Benjamin Fair
Community@bfairkun
Benjamin Fair's skill registry for computational genomics: RNA-seq pipelines, qPCR analysis, genomic APIs, and HPC cluster operations on UChicago Midway and UMich Great Lakes.
Agent Skills by Benjamin Fair
Showing 26 vetted skills indexed across 1 GitHub repositories.
bfairkunpaper-reading
Retrieve and verify scientific paper full text via Europe PMC, PMC, and bioRxiv before summarizing.
bfairkunsnakemake-rule
Generate and debug Snakemake rules following project conventions for logs, conda envs, and resources.
bfairkunigv-tracks
Visualize genomic signal tracks from bigWig, BED, and BAM files using IGV, pyGenomeTracks, and igv.js.
bfairkunauthoring-skills
Create, revise, and validate agent skill directories with portable SKILL.md frontmatter.
bfairkunparse-logs
Diagnose Snakemake and Slurm pipeline failures by parsing HPC job logs.
bfairkungreatlakes-hpc-setup
Configures new UMich Great Lakes HPC accounts with stow-based dotfiles, conda, and SLURM tooling.
bfairkunclearplots
Deletes all files in the RCC Midway agent plots directory except server.log.
bfairkunqpcr-analysis
Analyze QuantStudio qPCR data with ΔΔCT statistics and Quarto notebook visualizations.
bfairkunhi-gene-aso-targets
Evaluates five ASO strategies for up-regulating haploinsufficient genes using splicing, miRNA, and translation data.
bfairkundispatch
Spawn, list, resume, and kill Claude or Codex sessions in tmux windows.
bfairkunnew-notebook
Create date-prefixed Quarto analysis notebooks with Python or R kernels and structured prose conventions.
bfairkungrant-writing
Drafts, revises, and critiques research grant proposals including Specific Aims and Research Strategy sections.
bfairkuncompute-kernel
Connect Jupyter kernels running on HPC compute nodes via SLURM job submission.
bfairkunsnaptron
Query Snaptron for splice junction counts, RNA-seq metadata, and BigWig coverage.
bfairkunfind-skills
Searches and installs agent skills from the open skills ecosystem using the Skills CLI.
bfairkunquarto-python
Create, parameterize, and render Quarto notebooks with a Python Jupyter kernel.
bfairkunsvg-to-png
Convert standalone SVG files to PNG using cairosvg on the RCC Midway HPC cluster.
bfairkunnew-project
Scaffolds RNA-seq analysis projects using the cookiecutter-quarto-smk template with snakemake submodules.
bfairkunensembl-api
Query the Ensembl REST API for variant annotation, gene lookup, and sequence retrieval.
bfairkuninteractive-notebook
Co-author Quarto notebooks iteratively through Jupyter kernels in Python or R.
bfairkuncolab-mcp
Author, edit, and execute Google Colab notebook cells through a browser MCP bridge.
bfairkunagent-plots
Saves plots and dataframes to a local HTTP server directory for browser viewing.
bfairkunconda-env
Create and update conda environment YAML files for Snakemake bioinformatics pipelines.
bfairkunjupyter-kernel
Start, connect to, and execute code in Jupyter kernels via a stdio MCP server.
Frequently Asked Questions About Benjamin Fair
FAQPage SchemaWhat tasks can I accomplish with bfairkun's skills?▼
You can run RNA-seq projects from cookiecutter scaffolds, write and debug Snakemake rules, query Ensembl/UCSC/Snaptron/AlphaGenome genomic services, analyze qPCR plates with ΔCT/ΔΔCT/RQ statistics, evaluate ASO targets for haploinsufficient genes, and draft LaTeX manuscripts and grant proposals.
Who are these skills designed for?▼
Computational biologists and genomics researchers working on UChicago RCC Midway or UMich Great Lakes HPC clusters. They target scientists running Snakemake pipelines, authoring Quarto notebooks in Python or R, and wet-lab researchers planning qPCR experiments.
How do the HPC skills work in practice?▼
The hpc skill explains Slurm job submission on Midway2/Midway3 via sbatch and sinteractive, compute-kernel connects Jupyter to HPC compute nodes, parse-logs diagnoses failed jobs, globus-transfer moves data between clusters, and greatlakes-hpc-setup onboards new UMich accounts.
What are the prerequisites and dependencies?▼
Many skills are restricted to RCC Midway or UMich Great Lakes HPC environments. Dependencies include conda environments in code/envs/, the jupyter-kernel MCP server, globus-cli, cairosvg for SVG rasterization, and project conventions like stow-based dotfiles and the cookiecutter-quarto-smk template.
Can these skills help with scientific writing and collaboration?▼
Yes. latex-manuscript builds LaTeX/Markdown papers and exports drafts to Google Docs, grant-writing drafts Specific Aims and Research Strategy sections, notebook-transcript embeds conversation history in Quarto notebooks, and post-to-slack shares plots and tables directly to Slack.