# Biology, Health, and Medicine

**URL:** https://discourse.julialang.org/c/domain/bio/15.md?page=1

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

**Page:** 2

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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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## [DICOM series: Reading, Manipulation and Visualization](https://discourse.julialang.org/t/dicom-series-reading-manipulation-and-visualization/93851)

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**Author:** [@AvinashKotla](https://discourse.julialang.org/u/AvinashKotla)\
**Replies:** 1\
**Last updated:** [February 15, 2023, 4:41pm UTC](https://discourse.julialang.org/t/dicom-series-reading-manipulation-and-visualization/93851 "2023-02-15T16:41:16Z")

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I have a DICOM image series generated from Micro CT scanning. How does one read the series, store the intensity values in a 3D matrix so that data manipulation is possible? var = dcmdir\_parse(“/path/to/dicom/folder/”); …

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## [How do I distinguish the first in pair and second in pair in pair end bam using XAM?](https://discourse.julialang.org/t/how-do-i-distinguish-the-first-in-pair-and-second-in-pair-in-pair-end-bam-using-xam/92536)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 4\
**Last updated:** [January 8, 2023, 3:51pm UTC](https://discourse.julialang.org/t/how-do-i-distinguish-the-first-in-pair-and-second-in-pair-in-pair-end-bam-using-xam/92536 "2023-01-08T15:51:34Z")

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I have a pair end bam. And I want to know whether the record is the first in pair or the second in pair. I use the julia package called XAM.jl. using XAM bamfile="..." reader=open(BAM.Reader,bamfile) mapped\_chr1 = Itera…

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## [Large FASTA datasets?](https://discourse.julialang.org/t/large-fasta-datasets/90786)

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**Author:** [@M-PERSIC](https://discourse.julialang.org/u/M-PERSIC)\
**Replies:** 7\
**Last updated:** [December 15, 2022, 6:21am UTC](https://discourse.julialang.org/t/large-fasta-datasets/90786 "2022-12-15T06:21:59Z")

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Hello! Apologies if this is the wrong place to post this question. I’m playing around with TranscodingStreams and I want to compare the compression of FASTA files with different codecs. I can make my own randomized FAST…

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## [\[ANN\] qtc.jl](https://discourse.julialang.org/t/ann-qtc-jl/90919)

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**Author:** [@AdamWysokinski](https://discourse.julialang.org/u/AdamWysokinski)\
**Replies:** 5\
**Last updated:** [November 28, 2022, 12:10pm UTC](https://discourse.julialang.org/t/ann-qtc-jl/90919 "2022-11-28T12:10:33Z")

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qtc.jl is a small Julia script to calculate the length of corrected QT interval (QTc) using Bazett, Fridericia, Hodges Sagie formulas.

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## [Another question on eachoverlap in GenomicFeatures.jl](https://discourse.julialang.org/t/another-question-on-eachoverlap-in-genomicfeatures-jl/90426)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 3\
**Last updated:** [November 27, 2022, 11:41pm UTC](https://discourse.julialang.org/t/another-question-on-eachoverlap-in-genomicfeatures-jl/90426 "2022-11-27T23:41:29Z")

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using GenomicFeatures using DataFrames col = \[ Interval("chr1", 10628, 10683, '?', "abc") Interval("chr1", 10643, 10779, '?', "abc") Interval("chr1", 10645, 10748, '?', "abc") Interval("chr1", 10648, 10786, '?', "a…

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## [\[ANN\] NeuroJ.jl](https://discourse.julialang.org/t/ann-neuroj-jl/82665)

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**Author:** [@AdamWysokinski](https://discourse.julialang.org/u/AdamWysokinski)\
**Replies:** 9\
**Last updated:** [October 31, 2022, 2:00pm UTC](https://discourse.julialang.org/t/ann-neuroj-jl/82665 "2022-10-31T14:00:50Z")

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Hi, This is the first public release, I’m kinda nervous and excited :slight\_smile: NeuroJ.jl is a Julia package for analyzing of EEG data. Future versions will also process MEG and NIRS data and use MRI data for source…

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## [Exact the sequence of chr1 in XAM.jl](https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 1\
**Last updated:** [October 17, 2022, 1:37pm UTC](https://discourse.julialang.org/t/exact-the-sequence-of-chr1-in-xam-jl/88163 "2022-10-17T13:37:51Z")

