# Biology, Health, and Medicine

**URL:** https://discourse.julialang.org/c/domain/bio/15.md

[Latest](https://discourse.julialang.org/latest.md) · [Categories](https://discourse.julialang.org/categories.md) · [Tags](https://discourse.julialang.org/tags.md)

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## [Introducing me and my first Julia package SiCell.jl](https://discourse.julialang.org/t/introducing-me-and-my-first-julia-package-sicell-jl/137720)

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**Author:** [@Sizerta](https://discourse.julialang.org/u/Sizerta)\
**Replies:** 7\
**Last updated:** [September 18, 2026, 8:41pm UTC](https://discourse.julialang.org/t/introducing-me-and-my-first-julia-package-sicell-jl/137720 "2026-09-18T20:41:43Z")

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Hi everyone :waving\_hand: My name is Masoud, and I’m excited to finally share my first Julia package with the community: SiCell.jl. SiCell is a high-performance single-cell RNA-seq toolkit I’ve been working on for the …

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## [\[ANN\] NeuroAnalyzer.jl](https://discourse.julialang.org/t/ann-neuroanalyzer-jl/89574)

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**Author:** [@AdamWysokinski](https://discourse.julialang.org/u/AdamWysokinski)\
**Replies:** 42\
**Last updated:** [August 2, 2026, 10:59am UTC](https://discourse.julialang.org/t/ann-neuroanalyzer-jl/89574 "2026-08-02T10:59:16Z")

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NeuroAnalyzer.jl: EEG/MEG/NIRS/NIBS analysis with Julia v0.22.11 is out: https://codeberg.org/AdamWysokinski/NeuroAnalyzer.jl Major changes: user-managed preferences virtual channels progress meter continuous and dis…

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## [\[ANN\] UVAPadova.jl – High-Performance T1D (Diabetes) Dosing Simulationation of the UVA/Padova S2008 T1D model](https://discourse.julialang.org/t/ann-uvapadova-jl-high-performance-t1d-diabetes-dosing-simulationation-of-the-uva-padova-s2008-t1d-model/136588)

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**Author:** [@Aoxo\_MoxoA](https://discourse.julialang.org/u/Aoxo_MoxoA)\
**Replies:** 1\
**Last updated:** [July 30, 2026, 7:54pm UTC](https://discourse.julialang.org/t/ann-uvapadova-jl-high-performance-t1d-diabetes-dosing-simulationation-of-the-uva-padova-s2008-t1d-model/136588 "2026-07-30T19:54:07Z")

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Hi, I’ve implemented UVAPadova.jl, a native Julia port of the UVA/Padova model. The primary goal is to provide a reliable simulation environment for T1D-Dosis (calculating insulin doses and correction factors). Most ex…

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## [Julia Bioinformatics Algorithms New Project](https://discourse.julialang.org/t/julia-bioinformatics-algorithms-new-project/135501)

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**Author:** [@Stergios\_Papadimitri](https://discourse.julialang.org/u/Stergios_Papadimitri)\
**Replies:** 6\
**Last updated:** [April 15, 2026, 3:31pm UTC](https://discourse.julialang.org/t/julia-bioinformatics-algorithms-new-project/135501 "2026-04-15T15:31:05Z")

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Hi all, I started to develop a project for the implementation in Julia of the algorithms of the book “Bioinformatics Algorithms: An active learning approach” of Pavel Pevzner et. all The project URL is: https dot sour…

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## [Packages for mass spectrometry?](https://discourse.julialang.org/t/packages-for-mass-spectrometry/43481)

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**Author:** [@Eugeleo](https://discourse.julialang.org/u/Eugeleo)\
**Replies:** 14\
**Last updated:** [April 9, 2026, 8:55pm UTC](https://discourse.julialang.org/t/packages-for-mass-spectrometry/43481 "2026-04-09T20:55:45Z")

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My bachelor thesis concerns working mass spectrometry data; I’ll need to be able to load the spectra, visualise them, and most importantly, given a spectrum and a peptide fragment I’ll need to decide how likely it is tha…

