Tag: github

Bioconductor – planet (development version)

DOI: 10.18129/B9.bioc.planet     This is the development version of planet; for the stable release version, see planet. Placental DNA methylation analysis tools Bioconductor version: Development (3.17) This package contains R functions to infer additional biological variables to supplemental DNA methylation analysis of placental data. This includes inferring ethnicity/ancestry, gestational…

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Bioconductor – metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

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promoter analysis in plant

promoter analysis in plant 0 Hi I did promoter analysis of Hsp20 of one plant species, for which I extract 2kb upstream sequences from each 40 Hsp20 genes that I found in that particular plant species. GAD python script was used to extract this sequences (github.com/bio-projects/GAD / PMID: 32524530) and…

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golang-github-openapi-inflect-devel – Fedora Packages

golang-github-openapi-inflect-devel – Fedora Packages Go library to perform word transformations This is a Go library to perform word transformations like pluralization, singularization, etc. It is a fork of bitbucket.org/pkg/inflect. This package contains the source code needed for building packages that reference the following Go import paths: – github.com/go-openapi/inflect Releases Overview…

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youxianbo/oceanengine-api – Packagist

No description provided (generated by Openapi Generator github.com/openapitools/openapi-generator) This PHP package is automatically generated by the OpenAPI Generator project: API version: 1.0.0 Build package: org.openapitools.codegen.languages.PhpClientCodegen Requirements PHP 5.5 and later Installation & Usage Composer To install the bindings via Composer, add the following to composer.json: { “repositories”: [ { “type”:…

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Variant calling on synthesized DNA

Variant calling on synthesized DNA 1 Hi everyone, I want to ask your opinion on the following subject: Currently, we are producing synthesized DNA with the use of Multiply-Primed Rolling Circle Amplification. This allows for the production of a lot of DNA. Within that DNA there is a region which…

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pyCirclize – Circular visualization in Python

Tool:pyCirclize – Circular visualization in Python 0 pyCirclize is a circular visualization python package implemented based on matplotlib. This package is developed for the purpose of easily and beautifully plotting circular figure such as Circos Plot and Chord Diagram in Python. In addition, useful genome and phylogenetic tree visualization methods…

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Research Fellow, Bioinformatician, Cancer Science Institute, Dr Jason Pitt’s Lab 1 job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow with an emphasis on cancer genomics and bioinformatics is immediately available in the laboratory of Dr. Jason Pitt, which integrates data science and biological expertise to facilitate precision oncology. The Pitt Laboratory achieves this by developing cutting-edge software that allows rapid interrogation and…

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The Biostar Herald for Monday, February 06, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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RagTag patch error–“tuple index out of range”

RagTag patch error–“tuple index out of range” 0 I’m trying to correct a long-read assembly with a short-read scaffold; I’m hoping to fill in the short gaps in the scaffold with the matching long-read sections. The RagTag “patch” function, if I understand correctly, is supposed to do exactly this. I…

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How to set up LTI 1.3 authentication for Jupyterhub – JupyterHub

We want to upgrade our integration of Jupyterhub into our LMS at our university from LTI 1.1 to 1.3. Currently, I am trying to set up ltiauthenticator.lti13.auth.LTI13Authenticator (1.3.0) to work with the saltire LTI platform simulator to exclude any issues coming from the LMS we are using and to have…

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2. QC Raw Data Using FastQC

2. QC Raw Data Using FastQC – HackMD # 2. QC Raw Data Using FastQC ###### tags: `2. Main Steps` `tutorials` `fastQC` > Program required: fastqc ## Setup 1. Once you have retrieved the raw data using `sftp`, you should quality check all the raw `.fastq` files. Here, we use…

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Metagenome-atlas course Finnland 2021 – HackMD

Metagenome-atlas course Finnland 2021 – HackMD # Metagenome-atlas course Finnland 2021 <!– ![Atlas scheme](https://www.oulu.fi/sites/default/files/styles/full_width/public/content-images/Atlas_image_0.jpg?height=5cm) –> <!– ## Get to know Gather.Town and each other **Welcome to this course!** If you haven’t used Gather.Town before, you might need to some time to get acquainted. The vital feature of Gather is that…

