit-learn
DESCRIPTION
Machine learning in Python.
URL
SciPy
DESCRIPTION
Scientific computing ecosystem for Python.
URL
Seaborn
DESCRIPTION
Statistical data visualization.
URL
Shields.io
DESCRIPTION
Badge service for READMEs.
URL
Singularity (GitHub)
DESCRIPTION
Singularity source repository.
URL
Singularity / Apptainer user guide
DESCRIPTION
Sylabs Singularity documentation.
URL
Snakemake
DESCRIPTION
Workflow management for reproducible analyses.
URL
Snakemake (GitHub)
DESCRIPTION
Snakemake source repository.
URL
statannotations
DESCRIPTION
Statistical annotations on matplotlib plots.
URL
statsmodels
DESCRIPTION
Statistical models and tests.
URL
Sylabs Singularity
DESCRIPTION
Singularity / Apptainer ecosystem.
URL
TensorFlow
DESCRIPTION
End-to-end ML platform.
URL
The Bash Hackers Wiki
DESCRIPTION
Bash and shell scripting reference.
URL