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I only want to exact the sequence of chr1 not all. using XAM bamfile="..." reader=open(BAM.Reader,bamfile) for record in reader println(BAM.refname(record)) end This returns all the chromosomes.I just want chr1.But…

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## [Questions about XAM.jl](https://discourse.julialang.org/t/questions-about-xam-jl/86665)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 8\
**Last updated:** [October 4, 2022, 2:12am UTC](https://discourse.julialang.org/t/questions-about-xam-jl/86665 "2022-10-04T02:12:51Z")

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When I used Julia’s package called XAM.jl,I was convinced that it was extraordinarily fast. But when I aligned the reads to the genome and then generated a bam file, how do I restore sequenced reads to undeleted and un…

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## [Reading Leica .lif files in julia](https://discourse.julialang.org/t/reading-leica-lif-files-in-julia/87924)

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**Author:** [@pascal](https://discourse.julialang.org/u/pascal)\
**Replies:** 1\
**Last updated:** [September 29, 2022, 8:56am UTC](https://discourse.julialang.org/t/reading-leica-lif-files-in-julia/87924 "2022-09-29T08:56:38Z")

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Is there way how I can read in .lif files that are generated by Leica microscopes?

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## [ANN - Towards a (Bio)Julia powered Genome Graphs framework](https://discourse.julialang.org/t/ann-towards-a-bio-julia-powered-genome-graphs-framework/27695)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 25\
**Last updated:** [September 24, 2022, 7:01am UTC](https://discourse.julialang.org/t/ann-towards-a-bio-julia-powered-genome-graphs-framework/27695 "2022-09-24T07:01:26Z")

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Hello everyone, the GSoC period for the year is nearly over, and for anyone who was unaware, BioJulia had a student this year: Arda Akdemir has been helping the project under my supervision, working on a de-Bruijn graph …

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## [Some questions about eachoverlap in GenomicFeatures.jl](https://discourse.julialang.org/t/some-questions-about-eachoverlap-in-genomicfeatures-jl/85977)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 4\
**Last updated:** [August 21, 2022, 12:25pm UTC](https://discourse.julialang.org/t/some-questions-about-eachoverlap-in-genomicfeatures-jl/85977 "2022-08-21T12:25:06Z")

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During using the eachoverlap function in GenomicFeatures,I cannot know how to solve this problem. My problem is :if each interval in “col” contains any interval in “hhh” ,I will output interval "col ".Here is the pict…

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## [GenomicVectors.jl](https://discourse.julialang.org/t/genomicvectors-jl/86084)

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**Author:** [@zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)\
**Replies:** 0\
**Last updated:** [August 21, 2022, 11:55am UTC](https://discourse.julialang.org/t/genomicvectors-jl/86084 "2022-08-21T11:55:22Z")

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When I installed the packge named GenomicVectors，I got the error like the picture. When I removed the package XAM,I can install GenomicVectors,however it’s not the newest.It’s 0.4 and I can not install the XMA at al…

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## [\[ANN\] JuliaEpi: Collaborative Computational Epidemiology in Julia](https://discourse.julialang.org/t/ann-juliaepi-collaborative-computational-epidemiology-in-julia/85131)

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**Author:** [@InPhyT](https://discourse.julialang.org/u/InPhyT)\
**Replies:** 4\
**Last updated:** [August 10, 2022, 9:38pm UTC](https://discourse.julialang.org/t/ann-juliaepi-collaborative-computational-epidemiology-in-julia/85131 "2022-08-10T21:38:27Z")

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We’re building an open research community called JuliaEpi to develop an epidemiological modelling ecosystem written in Julia for the design, management, wrangling and quality assessment of multiple data types and sources…

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## [\[ANN\] NTupleKmers.jl](https://discourse.julialang.org/t/ann-ntuplekmers-jl/40474)

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**Author:** [@Ward9250](https://discourse.julialang.org/u/Ward9250)\
**Replies:** 0\
**Last updated:** [May 30, 2020, 4:09pm UTC](https://discourse.julialang.org/t/ann-ntuplekmers-jl/40474 "2020-05-30T16:09:20Z")

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Hi Everyone, Following my earlier murmerings on Kmers and NTuples on Slack and here: Ntuple aggressive specialisation and boxed values I decided to create an experimental package repo on BioJulia that can house my NTu…