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20 generative AI power players in Europe

As excitement around generative AI continues to sweep across the world of tech and startups, it can be difficult to know who to listen to, as just about everyone seems to be an expert on the topic now. So who are the European founders, experts and operators worth knowing in…

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AstraZeneca creates FRAGLER for DNA synthesis

“Plasmids are critical for so many processes in early drug discovery,” says David Öling, associate principal scientist at AstraZeneca.  “From protein production, cell line engineering, CAR-T cell therapy, viral vector generation, therapeutic genome editing, mRNA/vaccine production and more. The time it takes and the cost of producing plasmids for DNA…

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FastAPI – OpenAPI

Enter the following URL in the browser to generate automatically the interactive documentation. 127.0.0.1:8000/docs&#13; FastAPI uses Swagger UI to produce this documentation. The browser will display the following − Click the ‘try it out’ button and then ‘Execute’ button that appears afterward. You can see the Curl command internally…

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Use SageMath with Jupyter · Discussion #4231 · quarto-dev/quarto-cli · GitHub

👎 1 reacted with thumbs down emoji 🎉 1 reacted with hooray emoji ❤️ 1 reacted with heart emoji 👀 1 reacted with eyes emoji 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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InterSystems Open Exchange Applications Digest, January 2023

Hey Developers! Here is a digest of new solutions and applications submitted to the InterSystems Open Exchange in January 2023. General Stats: ✓ 18 new apps in January✓ 620 downloads in January✓ 728 applications all time✓ 23,089 downloads all time✓ 1,996 developers joined New Applications (18) xml-to-udl by Tommy HeydingA tool to…

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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article  Google Scholar  Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…

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mutect2 github – Iskanje Google

Piškotke in podatke uporabljamo za to: zagotavljanje in vzdrževanje Googlovih storitev; spremljanje izpadov delovanja in zaščito pred vsiljeno vsebino, prevarami in zlorabo; merjenje dejavnosti ciljnih skupin in statističnih podatkov glede spletnih mest zaradi razumevanja, kako se uporabljajo naše storitve, in izboljšanja kakovosti teh storitev. Če izberete »Sprejmi vse«, bomo piškotke…

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Recommendations on Dynamic PersistentVolumes on Newer AWS EKS Versions – Zero to JupyterHub on Kubernetes

Hello,I’ve been walking through z2jh documentation which is thorough and great! I set up an AWS EKS cluster with eksctl. I then helm install jupyterhub-2.0.0. The newer versions of EKS tend to use the EBS CSI driver for dynamic PersistentVolume provisioning using the annotation: volume.beta.kubernetes.io/storage-provisioner: kubernetes.io/aws-ebs Your older storage documentation…

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OpenAPI Validation | FortiWeb 6.3.21

OpenAPI Validation The OpenAPI Specification (OAS) defines a standard, language-agnostic interface to RESTful APIs, which allows both humans and computers to discover and understand the capabilities of the service without access to source code, documentation, or through network traffic inspection. When properly defined, you can understand and interact with the…

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Statistical Bioinformatics Analyst – Judge Group, Inc. – Hanover, NJ

Location: Hanover, NJ Salary: $60.00 USD Hourly – $75.00 USD Hourly Description: Our client is currently seeking a Statistical Bioinformatics Analyst**only W2- Fully remote role JOB DESCRIPTION- The primary responsibility of the Statistical Bioinformatics Analyst is to work independently and assume responsibility for data processing, annotation, and statistical analysis for…

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python – Pytorch Runtime Error: “nll_loss_forward_reduce_cuda_kernel_2d_index” not implemented for ‘Int’:

I am trying to implement the TGCN model in this github repo. I have installed all the necessary libraries and packages and my PyTorch is built with CUDA and can detect my Nvidia GPU properly. However, whenever I try and train the model on my local machine I get this…

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PhD fellowship in Bioinformatics/Data Science at the Department of Drug Design and Pharmacology – University of Copenhagen – job portal

