heuermh

Awesome, will check it out!

I mostly use it for learning things. How does this guitar pedal effect work? Why does this Eurorack module sound so good? How can I drive this MIDI instrument from this OSC controller? etc.

Ideally there would be an easy path from ChucK to implementing all of these things in hardware but I haven't quite got there yet.

https://github.com/heuermh/lick

Curious, would the rewrite allow for building on hardware platforms such as the Daisy?

Or maybe it is already possible, to be fair I haven't looked closely.

https://daisy.audio/hardware/, https://github.com/electro-smith/libDaisy

I have been using ChucK for a long time. Like others here, I appreciate Max/Pure Sound but would rather use my text editor.

  Delay delay;
  LPF filter;
  Reverb reverb;
  Gain feedback;
  
  adc => delay => filter => reverb => dac;
  filter => feedback => delay;

I had a PowerComputing desktop, sweet metal case, and good performance specs for the price. I can't recall the exact model though. Was still working fine when I donated it to a local vintage computer non-profit!

The link above does not mention a Founding Data Engineer role -- I sent an email but have not received any reply.

Thank you for writing up your experience!

I have done a ton of Swing over the years, and also a 2.5D zoomable scene graph API called Piccolo2D [0], which was one of the inspirations for JavaFX (or so I heard at the time).

As far as your advice, I will take a look at swapping Batik out for EchoSVG, and also see how you tackled the user data directory issue in KeenWrite.

[0] - https://github.com/piccolo2d/piccolo2d.java

I was at ISMB [0] and BOSC [1] conferences earlier this month and Venn and Euler diagrams were all over the poster session. Not sure why, but biologists love them!

I wrote an implementation of Venn and Euler diagrams for the bioinformatics data visualization application Cytoscape many years ago [2]. Sigh, thick clients in Java haven't aged all that well.

[0] - https://www.iscb.org/ismb2024/home

[1] - https://www.open-bio.org/events/bosc-2024/

[2] - https://apps.cytoscape.org/apps/vennandeulerdiagrams

Very cool!

I am curious if you might explain how/why this stack diverges from the upstream one (bebop/poly)? I see for example dnadesign has a version two of the seqhash algorithm that looks rather interesting.

All the time!

My most recent were tools to improve the AWS commandline experience for s3 and Athena

https://github.com/heuermh/cooper

https://github.com/heuermh/sea-eagle

Both are available via Homebrew

https://github.com/heuermh/homebrew-parquet-tools

I would next like to improve the TUI experience for tabular data, e.g. using the Charm_ Bubbles/Gum table component, but I have yet to investigate how the JVM <--> Go interaction might work.

Curious what it might take to add AWS Athena as another back end?

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

Cool! I have a 128k Mac in working but not restored condition, reach out to me if interested.

I also have a 512ke, which I'll not be able to part with, as it was my first computer. Still runs the copy of HardBall! I hacked to use the roster from my baseball team!

Since moving from GCP BigQuery to AWS Athena, I missed having something for Athena similar in functionality to the BigQuery bq command line tool.

Made this quickly, and then a python version based on awswrangler for work (not open source, unfortunately).

https://github.com/heuermh/sea-eagle

Hang in there, lots of folks having similar experience!

We have been pretty impressed with the closed-ish loop of the Dexcom and Omnipod, it handles daily fluctuations due to more/less exercise etc. fairly well.

Still two separate handheld devices though, and quality always falls off when the sensor (every 10ish days) and pump (every 3 days) approach expiration.

Nice to see Parquet support in DuckDB improving with each new release! In earlier versions, I had trouble with enums and nested schema, these issues have been resolved since.

The only missing feature for me now is full table, column, &c. metadata support in the DuckDB JDBC driver.

Thanks!

Had a glance at the team page on the Mammoth website, curious to learn more about how the various roles fit together. Mind sharing a way to get in touch?

> I'd love to set up a "you don't need software" design agency.

Sign me up!

If it helps, I have an large collection of antique and vintage knobs, switches, pots, buttons, and sliders. ;)

We presented using Parquet formats for bioinformatics 2012/13-ish at the Bioinformatics Open Source Conference (BOSC) and got laughed out of the place.

While using Apache Spark for bioinformatics [0] never really took off, I still think Parquet formats for bioinformatics [1] is a good idea, especially with DuckDB, Apache Arrow, etc. supporting Parquet out of the box.

0 - https://github.com/bigdatagenomics/adam

1 - https://github.com/bigdatagenomics/bdg-formats

I've been writing effects in ChucK for several years but have found it difficult to deploy to various platforms of interest.

Is it possible to build an effect written in Glicol into an iOS app or effect (AudioUnit v3? haven't been keeping up)? LV2 plugin to run on MOD devices guitar pedals? VCVRack, which has its own plugin interface? onto a Rasp Pi Zero?

As good a thread as any in which to post this, anyone else with a basement full of electronics parts interested in federating a web store for one-offs and interesting finds?

I have acquired plenty of cool stuff, but nothing in significant enough quantities to make it as an electronics supplier. I'm thinking more curated antique store vibe.

I got to use an SGI Octane for a while and fell in love with its keyboard, just the right amount of clicky. I later acquired an entire box of 'em, so hopefully those will last the rest of my lifetime.

There are automata restorers [0] featured on the television show Salvage Hunters: The Restorers [1].

[0] - https://thehouseofautomata.com

[1] - https://www.imdb.com/title/tt13405620

Yes, please

I do too, let me know if you know/think of a good place to host these. UG must be one of the most user hostile resources I've ever attempted to use.

Feel free to reach out, username at berkeley edu.

In open source bioinformatics we strive for reproducible science, which can be difficult in a field with tons of different methods and tools. One approach is to use a workflow language such as Nextflow [0] and Docker/Singularity such that the entire analysis is reproducible, see e.g. [1].

There is a vibrant community around Nextflow workflows called nf-core [2] which has a rare disease workflow in development [3], come join our slack!

[0] - https://nextflow.io

[1] - https://github.com/brentp/rare-disease-wf

[2] - https://nf-co.re

[3] - https://nf-co.re/raredisease

This is fairly close to what we generate for our change log, closed issues and closed and merged pull requests keyed by release milestone. Release notes are separate though, and written by hand.

Maven plugin, if you're interested

[1] https://github.com/heuermh/github-changes-maven-plugin

I'm interested in chatting with you about this, and genomics on Spark more generally, feel free to reach out on Github or via my username at the usual suspects.

We're here, still plugging along.

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

https://github.com/bigdatagenomics/adam

Totally agree! I would suggest adding KIR as well. Curious what your background/interest is?

I have consulted to National Marrow Donor Program/Be The Match [0] off and on for several years. There are typing labs using long reads but most reporting/matching/analysis is still performed at the nomenclature level [1].

I hope in the near future we'll be able to simply assemble the entire MHC for each sample, as messy as it might be, see e.g., "A diploid assembly-based benchmark for variants in the major histocompatibility complex" [2].

[0] https://bethematch.org [1] https://www.ebi.ac.uk/ipd/imgt/hla [2] https://www.nature.com/articles/s41467-020-18564-9