41554 blogs · [ { "id": "01a08789-1a72-7271-bcb8-f0224281ec0f", "title": "Announcing taxburst, an update of the Krona software for taxonomy exploration", "url": "http://ivory.idyll.org/blog/2025-announcing-taxburst-030.html", "published_at": "2025-08-07T22:00:00+00:00" }, { "id": "01a08789-1a72-7271-bcb8-f022429b10fd", "title": "Announcing: the chill-filter Web site - DNA sample composition at a glance!", "url": "http://ivory.idyll.org/blog/2024-announcing-chill-filter.html", "published_at": "2024-12-26T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52ecce91ea", "title": "Why Rust is an increasingly beloved part of my programming toolbox", "url": "http://ivory.idyll.org/blog/2024-why-i-like-rust.html", "published_at": "2024-10-15T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52ed69b981", "title": "Recent advances in the sourmash ecosystem (August 2024)", "url": "http://ivory.idyll.org/blog/2024-sourmash-advances.html", "published_at": "2024-08-15T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52edbb1078", "title": "Speeding sourmash the heck up", "url": "http://ivory.idyll.org/blog/2024-speeding-sourmash-the-heck-up.html", "published_at": "2024-02-19T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52ee3275e3", "title": "The history of the \"Tragedy of the Commons\"", "url": "http://ivory.idyll.org/blog/2024-tragedy-of-commons.html", "published_at": "2024-01-12T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52ef22d34e", "title": "Sourmash and branchwater licensing: thoughts on extractive engagement with projects", "url": "http://ivory.idyll.org/blog/2024-sourmash-branchwater-licensing.html", "published_at": "2024-01-06T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52ef7c9b10", "title": "snakemake for doing bioinformatics - inputs and outputs and more!", "url": "http://ivory.idyll.org/blog/2023-snakemake-slithering-input-outputs.html", "published_at": "2023-04-06T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f0268cec", "title": "snakemake for doing bioinformatics - using wildcards to generalize your rules", "url": "http://ivory.idyll.org/blog/2023-snakemake-slithering-wildcards.html", "published_at": "2023-03-02T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f0cd929b", "title": "conda & mamba on shared clusters works better now!", "url": "http://ivory.idyll.org/blog/2023-conda-mamba-shared.html", "published_at": "2023-02-08T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f1a655e6", "title": "A brief overview of automation and parallelization options in UNIX/on an HPC", "url": "http://ivory.idyll.org/blog/2023-automation-and-parallelization.html", "published_at": "2023-01-30T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f2826012", "title": "snakemake for doing bioinformatics - a beginner's guide (part 2)", "url": "http://ivory.idyll.org/blog/2023-snakemake-slithering-section-2.html", "published_at": "2023-01-22T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f2973d58", "title": "snakemake for doing bioinformatics - a beginner's guide (part 1)", "url": "http://ivory.idyll.org/blog/2023-snakemake-slithering-section-1.html", "published_at": "2023-01-13T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f334abe3", "title": "sourmash has a plugin interface!", "url": "http://ivory.idyll.org/blog/2023-sourmash-plugins-first-effort.html", "published_at": "2023-01-07T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f36d2c35", "title": "Reading \"Orwell's Roses\" by Rebecca Solnit", "url": "http://ivory.idyll.org/blog/2022-reading-orwells-roses.html", "published_at": "2022-12-30T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f385ac4a", "title": "So! You want to search all the public metagenomes with a genome sequence!", "url": "http://ivory.idyll.org/blog/2022-sourmash-mastiff.html", "published_at": "2022-08-30T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f3a6425a", "title": "Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers", "url": "http://ivory.idyll.org/blog/2022-announcing-ribbity-github-issue-munging.html", "published_at": "2022-05-22T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f48b4668", "title": "The second Common Fund Data Ecosystem hackathon - May 9-13, 2022!", "url": "http://ivory.idyll.org/blog/2022-second-cfde-hackathon.html", "published_at": "2022-04-30T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f500d1e8", "title": "Storing 64-bit unsigned integers in SQLite databases, for fun and profit", "url": "http://ivory.idyll.org/blog/2022-storing-ulong-in-sqlite-sourmash.html", "published_at": "2022-04-21T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f5191abe", "title": "The First Common Fund Data Ecosystem Hackathon", "url": "http://ivory.idyll.org/blog/2022-feb-hackathon.html", "published_at": "2022-03-04T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f56f77e1", "title": "On minimum metagenome covers, and calculating them for your own data.", "url": "http://ivory.idyll.org/blog/2022-calculating-minimum-metagenome-covers-with-genome-grist.html", "published_at": "2022-01-17T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f63d8ef0", "title": "A bioinformatics training career panel in the DIB Lab", "url": "http://ivory.idyll.org/blog/2021-training-career-panel.html", "published_at": "2021-11-07T23:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f6de8e43", "title": "Using snakemake to do simple wildcard operations on many, many, many files", "url": "http://ivory.idyll.org/blog/2021-snakemake-simple-operations.html", "published_at": "2021-08-29T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f79bd5f1", "title": "A biotech career panel in the DIB Lab", "url": "http://ivory.idyll.org/blog/2021-biotech-career-panel.html", "published_at": "2021-07-19T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f7f55d9d", "title": "Scaling sourmash to millions of samples", "url": "http://ivory.idyll.org/blog/2021-sourmash-scaling-to-millions.html", "published_at": "2021-07-12T22:00:00+00:00" }, { "id": "01a08789-1a73-7038-95ea-4d52f7f622bb", "title": "New