Cade Mirchandani
@cademirch.bsky.social
Reposted by Cade Mirchandani
Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...
#sciworkflows #reproducibility
#sciworkflows #reproducibility
Snakemake Hackathon March 2026
We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...
indico.cern.ch
October 17, 2025 at 4:49 PM
Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...
#sciworkflows #reproducibility
#sciworkflows #reproducibility
Reposted by Cade Mirchandani
Check out the latest paper from the CCGP on California Quail and the ecological and anthropogenic factors that impact genomic variation. Led by Phred Benham and the Bowie group: onlinelibrary.wiley.com/doi/10.1111/...
Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes
Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often rely on a...
onlinelibrary.wiley.com
October 16, 2025 at 8:40 PM
Check out the latest paper from the CCGP on California Quail and the ecological and anthropogenic factors that impact genomic variation. Led by Phred Benham and the Bowie group: onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Cade Mirchandani
Want to make publication-ready figures come straight from Python without having to do any manual editing? Are you fed up with axes labels being unreadable during your presentations? Follow this short tutorial including code examples! 👇🧵
October 16, 2025 at 8:26 AM
Want to make publication-ready figures come straight from Python without having to do any manual editing? Are you fed up with axes labels being unreadable during your presentations? Follow this short tutorial including code examples! 👇🧵
Reposted by Cade Mirchandani
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST!
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
September 29, 2025 at 5:33 PM
Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST!
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects.
DM me to join!
#snakemake #workflows #opensource #bioinformatics #oss
Reposted by Cade Mirchandani
Preview of an important slide:
September 24, 2025 at 4:02 PM
Preview of an important slide:
snkmt 0.2.0 is out! New features:
1. Multi-database support - switch between dbs via ctrl+p (like VSCode)
2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation
github.com/cademirch/sn...
#snakemake #bioinformatics #workflow #opensource #python #cli #tui
1. Multi-database support - switch between dbs via ctrl+p (like VSCode)
2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation
github.com/cademirch/sn...
#snakemake #bioinformatics #workflow #opensource #python #cli #tui
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
github.com
September 22, 2025 at 7:46 PM
snkmt 0.2.0 is out! New features:
1. Multi-database support - switch between dbs via ctrl+p (like VSCode)
2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation
github.com/cademirch/sn...
#snakemake #bioinformatics #workflow #opensource #python #cli #tui
1. Multi-database support - switch between dbs via ctrl+p (like VSCode)
2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation
github.com/cademirch/sn...
#snakemake #bioinformatics #workflow #opensource #python #cli #tui
Reposted by Cade Mirchandani
Recording of the tutorial now up on the @scipyconf.bsky.social YouTube channel: www.youtube.com/watch?v=8AYp...
Arts, Feickert, & Kirkham - Reproducible Machine Learning Workflows for Scientists with pixi
YouTube video by SciPy
www.youtube.com
September 10, 2025 at 2:50 PM
Recording of the tutorial now up on the @scipyconf.bsky.social YouTube channel: www.youtube.com/watch?v=8AYp...
Reposted by Cade Mirchandani
Link to the new documentation pages:
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
Rust packages | conda-forge | community-driven packaging for conda
If you want to package a Rust package to conda-forge, you can use this recipe template:
conda-forge.org
July 4, 2025 at 8:10 AM
Link to the new documentation pages:
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
- conda-forge.org/docs/mainta...
Reposted by Cade Mirchandani
Some great tips on making better #dataviz 👇 In my experience, the final point—feedback—is invaluable
Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪
www.nature.com/articles/s41...
Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪
www.nature.com/articles/s41...
A checklist for designing and improving the visualization of scientific data - Nature Cell Biology
Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data visualization research in a checkl...
www.nature.com
July 4, 2025 at 4:31 AM
Some great tips on making better #dataviz 👇 In my experience, the final point—feedback—is invaluable
Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪
www.nature.com/articles/s41...
Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪
www.nature.com/articles/s41...
Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
June 3, 2025 at 2:52 PM
Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3