# \#biology

**URL:** https://discourse.julialang.org/tag/biology/234.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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## [Research / Scientific Computing Collaboration – Julia Modelling for Subak Water Filtration](https://discourse.julialang.org/t/research-scientific-computing-collaboration-julia-modelling-for-subak-water-filtration/139586)

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**Author:** [@Fen\_Steckenborn](https://discourse.julialang.org/u/Fen_Steckenborn)\
**Replies:** 5\
**Last updated:** [September 26, 2026, 3:07pm UTC](https://discourse.julialang.org/t/research-scientific-computing-collaboration-julia-modelling-for-subak-water-filtration/139586 "2026-09-26T15:07:04Z")

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Location: Remote / Germany–Indonesia collaboration Project: Bali Ecofiltration – Subak Water Management, Bali, Indonesia Engagement: Research collaboration / contract / student or PhD project Start: Flexible / as soon…

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## [First ever BioJulia community call - Poll](https://discourse.julialang.org/t/first-ever-biojulia-community-call-poll/139645)

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**Author:** [@kevbonham](https://discourse.julialang.org/u/kevbonham)\
**Replies:** 0\
**Last updated:** [September 24, 2026, 12:08pm UTC](https://discourse.julialang.org/t/first-ever-biojulia-community-call-poll/139645 "2026-09-24T12:08:42Z")

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Hello everyone, as discussed at JuliaCon, @jakobnissen and I are planning to host periodic (roughly quarterly) community calls for folks interested in biology, bioinformatics, and related ecosystems, please take this pol…

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## [\[ANN\] ReactionDiffusion.jl v1.0.0 - Simulation and visualization for 1D reaction-diffusion systems](https://discourse.julialang.org/t/ann-reactiondiffusion-jl-v1-0-0-simulation-and-visualization-for-1d-reaction-diffusion-systems/139041)

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**Author:** [@homocarbonis](https://discourse.julialang.org/u/homocarbonis)\
**Replies:** 0\
**Last updated:** [August 25, 2026, 6:36pm UTC](https://discourse.julialang.org/t/ann-reactiondiffusion-jl-v1-0-0-simulation-and-visualization-for-1d-reaction-diffusion-systems/139041 "2026-08-25T18:36:45Z")

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I’d like to announce a brand new version of ReactionDiffusion.jl, a general purpose toolkit for anyone interested in modelling reaction-diffusion systems on a 1D domain. This release builds on the design of its predece…

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## [Spiking Neural Networks](https://discourse.julialang.org/t/spiking-neural-networks/63270)

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**Author:** [@mefob](https://discourse.julialang.org/u/mefob)\
**Replies:** 33\
**Last updated:** [July 9, 2026, 4:32pm UTC](https://discourse.julialang.org/t/spiking-neural-networks/63270 "2026-07-09T16:32:19Z")

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What is the state of the art for modeling spiking neural networks in Julia? I haven’t found much recent work: Spiking Neural Network (Discussion from 2019 on implementing a SNN as an ODE) GitHub - AStupidBear/Spikin…

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## [\[ANN\] Announcing ImageTally.jl — Interactive image counting and landmark placement for scientific images](https://discourse.julialang.org/t/ann-announcing-imagetally-jl-interactive-image-counting-and-landmark-placement-for-scientific-images/136705)

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**Author:** [@alejandromerchan](https://discourse.julialang.org/u/alejandromerchan)\
**Replies:** 3\
**Last updated:** [June 9, 2026, 12:09am UTC](https://discourse.julialang.org/t/ann-announcing-imagetally-jl-interactive-image-counting-and-landmark-placement-for-scientific-images/136705 "2026-06-09T00:09:57Z")

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Hi Julia community! I’m excited to share ImageTally.jl, a package I’ve been working on for interactive counting and tagging of objects in scientific images. \[EDIT\] ImageTally.jl is now part of the General registry! T…

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## [Modeling scale-up and economic factors in DYAD (bioprocess / fermentation)](https://discourse.julialang.org/t/modeling-scale-up-and-economic-factors-in-dyad-bioprocess-fermentation/136777)

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**Author:** [@mpampuch](https://discourse.julialang.org/u/mpampuch)\
**Replies:** 1\
**Last updated:** [April 21, 2026, 6:27pm UTC](https://discourse.julialang.org/t/modeling-scale-up-and-economic-factors-in-dyad-bioprocess-fermentation/136777 "2026-04-21T18:27:29Z")

