Tag: shell

‘info jupyterhub’ displays the manpage although it suggests ‘info’ to get the full doc

Package: jupyterhub Version: 2.0.0+ds1-2 Severity: normal X-Debbugs-Cc: gkni…@australdx.fr Dear Maintainer, ‘man jupyterhub’ ends with: > The full documentation for jupyterhub is maintained as a Texinfo manual. If the info and jupyterhub programs are properly installed at your site, the command > info jupyterhub > should give you access to the complete manual. although…

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ACENET Basics: Job Scheduling with Slurm Tickets, Fri, 23 Sep 2022 at 10:00 AM

This session teaches participants how to use the Digital Research Alliance of Canada’s queuing environment on the national systems, using the job scheduler Slurm. Learn how the scheduler works, how it allocates jobs, what are reasonable requests to minimize wait time, how to make the best use of the resources…

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Bioinformatics job in Riyadh

Riyadh, Saudi Arabia Center for Genomic Medicine Full time The Center for Genomic Medicine (CGM) plans to expand its IT and bioinformatics teams with experts who will be responsible for maintaining the bioinformatics IT infrastructure and developing, maintaining, and execution of computational pipelines…

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Eyam Vaccines and Immunotherapeutics hiring Bioinformatician in Vancouver, British Columbia, Canada

Postdoctoral Position at Eyam Vaccines and Immunotherapeutics – Bioinformatician  Eyam Vaccines and Immunotherapeutics (Eyam) is seeking an outstanding Bioinformatician. This is a unique opportunity to experience collaborative research with leading industry and academic experts. Under the direction of the Director of Bioinformatics and the Chief Scientific Officer, Dr. Paolo Ribeca…

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[Internship] Bioinformatics Intern, Fall 2022 at Harmonic Discovery (United States)

About Us Based in NYC, Harmonic Discovery is a biotechnology company leveraging biology, medicinal chemistry, and machine learning to create a new generation of therapeutics for oncology and autoimmune disorders. We look for passionate innovators, radical thinkers, and collaborative builders. It’s time to integrate our understanding of biology and chemistry…

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Bioinformatics Analyst in Minneapolis, MN for University of Minnesota, Twin Cities

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in WORLDWIDE

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. This opportunity is…

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Cornell Virtual Workshop: Execution: idev (at TACC)

TACC also offers their idev command (for interactive development) as a convenient way to initiate interactive work on their compute nodes, via Slurm. It works very much like srun and even takes many of the same options. But by making a few assumptions, idev shortens the path for you…

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Postdoc in Computational method development for precision medicine in

Area of research: Scientific / postdoctoral posts Job description: : Discover personalized medical solutions for environmentally triggered diseases to promote a healthier society in a rapidly changing world. The Institute of Computational Biology (ICB) is globally recognised for its innovations in data analysis and modelling of biological systems and diseases,…

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Gene Therapy Delivered via High-Capacity Baculovirus

Some of the newest and most exciting gene therapy technologies share a problem: They’re too bulky. They rely on multiple functional DNA and protein elements that must reach target cells all at the same time, even though they have trouble fitting into the usual delivery vehicles, which include vector systems…

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Bioinformatic jobs in Marina South City Park – July 2022

Bayes–Central Singapore The ideal candidate will have an established track record in the field of structural biology, molecular dynamics and possess a broad base… National Cancer Centre Singapore–Outram We are recruiting Bioinformatics Specialists and Postdoctoral Fellows at the Cancer Discovery Hub, National Cancer Centre Singapore. You… $1,000 – $1,000 per…

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Sr. Bioinformatics-Clinical Database Developer – CBL Path, Inc

Job Functions, Duties, Responsibilities and Position Qualifications: POSITION TITLE:Senior Bioinformatics-Clinical Database Developer STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics EXEMPT STATUS:  Exempt POSITION SUMMARY: Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected…

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‘Self-boosting’ vaccines could soon replace the need for multiple COVID shots