Job Portal PhD fellowship in Bioinformatics/Data Science at the Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen We are looking for a highly motivated and ambitious bioinformatician / data scientist for a three-year PhD fellowship commencing 1 May 2023 or as soon as…

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Google Q4 Earnings: AI Invests, Trying To Make Cloud Profitable

Cloud News Wade Tyler Millward February 02, 2023, 07:20 PM EST Google has ‘been investing for awhile, and it‘s clear that the market is ready’ for AI, CEO Sundar Pichai tells analysts. Google’s rough performance in advertising didn’t mask gains made in…

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Can’t access TLJH via a browser – JupyterHub

Hello, I installed TLJH on Ubuntu Server 22.04 (This should work: [removed bc I can only include 2 links] github[dot]com/jupyterhub/the-littlest-jupyterhub/issues/813) on a local machine – following these instructions: The Littlest JupyterHub Installing on your own server Follow this guide if your cloud provider doesn’t have a direct tutorial, or you…

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Opening for a PLUMED developer position – LAMMPS

Dear all, I am sending this email here in case someone in the LAMMPS community is interested. We are opening a full-time position for PLUMED software development based at SISSA (Trieste, Italy). The opening will be for a “Tecnologo” (EP level) position funded by the “Centro Nazionale di Ricerca in…

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docker – “Nbextensions” tab not showing in jupyterhub

can anyone explain how to fix or troubleshoot this issue ? How i understand i already install packages and enable all modules. There are no any issue(at least i can’t see any) with requirements or versions. But after login in jupyterhub, the “Nbextensions” tab is not showing. Output of commands…

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Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

Isolation of pure populations of MuSCs and niche cells by fluorescence-activated cell sorting (FACS) Hindlimb muscles were dissected from young (4–6 weeks old) or aged (22–26 months old) C57BL/6J (Jackson Laboratory, 000664) mice and minced until no visible tissue chunks were visible. Muscle was then digested in a 15 ml Falcon…

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Postdoc in Bioinformatics/Data Science at Department of Drug Design and Pharmacology – University of Copenhagen – job portal

Job Portal Postdoc in Bioinformatics/Data Science at Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen We are looking for a highly motivated and dynamic postdoc for an ambitious bioinformatician / data scientist for a two-year Postdoc with possibilities for extension commencing 1 May…

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How to use gseapy after scanpy?

Hello, I analyzed some data using scanpy and now I want to do some pathway analysis. I have done DE analysis between each cluster and the rest and I want to do the pathway analysis for each cluster but I have a few questions. I initially followed the instructions from…

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Leveraging 16S rRNA data to uncover vaginal microbial signatures in women with cervical cancer

1 Introduction Cervical cancer (CC) remains the fourth most common cancer in women worldwide, with 604,127 new cases in 2020 and more than 341,831 deaths, accounting for nearly 8% of all female cancer-related deaths annually (Sung et al., 2021). This common infection-related neoplasm and its premalignant precursor are caused by high-risk…

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Bioconductor – TSRchitect

DOI: 10.18129/B9.bioc.TSRchitect     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TSRchitect. Promoter identification from large-scale TSS profiling data Bioconductor version: 3.14 In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in…

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Bioinformatics Scientist – GreenLight Biosciences |

GreenLight Biosciences is a mission-driven public-benefit corporation using the power of RNA to tackle some of humanity’s greatest challenges, including pandemics, rare diseases, biodiversity and climate change. ABOUT GREENLIGHT At GreenLight we are working to solve two of the world’s greatest problems: global food insecurity and equal access to vaccines…

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OpenAPI Suite | InterSystems Developer Community

I would like to present my last package OpenAPI-Suite, this is a set of tools to generate ObjectScript code from an OpenAPI specification version 3.0.  In short, these packages allow to:  Generate server-side class.  It’s pretty similar to the generated code by ^%REST but the added value is the version…

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python – convert pytorch MAT model in github reposity to onnx