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Hi all, I’m new to DYAD, so apologies if this is a basic question. I’m exploring whether DYAD is a good fit for modeling for my purposes, particularly modelling and analyzing the feasibility of fermentation systems. My…

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## [NeuralIntegrator: Spiking neural network and synaptic plasticity in DifferentialEquations.jl](https://discourse.julialang.org/t/neuralintegrator-spiking-neural-network-and-synaptic-plasticity-in-differentialequations-jl/130295)

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**Author:** [@flmuk](https://discourse.julialang.org/u/flmuk)\
**Replies:** 1\
**Last updated:** [July 1, 2025, 8:09am UTC](https://discourse.julialang.org/t/neuralintegrator-spiking-neural-network-and-synaptic-plasticity-in-differentialequations-jl/130295 "2025-07-01T08:09:13Z")

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NeuralIntegrator: simulating spiking neural networks with discontinuities I work in the field of computational neuroscience and model spiking neural networks (SNNs) with different synaptic plasticity rules, i.e. rules o…

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## [PhD Student & Bioinformatics Engineer – SPPICES project at I2BC (Gif-sur-Yvette, France)](https://discourse.julialang.org/t/phd-student-bioinformatics-engineer-sppices-project-at-i2bc-gif-sur-yvette-france/130021)

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**Author:** [@Diego\_Javier\_Zea](https://discourse.julialang.org/u/Diego_Javier_Zea)\
**Replies:** 0\
**Last updated:** [June 19, 2025, 10:09am UTC](https://discourse.julialang.org/t/phd-student-bioinformatics-engineer-sppices-project-at-i2bc-gif-sur-yvette-france/130021 "2025-06-19T10:09:42Z")

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We’re recruiting for two positions at the MAGI (Molecular Assemblies and Genome Integrity) team at I2BC (Institute for Integrative Biology of the Cell), within the ANR-funded SPPICES (Scoring and Predicting Protein Inter…

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## [Sequence motifs in pure Julia](https://discourse.julialang.org/t/sequence-motifs-in-pure-julia/128047)

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**Author:** [@candidaorelmex](https://discourse.julialang.org/u/candidaorelmex)\
**Replies:** 4\
**Last updated:** [April 15, 2025, 8:46pm UTC](https://discourse.julialang.org/t/sequence-motifs-in-pure-julia/128047 "2025-04-15T20:46:42Z")

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Hi everyone, I’m writing for a little package for myself and to maybe share with the community one day, if it’s mature enough. I want to plot sequence motifs of letters (or peptides for those who are curious about the c…

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## [\[ANN\] EcologicalNetworksDynamics.jl: simulate the temporal dynamics of complex ecological networks](https://discourse.julialang.org/t/ann-ecologicalnetworksdynamics-jl-simulate-the-temporal-dynamics-of-complex-ecological-networks/112130)

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**Author:** [@ismael-lajaaiti](https://discourse.julialang.org/u/ismael-lajaaiti)\
**Replies:** 1\
**Last updated:** [March 4, 2025, 3:41pm UTC](https://discourse.julialang.org/t/ann-ecologicalnetworksdynamics-jl-simulate-the-temporal-dynamics-of-complex-ecological-networks/112130 "2025-03-04T15:41:33Z")

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Together with @iago-lito, we’re delighted to present our new package. In short, EcologicalNetworksDynamics.jl offers a robust toolkit in Julia for researchers, and curious Julia users, to simulate and analyse the tem…

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## [Training Universal PINNs using NeuralPDE?](https://discourse.julialang.org/t/training-universal-pinns-using-neuralpde/125948)

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**Author:** [@John\_Nardini](https://discourse.julialang.org/u/John_Nardini)\
**Replies:** 4\
**Last updated:** [February 18, 2025, 2:34pm UTC](https://discourse.julialang.org/t/training-universal-pinns-using-neuralpde/125948 "2025-02-18T14:34:44Z")

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I am interested Universal PINNs (UPINNs) to describe some data. UPINNs are similar to a PINN, but we assume that the underlying DE model has known and unknown dynamics: \\dfrac{d\\vec{u}}{dt} = F\_{known}(\\vec{u}) + F\_{unk…