CAMBRIDGE, Mass. — A one-jab, self-boosting vaccine that provides patients with several doses at different times is currently under development. Scientists from the Massachusetts Institute of Technology say the one-shot would provide multiple stages of vaccination thanks to microparticles that release payloads at different intervals. These microparticles resemble tiny coffee…

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How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

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Dimorphic life cycle through transverse division in burrowing hard coral Deltocyathoides orientalis

Transverse division of Deltocyathoides orientalis In this study, we conducted a detailed morphological analysis of an undescribed species and D. orientalis. The results showed that the two species were different in terms of their mode of life (attached vs. free-living) and GCD size (Figs. 3 and 5, Supplementary Table S3)….

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main-i386-default][science/cp2k] Failed for cp2k-9.1.0 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy17.nyi.freebsd.org/data/main-i386-default/p429f3de9bdcd_s2573e6ced9/logs/cp2k-9.1.0.log Build URL: beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p429f3de9bdcd_s2573e6ced9 Log: =>> Building science/cp2k build started at Sat Jun 4…

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Convenience-sized RNA editing | MIT News

Last year, researchers at MIT’s McGovern Institute for Brain Research discovered and characterized Cas7-11, the first CRISPR enzyme capable of making precise, guided cuts to strands of RNA without harming cells in the process. Now, working with collaborators at the University of Tokyo, the same team has revealed that Cas7-11…

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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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Open API Market Size, Trends and Forecast to 2029

New Jersey, United States – The Open API Market report includes the upcoming challenges and opportunities in the market. It ensures a strengthened position in the market and a growing product portfolio by providing all the important details related to the market growth. It reveals some of the key insights and focuses…

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Database Administrator at European Molecular Biology Laboratory (EMBL)

About the team/job In this role you will join an established Database team of database administrators in order to support the ongoing database operations. The main duties for this post are: DBA of MySQL and MongoDB.The Database Team provides day-to-day Database Administration support , database performance tuning and query optimization…

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Description, Programming Languages, Similar Projects of Python-for-Text-Classification

Python for Text Classification with Machine Learning in Python 3.6. Installation Guide Start your environment by picking either pipenv (recommended) or virtualenv. Simple guides are below. Using pipenv Initialize pipenv (setup guide): cd path/to/your/dev/folder mkdir text-classify cd text-classify pipenv install –three After installation of pipenv works, just activate it (same…

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Senior Research Associate, Bioinformatics at Kite Pharma

Job details Job type full-time Full job description Job description At kite pharma we are revolutionizing the treatment for cancers through immunotherapy through novel breakthrough technologyWe have developed and launched best in class car-t therapy yescarta, currently curing patients from previously intractable b-cell malignanciesWe are using our expertise to apply…

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Anthony Nolan hiring Bioinformatics Developer in Swiss Cottage, England, United Kingdom

We’re Anthony Nolan and we save the lives of people with blood cancer who need a stem cell transplant. We’re unique. Thanks to the incredible donors on our register, our pioneering research and our passionate fundraisers, we give the chance of life to three people a day. But we won’t…

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Distributed training on slurm cluster – distributed

chinmay5 (Chinmay5) April 29, 2022, 12:48pm #1 Sorry for the naive question but I am confused about the integration of distributed training in a slurm cluster. Do we need to explicitly call the distributed.launch when invoking the python script or is this taken care of automatically? In other words, is…

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Exploring oncolytic viral therapeutics and immunotherapies derived from DNA and RNA

Due to the high priority and growing need for treatment to alleviate the symptoms associated with potentially fatal prognoses, cancer treatments are continually being developed. Cancer therapies are being developed to prevent malignant cells from forming, proliferating, and metastasizing, as well as assisting in the control of symptoms associated with advanced…

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Euro-BioImaging Bio-Hub – FAIR Image Data Steward at European Molecular Biology Laboratory (EMBL)

About the team/job Euro-BioImaging ERIC (www.eurobioimaging.eu) is a leading pan-European research infrastructure that provides the research community open access to cutting-edge imaging services. The Euro-BioImaging Bio-Hub hosted by European Molecular Biology Laboratory (EMBL) is looking for a highly motivated FAIR Image Data Steward to develop general guidelines and technically support…