Unsupported: ONNX export of convolution for kernel of unknown shape. [Caused by the value ‘x.47 defined in (%x.47 : Float(*, *, *, *, strides=[12168000, 67600, 260, 1], requires_grad=0, device=cpu) = onnx::Slice(%874, %875, %876, %877, %878), scope: torch_utils.persistence.persistent_class..Decorator::/torch_utils.persistence.persistent_class..Decorator::synthesis/torch_utils.persistence.persistent_class..Decorator::first_stage/torch_utils.persistence.persistent_class..Decorator::enc_conv.1/torch_utils.persistence.persistent_class..Decorator::conv # /Users/QSoft019/Documents/ai-image-research/MAT/torch_utils/ops/upfirdn2d.py:190:0 )’ (type ‘Tensor’) in the TorchScript graph. The containing node has…

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Jupyterhub is not tracking Keycloak’s sessions – Zero to JupyterHub on Kubernetes

Hello,I have installed the Jupyterhub chart with this chart.yaml: annotations: artifacthub.io/images: | – image: jupyterhub/configurable-http-proxy:4.5.3 name: configurable-http-proxy – image: jupyterhub/k8s-hub:2.0.0 name: k8s-hub – image: jupyterhub/k8s-image-awaiter:2.0.0 name: k8s-image-awaiter – image: jupyterhub/k8s-network-tools:2.0.0 name: k8s-network-tools – image: jupyterhub/k8s-secret-sync:2.0.0 name: k8s-secret-sync – image: jupyterhub/k8s-singleuser-sample:2.0.0 name: k8s-singleuser-sample – image: k8s.gcr.io/kube-scheduler:v1.23.10 name: kube-scheduler – image: k8s.gcr.io/pause:3.8…

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Cost-effective and accurate genomics analysis with Sentieon on AWS

This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…

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Research Fellow, Bioinformatician (Cancer Science Institute of Singapore) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) — with an emphasis on computational cancer genomics — is immediately available at The Cancer Science Institute of Singapore (a part of The National University of Singapore). The postholder will work with the laboratories of Prof. Ashok Venkitaraman, on a project studying the…

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CABSdock issue: DSSP call failing

So, slightly niche but i figure there might be somebody with knowledge of either CABSDock or DSSP. I’ve installed CABSDock, software for docking peptides to proteins, on an ubuntu HPC, following: bitbucket.org/lcbio/cabsdock/src/master/ CABSdock makes use of DSSP, a database of secondary structures for proteins. I installed DSSP following github.com/cmbi/hssp However,…

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deep learning – pytorch implementation using object oriented programming

Closed. This question is opinion-based. It is not currently accepting answers. Want to improve this question? Update the question so it can be answered with facts and citations by editing this post. I am fairly new to pytorch and machine learning and deep learning in…

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Sharing GWAS summary statistics results in more citations

Analyses The GWAS Catalog10 is an established and high-quality repository of curated human GWAS results, providing easy access to summary statistics made public by authors (via curator inclusion or author submission). Its large coverage (400,000+ associations from 5690 publications as of May 2022) and its easy-to-access statistics make it an…

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Bioinformatics Software Engineer II/III – Frederick National Laboratory for Cancer Research

Bioinformatics Software Engineer II/III Job ID: req2614Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses…

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sagemath package currently absent from bookworm

Successfully built Sagemath 9.6 on Bookworm (“apt dist-upgrade”-ed as of 25 January 2023) using the following script. (It seems to have partially built 9.7, and that build might be fixable by an interested someone.) The important piece seems to be ./configure –without-system-gcc –without-system-pari –without-system-singular to avoid the version conflicts reported…

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Downloads | SchedMD

Download the latest stable version of Slurm® slurm-22.05.8.tar.bz2md5: 6a3b5071e36ff05cf06f87abdafb235dsha1: b808bc7b39ec6e7df28af6866127463bc273a0b5 Get Commercial Support The Slurm developers at SchedMD® provide commercial support at competitive prices. Git Repository You can obtain the latest bleeding-edge SchedMD source code by anonymous Git access. git clone github.com/SchedMD/slurm.git For more information about using Git, including tutorials…

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CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA. 2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA. 3 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 4 Curriculum in…

