Tag: github

Jupyter notebook not loading the correct virtual environment

We deployed Jupyterhub in Kubernetes using the helm chart , the chart version is 0.9.0 github.com/jupyterhub/zero-to-jupyterhub-k8s/tree/main/jupyterhub zero-to-jupyterhub.readthedocs.io/en/latest/jupyterhub/installation.html Users creating virtual environments using the terminal and created kernals as well, But when they accessing the jupyter notebook using the newly created kernal and run the command !conda info It is not…

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fix checkpatch.pl struct should normally be const — DRI Development

Hi Uri, Thank you for the patch! Yet something to improve: [auto build test ERROR on staging/staging-testing] url: github.com/intel-lab-lkp/linux/commits/Uri-Arev/staging-fbtft-fix-checkpatch-pl-struct-should-normally-be-const/20220520-012948 base: git.kernel.org/pub/scm/linux/kernel/git/gregkh/staging.git 4d0cc9e0e53e9946d7b8dc58279c62dfa7a2191b config: arm64-randconfig-r011-20220519 (download.01.org/0day-ci/archive/20220520/202205200821.nJQ0IfFt-lkp@xxxxxxxxx/config) compiler: clang version 15.0.0 (github.com/llvm/llvm-project e00cbbec06c08dc616a0d52a20f678b8fbd4e304) reproduce (this is a W=1 build): wget raw.githubusercontent.com/intel/lkp-tests/master/sbin/make.cross -O ~/bin/make.cross chmod +x ~/bin/make.cross # install arm64 cross compiling tool…

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Issue with certificates when performing mbedtls handshake with AWS – AWS

Hello, We want our device (STM32-F446RE running FreeRTOS + SIM7000G modem) to communicate to the AWS cloud. We are trying to follow the Cellular Interface Library Demo, in particular following the diagram We are using coreMQTT, MbedTLS 2.16 libraries, the amazon communication interface implementation for UART, and amazon UART API…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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GitHub – akonecny/Bulk-RNAseq-Tumor_vs_Inflamed: TBD

GitHub – akonecny/Bulk-RNAseq-Tumor_vs_Inflamed: TBD This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in…

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clara-parabricks/NVIDIA-Clara-Parabricks-Somatic-Variant-Calling-AWS-Blog: AWS Blog (Somatic Variant Calling )

GitHub – clara-parabricks/NVIDIA-Clara-Parabricks-Somatic-Variant-Calling-AWS-Blog: AWS Blog (Somatic Variant Calling ) This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your…

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Recent questions tagged fasta – Q&A

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

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Visualizing Transcript Structure and Annotation using ‘ggplot2’ version 0.99.8 from GitHub

The goal of ggtranscript is the simplify the process of visualizing transcript structure and annotation. To achieve this, ggtranscript introduces 5 new geoms (geom_range(), geom_half_range(), geom_intron(), geom_junction() and geom_junction_label_repel()) as well as several helper functions. As a ‘ggplot2’ extension, ggtranscript inherits ‘ggplot2’s familiarity and flexibility, enabling users to intuitively adjust…

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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vineethk57/Bank-Note-Authentication: Kaggle problem is converted into an end to end project.

GitHub – vineethk57/Bank-Note-Authentication: Kaggle problem is converted into an end to end project. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window….

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Programmer or Software Developer in Bioinformatics

Job:Programmer or Software Developer in Bioinformatics 0 Dr. Vikas Bansal’s research group (bansal-lab.github.io) in the School of Medicine at the University of California San Diego is looking for a programmer or software developer to advance the development of computational tools and methods for human genome analysis. Research in the group…

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GitHub – newtonsgrandson/titanic-prediction: Kaggle Titanic Competition

GitHub – newtonsgrandson/titanic-prediction: Kaggle Titanic Competition This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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BenchSci hiring Bioinformatics Engineer (Remote) in Toronto, Ontario, Canada