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Biomedical/BioInformatics Intern in Rockville, MD

Description Job Description: The Government Health and Safety Solutions Group within the Health group has an opening for a  Biomedical/Bioinformatics Intern. The intern will work alongside data scientists and managers and use biomedical or genomics data to inform health-related research questions. Primary Responsibilities: Under the guidance of Leidos staff, the…

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Molecular Modeling Software for Chemistry Market Size, Scope And Forecast

New Jersey, United States – The Molecular Modeling Software for Chemistry Market report is the ultimate tool to help industries, companies, and organizations make informed decisions for business growth. With the help of the market tactics and strategies covered here, it becomes easy for business players to maintain their position in…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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Science Papers on Cancer Mutational Signatures, System to Deliver CRISRP-Cas9 Machinery Across Blood-Brain Barrier

By sequencing tumors from thousands of cancer patients and comparing them to similar datasets generated by other research groups, a team led by scientists from the University of Cambridge has identified new mutational signatures of cancer, while also uncovering details about organ-specific common and rare signatures. In the study, which…

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Medical Alert System/Personal Emergency Response System Market Size And Forecast

New Jersey, United States – Medical Alert System/Personal Emergency Response System Market Research Report provides you with detailed and accurate analysis to strengthen your position in the market. It provides the latest updates and powerful insights on the Medical Alert System/Personal Emergency Response System industry to help you improve your business…

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Cannot compile any CUDA program – CUDA Programming and Performance

I am getting the following error when I run sample programs on vs 2022.My details:Windows 11 x64GTX 1650i7 9gen8 gb ram Severity Code Description Project File Line Suppression State Error MSB3721 The command C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\bin\nvcc.exe -gencode=arch=compute_35,code=\sm_35,compute_35\ -gencode=arch=compute_37,code=\sm_37,compute_37\ -gencode=arch=compute_50,code=\sm_50,compute_50\ -gencode=arch=compute_52,code=\sm_52,compute_52\ -gencode=arch=compute_60,code=\sm_60,compute_60\ -gencode=arch=compute_61,code=\sm_61,compute_61\ -gencode=arch=compute_70,code=\sm_70,compute_70\ -gencode=arch=compute_75,code=\sm_75,compute_75\ -gencode=arch=compute_80,code=\sm_80,compute_80\ -gencode=arch=compute_86,code=\sm_86,compute_86\ –use-local-env -ccbin…

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Problem with Python environment and Slurm (srun/sbatch)

I had a similar issue with Slurm Version 20.11.7I had a virtual environment created with the systems python3, which was Python 3.6.8When activating the venv on the logging-node calling an installed module worked fine, but from within the following shell script for example it did not and resulted in ModuleNotFound:…

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Loading environment modules on a cluster from my python script

I recently ran into this. A simple way around this would be to include the dependencies before the command you want, and separate them with a semi-colon cmd = ‘module load intel/2016.4; “gromacs command”‘ p = sub.Popen(cmd, shell=True, stderr = sub.STDOUT, stdout = sub.PIPE).communicate()[0] where “gromacs command” represents however you…

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Enable MBEDTLS debugging Nordic provided security backend (for CoAP Secure via OpenThread on nRF5340) – Nordic Q&A – Nordic DevZone

Goal Hi guys, is there an option to enable MBEDTLS debugging as with the CONFIG_MBEDTLS_DEBUG_LEVEL=4 for the MBEDTLS_BUILTIN? I am trying to setup a DTLS client based in order to establish a CoAP Secure Session via Openthread to a Borderrouter and I am struggling in the handshake process. It would…

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IRC issues on Gaussian : comp_chem

Hi r/comp_chem I am attempting to calculate the for several hydrogen abstraction steps using different heteroatoms on a doublet surface in Gaussian09. When look at the Gibbs energy energy difference between the separated species and the TS I get a positive barrier, but when I look at the enthalpy difference…

