# Biology, Health, and Medicine

**URL:** https://discourse.julialang.org/c/domain/bio/15.md?page=3

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

**Page:** 4

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## [DiffEqBiological: getting the error "type Symbol has no field head"](https://discourse.julialang.org/t/diffeqbiological-getting-the-error-type-symbol-has-no-field-head/42296)

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**Author:** [@Sanji\_Vinsmoke](https://discourse.julialang.org/u/Sanji_Vinsmoke)\
**Replies:** 5\
**Last updated:** [June 30, 2020, 9:43pm UTC](https://discourse.julialang.org/t/diffeqbiological-getting-the-error-type-symbol-has-no-field-head/42296 "2020-06-30T21:43:21Z")

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I want to make a simple model of enzyme kinetics,but I keep getting some errors This is what I tried: rn = @reaction\_network begin k\_f, E + S → ES k\_r, ES → E + S k\_p, ES → P end and I get the error: type Sym…

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## [DifferentialEquations: Confusion regarding time points and values in the solution array](https://discourse.julialang.org/t/differentialequations-confusion-regarding-time-points-and-values-in-the-solution-array/41730)

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**Author:** [@Sanji\_Vinsmoke](https://discourse.julialang.org/u/Sanji_Vinsmoke)\
**Replies:** 10\
**Last updated:** [June 19, 2020, 5:54pm UTC](https://discourse.julialang.org/t/differentialequations-confusion-regarding-time-points-and-values-in-the-solution-array/41730 "2020-06-19T17:54:39Z")

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I am a bit confused about the timepoints that the solution array represents. Since the algorithms used to solve are adaptive, the size of solutions might be different. Now, if I say that all my growth rates of species h…

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## [lhe/Biofast benchmark | FASTQ parsing \[Julia,Nim,Crystal,Python,...\]](https://discourse.julialang.org/t/lhe-biofast-benchmark-fastq-parsing-julia-nim-crystal-python/39747)

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**Author:** [@ImreSamu](https://discourse.julialang.org/u/ImreSamu)\
**Replies:** 54\
**Last updated:** [May 25, 2020, 8:17pm UTC](https://discourse.julialang.org/t/lhe-biofast-benchmark-fastq-parsing-julia-nim-crystal-python/39747 "2020-05-25T20:17:43Z")

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from the community news: " Biofast is a small benchmark for evaluating the performance of programming languages and implementations on a few common tasks in the field of Bioinformatics. It currently includes two benchma…

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## [Simple SEIR model for simulating Covid-19 outbreak](https://discourse.julialang.org/t/simple-seir-model-for-simulating-covid-19-outbreak/35854)

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**Author:** [@Bernd\_Blasius](https://discourse.julialang.org/u/Bernd_Blasius)\
**Replies:** 1\
**Last updated:** [April 3, 2020, 9:07am UTC](https://discourse.julialang.org/t/simple-seir-model-for-simulating-covid-19-outbreak/35854 "2020-04-03T09:07:12Z")

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Implementation of a SEIR-like model describing the Coronavirus Covid-19 outbreak 2019/20, based on the publication: Wang et al. (2020) Evolving epidemiology and impact of non-pharmaceutical interventions on the outbreak …

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## [BioJulia dependencies and JuliaRegistrator](https://discourse.julialang.org/t/biojulia-dependencies-and-juliaregistrator/36400)

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**Author:** [@phaverty](https://discourse.julialang.org/u/phaverty)\
**Replies:** 4\
**Last updated:** [March 23, 2020, 9:52pm UTC](https://discourse.julialang.org/t/biojulia-dependencies-and-juliaregistrator/36400 "2020-03-23T21:52:08Z")

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GenomicVectors.jl is registered with the main julia registry. I’ve added XAM.jl as a dependency. When I try to register a new version of GenomicVectors.jl, the JuliaRegistrator complains that it can’t find XAM.jl. Is the…

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## [Renaming IDs in a GFF3](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687)

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**Author:** [@mictadlo](https://discourse.julialang.org/u/mictadlo)\
**Replies:** 42\
**Last updated:** [January 28, 2020, 3:51pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687 "2020-01-28T15:51:28Z")

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Hi, are there any examples of renaming IDs in a GFF3 file? Thank you in advance,

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## [Extract alignments from BAM and associated FASTA reference genome](https://discourse.julialang.org/t/extract-alignments-from-bam-and-associated-fasta-reference-genome/30294)

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**Author:** [@Gio](https://discourse.julialang.org/u/Gio)\
**Replies:** 2\
**Last updated:** [October 28, 2019, 11:49am UTC](https://discourse.julialang.org/t/extract-alignments-from-bam-and-associated-fasta-reference-genome/30294 "2019-10-28T11:49:10Z")