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## [Postdoc and PhD positions in mathematical biology and data-driven modelling of biological systems](https://discourse.julialang.org/t/postdoc-and-phd-positions-in-mathematical-biology-and-data-driven-modelling-of-biological-systems/119124)

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**Author:** [@twhiscock](https://discourse.julialang.org/u/twhiscock)\
**Replies:** 0\
**Last updated:** [September 6, 2024, 1:30pm UTC](https://discourse.julialang.org/t/postdoc-and-phd-positions-in-mathematical-biology-and-data-driven-modelling-of-biological-systems/119124 "2024-09-06T13:30:43Z")

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The Hiscock lab is hiring! Funded by an ERC Starting Grant, we are looking to recruit people with a strong quantitative background to work on some of the most fundamental problems in developmental biology. We particularl…

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## [Postdoc position in SciML + engineering biology at University of Bristol (UK)](https://discourse.julialang.org/t/postdoc-position-in-sciml-engineering-biology-at-university-of-bristol-uk/118278)

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**Author:** [@dawbarton](https://discourse.julialang.org/u/dawbarton)\
**Replies:** 0\
**Last updated:** [August 16, 2024, 2:32pm UTC](https://discourse.julialang.org/t/postdoc-position-in-sciml-engineering-biology-at-university-of-bristol-uk/118278 "2024-08-16T14:32:52Z")

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TLDR: there is a research associate (postdoc) position available at the University of Bristol, UK, focusing on SciML + engineering biology/synthetic biology in Julia/Rust. See below for details. We’re also starting a cen…

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## [Northeastern University: Looking for Research Projects for Student Teams!](https://discourse.julialang.org/t/northeastern-university-looking-for-research-projects-for-student-teams/114880)

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**Author:** [@TheCedarPrince](https://discourse.julialang.org/u/TheCedarPrince)\
**Replies:** 15\
**Last updated:** [June 26, 2024, 5:52pm UTC](https://discourse.julialang.org/t/northeastern-university-looking-for-research-projects-for-student-teams/114880 "2024-06-26T17:52:37Z")

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Hello everyone :wave: I have some very exciting news to share for the Julia Community! After discussion with Northeastern University, I am pleased to share that we have the opportunity to bring in Julia-related project…

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## [\[blogpost\] From FASTQ to CNV calls in Julia](https://discourse.julialang.org/t/blogpost-from-fastq-to-cnv-calls-in-julia/113084)

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**Author:** [@jonathanBieler](https://discourse.julialang.org/u/jonathanBieler)\
**Replies:** 0\
**Last updated:** [April 17, 2024, 4:21pm UTC](https://discourse.julialang.org/t/blogpost-from-fastq-to-cnv-calls-in-julia/113084 "2024-04-17T16:21:35Z")

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## [Optimizing dinucleotides count in a DNA sequence type \`LongDNA\`](https://discourse.julialang.org/t/optimizing-dinucleotides-count-in-a-dna-sequence-type-longdna/101583)

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**Author:** [@camilogarciabotero](https://discourse.julialang.org/u/camilogarciabotero)\
**Replies:** 21\
**Last updated:** [July 17, 2023, 5:33pm UTC](https://discourse.julialang.org/t/optimizing-dinucleotides-count-in-a-dna-sequence-type-longdna/101583 "2023-07-17T17:33:43Z")

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I am working with the BioSequences.jl package, particularly a LongSequence{DNAAlphabet{4}} (a very efficient string) type like the following random DNA sequence seq = dna"ACACATCATCTACTATCAT" and I want a function that c…

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## [CUBScout.jl: Codon Usage Bias in Julia](https://discourse.julialang.org/t/cubscout-jl-codon-usage-bias-in-julia/99774)

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**Author:** [@gus-pendleton](https://discourse.julialang.org/u/gus-pendleton)\
**Replies:** 0\
**Last updated:** [June 2, 2023, 3:04pm UTC](https://discourse.julialang.org/t/cubscout-jl-codon-usage-bias-in-julia/99774 "2023-06-02T15:04:05Z")

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CUBScout is a new package to calculate Codon Usage Bias in Julia. Currently, CUBScout calculates: Six measures of codon usage bias: B, from Karlin and Mrazek, 1996 ENC, from Wright 1990 ENC’, from Novembre, 2002 MCB, …