sourmash databases are available!", "url": "http://ivory.idyll.org/blog/2021-sourmash-new-databases.html", "published_at": "2021-06-28T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462d7f1b2bb", "title": "Moving sourmash towards more community engagement - a funding application", "url": "http://ivory.idyll.org/blog/2021-sourmash-czi-application.html", "published_at": "2021-06-08T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462d848e04a", "title": "Searching all public metagenomes with sourmash", "url": "http://ivory.idyll.org/blog/2021-MAGsearch.html", "published_at": "2021-06-07T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462d8cddee2", "title": "sourmash 4.1.0 released!!", "url": "http://ivory.idyll.org/blog/2021-sourmash-v4.1.0-released.html", "published_at": "2021-05-16T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462d8e30ec7", "title": "sourmash 4.0 is now available! Low low cost if you buy now!", "url": "http://ivory.idyll.org/blog/2021-sourmash-v4-released.html", "published_at": "2021-03-03T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462d978409b", "title": "sourmash v4.0.0 release candidate 1 is now available for comment!", "url": "http://ivory.idyll.org/blog/2021-sourmash-v4-rc1-now-available.html", "published_at": "2021-02-18T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462da11a907", "title": "Transition your Python project to use pyproject.toml and setup.cfg! (An example.)", "url": "http://ivory.idyll.org/blog/2021-transition-to-pyproject.toml-example.html", "published_at": "2021-02-01T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462daa7e13c", "title": "A snakemake hack for checkpoints", "url": "http://ivory.idyll.org/blog/2021-snakemake-checkpoints.html", "published_at": "2021-01-24T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462db6aa07b", "title": "Improved workflows-as-applications: tips and tricks for building applications on top of snakemake", "url": "http://ivory.idyll.org/blog/2020-improved-workflows-as-applications.html", "published_at": "2020-08-05T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462db7ab08b", "title": "sourmash databases as zip files, in sourmash v3.3.0", "url": "http://ivory.idyll.org/blog/2020-sourmash-databases-as-zip-files.html", "published_at": "2020-05-06T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dbed20b0", "title": "Software and workflow development practices (April 2020 update)", "url": "http://ivory.idyll.org/blog/2020-software-and-workflow-dev-practices.html", "published_at": "2020-04-19T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dc65c931", "title": "How to give a bad online talk", "url": "http://ivory.idyll.org/blog/2020-bad-online-talk.html", "published_at": "2020-04-12T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dcca1b48", "title": "Some snakemake hacks for dealing with large collections of files", "url": "http://ivory.idyll.org/blog/2020-snakemake-hacks-collections-files.html", "published_at": "2020-03-08T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dceae538", "title": "Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.", "url": "http://ivory.idyll.org/blog/2020-talks-at-jgi.html", "published_at": "2020-02-16T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dcfa94c8", "title": "sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes", "url": "http://ivory.idyll.org/blog/2020-sourmash-oddify.html", "published_at": "2020-01-01T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dd5b941a", "title": "Finding problematic bacterial/archaeal genomes using k-mers and taxonomy", "url": "http://ivory.idyll.org/blog/2020-sourmash-gtdb-oddities.html", "published_at": "2019-12-31T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462ddb8b6b0", "title": "How does sourmash's lca classification routine compare with GTDB classifications?", "url": "http://ivory.idyll.org/blog/2019-sourmash-lca-vs-gtdb-classify.html", "published_at": "2019-12-30T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462de5f9e6a", "title": "Sourmash LCA databases now available for the GTDB taxonomy", "url": "http://ivory.idyll.org/blog/2019-sourmash-lca-db-gtdb.html", "published_at": "2019-12-29T23:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462df22330d", "title": "An initial report on the Common Fund Data Ecosystem", "url": "http://ivory.idyll.org/blog/2019-cfde-july-report.html", "published_at": "2019-08-14T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dfc0290c", "title": "Comparing two genome binnings quickly with sourmash", "url": "http://ivory.idyll.org/blog/2019-comparing-binnings.html", "published_at": "2019-07-22T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462dfee2a81", "title": "How to encourage participation in teleconferences", "url": "http://ivory.idyll.org/blog/2019-encourage-participation-teleconferences.html", "published_at": "2019-06-23T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462e0650afe", "title": "Using GitHub for janky project reporting - some code", "url": "http://ivory.idyll.org/blog/2019-github-project-reporting.html", "published_at": "2019-05-14T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462e0fc4523", "title": "Some questions and thoughts on journal peer review.", "url": "http://ivory.idyll.org/blog/2019-questions-and-thoughts-peer-review.html", "published_at": "2019-04-15T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462e159bbf1", "title": "Things to think about when developing shotgun metagenome classifiers", "url": "http://ivory.idyll.org/blog/2019-developing-metagenome-classifiers.html", "published_at": "2019-04-10T22:00:00+00:00" }, { "id": "01a08789-1a74-7324-aa63-1462e1aecddf", "title": "Our submission for the NHGRI Human Genome Reference Center call", "url": "http://ivory.idyll.org/blog/2019-nih-hgrc-proposal.html", "published_at": "2019-04-09T22:00:00+00:00" } ] posts Claim your blog