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Hello everybody, I’m new to Julia/BioJulia but I’m already appreciating some features of both the language and the Bio libraries (really nice work!). I’m currently trying to do simple stuff to get acquainted with the Bi…

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## [Bioinitio Project?](https://discourse.julialang.org/t/bioinitio-project/29166)

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**Author:** [@kevbonham](https://discourse.julialang.org/u/kevbonham)\
**Replies:** 1\
**Last updated:** [October 8, 2019, 3:40pm UTC](https://discourse.julialang.org/t/bioinitio-project/29166 "2019-10-08T15:40:41Z")

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I just came across https://github.com/bionitio-team/bionitio, which provides templates for bioinformatics command line tools. I was thinking it might be good to submit something in julia as a sort of advertisement. I do…

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## [Developing a kmer counter in Julia](https://discourse.julialang.org/t/developing-a-kmer-counter-in-julia/292)

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**Author:** [@bpr](https://discourse.julialang.org/u/bpr)\
**Replies:** 7\
**Last updated:** [September 19, 2019, 3:42pm UTC](https://discourse.julialang.org/t/developing-a-kmer-counter-in-julia/292 "2019-09-19T15:42:59Z")

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Hi, I was looking at some data using the Jellyfish program (a fast parallel kmer counter written in C++) and I was wondering how close I could get to it’s performance in Julia. Just so you know where I’m coming from, my…

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## [CRAM support?](https://discourse.julialang.org/t/cram-support/28222)

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**Author:** [@brendanofallon](https://discourse.julialang.org/u/brendanofallon)\
**Replies:** 5\
**Last updated:** [September 1, 2019, 2:10pm UTC](https://discourse.julialang.org/t/cram-support/28222 "2019-09-01T14:10:56Z")

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Hello, I’m wondering if there’s support, or plans for support, of the CRAM alignment format in BioJulia? I didn’t come across anything obvious reading the documentation, but perhaps it’s hiding somewhere, or a work in pr…

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## [Biostar Handbook, computational genomics, and Julia - to be or not to be?](https://discourse.julialang.org/t/biostar-handbook-computational-genomics-and-julia-to-be-or-not-to-be/25732)

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**Author:** [@XVilka](https://discourse.julialang.org/u/XVilka)\
**Replies:** 23\
**Last updated:** [August 21, 2019, 2:03pm UTC](https://discourse.julialang.org/t/biostar-handbook-computational-genomics-and-julia-to-be-or-not-to-be/25732 "2019-08-21T14:03:56Z")

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How many people started to learn bioinformatics with Julia, not Python? I guess not many. There is a unique opportunity to change that - one of the most recommended books for the beginners in this area is Biostar Handboo…

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## [Bioinformatics.jl - Helper functions for bioinformatics and rosalind.info problems](https://discourse.julialang.org/t/bioinformatics-jl-helper-functions-for-bioinformatics-and-rosalind-info-problems/27506)

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**Author:** [@mrtkp9993](https://discourse.julialang.org/u/mrtkp9993)\
**Replies:** 1\
**Last updated:** [August 13, 2019, 9:06pm UTC](https://discourse.julialang.org/t/bioinformatics-jl-helper-functions-for-bioinformatics-and-rosalind-info-problems/27506 "2019-08-13T21:06:51Z")

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https://github.com/mrtkp9993/Bioinformatics.jl

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## [Streaming gzipped BCF files: issue with CHROM field](https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194)

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**Author:** [@kaskarn](https://discourse.julialang.org/u/kaskarn)\
**Replies:** 1\
**Last updated:** [June 12, 2019, 3:55pm UTC](https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194 "2019-06-12T15:55:34Z")

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Hello, I first posted this as an issue on the GeneticVariation github: github.com/BioJulia/GeneticVariation.jl/issues/25 However, I suspect this may be a better place for it, since the package may not be at fault here…

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## [Reading/parsing .ab1 sequencing files](https://discourse.julialang.org/t/reading-parsing-ab1-sequencing-files/23555)

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**Author:** [@solf1re2](https://discourse.julialang.org/u/solf1re2)\
**Replies:** 10\
**Last updated:** [May 29, 2019, 12:42pm UTC](https://discourse.julialang.org/t/reading-parsing-ab1-sequencing-files/23555 "2019-05-29T12:42:27Z")

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Hi, We currently get some sequencing done on 96 well plates. The lab guys manually check the chromatograms (ab1) files for clean reads. But I was wondering if there was a julia package able to open and retrieve the info…

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## [ANN: Pseudoseq.jl - Simulating DNA sequencing experiments](https://discourse.julialang.org/t/ann-pseudoseq-jl-simulating-dna-sequencing-experiments/21736)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 6\
**Last updated:** [May 7, 2019, 3:00pm UTC](https://discourse.julialang.org/t/ann-pseudoseq-jl-simulating-dna-sequencing-experiments/21736 "2019-05-07T15:00:24Z")