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Bioinformatics Application Scientist – Carlsbad

Job Description Bioinformatics Application Scientist (Actual title will depend on qualification and experience, including director level appointment) The Company: Universal Sequencing Technology Corporation (universalsequencing.com), a leading NGS biotechnology company engaged in long range/long read sequencing technology is relocating its headquarters from the greater Boston area to Carlsbad, CA where R&D…

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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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Running bash commands from within python script : bioinformatics

Hi all, I wanted to ask whether anyone has ever come across the problem I have. In my project we need to run few tools on multiple genes. I have written python script that chooses right genes, runs tools and then aggregates results. The problem I have is that after…

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Install Jupyter Notebook on Debian 11 Bullseye Linux

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…

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GROMACS – SBGrid Consortium – Supported Software

Usage Notes SBGrid Usage Info GROMACS is GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : sbgrid.org/wiki/gpu CUDA builds of GROMACS are designated by a ‘_cu’ suffix in the version of the application. For example, 2020.2_cu9.2.88 is linked against…

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Dissertations.se: INITIATION OF DNA REPLICATION

Showing result 1 – 5 of 43 swedish dissertations containing the words initiation of DNA replication. Author : Elisabeth Jemt; Göteborgs universitet; Göteborgs universitet; Gothenburg University; []Keywords : NATURVETENSKAP; NATURAL SCIENCES; mitochondria; mtDNA; DNA replication; Abstract : Mitochondria produce most of the adenosine triphosphate required in a eukaryotic cell and…

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Generation of Hook Ischemia-Reperfusion Model using a Three-Day Developing Chick Embryo

This paper describes ischemia-reperfusion (I/R) modeling in a 3-day chick embryo using a spinal needle customized hook to better understand I/R development and treatment. This model is simple, quick, and inexpensive. Hi, I am Dr.Syed Shadab Raza, the principal investigator for the Laboratory for Stem Cells and Restorative Neurology, located…

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Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

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Processing two lists of files with snakemake

I want to use snakemake to do bowtie2 mapping of split read files to a reference genome, and I’d like that rule to be integrated in the general workflow. For that purpose, I first defined a rule to create a bowtie index rule build_bowtie_index: input: referenceGenomeFasta output: expand(“{name}.{index}.bt2”, index=range(1,5), name…

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bash – Python argparse error

It is certainly possible the ‘error’ is the input file 2. However, both try: routines are weird and if this is the real code it would fall over. Something isn’t quite right however, which I’ll touch on at the end. What the code is supposed to say is: try: load…

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Snakemake using multi inputs – Stackify

You need to define target output files using rule all. SAMPLES = [‘1’, ‘2’, ‘3’, ‘4’] rule all: input: expand(“sample{sample}.R{read_no}.fq.gz.out”, sample=SAMPLES, read_no=[‘1’, ‘2’]) rule fastp: input: reads1=”sample{sample}.R1.fq.gz”, reads2=”sample{sample}.R2.fq.gz” output: reads1out=”sample{sample}.R1.fq.gz.out”, reads2out=”sample{sample}.R2.fq.gz.out” shell: “fastp -i {input.reads1} -I {input.reads2} -o {output.reads1out} -O {output.reads2out}” This is the output of command snakemake -np, with…

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Bioactive nanomaterials treat inflammatory bowel disease by scavenging multiple dangerous molecules

With the modernization of the Chinese people’s eating habits and lifestyles, the incidence of inflammatory bowel disease (IBD) has shown a sustained and rapid growth trend. The pathogenesis of IBD is complex, and clinical treatment is often dominated by anti-inflammatory drugs such as salicylic acid, glucocorticoids, and immunosuppressants, which have…

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What are the likely causes of Breast Implant Associated Anaplastic Large Cell Lymphoma (BIA-ALCL)?

