# Biology, Health, and Medicine

**URL:** https://discourse.julialang.org/c/domain/bio/15.md?page=2

[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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## [FASTX.FASTA.Reader, no method matching error](https://discourse.julialang.org/t/fastx-fasta-reader-no-method-matching-error/72240)

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**Author:** [@Lamma](https://discourse.julialang.org/u/Lamma)\
**Replies:** 7\
**Last updated:** [November 30, 2021, 1:21pm UTC](https://discourse.julialang.org/t/fastx-fasta-reader-no-method-matching-error/72240 "2021-11-30T13:21:34Z")

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I am using the ´FASTX\` package to stream over a large fasta file but am getting a no method matching error: ERROR: LoadError: TaskFailedException Stacktrace: \[1\] wait @ ./task.jl:334 \[inlined\] \[2\] threading\_run(fun…

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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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## [Adaptive methods for image contrast stretching?](https://discourse.julialang.org/t/adaptive-methods-for-image-contrast-stretching/67774)

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**Author:** [@babaq](https://discourse.julialang.org/u/babaq)\
**Replies:** 1\
**Last updated:** [September 8, 2021, 7:51am UTC](https://discourse.julialang.org/t/adaptive-methods-for-image-contrast-stretching/67774 "2021-09-08T07:51:50Z")

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Hi, I have an image with small repeating structures, which need to be stretched in the same range(0-1). My intuition is to partition the image to many small tiles, and apply contrast linear stretching for each tile,…

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## [Simulating evolutionary birth-death processes with EvoId.jl](https://discourse.julialang.org/t/simulating-evolutionary-birth-death-processes-with-evoid-jl/65867)

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**Author:** [@boutor2](https://discourse.julialang.org/u/boutor2)\
**Replies:** 1\
**Last updated:** [September 6, 2021, 7:47pm UTC](https://discourse.julialang.org/t/simulating-evolutionary-birth-death-processes-with-evoid-jl/65867 "2021-09-06T19:47:05Z")

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Hello guys, I am posting here a link to EvoId.jl, a package that I have been developing for my research. EvoId.jl is purposed for numerical experiments in theoretical evolutionary biology, and implements a few algorithm…

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## [SequenceVariation: Brainstorming for new package](https://discourse.julialang.org/t/sequencevariation-brainstorming-for-new-package/66918)

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**Author:** [@jakobnissen](https://discourse.julialang.org/u/jakobnissen)\
**Replies:** 3\
**Last updated:** [August 26, 2021, 6:04pm UTC](https://discourse.julialang.org/t/sequencevariation-brainstorming-for-new-package/66918 "2021-08-26T18:04:29Z")

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I’d like to make a new package for BioJulia. I’ve made a crude prototype, but I’m still unsure about the design and API and would like some feedback, and maybe pushback if my current design has problems. I think I asked …

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## [3d medical app stencil](https://discourse.julialang.org/t/3d-medical-app-stencil/64019)

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**Author:** [@Jakub\_Mitura](https://discourse.julialang.org/u/Jakub_Mitura)\
**Replies:** 6\
**Last updated:** [July 14, 2021, 12:14pm UTC](https://discourse.julialang.org/t/3d-medical-app-stencil/64019 "2021-07-14T12:14:43Z")

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Hello I am trying to apply fantactic ParallelStencil.jl (https://github.com/omlins/ParallelStencil.jl) library to 3d medical imaging, as it seems ideal yet I have problems with application of code to my domain. For the…

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## [\[ANN\]: Announcing RxNav.jl interface to National Library of Medicine RxNav database](https://discourse.julialang.org/t/ann-announcing-rxnav-jl-interface-to-national-library-of-medicine-rxnav-database/64020)

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**Author:** [@wherrera](https://discourse.julialang.org/u/wherrera)\
**Replies:** 0\
**Last updated:** [July 4, 2021, 5:27am UTC](https://discourse.julialang.org/t/ann-announcing-rxnav-jl-interface-to-national-library-of-medicine-rxnav-database/64020 "2021-07-04T05:27:18Z")

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and

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## [SBML parser](https://discourse.julialang.org/t/sbml-parser/54915)

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**Author:** [@Elmo](https://discourse.julialang.org/u/Elmo)\
**Replies:** 4\
**Last updated:** [June 16, 2021, 7:04am UTC](https://discourse.julialang.org/t/sbml-parser/54915 "2021-06-16T07:04:21Z")

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Is anyone actively working on an SBML parser? I saw this and this but can’t find any status updates. I am busy building a Julia version of Cobrapy (much more expansive than COBRA.jl, which seems to be restricted to distr…

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## [What are the popgen and bioinformatics weaknesses](https://discourse.julialang.org/t/what-are-the-popgen-and-bioinformatics-weaknesses/62469)

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**Author:** [@EvoArt](https://discourse.julialang.org/u/EvoArt)\
**Replies:** 7\
**Last updated:** [June 7, 2021, 3:42pm UTC](https://discourse.julialang.org/t/what-are-the-popgen-and-bioinformatics-weaknesses/62469 "2021-06-07T15:42:17Z")

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Just wondering if any Julia users still call python/R or just straight don’t use Julia for any area of bioinformatics or population genetics analyses? And why?