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## [Implementing custom learning rule in Neuroblox.jl](https://discourse.julialang.org/t/implementing-custom-learning-rule-in-neuroblox-jl/133063)

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**Author:** [@dmaioli](https://discourse.julialang.org/u/dmaioli)\
**Replies:** 3\
**Last updated:** [March 5, 2026, 5:45pm UTC](https://discourse.julialang.org/t/implementing-custom-learning-rule-in-neuroblox-jl/133063 "2026-03-05T17:45:40Z")

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Hi, I am interested in doing spiking neural networks simulations in Julia. The package Neuroblox.jl seems very promising, and the lectures posted on MIT OpenCourseware on it make it clear that it is possible to build cu…

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## [Genomic Annotation Package?](https://discourse.julialang.org/t/genomic-annotation-package/98255)

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**Author:** [@hkhalil](https://discourse.julialang.org/u/hkhalil)\
**Replies:** 3\
**Last updated:** [December 20, 2025, 3:39pm UTC](https://discourse.julialang.org/t/genomic-annotation-package/98255 "2025-12-20T15:39:20Z")

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Hi everyone, I am new to Julia and BioJulia so this serves as an introduction as well! In my work, I make extensive use of R/Bioconductor and am excited to see the development of BioJulia and am looking to use Julia mor…

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## [Building a JuliaHealth-specific Genie.jl Dashboard](https://discourse.julialang.org/t/building-a-juliahealth-specific-genie-jl-dashboard/133085)

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**Author:** [@kosuri-indu](https://discourse.julialang.org/u/kosuri-indu)\
**Replies:** 6\
**Last updated:** [November 16, 2025, 2:17pm UTC](https://discourse.julialang.org/t/building-a-juliahealth-specific-genie-jl-dashboard/133085 "2025-11-16T14:17:31Z")

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Hello everyone! :waving\_hand: I am currently working towards building a JuliaHealth-specific Dashboard using Genie.jl. The main idea is to have one simple, unified interface where users can: Load or connect to health …

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## [Confusion about BioJulia site?](https://discourse.julialang.org/t/confusion-about-biojulia-site/132708)

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**Author:** [@Marco\_Antoniotti](https://discourse.julialang.org/u/Marco_Antoniotti)\
**Replies:** 2\
**Last updated:** [September 28, 2025, 9:08am UTC](https://discourse.julialang.org/t/confusion-about-biojulia-site/132708 "2025-09-28T09:08:23Z")

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Hi I am back to BioJulia and I see that the main indexed site appears to be https://biojulia.dev. Alas, that appears… old (2024). OTOH, there is a BioJulia Unified Docs which appears to be up to date. What gives? Al…

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## [\[GSoC 2025\] Supporting Patient-Level Pipelines within JuliaHealth](https://discourse.julialang.org/t/gsoc-2025-supporting-patient-level-pipelines-within-juliahealth/132534)

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**Author:** [@kosuri-indu](https://discourse.julialang.org/u/kosuri-indu)\
**Replies:** 0\
**Last updated:** [September 21, 2025, 8:29am UTC](https://discourse.julialang.org/t/gsoc-2025-supporting-patient-level-pipelines-within-juliahealth/132534 "2025-09-21T08:29:10Z")

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Hello Julia Community! :waving\_hand: I’m thrilled to share a major milestone: I’ve officially completed my Google Summer Of Code 2025 project with JuliaHealth! This summer, I had the incredible opportunity to improve to…

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## [Request for comments: Upcoming Kmers.jl version 1.0](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203)

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**Author:** [@jakobnissen](https://discourse.julialang.org/u/jakobnissen)\
**Replies:** 4\
**Last updated:** [December 23, 2024, 6:38pm UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203 "2024-12-23T18:38:07Z")

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Dear BioJulia users and stakeholders, I’m pleased to announce a preview of the first stable release of Kmers.jl, namely version 1.0. The release is essentially done and just needs some more testing and polishing, but b…

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## [\[ANN\] PairwiseMappingFormat.jl](https://discourse.julialang.org/t/ann-pairwisemappingformat-jl/121714)