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ivory.idyll.org

2025

Announcing taxburst, an update of the Krona software for taxonomy exploration original ↗

7 Aug 2025

2024

Announcing: the chill-filter Web site - DNA sample composition at a glance!original ↗

26 Dec 2024

Why Rust is an increasingly beloved part of my programming toolbox original ↗

15 Oct 2024

Recent advances in the sourmash ecosystem (August 2024)original ↗

15 Aug 2024

Speeding sourmash the heck up original ↗

19 Feb 2024

The history of the "Tragedy of the Commons"original ↗

12 Jan 2024

Sourmash and branchwater licensing: thoughts on extractive engagement with projects original ↗

6 Jan 2024

2023

snakemake for doing bioinformatics - inputs and outputs and more!original ↗

6 Apr 2023

snakemake for doing bioinformatics - using wildcards to generalize your rules original ↗

2 Mar 2023

conda & mamba on shared clusters works better now!original ↗

8 Feb 2023

A brief overview of automation and parallelization options in UNIX/on an HPC original ↗

30 Jan 2023

snakemake for doing bioinformatics - a beginner's guide (part 2)original ↗

22 Jan 2023

snakemake for doing bioinformatics - a beginner's guide (part 1)original ↗

13 Jan 2023

sourmash has a plugin interface!original ↗

7 Jan 2023

2022

Reading "Orwell's Roses" by Rebecca Solnit original ↗

30 Dec 2022

So! You want to search all the public metagenomes with a genome sequence!original ↗

30 Aug 2022

Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers original ↗

22 May 2022

The second Common Fund Data Ecosystem hackathon - May 9-13, 2022!original ↗

30 Apr 2022

Storing 64-bit unsigned integers in SQLite databases, for fun and profit original ↗

21 Apr 2022

The First Common Fund Data Ecosystem Hackathon original ↗

4 Mar 2022

On minimum metagenome covers, and calculating them for your own data.original ↗

17 Jan 2022

2021

A bioinformatics training career panel in the DIB Lab original ↗

7 Nov 2021

Using snakemake to do simple wildcard operations on many, many, many files original ↗

29 Aug 2021

A biotech career panel in the DIB Lab original ↗

19 Jul 2021

Scaling sourmash to millions of samples original ↗

12 Jul 2021

New sourmash databases are available!original ↗

28 Jun 2021

Moving sourmash towards more community engagement - a funding application original ↗

8 Jun 2021

Searching all public metagenomes with sourmash original ↗

7 Jun 2021

sourmash 4.1.0 released!!original ↗

16 May 2021

sourmash 4.0 is now available! Low low cost if you buy now!original ↗

3 Mar 2021

sourmash v4.0.0 release candidate 1 is now available for comment!original ↗

18 Feb 2021

Transition your Python project to use pyproject.toml and setup.cfg! (An example.)original ↗

1 Feb 2021

A snakemake hack for checkpoints original ↗

24 Jan 2021

2020

Improved workflows-as-applications: tips and tricks for building applications on top of snakemake original ↗

5 Aug 2020

sourmash databases as zip files, in sourmash v3.3.0 original ↗

6 May 2020

Software and workflow development practices (April 2020 update)original ↗

19 Apr 2020

How to give a bad online talk original ↗

12 Apr 2020

Some snakemake hacks for dealing with large collections of files original ↗

8 Mar 2020

Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.original ↗

16 Feb 2020

sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes original ↗

1 Jan 2020

2019

Finding problematic bacterial/archaeal genomes using k-mers and taxonomy original ↗

31 Dec 2019

How does sourmash's lca classification routine compare with GTDB classifications?original ↗

30 Dec 2019

Sourmash LCA databases now available for the GTDB taxonomy original ↗

29 Dec 2019

An initial report on the Common Fund Data Ecosystem original ↗

14 Aug 2019

Comparing two genome binnings quickly with sourmash original ↗

22 Jul 2019

How to encourage participation in teleconferences original ↗

23 Jun 2019

Using GitHub for janky project reporting - some code original ↗

14 May 2019

Some questions and thoughts on journal peer review.original ↗

15 Apr 2019

Things to think about when developing shotgun metagenome classifiers original ↗

10 Apr 2019

Our submission for the NHGRI Human Genome Reference Center call original ↗

9 Apr 2019