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## [OHDSICohortExpressions.jl](https://discourse.julialang.org/t/ohdsicohortexpressions-jl/62525)

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**Author:** [@cce](https://discourse.julialang.org/u/cce)\
**Replies:** 1\
**Last updated:** [June 7, 2021, 3:07pm UTC](https://discourse.julialang.org/t/ohdsicohortexpressions-jl/62525 "2021-06-07T15:07:57Z")

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Observational Health Data Sciences and Informatics (or OHDSI) is a program to bring out the value of health data through large-scale analytics. OHDSI defines the OMOP CDM, a data warehouse database schema for storing …

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## [What Package would you suggest to represent sequence alteration events?](https://discourse.julialang.org/t/what-package-would-you-suggest-to-represent-sequence-alteration-events/62423)

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**Author:** [@Marco\_Antoniotti](https://discourse.julialang.org/u/Marco_Antoniotti)\
**Replies:** 7\
**Last updated:** [June 7, 2021, 10:02am UTC](https://discourse.julialang.org/t/what-package-would-you-suggest-to-represent-sequence-alteration-events/62423 "2021-06-07T10:02:58Z")

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Hi I am looking for a package that would allow me to represent changes to a sequence. Is there something like that around? I looked at GenomeGraph and PopGen (and PopGenSim) but their documentation is quite sparse to …

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## [Building RNA Sequencing and Analysis Apps Webinar 5/20/2021](https://discourse.julialang.org/t/building-rna-sequencing-and-analysis-apps-webinar-5-20-2021/61392)

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**Author:** [@jdamiba](https://discourse.julialang.org/u/jdamiba)\
**Replies:** 0\
**Last updated:** [May 18, 2021, 8:41pm UTC](https://discourse.julialang.org/t/building-rna-sequencing-and-analysis-apps-webinar-5-20-2021/61392 "2021-05-18T20:41:45Z")

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Hello! I just wanted to let interested parties know that on Thursday, May 20th at 1PM, Plotly is hosting a free webinar with UC Berkeley PhD Candidate, Alyssa Morrow on the topic of using the Dash framework and the Pile…

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## [BioProfiling.jl](https://discourse.julialang.org/t/bioprofiling-jl/60727)

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**Author:** [@koalive](https://discourse.julialang.org/u/koalive)\
**Replies:** 1\
**Last updated:** [May 7, 2021, 4:54pm UTC](https://discourse.julialang.org/t/bioprofiling-jl/60727 "2021-05-07T16:54:17Z")

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Hi there, I’m glad to announce the release of BioProfiling.jl v1.0.0, now as a registered package! You might find it interesting if you’re analysing high-content imaging screens and eager to curate informative morpholo…

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## [Celltracker possibilities?](https://discourse.julialang.org/t/celltracker-possibilities/46736)

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**Author:** [@ervern](https://discourse.julialang.org/u/ervern)\
**Replies:** 11\
**Last updated:** [March 16, 2021, 7:31am UTC](https://discourse.julialang.org/t/celltracker-possibilities/46736 "2021-03-16T07:31:35Z")

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Hi im a student and was wondering if this would be a good language to make a program that tracks cells in a video rather than python or MATLAB. If so I was wondering where I should start. Thanks!

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## [How to bring a system of differential equations to zero with DifferentialEquations?](https://discourse.julialang.org/t/how-to-bring-a-system-of-differential-equations-to-zero-with-differentialequations/53659)

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**Author:** [@Luigi\_Marongiu](https://discourse.julialang.org/u/Luigi_Marongiu)\
**Replies:** 15\
**Last updated:** [January 24, 2021, 12:59pm UTC](https://discourse.julialang.org/t/how-to-bring-a-system-of-differential-equations-to-zero-with-differentialequations/53659 "2021-01-24T12:59:30Z")

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I have a population model described by this system of differential equations: dN/dt = μN(1-(N+I)/κ) -φNP -ωN dI/dt = φNP -ηI -ωI dP/dt = βηI -φNP -ωP with κ = 2.2 ⋅ 10^7 μ = 0.47 φ = 10^-9 β = 50 η = 1.0 ω = 0.05 Thi…

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## [Has Moderna used Pumas AI for mRNA modeling and simulation?](https://discourse.julialang.org/t/has-moderna-used-pumas-ai-for-mrna-modeling-and-simulation/53004)