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**Author:** [@jakobnissen](https://discourse.julialang.org/u/jakobnissen)\
**Replies:** 0\
**Last updated:** [October 24, 2024, 5:45pm UTC](https://discourse.julialang.org/t/ann-pairwisemappingformat-jl/121714 "2024-10-24T17:45:33Z")

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The newest BioJulia package has just been merged to the General Registry: PairwiseMappingFormat.jl. This package provide a parser for PAF (Pairwise mApping Format) files, which are used by some aligners such as minimap2…

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## [\[ANN\] BlindingIndex.jl](https://discourse.julialang.org/t/ann-blindingindex-jl/119161)

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**Author:** [@AdamWysokinski](https://discourse.julialang.org/u/AdamWysokinski)\
**Replies:** 0\
**Last updated:** [September 7, 2024, 9:01am UTC](https://discourse.julialang.org/t/ann-blindingindex-jl/119161 "2024-09-07T09:01:48Z")

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Compute James’ and Bang’s Blinding Indices, used in evaluating blinding of randomized, blinded clinical trials (RCTs). The code is based on R package BI by Marc Schwartz and Nate Mercaldo. repository: https://codeberg.…

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## [Genetic Epidemiology tools](https://discourse.julialang.org/t/genetic-epidemiology-tools/117764)

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**Author:** [@jromanowska](https://discourse.julialang.org/u/jromanowska)\
**Replies:** 7\
**Last updated:** [August 6, 2024, 3:59pm UTC](https://discourse.julialang.org/t/genetic-epidemiology-tools/117764 "2024-08-06T15:59:24Z")

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Hi, I am working with genotyping data (PLINK format) and DNA methylation data (large matrices of numbers in range 0-1). Are there any recommended packages, workflows, or tutorials for working with these data in Julia? …

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## [Falling Behind - Julia for genomics?](https://discourse.julialang.org/t/falling-behind-julia-for-genomics/116552)

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**Author:** [@SergeantMike67](https://discourse.julialang.org/u/SergeantMike67)\
**Replies:** 7\
**Last updated:** [July 8, 2024, 2:57pm UTC](https://discourse.julialang.org/t/falling-behind-julia-for-genomics/116552 "2024-07-08T14:57:04Z")

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I just saw in BioRxiv that a group has developed a pythonic pipeline for parallel processing of 3d epigenetic profiles. Other than the rather forced attempt at alliteration and the distinct lack of creativity in naming …

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## [Julia for processing Next-Generation Sequencing (NGS) datasets](https://discourse.julialang.org/t/julia-for-processing-next-generation-sequencing-ngs-datasets/113371)

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**Author:** [@Bonjour-Lemonde](https://discourse.julialang.org/u/Bonjour-Lemonde)\
**Replies:** 5\
**Last updated:** [April 23, 2024, 5:24pm UTC](https://discourse.julialang.org/t/julia-for-processing-next-generation-sequencing-ngs-datasets/113371 "2024-04-23T17:24:40Z")

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Hi all! I want to inquire how to use Julia for processing Next-Generation Sequencing (NGS) datasets, especially to merge paired-end sequencing reads. I think currently there seems no suitable packages in Julia as pandase…

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## [Biotools instalation](https://discourse.julialang.org/t/biotools-instalation/112116)

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**Author:** [@perrochico](https://discourse.julialang.org/u/perrochico)\
**Replies:** 6\
**Last updated:** [March 26, 2024, 4:00am UTC](https://discourse.julialang.org/t/biotools-instalation/112116 "2024-03-26T04:00:05Z")

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Hello! i have a situation installation Biotools and idk even what is about. A screenshoot of my problem

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## [\[BioSequences\] data structure to keep mutations (delta) of a sequence](https://discourse.julialang.org/t/biosequences-data-structure-to-keep-mutations-delta-of-a-sequence/111263)

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**Author:** [@Marco\_Antoniotti](https://discourse.julialang.org/u/Marco_Antoniotti)\
**Replies:** 4\
**Last updated:** [March 7, 2024, 9:38pm UTC](https://discourse.julialang.org/t/biosequences-data-structure-to-keep-mutations-delta-of-a-sequence/111263 "2024-03-07T21:38:40Z")