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Research Fellow, Bioinformatician, Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) in computational cancer genomics is immediately available at The Cancer Science Institute of Singapore (The National University of Singapore). This PDF will lead a newly funded project in the laboratory of Dr. Jason Pitt that will explore how germline genetics and cell-of-origin…

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GitHub Has 100 Million Active Users

In his keynote at GitHub Universe 2019, then CEO Nat Friedman announced GitHub had more than 40 million active users and predicted that by 2025 it would have 100 million. That target has already been reached. The announcement was made on January 25, 2023 by Thomas Dohmke  who…

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Bioinformatics Programmerother related Employment listings

Quick Apply Full-time 2 hours ago Full Job Description Job Summary Blue Marble Space Institute for Science (bmsis.org) is seeking a mid-level or senior Bioinformatics Programmer with experience in analyzing large-scale epigenomics, genomics, transcriptomics, proteomics, and metabolomics data to support the GeneLab Project at NASA Ames Research Center (genelab.nasa.gov/).The Bioinformatics…

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Time-dependent microbial shifts during crayfish decomposition in freshwater and sediment under different environmental conditions

Seilacher, A. Arbeitskonzept zur konstruktions-morphologie. Lethaia 3, 393–396 (1970). Google Scholar  Seilacher, B. A., Reif, W.-E. & Westphal, F. Sedimentological, ecological and temporal patterns of fossil Lagerstätten. Philos. Trans. R. Soc. Lond. B 311, 5–23 (1985). ADS  Google Scholar  Gibbons, N. E. & Reed, G. B. The effect of autolysis…

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Reconstruct 2D pmf – User discussions

GROMACS version: 2021.6-Colvars-2022-12-16-devGROMACS modification: NoHere post your questionHi all,I have performed a metadynamics simulation with the Colvars module; I decided to stop it before it got to the final step. In the simulation I biased three CV’s and I have the pmf file for each variable: I was wondering if…

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bwa-meth unrecognized reference name during sam_parse

bwa-meth unrecognized reference name during sam_parse 0 Dear all, I have some Enzymatic methyl sequencing data that I am trying to align using bwa-meth (github.com/brentp/bwa-meth). However, I am encountering the following issue in parsing of the sam file that the aligner is generating when I try to convert the sam…

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Please supply a reference FASTA/GBK/EMBL file with –reference

Error: Please supply a reference FASTA/GBK/EMBL file with –reference 0 Hi, i am trying to run snippy on multiple genomes, however it gives following error like Please supply a reference FASTA/GBK/EMBL file with –reference even after providing the reference file. i don’t understand why it is happen and here is…

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Degree symbol not appearing in ggplot output using sf file – RStudio IDE

I saw this thread github.com/r-lib/ragg/issues/51 . There is there is the reference to this stopgap: ragg.r-lib.org/#use-ragg-with-knitr which did fix the current problem. Is there a more permanent solution? I am using Windows 11 and :RStudio 2022.12.0+353 “Elsbeth Geranium” Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for WindowsMozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML,…

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pytorch FTBFS with Python 3.11 as default version

Hi, I was checking this bug log and realised, that the “Forwarded” field links to an old PR[1] that was merged long before this bug was filed. Checking upstream I realised that the Debian package is lagging behind upstream releases. Could someone please give a status update what might be…

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Running command in docker container results in directly shutting down the docker container

Im currently struggling to run a container and execute a command within this container.I’m trying to use NanoSNP (github.com/huangnengCSU/NanoSNP), which is an image available from dockerhub. After fulling this docker, the following command would be sufficient to run the the container: docker run \ -v “${INPUT_DIR}”:”${INPUT_DIR}” \ -v “${OUTPUT_DIR}”:”${OUTPUT_DIR}” \…

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Epidemiology of Clostridioides difficile infection

Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…

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Bioconductor – IntOMICS (development version)

DOI: 10.18129/B9.bioc.IntOMICS     This is the development version of IntOMICS; to use it, please install the devel version of Bioconductor. Integrative analysis of multi-omics data to infer regulatory networks Bioconductor version: Development (3.17) IntOMICS is an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression (GE),…

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Difference between python and biopython

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

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Could not introduce k8s.io/kube-openapi@master