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Hi Everyone, I’d like to announce a package I’ve been working on for my research group here at the Earlham Institute, (the first full julia project… I think I’m getting to them :wink: ) that is currently close to releas…

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## [Efficient memory representation of sequences with few mutations](https://discourse.julialang.org/t/efficient-memory-representation-of-sequences-with-few-mutations/23466)

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**Author:** [@e3c6](https://discourse.julialang.org/u/e3c6)\
**Replies:** 9\
**Last updated:** [May 1, 2019, 11:04am UTC](https://discourse.julialang.org/t/efficient-memory-representation-of-sequences-with-few-mutations/23466 "2019-05-01T11:04:14Z")

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I have a dataset which consists of a wild-type sequence and many (\\sim10^7 or more) mutated sequences which differ from the wild-type in only a few positions. I want to represent this efficiently in memory, by storing th…

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## [Does Bio support EMBL and/or IMGT/HLA format ?](https://discourse.julialang.org/t/does-bio-support-embl-and-or-imgt-hla-format/22541)

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**Author:** [@zimoun](https://discourse.julialang.org/u/zimoun)\
**Replies:** 7\
**Last updated:** [April 1, 2019, 5:03pm UTC](https://discourse.julialang.org/t/does-bio-support-embl-and-or-imgt-hla-format/22541 "2019-04-01T17:03:28Z")

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Dear, I am not able to find in the doc if the metapackage Bio supports the format EMBL and/or the specific one about HLA database \[1\] (hla.dat). The wiki \[2\] mentions EMBL but is it accurate ? Thank you in advance for…

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## ["A Comparison of Three Programming Languages for a Full-Fledged Next-Generation Sequencing Tool" selects...Go?](https://discourse.julialang.org/t/a-comparison-of-three-programming-languages-for-a-full-fledged-next-generation-sequencing-tool-selects-go/21126)

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**Author:** [@jballanc](https://discourse.julialang.org/u/jballanc)\
**Replies:** 5\
**Last updated:** [February 25, 2019, 5:40pm UTC](https://discourse.julialang.org/t/a-comparison-of-three-programming-languages-for-a-full-fledged-next-generation-sequencing-tool-selects-go/21126 "2019-02-25T17:40:09Z")

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Was wondering if anyone has had a chance to look at this paper posted to bioRxiv yesterday? I’ve only just briefly skimmed the paper and associated code, but I find the results…interesting. The authors appear to have tak…

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## [Package for genome graphics?](https://discourse.julialang.org/t/package-for-genome-graphics/20550)

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**Author:** [@aalexandersson](https://discourse.julialang.org/u/aalexandersson)\
**Replies:** 11\
**Last updated:** [February 21, 2019, 1:27am UTC](https://discourse.julialang.org/t/package-for-genome-graphics/20550 "2019-02-21T01:27:14Z")

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Are there any graphing capabilities in Julia 1.x specifically for genomics (“genome graphs”), for example a genome viewer? Ben Ward illustrated the Julia package GenomeBrowsers in his presentation at JuliaCon 2018. It h…

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## [Support for cancer data in GeneticVariation?](https://discourse.julialang.org/t/support-for-cancer-data-in-geneticvariation/18601)

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**Author:** [@aalexandersson](https://discourse.julialang.org/u/aalexandersson)\
**Replies:** 3\
**Last updated:** [December 13, 2018, 9:20am UTC](https://discourse.julialang.org/t/support-for-cancer-data-in-geneticvariation/18601 "2018-12-13T09:20:48Z")

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I want to try to use Julia for analyzing cancer genomics data but I am not sure how. BioJulia seems to cover the basics, and I have contacted Julia Computing for info about JuliaRun and JuliaDB. Genomics data are increa…

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## [Finding new packages and docs](https://discourse.julialang.org/t/finding-new-packages-and-docs/10417)

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**Author:** [@phaverty](https://discourse.julialang.org/u/phaverty)\
**Replies:** 11\
**Last updated:** [June 14, 2018, 3:52pm UTC](https://discourse.julialang.org/t/finding-new-packages-and-docs/10417 "2018-06-14T15:52:19Z")

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It looks like the Bio.jl documentation and such is moving from BioJulia · GitHub to https://biojulia.net/. I that right? Some cross-links and explanation would be very helpful. The “not for use with Julia 0.6” warning o…

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## [Is BioJulia team maintaining the IntervalTree package regularly?](https://discourse.julialang.org/t/is-biojulia-team-maintaining-the-intervaltree-package-regularly/10173)

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**Author:** [@sambitdash](https://discourse.julialang.org/u/sambitdash)\
**Replies:** 24\
**Last updated:** [April 7, 2018, 6:34pm UTC](https://discourse.julialang.org/t/is-biojulia-team-maintaining-the-intervaltree-package-regularly/10173 "2018-04-07T18:34:14Z")