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Hi we are looking to a data structure to keep tract of the “evolution” of a sequence. What suggestions do you have in this respect? LongSubSeq views look useful, but they always refer to the the “main” sequence. What…

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## [Bioinference conference 2024: Call for Abstract & Registration](https://discourse.julialang.org/t/bioinference-conference-2024-call-for-abstract-registration/108614)

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**Author:** [@Yongchao](https://discourse.julialang.org/u/Yongchao)\
**Replies:** 0\
**Last updated:** [January 10, 2024, 10:49am UTC](https://discourse.julialang.org/t/bioinference-conference-2024-call-for-abstract-registration/108614 "2024-01-10T10:49:10Z")

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BioInference 2024: save the date and call for abstract The BioInference 2024 conference (2024 Conference - BioInference) is taking place at the University of Warwick on the 5th-7th June 2024, and it will combine a data-…

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## [How to get location of sequence in GenomicAnnotations](https://discourse.julialang.org/t/how-to-get-location-of-sequence-in-genomicannotations/106731)

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**Author:** [@michikazjp](https://discourse.julialang.org/u/michikazjp)\
**Replies:** 2\
**Last updated:** [January 3, 2024, 3:02am UTC](https://discourse.julialang.org/t/how-to-get-location-of-sequence-in-genomicannotations/106731 "2024-01-03T03:02:54Z")

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Hello I am newcomer in BioJulia and getting interested in it. Now I am starting to use GenomicAnnotations package. For example, I open a genbank file of E. coli K12 as using GenomicAnnotations K12 = readgbk(“K12.gbff”…

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## [Add DICOMTree.jl to JuliaHealth organisation?](https://discourse.julialang.org/t/add-dicomtree-jl-to-juliahealth-organisation/102873)

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**Author:** [@fdekerme](https://discourse.julialang.org/u/fdekerme)\
**Replies:** 2\
**Last updated:** [October 10, 2023, 1:28pm UTC](https://discourse.julialang.org/t/add-dicomtree-jl-to-juliahealth-organisation/102873 "2023-10-10T13:28:54Z")

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Hello ! :grin: Continuing the discussion from \[ANN\] DICOMTree.jl: fdekerme/DICOMTree.jl: A small Julia tool for visualizing DICOM metadata. (github.com) I have recently published a new DICOMTree package which has just…

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## [How to get involved in BioJulia](https://discourse.julialang.org/t/how-to-get-involved-in-biojulia/102215)

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**Author:** [@Emiller](https://discourse.julialang.org/u/Emiller)\
**Replies:** 7\
**Last updated:** [July 31, 2023, 2:54pm UTC](https://discourse.julialang.org/t/how-to-get-involved-in-biojulia/102215 "2023-07-31T14:54:07Z")

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Hoping we could create a similar page for at least BioJulia. I’m happy to take on the leg work to make a PR to the site, but I don’t know what the process :grimacing: I’m hoping to mimic: Join nf-core

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## [Possible to subset XAM BAM reader object by contig?](https://discourse.julialang.org/t/possible-to-subset-xam-bam-reader-object-by-contig/101715)

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**Author:** [@nrminor](https://discourse.julialang.org/u/nrminor)\
**Replies:** 5\
**Last updated:** [July 18, 2023, 6:17pm UTC](https://discourse.julialang.org/t/possible-to-subset-xam-bam-reader-object-by-contig/101715 "2023-07-18T18:17:48Z")

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Hi all. I’m writing a script to plot depth of coverage for each contig in an alignment. So far, I haven’t found a way to subset the BAM IOStream by contig, so the loop I use to iterate through records has to invoke a con…

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## [Interest in RNA-seq specific convenience package based on BioJulia?](https://discourse.julialang.org/t/interest-in-rna-seq-specific-convenience-package-based-on-biojulia/96949)

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**Author:** [@maltesie](https://discourse.julialang.org/u/maltesie)\
**Replies:** 16\
**Last updated:** [July 17, 2023, 4:11pm UTC](https://discourse.julialang.org/t/interest-in-rna-seq-specific-convenience-package-based-on-biojulia/96949 "2023-07-17T16:11:13Z")