BenchSci’s vision is to bring novel medicine to patients 50% faster by 2025. We’re achieving it by empowering scientists with the world’s most advanced biomedical artificial intelligence. Backed by F-Prime, Gradient Ventures (Google’s AI fund), and Inovia Capital, our platform accelerates science at 15 top-20 pharmaceutical companies and over 4,300…

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python – Pymc3 install issues on windows 10

So I downloaded pymc3 (uninstalled and reinstalled a few times) and every time I try to import pymc3 into a jupyter notebook I get some kind of error. I am guessing that I am having an issue with how I am installing Pymc3, I followed this tutorial: github.com/pymc-devs/pymc/wiki/Installation-Guide-(Windows). After my…

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Mbedtls Application On Tcp

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

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archinetai/surgeon-pytorch: A library to inspect itermediate layers of PyTorch models.

GitHub – archinetai/surgeon-pytorch: A library to inspect itermediate layers of PyTorch models. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload…

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which of the following are the prerequisite packages for scikit-learn?

Mohammed Guys, does anyone know the answer? get which of the following are the prerequisite packages for scikit-learn? from screen. Installing scikit There are different ways to install scikit-learn: Install the latest official release. This is the best approach for most users. It will provide a stable version and pre-built…

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On a reference pan-genome model (Part II)

12 July 2019 I wrote a blog post on a potential reference pan-genome model. I had more thoughts in my mind. I didn’t write about them because they are immature. Nonetheless, a few readers raised questions related to my immature thoughts, so I decide to add this “Part II” as…

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dyxstat/HiFine: HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs

GitHub – dyxstat/HiFine: HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab…

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DNA sequencing with Python | Python | GitHub | Bioinformatics

Hello, i need to add a step into a script (find attached). The step is DNA sequencing with a Python library, for example: [login to view URL] [login to view URL] [login to view URL] You can find many on Github. Thanks Skills: Python, GitHub, Bioinformatics See more: need classified…

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Hard filtering on GATK HaplotypeCaller giving multiple warnings

I’m using this pipeline for deriving variants from RNA sequencing data: github.com/modupeore/VAP which uses specific versions of various tools, including HaplotypeCaller from GATK (v3.8-0-ge9d806836). The final step is a set of hard filters on the called variants (applied using VariantFilter), but looking at the log files, there are a lot…

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[Solved] ggplot with 2 y axes on each side and different

Sometimes a client wants two y scales. Giving them the “flawed” speech is often pointless. But I do like the ggplot2 insistence on doing things the right way. I am sure that ggplot is in fact educating the average user about proper visualization techniques. Starting with ggplot2 2.2.0 you can…

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Reproduce incorrect goa generation of MapOf in OpenAPI body

goa version 3.7.2 Design The field name anyobject with Attribute MapOf(String, Any) should describe a map of string to any unknown value. For HTTP requests, the field anyobject can be sent like the following (i.e. any json object): { “anyobject”: { “testkey”: 10, “test1”: “testval”, “myarr”: [ { “nestedk”: {…

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Ubuntu Manpage: Bio::Tools::Seg – parse “seg” output

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Seg – parse “seg” output SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => ‘seg.fasta’); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, ” is low complexity\n”; } } DESCRIPTION “seg” identifies low-complexity regions on a protein sequence. It is…

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Minimap2 detects too many 16S sequences in metagenome

16S is a very conserved sequence, which is why it’s used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which is built around the idea that matching scattered subsequences within a sequence is good enough for identifying matches…

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CRISPR-VAE: A Method for Explaining CRISPR/Cas12a Predictions, and an Efficiency-aware gRNA Sequence Generator

Abstract Deep learning has shown great promise in the prediction of the gRNA efficiency, which helps optimize the engineered gRNAs, and thus has greatly improved the usage of CRISPR-Cas systems in genome editing. However, the black box prediction of deep learning methods does not provide adequate explanation to the factors…

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GitHub – ErasmusMC-Bioinformatics/TTT