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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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## [Google Summer of Code plans and questions](https://discourse.julialang.org/t/google-summer-of-code-plans-and-questions/94761)

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**Author:** [@M-PERSIC](https://discourse.julialang.org/u/M-PERSIC)\
**Replies:** 1\
**Last updated:** [February 24, 2023, 2:02pm UTC](https://discourse.julialang.org/t/google-summer-of-code-plans-and-questions/94761 "2023-02-24T14:02:18Z")

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For background, I am a Systems and Information Biology student looking to plan for my undergraduate research thesis that would start in the summer. I have previous internship experience as part of my university’s Co-op p…

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## [\[ANN\] CellularPotts.jl: MultiScale Modeling of BIological Cells](https://discourse.julialang.org/t/ann-cellularpotts-jl-multiscale-modeling-of-biological-cells/92029)

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**Author:** [@RobertGregg](https://discourse.julialang.org/u/RobertGregg)\
**Replies:** 0\
**Last updated:** [December 23, 2022, 1:09am UTC](https://discourse.julialang.org/t/ann-cellularpotts-jl-multiscale-modeling-of-biological-cells/92029 "2022-12-23T01:09:55Z")

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Hi everyone, I want to introduce a package I’ve been working on for a while now called CellularPotts.jl (Here is the Github repo and the documention). The point of this package is to model cell behaviors like adhesion, …

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## [Fastq to OTU table pipeline in julia](https://discourse.julialang.org/t/fastq-to-otu-table-pipeline-in-julia/90183)

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**Author:** [@Ritu\_Lahkar](https://discourse.julialang.org/u/Ritu_Lahkar)\
**Replies:** 0\
**Last updated:** [November 13, 2022, 4:21am UTC](https://discourse.julialang.org/t/fastq-to-otu-table-pipeline-in-julia/90183 "2022-11-13T04:21:07Z")

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Is there any available julia pipeline for analysis of FASTQ data into OTU tables? If yes any reference of how to use or any documentation?

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## [How do I insert a specific string into a BioSequences DNA string?](https://discourse.julialang.org/t/how-do-i-insert-a-specific-string-into-a-biosequences-dna-string/86694)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 1\
**Last updated:** [September 2, 2022, 4:40pm UTC](https://discourse.julialang.org/t/how-do-i-insert-a-specific-string-into-a-biosequences-dna-string/86694 "2022-09-02T16:40:51Z")

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using BioSequences julia\> a=dna"ATCG" 4nt DNA Sequence: ATCG julia\> insert!(a,2,'C') 5nt DNA Sequence: ACTCG But if I inserted more than one chars,it will fail. julia\> insert!(a,2,"CG") ERROR: MethodError: Cannot \`conv…

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## [\[ANN\] ProtoSyn.jl v1.1: Molecular manipulation and simulation](https://discourse.julialang.org/t/ann-protosyn-jl-v1-1-molecular-manipulation-and-simulation/84158)

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**Author:** [@JosePereiraUA](https://discourse.julialang.org/u/JosePereiraUA)\
**Replies:** 2\
**Last updated:** [July 13, 2022, 12:39pm UTC](https://discourse.julialang.org/t/ann-protosyn-jl-v1-1-molecular-manipulation-and-simulation/84158 "2022-07-13T12:39:24Z")

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Hi everyone! I’m excited to officially share with you ProtoSyn.jl: a new tool for molecular simulation and general manipulation, with a strong emphasis on protein design. I’ve been showcasing ProtoSyn.jl for a while, but…

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## [\[ANN\] Nucleotide\_Essentials.jl - Support for some basic first steps in analyzing Illumina sequencing data!](https://discourse.julialang.org/t/ann-nucleotide-essentials-jl-support-for-some-basic-first-steps-in-analyzing-illumina-sequencing-data/79500)

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**Author:** [@patrickhorve](https://discourse.julialang.org/u/patrickhorve)\
**Replies:** 3\
**Last updated:** [April 15, 2022, 11:03am UTC](https://discourse.julialang.org/t/ann-nucleotide-essentials-jl-support-for-some-basic-first-steps-in-analyzing-illumina-sequencing-data/79500 "2022-04-15T11:03:37Z")

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I just finished up throwing together some useful commands for working with Illumina sequencing data and thought it could be useful for others as well! Nucleotide\_Essentials.jl is a collection of tools for working with I…