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## [Equivalent to Rosetta in Julia](https://discourse.julialang.org/t/equivalent-to-rosetta-in-julia/32168)

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**Author:** [@Seanny123](https://discourse.julialang.org/u/Seanny123)\
**Replies:** 4\
**Last updated:** [June 30, 2022, 10:24am UTC](https://discourse.julialang.org/t/equivalent-to-rosetta-in-julia/32168 "2022-06-30T10:24:43Z")

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I’ve recently started working at a biotech startup. One of the tools used by these types of companies is the macromolecular modelling tool Rosetta. I don’t totally understand Rosetta’s various capabilities/limitations. T…

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## [Morgan Finger print](https://discourse.julialang.org/t/morgan-finger-print/79258)

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**Author:** [@YitaoCai](https://discourse.julialang.org/u/YitaoCai)\
**Replies:** 1\
**Last updated:** [June 27, 2022, 3:50pm UTC](https://discourse.julialang.org/t/morgan-finger-print/79258 "2022-06-27T15:50:26Z")

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Is there any package we can get Morgan Finger print same as rdkit’s AllChem.GetMorganFingerprintAsBitVect(mol, radius=3, nBits=fp\_length) Thank you!

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## [Can we find a DDe's canstant from a table](https://discourse.julialang.org/t/can-we-find-a-ddes-canstant-from-a-table/81676)

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**Author:** [@Achraf\_el\_fadli](https://discourse.julialang.org/u/Achraf_el_fadli)\
**Replies:** 6\
**Last updated:** [May 26, 2022, 12:35pm UTC](https://discourse.julialang.org/t/can-we-find-a-ddes-canstant-from-a-table/81676 "2022-05-26T12:35:33Z")

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for finding a,b,c the most compatible with the model

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## [Memory issues generating a search space from protein sequences](https://discourse.julialang.org/t/memory-issues-generating-a-search-space-from-protein-sequences/80860)

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**Author:** [@candidaorelmex](https://discourse.julialang.org/u/candidaorelmex)\
**Replies:** 20\
**Last updated:** [May 17, 2022, 9:02am UTC](https://discourse.julialang.org/t/memory-issues-generating-a-search-space-from-protein-sequences/80860 "2022-05-17T09:02:25Z")

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Hi, I wrote two functions in order to generate a peptide search space from protein sequences. In the end, I need a dictionary that tells me in which protein I can find a certain peptide in. Now I have two questions ab…

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## [Question about Bayesian Survival Analysis with Cox (proportional hazards) regression method in Julia with Turing](https://discourse.julialang.org/t/question-about-bayesian-survival-analysis-with-cox-proportional-hazards-regression-method-in-julia-with-turing/80672)

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**Author:** [@RyanKuo](https://discourse.julialang.org/u/RyanKuo)\
**Replies:** 6\
**Last updated:** [May 10, 2022, 1:17pm UTC](https://discourse.julialang.org/t/question-about-bayesian-survival-analysis-with-cox-proportional-hazards-regression-method-in-julia-with-turing/80672 "2022-05-10T13:17:11Z")

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Dear All, I am trying to implement Bayesian Survival Analysis with Cox (proportional hazards) regression method in Julia based on the PyMC3 code written by Austin Rochford https://austinrochford.com/posts/2015-10-05-ba…

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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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## [Are there Julia packages for RNA/DNA/protein structure prediction?](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060)

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**Author:** [@BetaQ](https://discourse.julialang.org/u/BetaQ)\
**Replies:** 7\
**Last updated:** [March 18, 2022, 5:39pm UTC](https://discourse.julialang.org/t/are-there-julia-packages-for-rna-dna-protein-structure-prediction/78060 "2022-03-18T17:39:25Z")

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I am doing research about RNA and proteins. Therefore, I am looking for a method to simulate the secondary or 3D structure. I have used some methods based on other programming language constructs. But those methods are n…

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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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## [Medical segmentation framework are you intrested?](https://discourse.julialang.org/t/medical-segmentation-framework-are-you-intrested/77621)

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**Author:** [@Jakub\_Mitura](https://discourse.julialang.org/u/Jakub_Mitura)\
**Replies:** 1\
**Last updated:** [March 9, 2022, 1:33pm UTC](https://discourse.julialang.org/t/medical-segmentation-framework-are-you-intrested/77621 "2022-03-09T13:33:23Z")

