Andrea Zonca

Deploy the Dask Operator for JupyterHub on Kubernetes

kubernetes

jetstream2

jupyterhub

python

This post describes how to deploy the Dask Operator for Kubernetes alongside a Helm-based JupyterHub installation. The Operator provides a Kubernetes-native way to create…

Mixing Nextflow Executors for Hybrid Workflows

hpc

sdsc

nextflow

This post demonstrates how to combine different Nextflow executors within a single workflow, a powerful pattern for optimizing resource usage in scientific computing. By…

Implementing Conditional Logic in Nextflow Workflows

hpc

sdsc

nextflow

This post serves as a follow-up to my previous tutorial, “Running Nextflow on Expanse”, where I covered the foundational aspects of deploying Nextflow workflows on an HPC…

Hierarchical EZID DOIs with Python

python

This post refers to the ezid_api repository.

Going Full Agentic for Scientific Software Development

github

ai

python

The landscape of scientific software development is being transformed by AI coding agents. Over the past few weeks, I’ve been exploring GitHub Copilot’s AI coding agent…

Software Citation Station helper script

software

citation

Proof-of-concept generate_citation.py in the software_citation repo pulls PyPI metadata plus repo CITATION files to produce the Markdown block that Software Citation Station …

Updated Tutorial on The Littlest JupyterHub on Jetstream

jupyterhub

jetstream2

I’m excited to share that I’ve contributed an updated tutorial on how to deploy “The Littlest JupyterHub” (TLJH) on a Jetstream instance!

Tampermonkey Script for Audible Filtering

This Tampermonkey script helps filter Audible search results by hiding items that do not meet certain criteria. Specifically, it hides audiobooks with a rating less than 4.0…

Running Nextflow on Expanse with Seqera

hpc

sdsc

nextflow

This tutorial will guide you through setting up Nextflow on Expanse using the Seqera platform. Nextflow is a powerful and flexible workflow management system that enables…

Auto-merge GitHub Pull Requests After GitHub Actions Pass

github

Pull request auto-merge is a small feature that keeps teams from babysitting green builds. Once every required check is green, GitHub merges the PR for you—no extra clicks…

Manage calendar of a scientific collaboration using Google Groups

openscience

Managing a calendar for a large scientific collaboration can be challenging. Over the years, I have tried different approaches to solve this problem.

Building Singularity Containers with Conda Environments from requirements.txt

singularity

python

This post introduces a method for building Singularity containers that include a Conda environment based on a requirements.txt file. This approach provides a reproducible…

EZID DOI Management with Python

python

This project offers Python scripts for interacting with the EZID API to create and verify Digital Object Identifiers (DOIs).

Running Nextflow on Expanse

hpc

sdsc

nextflow

This tutorial will guide you through setting up Nextflow on Expanse. Nextflow is a powerful and flexible workflow management system that enables scalable and reproducible…

PySM 3.4.3 Released

openscience

pysm

python

PySM version 3.4.3 is now live. Install it from PyPI or upgrade existing environments with pip install --upgrade pysm3. Full details are available in the GitHub release notes.

Deploy a ChatGPT-like LLM on Jetstream with llama.cpp

jetstream

llm

This is a crosspost of the official Jetstream documentation: Deploy a ChatGPT-like LLM service on Jetstream. I built a brand new version of that tutorial that swaps in llama.…

PySM Methods Paper Published in ApJ

openscience

pysm

python

The Astrophysical Journal formally published our paper, Full-sky Models of Galactic Microwave Emission and Polarization at Sub-arcminute Scales for the Python Sky Model, on S…

Inspect SMTP sending through UCSD

Python

When configuring email sending through UCSD, it can be surprisingly unclear which SMTP server to use. The official documentation mentions three options: smtp.ucsd.edu, smtp.g…

OpenStack Unshelver Demo

openstack

jetstream

I recently vibe-coded a lightweight web application, using gpt-5-codex, that revives shelved OpenStack instances on demand. The stack is intentionally minimal: a FastHTML…

Deploy a 70B LLM to Jetstream

jetstream

llm

Deploying large language models on Jetstream is getting easier thanks to the official Jetstream LLM guide. Here I follow that walkthrough but scale the hardware and model so…

Timing the Unshelving of a Jetstream 70B LLM Instance

jetstream

llm

Following the work documented in Deploy a 70B LLM to Jetstream, the Meta-Llama-3.1-70B-Instruct-GGUF deployment is now running on a g3.xl instance. The goal of this…

Python for HPC

Python

hpc

sdsc

Python is often the first choice for prototyping research ideas, but scaling that prototype to thousands of cores and multi‑node workflows needs a different toolkit. This…

Execute Pegasus Jobs on Expanse

sdsc

hpc

Pegasus is a workflow management system that helps scientists and engineers execute complex computational workflows. It maps a user’s abstract workflow onto available…

Use VS Code on Expanse

Using VS Code directly on Expanse, or other HPC systems, is generally not recommended due to the high resource usage of the IDE itself. These systems are optimized for…

How to Use AI Chat Assistants While Traveling

ai

llm

Traveling often means unreliable or expensive internet access, especially on airplanes or in remote areas. Here are two practical ways to keep using AI chat assistants even…