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**Author:** [@empet](https://discourse.julialang.org/u/empet)\
**Replies:** 1\
**Last updated:** [January 7, 2021, 10:57pm UTC](https://discourse.julialang.org/t/has-moderna-used-pumas-ai-for-mrna-modeling-and-simulation/53004 "2021-01-07T22:57:56Z")

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A few days ago, I saw a Julia related tweet announcing that Pumas AI was involved in modeling and simulating Moderna’s mRNA. In a discussion with a friend about Julia vs Python I told him this news, but when I was aske…

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## [\[ANN\] PubChemCrawler](https://discourse.julialang.org/t/ann-pubchemcrawler/50935)

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**Author:** [@tim.holy](https://discourse.julialang.org/u/tim.holy)\
**Replies:** 0\
**Last updated:** [November 29, 2020, 2:03pm UTC](https://discourse.julialang.org/t/ann-pubchemcrawler/50935 "2020-11-29T14:03:17Z")

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For the chemistry- or cheminformatics-inclined among you, you may be interested in PubChemCrawler, which makes it easier to query the PubChem service. https://github.com/JuliaHealth/PubChemCrawler.jl

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## [Biostructures.jl and md trajectory files](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789)

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**Author:** [@bharland](https://discourse.julialang.org/u/bharland)\
**Replies:** 3\
**Last updated:** [November 26, 2020, 11:59am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789 "2020-11-26T11:59:01Z")

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I’m wondering how horrendous it would be to include parsing of popular trajectory files, so I had a look at how MDTraj did it with (e.g.) the xtc format. A layer of python, then cython and then a set of c files adapted …

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## [How can I set a Specific chain name for a Structure？(BioStrcuture Package)](https://discourse.julialang.org/t/how-can-i-set-a-specific-chain-name-for-a-structure-biostrcuture-package/50211)

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**Author:** [@Wang-Lin-boop](https://discourse.julialang.org/u/Wang-Lin-boop)\
**Replies:** 6\
**Last updated:** [November 18, 2020, 3:26pm UTC](https://discourse.julialang.org/t/how-can-i-set-a-specific-chain-name-for-a-structure-biostrcuture-package/50211 "2020-11-18T15:26:13Z")

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Recently, I was working on a project dealing with a large number of coordinate files, which required me to convert each chain in some coordinate files with MMCIF/PDBXML/MMTF/PDB format into PDB format. Some of the chains…

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## [\[ANN\] PopGen.jl v0.4.0 and PopGenSims.jl v0.0.2](https://discourse.julialang.org/t/ann-popgen-jl-v0-4-0-and-popgensims-jl-v0-0-2/50316)

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**Author:** [@pdimens](https://discourse.julialang.org/u/pdimens)\
**Replies:** 4\
**Last updated:** [November 17, 2020, 9:47pm UTC](https://discourse.julialang.org/t/ann-popgen-jl-v0-4-0-and-popgensims-jl-v0-0-2/50316 "2020-11-17T21:47:05Z")

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Hello all, I’m thrilled to announce the next release of PopGen.jl v0.4.0 (although incorrectly versioned in the release, oops). Internal tweaks removing CategoricalArrays in favor of PooledArrays cleaning up and adding…

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## [SciMl/Differential equations for modeling clinic medicine](https://discourse.julialang.org/t/sciml-differential-equations-for-modeling-clinic-medicine/48982)

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**Author:** [@timothyhartzog](https://discourse.julialang.org/u/timothyhartzog)\
**Replies:** 8\
**Last updated:** [October 30, 2020, 5:30am UTC](https://discourse.julialang.org/t/sciml-differential-equations-for-modeling-clinic-medicine/48982 "2020-10-30T05:30:42Z")

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After watching numerous lectures by Dr. Christopher Rackauckas, i am trying to develop the theory/understanding of using SciMl/differential equations vs biostats in modeling clinical medicinal problems? Biostats/eviden…

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## [Celltracker updates](https://discourse.julialang.org/t/celltracker-updates/48781)

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**Author:** [@ervern](https://discourse.julialang.org/u/ervern)\
**Replies:** 1\
**Last updated:** [October 22, 2020, 12:10am UTC](https://discourse.julialang.org/t/celltracker-updates/48781 "2020-10-22T00:10:13Z")

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Hi so I recently posted and found some useful information on how to make code that would track cells. However I’m running into an issue where I think the cells are too close to the background to use most of the detection…

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## [Pairwise Alignment Score function: From Python to Julia. Suggestions](https://discourse.julialang.org/t/pairwise-alignment-score-function-from-python-to-julia-suggestions/48089)

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**Author:** [@aadam](https://discourse.julialang.org/u/aadam)\
**Replies:** 3\
**Last updated:** [October 10, 2020, 1:23pm UTC](https://discourse.julialang.org/t/pairwise-alignment-score-function-from-python-to-julia-suggestions/48089 "2020-10-10T13:23:24Z")