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Hi all, I’m working in Bioinformatics research and started using Julia 2 years ago and now use it as my main language for everything I do. I organize the reusable part of my code in form of a Julia package which I try t…

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## [Change record sequence in a BAM file using XAM](https://discourse.julialang.org/t/change-record-sequence-in-a-bam-file-using-xam/98141)

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**Author:** [@ForestRaven](https://discourse.julialang.org/u/ForestRaven)\
**Replies:** 2\
**Last updated:** [June 4, 2023, 8:19am UTC](https://discourse.julialang.org/t/change-record-sequence-in-a-bam-file-using-xam/98141 "2023-06-04T08:19:05Z")

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Hi, I would like to update the sequence of a list of records in a BAM file. Looking at the code of record.jl, data is stored as Vector{UInt64} and some dark magic is used to convert to a DNA sequence. As it looks very …

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## [Optimizing performance with FASTX I/O stream and Codon Counting](https://discourse.julialang.org/t/optimizing-performance-with-fastx-i-o-stream-and-codon-counting/97918)

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**Author:** [@gus-pendleton](https://discourse.julialang.org/u/gus-pendleton)\
**Replies:** 5\
**Last updated:** [April 26, 2023, 8:05pm UTC](https://discourse.julialang.org/t/optimizing-performance-with-fastx-i-o-stream-and-codon-counting/97918 "2023-04-26T20:05:38Z")

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Hello, I am working to write code for codon usage bias, and my slowest step by far is calculating counts of individual codons for each gene in a fasta sequence of a genome. The general idea is that I’m using FASTX to s…

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## [Missing functions in namespace from BioSequences](https://discourse.julialang.org/t/missing-functions-in-namespace-from-biosequences/97871)

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**Author:** [@gus-pendleton](https://discourse.julialang.org/u/gus-pendleton)\
**Replies:** 4\
**Last updated:** [April 26, 2023, 4:40am UTC](https://discourse.julialang.org/t/missing-functions-in-namespace-from-biosequences/97871 "2023-04-26T04:40:37Z")

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I feel like I’m missing something fundamental, but I’m unable to follow many of the examples in the BioSequences documentation, because many of the functions they use remain undefined in my namespace. A few key ones that…

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## [Biojulia website not accessible](https://discourse.julialang.org/t/biojulia-website-not-accessible/94870)

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**Author:** [@ForestRaven](https://discourse.julialang.org/u/ForestRaven)\
**Replies:** 6\
**Last updated:** [March 23, 2023, 10:50pm UTC](https://discourse.julialang.org/t/biojulia-website-not-accessible/94870 "2023-03-23T22:50:31Z")

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Hi, I’m interested in doing bioinformatics with Julia and Google keeps redirecting me to Biojulia. However, the website does not seem to be up for at least two days. Is it still online ? Thanks,

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## [BioJulia Fastx import long{4}](https://discourse.julialang.org/t/biojulia-fastx-import-long-4/78098)

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**Author:** [@Jdbeck66](https://discourse.julialang.org/u/Jdbeck66)\
**Replies:** 1\
**Last updated:** [March 14, 2023, 4:19am UTC](https://discourse.julialang.org/t/biojulia-fastx-import-long-4/78098 "2023-03-14T04:19:35Z")

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I have a fast file that I loaded with FASTX and it seems that the data is stored as a LongDNA{4}. There are no ambiguities in the reads and I’d like to work with them as 2 bit sequences but I get an error when I try to …

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## [TextFormats parser generator](https://discourse.julialang.org/t/textformats-parser-generator/95505)

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**Author:** [@tp2750](https://discourse.julialang.org/u/tp2750)\
**Replies:** 5\
**Last updated:** [March 5, 2023, 9:31am UTC](https://discourse.julialang.org/t/textformats-parser-generator/95505 "2023-03-05T09:31:47Z")

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Came across this library: GitHub - ggonnella/textformats and paper: TextFormats: Simplifying the definition and parsing of text formats in bioinformatics They define a way to describe a text-based file format (like FAST…

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