GitHub – ErasmusMC-Bioinformatics/TTT This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Brew Conda Recipes

conda-forge community driven packaging for conda Recipes Details: About conda-forge. conda-forge is a GitHub organization containing repositories of conda recipes. Thanks to some awesome continuous integration providers (AppVeyor, Azure Pipelines, CircleCI and TravisCI), each repository, also known as a feedstock, automatically builds its own recipe in a clean and repeatable…

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Learn to draw with Nature Genetics: a simple example of R language ggplot2 drawing a world map

Whole genome resequencing of 445 Lactuca access requests the household history of cultivated lettuce image.png The data of this paper is public. We can try to reproduce the graph used to display the data in the paper with the public data. The first figure uses a map to show the…

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How to link GCP VM disks allocated by dynamic pvc-HEXHEXHEX and `claim-username` again after irrevocably losing all kubernetes yaml? – Zero to JupyterHub on Kubernetes

TL;DR I destroyed my claim-usernames on a prod cluster deployed using current z2jh, and have a mob of nervous scientists scared they lost their data… how do I go about rebinding a hundred disk-HEXHEX GCP VM disks to the appropriate jupyterhub users? In the process of finally deploying / converting…

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Foundations of Git connectivity with RStudio

Good ay all, R-Ladies has another educational webinar on how to use Git. Gracielle Higino will cover foundations of version control, useful git commands and connections with RStudio. Saturday, April 30, 2022 10:00 AM to 11:30 AM SAST passcode:   000111 Gracielle is an open science enthusiast and advocate. Her research…

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ebi-wp/sss_json_schema: JSON schema for EBI’s Job Dispatcher sequence similarity search outputs

GitHub – ebi-wp/sss_json_schema: JSON schema for EBI’s Job Dispatcher sequence similarity search outputs This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window….

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There is no speed up with trt model compared with pytorch – TensorRT

Description After I convert my pth model to onnx to trt, the result shows no speedup, even slower… Environment TensorRT Version: 8.4.0GPU Type: Tesla T4Nvidia Driver Version: 460.106.00CUDA Version: 10.2CUDNN Version: 8.1.1Operating System + Version: ubuntu 18.04Python Version (if applicable):TensorFlow Version (if applicable):PyTorch Version (if applicable):Baremetal or Container (if container…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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3 arguments passed to .Internal(is.unsorted) which requires 2 #95

Kevinrue I am getting this error, using R 4.2.0 and Bioconductor 3.15: library(scRNAseq) > sce <- HermannSpermatogenesisData() […] Error in ..Internal(is.unsorted(x, FALSE, FALSE)) : 3 arguments passed to .Internal(is.unsorted) which requires 2 I’ve chased the issue down to this line (and the next) github.com/Bioconductor/S4Vectors/blob/338534bfb5fb6ada3f2abc144017bc8ce0aab6c3/R/isSorted.R#L149 That’s as far as I managed…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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GitHub – mjfrigaard/ggplot2-graph-gallery: ggplot2 graph gallery

GitHub – mjfrigaard/ggplot2-graph-gallery: ggplot2 graph gallery This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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RStudio AI Weblog: pins 0.4: Versioning

A new version of pins is available on CRAN today, which adds support for versioning your datasets and DigitalOcean Spaces boards! As a quick recap, the pins package allows you to cache, discover and share resources. You can use pins in a wide range of situations, from downloading a dataset…

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[Bug 1960449] Autopkgtest regression report (docker.io/20.10.12-0ubuntu2~20.04.1)

All autopkgtests for the newly accepted docker.io (20.10.12-0ubuntu2~20.04.1) for focal have finished running. The following regressions have been reported in tests triggered by the package: golang-github-fsouza-go-dockerclient/1.6.0-2 (arm64, amd64, ppc64el, s390x, armhf) golang-github-openshift-imagebuilder/1.1.0-2 (arm64, amd64, ppc64el, s390x, armhf) ubuntu-fan/0.12.13 (arm64, amd64, ppc64el, s390x) Please visit the excuses page listed below and…

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L-BFGS-B needs finite values of ‘fn’

