Jayaram Kancherla
@jkanche.bsky.social
Research Software Engineer. Develops bioinformatics tools and software: github.com/jkanche
Thanks Tommy for sharing our work. we recently updated some of our core packages in Python, especially Genomic Ranges that can perform some very fast interval operations, more here - bsky.app/profile/jkan...
The GenomicRanges (github.com/BiocPy/GenomicRanges) package for Python got a major speed boost (v0.7.0+) thanks to Aaron’s blazing-fast C++ nclist interval indexing!
#Bioinformatics #Genomics #Bioconductor
#Bioinformatics #Genomics #Bioconductor
GitHub - BiocPy/GenomicRanges: Container class to represent genomic locations and support genomic analysis
Container class to represent genomic locations and support genomic analysis - BiocPy/GenomicRanges
github.com
November 26, 2025 at 1:07 AM
Thanks Tommy for sharing our work. we recently updated some of our core packages in Python, especially Genomic Ranges that can perform some very fast interval operations, more here - bsky.app/profile/jkan...
github.com/BiocPy/tutor..., happy to help if you need any details
GitHub - BiocPy/tutorial: tutorial for all bioconductor representations in Python
tutorial for all bioconductor representations in Python - BiocPy/tutorial
github.com
October 17, 2025 at 2:24 PM
github.com/BiocPy/tutor..., happy to help if you need any details
another good read around the same topic - www.mbi-deepdives.com/reader-respo...
Reader Response to "AI Overinvestment"
A couple of days ago, I wrote a piece titled “What if there’s an overinvestment in AI?”
I received some thoughtful emails in response to that piece. One reader named Craig Melillo took the time to sh...
www.mbi-deepdives.com
September 29, 2025 at 2:10 PM
another good read around the same topic - www.mbi-deepdives.com/reader-respo...
If you're building Python pipelines for genomics, check out GenomicRanges. For feature requests or feedback, reach out to us on GitHub!
Try it: `pip install genomicranges`
Contribute: github.com/BiocPy/Genom...
#BiocPy
Try it: `pip install genomicranges`
Contribute: github.com/BiocPy/Genom...
#BiocPy
August 25, 2025 at 3:56 AM
If you're building Python pipelines for genomics, check out GenomicRanges. For feature requests or feedback, reach out to us on GitHub!
Try it: `pip install genomicranges`
Contribute: github.com/BiocPy/Genom...
#BiocPy
Try it: `pip install genomicranges`
Contribute: github.com/BiocPy/Genom...
#BiocPy
Now with nclist, it performs fast, complex overlap queries, all while keeping the same interface as the R equivalent. Check out Aaron's nclist @ github.com/LTLA/nclist-...
GitHub - LTLA/nclist-cpp: Nested containment lists in C++
Nested containment lists in C++. Contribute to LTLA/nclist-cpp development by creating an account on GitHub.
github.com
August 25, 2025 at 3:56 AM
Now with nclist, it performs fast, complex overlap queries, all while keeping the same interface as the R equivalent. Check out Aaron's nclist @ github.com/LTLA/nclist-...
while I agree on the h5 format, my last 5 years working with h5ad has not been easy. there's a lot of language assumptions baked in. hoping anndataR will be more stable soon
August 5, 2025 at 3:35 PM
while I agree on the h5 format, my last 5 years working with h5ad has not been easy. there's a lot of language assumptions baked in. hoping anndataR will be more stable soon
A solution I've been thinking of or may be I am unaware of is a community of developers brought together across rust, python and R. Bioconductor is organizing a rust workshop soon and seems like more of this should be happenning to bring everyone together. thoughts?
August 4, 2025 at 2:26 AM
A solution I've been thinking of or may be I am unaware of is a community of developers brought together across rust, python and R. Bioconductor is organizing a rust workshop soon and seems like more of this should be happenning to bring everyone together. thoughts?
Most end users of bioinformatics tools work in R or Python, which creates a language barrier and overhead for users who want to contribute back or for newcomers getting started. Second, while I do know many awesome Rust packages, some of them often lack the user base because of limited interfaces.