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Hi BioJulia Team, Just wanted to check if this team is actively maintaining the IntervalTree package. I have raised a few issues and submitted a PR today. Will request quick turnaround or a time line when you can do so.…

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## [Using bgzipped VCF files with GeneticVariation.jl](https://discourse.julialang.org/t/using-bgzipped-vcf-files-with-geneticvariation-jl/5187)

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**Author:** [@weinstockj](https://discourse.julialang.org/u/weinstockj)\
**Replies:** 3\
**Last updated:** [August 3, 2017, 7:46pm UTC](https://discourse.julialang.org/t/using-bgzipped-vcf-files-with-geneticvariation-jl/5187 "2017-08-03T19:46:41Z")

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I’m interested in using GeneticVariation.jl to work with VCF files. My VCF files are compressed with bgzip and are indexed using tabix. I’m looking at the documentation for reading in VCF files here: https://github.com/…

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## [Genomic Interval Metadata & Annotation](https://discourse.julialang.org/t/genomic-interval-metadata-annotation/4721)

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**Author:** [@snystrom](https://discourse.julialang.org/u/snystrom)\
**Replies:** 9\
**Last updated:** [July 21, 2017, 2:24am UTC](https://discourse.julialang.org/t/genomic-interval-metadata-annotation/4721 "2017-07-21T02:24:45Z")

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Hi, Pretty new to Julia but looking forward to its continued growth and use for genomic data. Given that the current BioJulia documentation is a bit sparse, I wanted to get the opinion of people who are more familiar wi…

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## [BigWig Reader](https://discourse.julialang.org/t/bigwig-reader/4677)

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**Author:** [@PoisonAlien](https://discourse.julialang.org/u/PoisonAlien)\
**Replies:** 5\
**Last updated:** [July 7, 2017, 3:00am UTC](https://discourse.julialang.org/t/bigwig-reader/4677 "2017-07-07T03:00:29Z")

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Hi, Before julia 0.6, I would read BigWig files without any problem BigWig.Reader(open("foo.bw")) but after the update, BigWig.Reader seems to be missing. This is the error I am getting: ERROR: LoadError: type DataTy…

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## [BioJulia Package: BioSequences.jl](https://discourse.julialang.org/t/biojulia-package-biosequences-jl/4197)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 1\
**Last updated:** [June 10, 2017, 4:58pm UTC](https://discourse.julialang.org/t/biojulia-package-biosequences-jl/4197 "2017-06-10T16:58:16Z")

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I am pleased to announced v0.5.0 of BioSequences.jl is released. https://github.com/BioJulia/BioSequences.jl

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## [Stuck on BAMWriter](https://discourse.julialang.org/t/stuck-on-bamwriter/1671)

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**Author:** [@amckay1](https://discourse.julialang.org/u/amckay1)\
**Replies:** 4\
**Last updated:** [January 25, 2017, 4:52pm UTC](https://discourse.julialang.org/t/stuck-on-bamwriter/1671 "2017-01-25T16:52:57Z")

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Looking for example code for wrapping with BGZFStream

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## [BioArgParse.jl](https://discourse.julialang.org/t/bioargparse-jl/959)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 0\
**Last updated:** [December 14, 2016, 11:54pm UTC](https://discourse.julialang.org/t/bioargparse-jl/959 "2016-12-14T23:54:32Z")

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I’ve been making scripts/packages with BioJulia packages which read in command line arguments, and I had to write some custom functions to take strings from command line and make Bio.jl types. Well, I’m lazy, ArgParse.jl…

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## [Use of this platform for Bio.jl - Am I doing this right?](https://discourse.julialang.org/t/use-of-this-platform-for-bio-jl-am-i-doing-this-right/167)

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**Author:** [@kevbonham](https://discourse.julialang.org/u/kevbonham)\
**Replies:** 5\
**Last updated:** [November 8, 2016, 11:28am UTC](https://discourse.julialang.org/t/use-of-this-platform-for-bio-jl-am-i-doing-this-right/167 "2016-11-08T11:28:04Z")

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Branching from a conversation on gitter (starting about here) on the uses of Discourse vs other platforms. I think the distinction between Gitter and Discourse is clear, at least to me. There’s value in extemporaneous c…

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## [BioJulia Package: Bio.jl](https://discourse.julialang.org/t/biojulia-package-bio-jl/117)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 5\
**Last updated:** [November 6, 2016, 5:28pm UTC](https://discourse.julialang.org/t/biojulia-package-bio-jl/117 "2016-11-06T17:28:31Z")

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Bioinformatics and Computational Biology Infrastructure for Julia https://biojulia.github.io/Bio.jl As the flagship package of the BioJulia organisation, Bio.jl provides core julia modules containing efficient data type…

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