Let me preface this with the admission that I am not an “expert” here by any means, which means I’m learning as I’m going. I have been tasked with the analysis of high dimensional (spectral) flow cytometry data with 32 parameters (time, six linear parameters (FSC and SSC) and 24…

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Polyphen2, Sift, etc filter-based annotation with annovar

use dbnsfp42a, which includes sift, polyphen and dozens of other scores. On Wed, Aug 25, 2021 at 8:32 PM BeeSam-code ***@wrote: Hi, Could someone help me figure out the correct command for filter-based annotation using polyphen2 and sift? Without the ljb23 files, I’m not sure how to approach this. —…

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Genomic Mate Selection version 0.2.0 from GitHub

Predict the usefulness of a cross. Multi-trait selection index mean and variance prediction based on parental haplotypes, a genetic map, and marker effects. Implement cross-validation procedures to estimate the accuracy predicting the performance (breeding value, total genetic value including dominance) of previously unobserved individuals as well as cross means and…

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moshi4/ANIclustermap: A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

GitHub – moshi4/ANIclustermap: A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with…

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Building custom hg38 – alt contigs

I am exploring modifications of hg38 like these: github.com/mebbert/Dark_and_Camouflaged_genes Starting from the regular bcbio hg38 data installation Masking hg38.fa using bedtools maskfasta Generating indexes using bcbio_setup_genome.py for seq and bwa as described in the manual The bwa directory then contains ├── bwa │   ├── hg38_masked.fa.amb │   ├── hg38_masked.fa.ann │   ├──…

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Create a generator for SciRuby gems

I like the idea, we must define a small set of specifications. I have a ready to go version in a Dev branch which uses rails style commands and let devs upgrade the library to a railsengine , web is behind the corner Il 23/ott/2013 18:50 “Pjotr Prins” [email protected] ha…

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adRn-s/ukbbgwas – githubhot

Explore SNVs associations with traits of UK BioBank. GWAS study results where made publicly available courtesy of Neale’s Lab on August 1st, 2018. For more information please visit: www.nealelab.is/uk-biobank INSTALL In R: devtools::install_github(“adRn-s/ukbbgwas”). DEV(s) Dependencies Mandatory and optional dependencies can all be handled with bioconda. Here’s a complete YAML specification…

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Keep IUC Galaxy bedtools tool wrappers in sync with the command line bedtools releases

For example, as of the time of the writing, IUC Galaxy bedtools still uses only the command line options available in the release v2.28.0 (Mar 23, 2019): github.com/galaxyproject/tools-iuc/commit/2962180c31dea5883b2ee529fe26b51c4dbc4d36 But the main (this) bedtools repo has already the release v2.29.2 (Dec 17, 2019): github.com/arq5x/bedtools2/releases/tag/v2.29.2 IUC Galaxy bedtools are widely used. It…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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Implement tests with pytest-workflow – githubhot

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs. cf. github.com/nf-core/tools/issues/605, github.com/nf-core/rnaseq/pull/546, github.com/nf-core/sarek/tree/dev/tests Testing scenarios: Run pipeline with more than one file different parameter combinations different filenames and folder structures for cellranger run subworkflows with and without index different protocols, if we manage…

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dx: error: unrecognized arguments: running swiss army knife plink2

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

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juharris/train-pytorch-in-js: Convert a PyTorch model to train it in JavaScript using ONNX Runtime Web

GitHub – juharris/train-pytorch-in-js: Convert a PyTorch model to train it in JavaScript using ONNX Runtime Web This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another…

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AutoDock Zn forcefield – githubhot

Yes 🙂 We have recently made the AD4Zn forcefield available in Vina and wrote this tutorial: autodock-vina.readthedocs.io/en/latest/docking_zinc.html The associated scripts are available in the Vina repository: github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/autodock_scripts You can follow steps 1, 2, and 3 from that tutorial and then instead of running Vina you run AutoDock-GPU: autodock-gpu –lfile 1s63_ligand.pdbqt…

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Description, Programming Languages, Similar Projects of Ggtree