August 4, 2025 at 2:26 AM
Most end users of bioinformatics tools work in R or Python, which creates a language barrier and overhead for users who want to contribute back or for newcomers getting started. Second, while I do know many awesome Rust packages, some of them often lack the user base because of limited interfaces.
h5ad/AnnData have similar problems with how its implemented in Python. it's not really language agnostic.
July 25, 2025 at 11:45 AM
h5ad/AnnData have similar problems with how its implemented in Python. it's not really language agnostic.
not ragnar, but I've been meaning to try out the llm extension in kuzu for something similar, might be worth to check this out - docs.kuzudb.com/extensions/l...
Kuzu - Graph Database
Documentation for Kuzu, an open source, embedded graph database
docs.kuzudb.com
July 22, 2025 at 5:44 PM
not ragnar, but I've been meaning to try out the llm extension in kuzu for something similar, might be worth to check this out - docs.kuzudb.com/extensions/l...
It feels like all the AI companies are getting caught up in the hype. soon they'll realize overemphasizing prompt engineering has led to a decline in deeper technical capabilities and probably hurts them in the long run. They'll probably find a way to spin a different narrative by then...
July 20, 2025 at 1:49 AM
It feels like all the AI companies are getting caught up in the hype. soon they'll realize overemphasizing prompt engineering has led to a decline in deeper technical capabilities and probably hurts them in the long run. They'll probably find a way to spin a different narrative by then...
Aaron tried switching over to the experimental 64 bit support for Kana at the beginning of the year, and I believe he mentioned there were too many issues at the time.
July 19, 2025 at 1:11 AM
Aaron tried switching over to the experimental 64 bit support for Kana at the beginning of the year, and I believe he mentioned there were too many issues at the time.
BiocPy has been open sourced for a while now and we continue to develop new functionality. Currently our focus has been around spatial and ml interop with bioc data structures.
July 18, 2025 at 7:07 PM
BiocPy has been open sourced for a while now and we continue to develop new functionality. Currently our focus has been around spatial and ml interop with bioc data structures.
while uv is great, I had issues using it inside vpn or installing from private registries.
July 10, 2025 at 1:42 PM
while uv is great, I had issues using it inside vpn or installing from private registries.
i watched the anime a few years ago and it was awesome. Didn't know they have a live action now..
June 14, 2025 at 12:34 AM
i watched the anime a few years ago and it was awesome. Didn't know they have a live action now..
Theres quite a few examples demonstrating scientific uses of webassembly, starting with our own application for single-cell analysis - www.kanaverse.org/kana/, and many others like biowasm.com, viralwasm, onnx's js runtime etc ..
February 3, 2025 at 5:05 AM
Theres quite a few examples demonstrating scientific uses of webassembly, starting with our own application for single-cell analysis - www.kanaverse.org/kana/, and many others like biowasm.com, viralwasm, onnx's js runtime etc ..
combined with kuzu (github.com/kuzudb/kuzu), it's all I use for most of my work
GitHub - kuzudb/kuzu: Embeddable property graph database management system built for query speed and scalability. Implements Cypher.
Embeddable property graph database management system built for query speed and scalability. Implements Cypher. - kuzudb/kuzu
github.com
December 28, 2024 at 4:21 PM
combined with kuzu (github.com/kuzudb/kuzu), it's all I use for most of my work
I literally just installed it after reading their 1.0 release and found it very slick and minimal. I don't use many of the features from wezterm but curious to see other replies. Also simple key-value config is easy to setup.
December 28, 2024 at 4:16 PM
I literally just installed it after reading their 1.0 release and found it very slick and minimal. I don't use many of the features from wezterm but curious to see other replies. Also simple key-value config is easy to setup.
They need a new investor pitch now that the AI boom is winding down ...
December 12, 2024 at 12:50 AM
They need a new investor pitch now that the AI boom is winding down ...
I believe you can choose custom vm configuration on google colab, need to be on a pay for use model. posit cloud also supports jupyter notebooks.
September 26, 2024 at 1:30 PM
I believe you can choose custom vm configuration on google colab, need to be on a pay for use model. posit cloud also supports jupyter notebooks.