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Hello I developed medical image viewer plus annotator based on OpenGL \[1\] And set of CUDA accelerated medical segmentation metrics \[2\] Currently I am working on example of using those two with some user defined CUDA.jl…

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## [Community members currently working on writing Bioconductor packages in Julia?](https://discourse.julialang.org/t/community-members-currently-working-on-writing-bioconductor-packages-in-julia/75993)

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**Author:** [@BioinfoBuggaBoo](https://discourse.julialang.org/u/BioinfoBuggaBoo)\
**Replies:** 4\
**Last updated:** [March 2, 2022, 2:12am UTC](https://discourse.julialang.org/t/community-members-currently-working-on-writing-bioconductor-packages-in-julia/75993 "2022-03-02T02:12:19Z")

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Hi all, Not sure if this is the right section sorry: I’m looking to get involved with people who may be actively working on writing equivalent packages from Bioconductor in Julia. From my own limited experience R havin…

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## [BioJulia OpenCollective](https://discourse.julialang.org/t/biojulia-opencollective/75997)

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**Author:** [@XVilka](https://discourse.julialang.org/u/XVilka)\
**Replies:** 2\
**Last updated:** [February 16, 2022, 5:52pm UTC](https://discourse.julialang.org/t/biojulia-opencollective/75997 "2022-02-16T17:52:46Z")

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Sorry for the annoyance, but I wonder why BioJulia OpenCollective and blog wasn’t updated for years: https://opencollective.com/biojulia As a small backer of the package I hope those money don’t sit idle and help the de…

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## [Molecular mass of proteins and peptides](https://discourse.julialang.org/t/molecular-mass-of-proteins-and-peptides/76439)

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**Author:** [@tp2750](https://discourse.julialang.org/u/tp2750)\
**Replies:** 5\
**Last updated:** [February 14, 2022, 5:10pm UTC](https://discourse.julialang.org/t/molecular-mass-of-proteins-and-peptides/76439 "2022-02-14T17:10:53Z")

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Is there a package that can compute the molecular mass based on an amino acid sequence? MolecularGraph has the machinery, but that appears to be focused on small molecules. I can’t find a method in BioSequences

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## [Missing records in my FASTA file when writing new FASTAs](https://discourse.julialang.org/t/missing-records-in-my-fasta-file-when-writing-new-fastas/74032)

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**Author:** [@Lamma](https://discourse.julialang.org/u/Lamma)\
**Replies:** 3\
**Last updated:** [January 5, 2022, 10:27am UTC](https://discourse.julialang.org/t/missing-records-in-my-fasta-file-when-writing-new-fastas/74032 "2022-01-05T10:27:36Z")

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I have a co-assembly and some alignment data telling me if a reads from a sample that helped spawn that co-assembly align to a contig. I am using this to write a fasta file for that sample. t1 = Threads.@spawn DataF…

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## [Scalable ODE solver for Bayesian multi-type compartmental models](https://discourse.julialang.org/t/scalable-ode-solver-for-bayesian-multi-type-compartmental-models/72845)

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**Author:** [@bernadette-eu](https://discourse.julialang.org/u/bernadette-eu)\
**Replies:** 2\
**Last updated:** [December 10, 2021, 11:43am UTC](https://discourse.julialang.org/t/scalable-ode-solver-for-bayesian-multi-type-compartmental-models/72845 "2021-12-10T11:43:29Z")

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Hello everyone, First time posting here. I provide a lengthy intro to my research problem with hopefully enough details, aiming to discuss scalable solvers for Nonlinear systems of ODES. The question is at the end of th…

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## [Indexing a fasta file with FASTX.jl](https://discourse.julialang.org/t/indexing-a-fasta-file-with-fastx-jl/72457)

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**Author:** [@Lamma](https://discourse.julialang.org/u/Lamma)\
**Replies:** 1\
**Last updated:** [December 2, 2021, 4:18pm UTC](https://discourse.julialang.org/t/indexing-a-fasta-file-with-fastx-jl/72457 "2021-12-02T16:18:02Z")

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I have been informed it is possible to use FASTX.jl to index a file. However I am struggling to do this. I think I am meant to use FASTA:Record() but am unsure how to pass the data to the function. reader = FASTA.Reader…

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