🎄Visualization and annotation of phylogenetic trees 206 Projects Similar to Ggtree Tidytuesday 📊 My contributions to the #TidyTuesday challenge Tracklytics ✔️ Annotation based tracking handler with aspect oriented programming Mirador An open-source, web-based ‘multi-up’ viewer that supports zoom-pan-rotate functionality, ability to display/compare simple images, and images with annotations. S Mall…

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JupyterHub apiUrl detection fails when hub.baseUrl is set

The Jupyterhub helm chart includes a hub.baseUrl for serving the hub under a path other than /, e.g. /jupyter/. I believe this breaks the automatic API setting at github.com/dask/dask-gateway/blob/7d1659db8b2122d1a861ea820a459fd045fc3f02/resources/helm/dask-gateway/templates/gateway/configmap.yaml#L97. I’m not sure if the baseUrl is available where that code is running, so it may be hard to detect the…

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golang-github-albenik-go-serial: autopkgtest regression on ppc64el: undefined: unix.TCGETS2

Source: golang-github-albenik-go-serial Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of golang-github-albenik-go-serial the autopkgtest of golang-github-albenik-go-serial fails in testing when that autopkgtest is run with the binary packages of golang-github-albenik-go-serial from unstable. It passes when run with only packages from testing. In tabular form:…

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StefanieGrosser/Kea_RH2opsin: This repository contains code used for the analyses described in Grosser et al. “Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control”

GitHub – StefanieGrosser/Kea_RH2opsin: This repository contains code used for the analyses described in Grosser et al. “Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control” This commit does not belong to any branch on this repository, and may belong to a fork outside…

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R package with CRAN and Bioconductor dependencies

The short answer: setRepositories(ind=1:2) tl;dr The documentation for setRepositories tells us that the “default list of known repositories is stored in the file ‘R_Home/etc/repositories’”. We can track this down a couple of ways, but for convenience, let’s read the table of repositories into R (this will cut off all of…

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Bioinformatics Scientist – GWAS – Invitae

Invitae is a rapidly growing, purposeful company. Our mission is to empower doctors and patients with genetic information to help them make informed medical decisions at all stages of life. The Integrated Risk Assessment Platform plays a meaningful role in rapidly growing our understanding of genomic health and personalized medicine….

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GitHub – pymc-devs/pymc_resources: PyMC3 educational resources

GitHub – pymc-devs/pymc_resources: PyMC3 educational resources This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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Python JupyterHub Developer at Pachyderm

Posted on: 03/22/2022 Location: (REMOTE) full time Crunchbase | Original Source Tags: jupyter github ml typescript docker kubernetes aws javascript python **About Pachyderm** At Pachyderm, we’re building an open-source enterprise-grade data science platform that lets you deploy and manage multi-stage, language-agnostic data pipelines while maintaining complete reproducibility and provenance. If…

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Tutorial: How to Connect Jupyter Notebooks to Ocean for Apache Spark – The Spot by NetApp Blog

Jupyter Notebook is a web-based interactive computational environment for creating notebook documents. It supports programming languages – such as Python, Scala, R – and is largely used for data engineering, data analysis, machine learning, and further interactive, exploratory computing. Think of notebooks like a developer console or terminal, but with…

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Parsing error(s): The input OpenAPI file is not valid for the OpenAPI specification #2770 | Support Center

ABP Framework version: v5.1 UI type: MVC DB provider: EF Core / MongoDB Tiered (MVC) or Identity Server Separated (Angular): yes / no Exception message and stack trace: Steps to reproduce the issue:” Add new solution add the Page with CURD operation using ABP Suite When we are validating the…

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Installation

🤗 Accelerate is tested on Python 3.6+, and PyTorch 1.6.0+. You should install 🤗 Accelerate in a virtual environment. If you’re unfamiliar with Python virtual environments, check out the user guide. Create a virtual environment with the version of Python you’re going to use and activate it. Now, if you…

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Assist in drug research and development, accelerate alphafold training at low cost from 11 days to 67 hours, and accelerate reasoning 11 times