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I wanted a function to compute the Pairwise Alignment Score in Julia, but didn’t find any in the BioJulia repository. I submitted an issue, asking for some guidance, but no response till now. So, after waiting a long tim…

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## [Package for cell (morphological) profiling](https://discourse.julialang.org/t/package-for-cell-morphological-profiling/47500)

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**Author:** [@koalive](https://discourse.julialang.org/u/koalive)\
**Replies:** 3\
**Last updated:** [October 1, 2020, 5:34pm UTC](https://discourse.julialang.org/t/package-for-cell-morphological-profiling/47500 "2020-10-01T17:34:09Z")

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Hi there. I am currently working on a package compiling useful tools and structures for handling morphological profiles: https://github.com/menchelab/RMP.jl Concretely, part of my research work involves High Content S…

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## [Current state of PopGen.jl](https://discourse.julialang.org/t/current-state-of-popgen-jl/41616)

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**Author:** [@pdimens](https://discourse.julialang.org/u/pdimens)\
**Replies:** 18\
**Last updated:** [September 23, 2020, 12:41am UTC](https://discourse.julialang.org/t/current-state-of-popgen-jl/41616 "2020-09-23T00:41:48Z")

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Hello all, For the past (I honestly don’t know how many) months, I’ve been writing and rewriting my fork of PopGen.jl (found here). The vast majority of the work involved was establishing a data structure and a million…

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## [Modify FASTQ file description with a new string using FASTX](https://discourse.julialang.org/t/modify-fastq-file-description-with-a-new-string-using-fastx/46672)

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**Author:** [@Gopi1616](https://discourse.julialang.org/u/Gopi1616)\
**Replies:** 3\
**Last updated:** [September 22, 2020, 8:51am UTC](https://discourse.julialang.org/t/modify-fastq-file-description-with-a-new-string-using-fastx/46672 "2020-09-22T08:51:53Z")

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Hi, I am a python programmer and new to Julia. One of the tasks I am working on needs modification of description lines in Fastq sequence files. Doing this in python was pretty time-consuming. So wanted to try the same …

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## [Is any package of CFD to simulate the hydrodynamic behaviour?](https://discourse.julialang.org/t/is-any-package-of-cfd-to-simulate-the-hydrodynamic-behaviour/44251)

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**Author:** [@PharmCat](https://discourse.julialang.org/u/PharmCat)\
**Replies:** 7\
**Last updated:** [August 4, 2020, 3:48pm UTC](https://discourse.julialang.org/t/is-any-package-of-cfd-to-simulate-the-hydrodynamic-behaviour/44251 "2020-08-04T15:48:38Z")

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Is any package to simulate the hydrodynamic behaviour of a bioreactor with a impeller? PS Something like ANSYS Fluent/THINK Fluid Dynamix.

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## [Implementing dosing regimens in diffeq](https://discourse.julialang.org/t/implementing-dosing-regimens-in-diffeq/43173)

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**Author:** [@Janssena](https://discourse.julialang.org/u/Janssena)\
**Replies:** 2\
**Last updated:** [July 28, 2020, 6:15am UTC](https://discourse.julialang.org/t/implementing-dosing-regimens-in-diffeq/43173 "2020-07-28T06:15:18Z")

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Hey all, I’ve been working to implement a complex dosing regimen consisting of both IV bolus doses and continuous IV infusions. An example would be: t = -80, dose = 1000, rate = 0 t = -2, dose = 2500, rate = 100 t =…

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## [Equivalent of MDAnalysis in Julia](https://discourse.julialang.org/t/equivalent-of-mdanalysis-in-julia/43070)

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**Author:** [@Seanny123](https://discourse.julialang.org/u/Seanny123)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 5:55pm UTC](https://discourse.julialang.org/t/equivalent-of-mdanalysis-in-julia/43070 "2020-07-14T17:55:37Z")

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Continuing with the theme of my previous question, Equivalent to Rosetta in Julia, I am still trying to understand the Computational Biology tool ecosystem. Currently, I’m trying to use MDAnalysis, which is a Python pac…

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## [\[ANN\] GeneticCrosses.jl](https://discourse.julialang.org/t/ann-geneticcrosses-jl/43041)

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**Author:** [@pdimens](https://discourse.julialang.org/u/pdimens)\
**Replies:** 0\
**Last updated:** [July 14, 2020, 12:50pm UTC](https://discourse.julialang.org/t/ann-geneticcrosses-jl/43041 "2020-07-14T12:50:36Z")

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Hello all, This past weekend I wrote a tiny offshoot to PopGen.jl that simulates the offspring resulting from breeding two individuals and it’s called GeneticCrosses.jl :sunglasses:. https://github.com/pdimens/GeneticCr…

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