How to reproduce? cd ${GOPATH}/src/github.com/kubeflow git clone git@github.com:kubeflow/tf-operator.git dep ensure Error message Solving failure: Could not introduce k8s.io/kube-openapi@master, as it requires package k8s.io/klog/v2 from k8s.io/klog, but in version v2.2.0 that package is missing. I’ve done with github.com/kubeflow/tf-operator/issues/1170, but I can’t generate openapi_generated.go $ ./hack/update-codegen.sh # output enerating deepcopy funcs Generating…

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CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

Development of the CusProSe software CustomProteinSearch (CusProSe) is a generic genome mining software, consisting of two distinct but complementary customizable programs: IterHMMBuild and ProSeCDA. IterHMMBuild is an HMM profile building tool based on an iterative learning process. ProSeCDA is a protein search and annotation tool based on user-defined domain architectures….

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AbbVie – 2023 Experiential Internship – Computational Biology/Bioinformatics Intern (Illinois) – Tallahassee, FL

**ABOUT ABBVIE** AbbVie’s mission is to discover and deliver innovative medicines that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people’s lives across several key therapeutic areas: immunology, oncology, neuroscience, eye care, virology, women’s health, and gastroenterology, in…

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Wildcard mapping in AzureAdOAuthenticator.username_map – JupyterHub

ebeb January 25, 2023, 7:53pm #1 Hello, While I can do mapping for individual users from email to local user, I am interested in doing a wildcard mapping for all users for example some regex or * like below:c.AzureAdOAuthenticator.username_map = {‘*@xyz.com’: ‘*’} The expected result is that any username like…

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Low alignment rates for randomly shredded TCR-B library with MixCR

Low alignment rates for randomly shredded TCR-B library with MixCR 1 Hello community, Apologies for cross-posting my query here along with the github page for MixCR. I am hoping to seek help from a wider community here. I recently applied the MiXCR pipeline in ‘shotgun’ mode to analyze my randomly…

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SALMON Index build Process Killed!

SALMON Index build Process Killed! 0 Hello, I was trying to create an decoy-aware index with Salmon (v1.4.0). So I used primary-assembly genome file and transcript file from Gencode library and followed the steps mentioned in the combine-lab.github.io/alevin-tutorial/2019/selective-alignment. Concatenated transcript file with genome to create gentrome.fa.gz. Then tried to create…

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Mutated genes on ctDNA detecting postoperative recurrence presented reduced neoantigens in primary tumors in colorectal cancer cases

Enrolled patients and plasma samples We used WES and RNA sequencing on ten primary tumors and ten postoperative metastatic tumors (the first one of metastases in each case) from ten cases of CRC from our previous study14 and established a cancer panel in the current study (Fig. S3). Therefore, we…

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transformers 4.26.0 – Download, Browsing & More

transformers 4.26.0 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of transformers-4.26.0.tar.gz (24 Jan 16:55, 12404584 Bytes) About: Transformers supports Machine Learning for Pytorch, TensorFlow, and JAX by providing thousands of pretrained models to perform tasks on different modalities such as…

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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7 Best Libraries for Machine Learning Explained

Image by rawpixel.com on Freepik   Key Takeaways   Machine learning libraries are an important tool for building and deploying machine learning models They provide a range of functions and algorithms that can be used to train and test models as well as make predictions and decisions based on data. …

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[BUG][JAVA] Exception in thread “main” java.lang.OutOfMemoryError: Java heap space

Bug Report Checklist Have you provided a full/minimal spec to reproduce the issue? Have you validated the input using an OpenAPI validator (example)? What’s the version of OpenAPI Generator used? Have you search for related issues/PRs? What’s the actual output vs expected output? Description Trying to generate a quite large…

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Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

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Ubuntu Manpage: Bio::Factory::SequenceFactoryI – This interface allows for generic building of sequences

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::Factory::SequenceFactoryI – This interface allows for generic building of sequences in factories which create sequences (like SeqIO) SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my $seqbuilder = Bio::Seq::SeqFactory->new(‘-type’ => ‘Bio::PrimarySeq’); my $seq =…