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## [What happened to composition function of BioSequences?](https://discourse.julialang.org/t/what-happened-to-composition-function-of-biosequences/78759)

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**Author:** [@kwicher](https://discourse.julialang.org/u/kwicher)\
**Replies:** 2\
**Last updated:** [March 30, 2022, 10:45pm UTC](https://discourse.julialang.org/t/what-happened-to-composition-function-of-biosequences/78759 "2022-03-30T22:45:42Z")

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I am trying to implement an older package that uses BioSequences, especially the composition function. This function is however gone from the newest BioSequences, so e everything breaks. Has composition been replaced by…

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## [Extract start and end positions from a PairwiseAlignment](https://discourse.julialang.org/t/extract-start-and-end-positions-from-a-pairwisealignment/77610)

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**Author:** [@rohan.m](https://discourse.julialang.org/u/rohan.m)\
**Replies:** 6\
**Last updated:** [March 10, 2022, 3:02am UTC](https://discourse.julialang.org/t/extract-start-and-end-positions-from-a-pairwisealignment/77610 "2022-03-10T03:02:03Z")

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Hello, I am dealing with PairwiseAlignments of the form: PairwiseAlignment{LongDNASeq, LongDNASeq}: seq: 2 TGTCTTTCGCTGCTGAGGGTAGA 24 | | | | | | | | | | | | | | | | | | | | | | ref: 307 TGTCTTTCGCTGC…

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## [What are some recommended ways to create networks of ensembles of neurons?](https://discourse.julialang.org/t/what-are-some-recommended-ways-to-create-networks-of-ensembles-of-neurons/72673)

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**Author:** [@yohan](https://discourse.julialang.org/u/yohan)\
**Replies:** 0\
**Last updated:** [December 6, 2021, 6:35pm UTC](https://discourse.julialang.org/t/what-are-some-recommended-ways-to-create-networks-of-ensembles-of-neurons/72673 "2021-12-06T18:35:18Z")

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Hi! I’m very new to Julia and considering migrating my Izhikevich neuronal network simulations to Julia from MATLAB. I was wondering about ways of implementing interactions among ensembles of units. I’d like to have pop…

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## [Julia package to calculate coverage and depth from sam/bam files](https://discourse.julialang.org/t/julia-package-to-calculate-coverage-and-depth-from-sam-bam-files/71888)

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**Author:** [@Lamma](https://discourse.julialang.org/u/Lamma)\
**Replies:** 4\
**Last updated:** [November 23, 2021, 7:42am UTC](https://discourse.julialang.org/t/julia-package-to-calculate-coverage-and-depth-from-sam-bam-files/71888 "2021-11-23T07:42:27Z")

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Hi there, I am wanting to generate coverage and depth statistic for some sam/bam files I have and was wondering if Julia has a package that can do this for me?

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## [\[ANN\] BioRecordsProcessing.jl - Easily process your biological records](https://discourse.julialang.org/t/ann-biorecordsprocessing-jl-easily-process-your-biological-records/70149)

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**Author:** [@jonathanBieler](https://discourse.julialang.org/u/jonathanBieler)\
**Replies:** 0\
**Last updated:** [October 21, 2021, 1:10pm UTC](https://discourse.julialang.org/t/ann-biorecordsprocessing-jl-easily-process-your-biological-records/70149 "2021-10-21T13:10:53Z")

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This is a small utility package that help reduce the boilerplate when processing files containing biological records (fastqs, bams, vcfs, …). It deals with files management, opening & closing readers and writers, process…

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## [Agent-based model performance](https://discourse.julialang.org/t/agent-based-model-performance/68758)

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**Author:** [@Peter\_Uhl](https://discourse.julialang.org/u/Peter_Uhl)\
**Replies:** 14\
**Last updated:** [September 27, 2021, 5:39am UTC](https://discourse.julialang.org/t/agent-based-model-performance/68758 "2021-09-27T05:39:14Z")

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Hi all, I am working to improve the performance of an agent-based model. The model is of two bacterial species whose growth and death probabilities are determined by the amount of a nutrient available locally. I’m aware…

[Next page](https://discourse.julialang.org/tag/biology/234.md?match_all_tags=true&page=1&tags%5B%5D=biology)