AlphaFold By Science and Nature The selection of 2021 year The top ten scientific breakthroughs . LuChen technology and Huashen Zhiyao jointly open source AlphaFold Training reasoning acceleration scheme FastFold, take GPU Optimization and large model training technology are introduced AlphaFold The training and reasoning of , Will succeed AlphaFold…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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An R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data

Overview of protti functions. protti can be used on the output of any software package for quantitative analysis of bottom-up proteomics experiments and provides a flexible set of functions for quality control, as well as data pre-processing, data analysis and data interpretation. Credit: Bioinformatics Advances (2021). DOI: 10.1093/bioadv/vbab041 A recent…

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HPC-AI’s FastFold Shortens AlphaFold Training Time from 11 Days to 67 Hours

DeepMind’s AlphaFold 2 grabbed headlines last year by leveraging a transformer-based model architecture to achieve atomic accuracy in protein structure prediction. While the development of deep neural networks (DNNs) has enabled significant performance improvements across a variety of natural language processing and computer vision tasks, AlphaFold’s success showed that DNNs…

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Data Scientist II

Data Scientist II Overview Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the…

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Bioconductor – cytoKernel

DOI: 10.18129/B9.bioc.cytoKernel     Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…

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r – RC Bray function not accepting phyloseq otu_table as argument

I am using James Stegen et al’s code here to calculate an abundance-weighted raup-crick value for my 16S dataset. I load in my phyloseq object then extract the otu_table. I then use the otu_table as the spXsite argument in the function raup_crick_abundance(). My otu_table is available as a dput() below…

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Easily document your Kotlin / Ktor web applications with an OpenAPI DSL

Koa intends to be a fully functional DSL for OpenAPI in Kotlin, including a Ktor plugin to add OpenAPI to your server Kotlin applications. install(Koa) { title = “Koa example” description = “Ktor + OpenAPI (+ Swagger UI) = Koa!” version = “1.2.3” } install(KoaSwaggerUi) // Optional, you can remove…

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Ubuntu Manpage: sambamba-view – tool for extracting information from SAM/BAM files

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

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griffithlab/cloud-workflows: Infrastructure and tooling required to get genomic workflows running in the cloud

GitHub – griffithlab/cloud-workflows: Infrastructure and tooling required to get genomic workflows running in the cloud This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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Installation and set up of R6 rocker object

Installation of current released version from CRAN install.packages(“rocker”) Installation of current development version from GitHub install.packages(“devtools”) devtools::install_github(“nikolaus77/rocker”) Create new rocker database handling object Option 1 db <- rocker::newDB() # New database handling object #> dctr | New object Option 2 db <- rocker::rocker$new() # New database handling object #> dctr…

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jessicastockdale/genomicSIs: Estimate the serial interval distribution with genomic data

GitHub – jessicastockdale/genomicSIs: Estimate the serial interval distribution with genomic data This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to…

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EvanBacon/App-Store-Connect-OpenAPI-Spec: Automatically tracks every copy of the App Store Connect OpenAPI JSON Spec

GitHub – EvanBacon/App-Store-Connect-OpenAPI-Spec: Automatically tracks every copy of the App Store Connect OpenAPI JSON Spec This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab…

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AlphaFold, GPT-3 and How to Augment Intelligence with AI

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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mbedtls_ctr_drbg_reseed_internal() goes straight to z_arm_usage_fault() in mbedtls cert req example – Nordic Q&A – Nordic DevZone

I am trying to get this example program github.com/ARMmbed/mbedtls/blob/mbedtls-2.11.0/programs/x509/cert_req.c (stripped out all the file handling stuff) to run on an nrf9160, but it fails to seed the RNG. I stepped through the mbedtls_ctr_drbg_seed() function, right to the call to mbedtls_ctr_drbg_reseed_internal(), in which the first line is this: if( ctx->entropy_len >…

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dbSNP. er diagram code example