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6 Great Sites to Host Your Data Science Portfolio

Data Science Portfolio Hosting Platforms Canva Where to Host Your Data Science Portfolio As a data scientist, having a portfolio of your work is essential for showcasing your skills and achievements to potential employers and clients. Data science portfolios contain your best projects and information about your education, experience, and…

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Transition to PyMC3

Sounds great! I seem to remember running into that issue before when I was playing around with pymc3 and thinking of upgrading. It’d be great if you sorted it out! Your changes look good so far. There was one that needs to be reverted (for efficiency). Thanks for contributing!!! Best,…

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cdma-numiscorner/ebay-developer-key-management-api – Packagist

Due to regulatory requirements applicable to our EU/UK sellers, for certain APIs, developers need to add digital signatures to the respective HTTP call. The Key Management API creates keypairs that are required when creating digital signatures for the following APIs: All methods in the <a href=”packagist.org/api-docs/sell/finances/resources/methods&#8221; target=”_blank “>Finances API <a…

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Using genelab-utils to download GeneLab workflows

Using genelab-utils to download GeneLab workflows – HackMD — tags: GeneLab title: Using genelab-utils to download GeneLab workflows — # Using genelab-utils to download GeneLab workflows > New download program added (as of v1.1.03) for downloading GeneLab workflows based on our plan on releasing assets with a zip of specific…

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Ubuntu Manpage: Bio::Tools::Primer::Pair – two primers on left and right side

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Primer::Pair – two primers on left and right side SYNOPSIS use Bio::Tools::Primer::Pair; my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp); # helper functions print “GC percentage different”,$pf->gc_difference(),”\n”; print “product length is “,$pf->product_length,”\n”; DESCRIPTION Primer Pairs represents one primer in a primer pair. This…

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siRNA Details

siRNA Details Display Info:cookie.CK_ISO_CODE.value:sicookie.CK_LANG_CODE.value:encookie.CK_DISPLAY_TYPE.value:pageContext.request:org.apache.struts2.dispatcher.StrutsRequestWrapper@33b9b7aRequest attributes: pageContext.request.scheme:http(not used)syndicationProtocol:httpssyndicationExtensionPrefix:syndicationDisplayType: This product has been added to your favorites list. Go to My Favorites LOADING Gene Symbol: Csdc2 Gene Name: cold shock domain containing C2, RNA binding Gene Aliases: Pippin Chromosome Location: Chr.7: 123168811…

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Bioconductor – MSstatsShiny

DOI: 10.18129/B9.bioc.MSstatsShiny     MSstats GUI for Statistical Anaylsis of Proteomics Experiments Bioconductor version: Release (3.16) MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs….

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an R/Bioconductor package for the inference and analysis of synteny networks

Please use this url to cite or link to this publication: hdl.handle.net/1854/LU-01GP3AHHZ8VR3BTBCPA6FEXGM0 MLA De Almeida Silva, Fabricio, Tao Zhao, Kristian K Ullrich, M Eric Schranz, and Yves Van de Peer. 2023. “Syntenet: An R/Bioconductor Package for the Inference and Analysis of Synteny Networks.” Ed by. Pier Luigi Martelli. Bioinformatics. doi:10.1093/bioinformatics/btac806….

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Andrej Karpathy Launches Advanced NanoGPT

Former Tesla AI head Andrej Karpathy recently released an updated version of minGPT, NanoGPT, a new fast repository for training and fine-tuning medium-sized GPTs. Prior to this, in 2020, he unveiled the minGPT library for the GPT language model to address the existing implementations of GPT on PyTorch.  Check out…

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CP2K version 2023.1 released

Dear CP2K users, we are pleased to announce the release of the CP2K version 2023.1. The CP2K source tarball can be downloaded from:   github.com/cp2k/cp2k/releases/tag/v2023.1 A container image is available on Docker Hub:   hub.docker.com/r/cp2k/cp2k/tags Pre-compiled binaries are still in the making and will be uploaded soon. Further information about…

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Bioconductor – CONSTANd (development version)