Menu PythonJavascriptLinuxCheat sheet Contact Python Javascript Linux Cheat sheet Contact Example: how to create er diagram in dbeaver DBeaver Er Diagram Tags: Misc Example Related find max in array code examplecomposer specify version code examplegit stash erase code exampleheroku clli code examplehow to plot a scatter plot in python code…

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Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification

Please use this url to cite or link to this publication: hdl.handle.net/1854/LU-8743723 MLA Vromman, Marieke, et al. “CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.” Frontiers in Bioinformatics, 2022, doi:10.3389/fbinf.2022.834655. APA Vromman, M., Anckaert, J., Vandesompele, J., & Volders, P.-J. (2022). CIRCprimerXL: Convenient and High-Throughput PCR Primer…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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python – PyTorch working in Miniconda but “not compiled with CUDA enabled” in PyCharm

I have had quite the journey trying to get PyCharm to use my GPU (NVIDIA GeForce GTX 1080 ti) when running code from this github: github.com/gordicaleksa/pytorch-neural-style-transfer After a whole lot of back and forth setting up CUDA, cuDNN etc., I have finally got PyTorch working (pretty sure) in my Miniconda…

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[slurm-users] Slurm-PMIx integration

Current Slurm official repository branches contain only a limited PMIx integration, primarily constrained to providing support for the traditional put-get exchange of key-value pairs. The support is also restricted to PMIx v3.x releases and below, though this restriction is due to a configure limitation as opposed…

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Post-doctoral Research Fellow job with KINGS COLLEGE LONDON

Job description We are seeking an enthusiastic and experience postgraduate researcher with a PhD in psychiatric genetics or a related field, to work with the Biomarkers and Genomics theme of the NIHR Maudsley BRC.  In this role, you will lead on development of collaborative genetic projects in the BRC, including…

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METASnake: a Snakemake workflow to facilitate…

Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…

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Openapi2apigee NPM | npm.io

0.8.0 • Published 1 year ago Share package openapi-apigee-node-utility openapi2apigee module converts a standard Open API spec (previously known as Swagger) into an Apigee API Proxy bundle and deploys into an Apigee Edge Organization. Now supports OAS v3 as well Pre-requisite Installation You can install openapi2apigee either through npm or…

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HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…

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molmd/mdproptools: A Python package for LAMMPS analysis tools

GitHub – molmd/mdproptools: A Python package for LAMMPS analysis tools This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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bwa-mem2/mm2-fast: Accelerated version of minimap2; up to 1.8x faster

GitHub – bwa-mem2/mm2-fast: Accelerated version of minimap2; up to 1.8x faster This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to…

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ESP32 (Sparkfun ESP32 Thing), Arduino IDE, BLE connections – Networking, Protocols, and Devices

Hello,I’m using a Sparkfun ESP32 Thing with the Arduino framework, trying to connect to and read from services on some W4 beacons – www.mokosmart.com/positioning-beacon-w3-w4/ I can successfully scan for the beacons, get the address, local name etc. however, actually connecting never succeeds – the call to client->connect() never returns. My…

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GitHub – HanifaElahi/AutoML

GitHub – HanifaElahi/AutoML This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another…

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GitHub – freidavid/Genomic-Consequences-of-Speciation-Reversal

GitHub – freidavid/Genomic-Consequences-of-Speciation-Reversal This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another…

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UMD Genome group

An email was successfully sent. MaSuRCA assembler MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and…

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u-net deployment based on tensorrt

The code used in this project is pytorch-Unet, Link to :GitHub – milesial/Pytorch-UNet: PyTorch implementation of the U-Net for image semantic segmentation with high quality images. The project is based on the scale of the original image as the final input , This for data If the size of the…

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Duke doctoral student Devang Thakkar shares inspiration, methodology for creating Wordle archive

Wordle, a daily internet game invented by Josh Wardle where users have six opportunities to guess a random five-letter word, has skyrocketed to popularity since its creation in October 2021. But Wordle resets each day, leaving users out of luck if they wish to go back to previous Wordles they…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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