DOI: 10.18129/B9.bioc.CONSTANd     This is the development version of CONSTANd; for the stable release version, see CONSTANd. Data normalization by matrix raking Bioconductor version: Development (3.17) Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the…

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Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

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Performance evaluation of six popular short-read simulators

Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71(12):8966–8969 Article  CAS  Google Scholar  Alosaimi S, Bandiang A, van Biljon N, Awany D, Thami PK, Tchamga MSS et…

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Preparing files for picrust with mothur

Dear mothur enthusiasts, A colleague advised me to try and run picrust on my dataset in order to get some functional inference from 16S sequences. He told me to “classify the OTU on GreenGenes” and prepare a biom file. I have tried to follow the commands listed in an earlier…

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go – OpenApi Generator Golang – Adding headers to request ending up in query params how to fix?

I’m trying to generate a go client but the generator won’t recognise a header and won’t let me pass it to the server as a header – instead it’s sent as a query param. info: title: API version: “1.2” servers: – url: example.com paths: /ping: get: summary: Checks if the…

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genbank sequence format

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

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Espressif’s Ali Hassan Shah Walks Through Putting a TinyML Gesture Recognition Model on an ESP32-S3

Espressif’s Ali Hassan Shah has penned a guide to getting started with the company’s ESP-DL TinyML edge AI framework, using it to deploy a gesture recognition model on to an ESP32-S3 microcontroller. “Artificial intelligence transforms the way computers interact with the real world. Decisions are carried by getting data from…

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A high-throughput multispectral imaging system for museum specimens

The two-dimensional nature of many pinned Lepidoptera specimens allows us to omit some technical considerations, such as the variable incident angles that need to be carefully considered when imaging 3D objects, and our multi-spectral imaging rig with its custom designed platform can image both the dorsal and ventral sides of…

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Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

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This Python Library ‘Imitation,’ Provides Open-Source Implementations of Imitation and Reward Learning Algorithms in PyTorch

In areas with clearly defined reward functions, like games, reinforcement learning (RL) has outperformed human performance. Unfortunately, it is difficult or impossible for many tasks in the real world to design the reward function procedurally. Instead, they must immediately absorb a reward function or policy from user feedback. Furthermore, even…

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[slurm-users] How to launch slurm services after installation

Hello, all supported build flags are available with “./configure –help” command. On of them is “–with-systemdsystemunitdir=DIR”, which will allow you to specify the directory for the systemd service files for all Slurm daemons. The most important of the flags is imho the “–prefix”, which sets the installation directory. I’ll describe my build setup shortly…

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StevenRice99/COMP-4730-Project-2: Kaggle Challenges in Representation Learning: Facial Expression Recognition Challenge

GitHub – StevenRice99/COMP-4730-Project-2: Kaggle Challenges in Representation Learning: Facial Expression Recognition Challenge 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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Ontology Development Kit Looks to Harmonize, Streamline Management of Biomedical Semantics

CHICAGO – Nearly seven years after it first appeared online as a beta release, the Ontology Development Kit (ODK) has matured into an open-source software package used by the developers and keepers of dozens of biomedical ontologies. The ODK is meant to implement the principles of the Open Biological and…

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parallel-fastq-dump install failed

parallel-fastq-dump install failed 0 Good morning, I am trying to install parallel-fastq-dump but I failed. And here is what ssh sever say: conda install parallel-fastq-dump Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current…

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No module named ‘upstream_ontologist.tests’ (and more)

Source: lintian-brush Version: 0.134 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of lintian-brush the autopkgtest of lintian-brush fails in testing when that autopkgtest is run with the binary packages of lintian-brush from unstable. It passes when run with only packages from testing. In tabular form:…

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logits to softmax pytorch

A tag already exists with the provided branch name. Join the PyTorch developer community to contribute, learn, and get your questions answered. Space – falling faster than light? We are converting the layers using ReLu and other neural networks. Learn more, including about available controls: Cookies Policy. In addition, the…

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pipeline launch from nf-core website

pipeline launch from nf-core website – input csv bug · Issue #811 · nf-core/sarek · GitHub Labels bug Something isn’t working 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 tab or window….

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