Available online 16 January 2022 doi.org/10.1016/j.jpra.2021.11.006Get rights and content Abstract Breast implant–associated anaplastic large cell lymphoma (BIA-ALCL) is a CD30-positive, anaplastic lymphoma kinase–negative T-cell lymphoma. Where implant history is known, all confirmed cases to date have occurred in patients with exposure to textured implants. The etiopathogenesis of BIA-ALCL is likely…

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Ubuntu Manpage: samtools reheader – replaces the header in the input file

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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Running Jobs on Titan

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

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make Pyspark working inside jupyterhub

You need to configure the pyspark kernel. On my server jupyter kernels are located at: /usr/local/share/jupyter/kernels/ You can create a new kernel by making a new directory: mkdir /usr/local/share/jupyter/kernels/pyspark Then create the kernel.json file – I paste my as a reference: { “display_name”: “pySpark (Spark 1.6.0)”, “language”: “python”, “argv”: […

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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How To Install RStudio IDE on Fedora 35

In this tutorial, we will show you how to install RStudio IDE on Fedora 35. For those of you who didn’t know, RStudio provides free and open-source tools for R and enterprise-ready professional software for data science teams to develop and share their work at scale. RStudio makes it easier…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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La Jolla Institute for Immunology hiring Bioinformatics Postdoc – Systems Immunology of Infectious Diseases in San Diego, California, United States

The Peters Lab at the La Jolla Institute for Immunology (LJI) is looking for a bioinformatics postdoc to join our efforts in profiling immune system responses to a variety of infectious agents, such as M. tuberculosis and B. Pertussis, as well as various cancers. Qualified applicants will have the opportunity…

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Bioinformatics Analyst in Evanston, IL for Northwestern University

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

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[lammps-users] using the solid liquid interface to calculate melting point of LiAlO2 – LAMMPS Mailing List Mirror

Hello,I am using the solid liquid interface method to calculate the melting point of LiAlO2 (melting temperature is roughly 2000K). I am taking a long cuboidal simulation cell of LiAlO2 and melting a small slab section in the middle of the long box to 6000 K while the rest of…

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sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…

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main-armv7-default][science/cp2k-data] Failed for cp2k-data-7.1.0 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy12.nyi.freebsd.org/data/main-armv7-default/p772274a15b8b_s0630a06b2a/logs/cp2k-data-7.1.0.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=p772274a15b8b_s0630a06b2a Log: =>> Building science/cp2k-data build started at Sun Dec 19…

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docker – SLURM cluster inside k8s cannot run srun command

I’m a beginner k8s user, I’m trying to recreate this docker-compose SLURM cluster with kubernetes. First I converted the docker-compose.yaml file into k8s yaml file in order to use kubectl apply -f . to create pods and services. I’m using minikube on my computer with the none driver (like this…

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laboratory jobs in germany

We wish you a good luck and have a prosperous career. Working at Labcorp | Jobs and Careers at Labcorp 15 GNeuS Postdoc Positions in Neutron Science of 24 Months Each (Full-time Job) FZJ – Forschungszentrum Jülich. What other similar jobs are there to Laboratory jobs in Germany? Clinical Laboratory…

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Novo Nordisk hiring Scientist I – Bioinformatics in Seattle, Washington, United States

About The DepartmentAt Novo Nordisk Research Center Seattle, Inc. (NNRCSI) our scientists apply cutting-edge technologies to early R&D projects with the goal of bringing real change to People with Diabetes and Obesity. Your skills, dedication and ambition will help change lives for the better and you will work with extraordinary…

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snakemake truncating shell codes

snakemake truncating shell codes 0 I’m trying to change the chromosome number notation from [0-9XY] to Chr[0-9XY] using the samtools reheader in the shell command of the snakemake. rule rename: input: os.path.join(config[“input”], “{sample}.bam”), output: os.path.join(config[“output”], “new_sample/{sample}_chr.bam”) log: os.path.join(config[“log”], “samtools/{sample}”) shell: “samtools view -H {input} | sed -e ‘s/SN:([0-9XY]*)/SN:chr1/’ -e ‘s/SN:MT/SN:chrM/’…

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Issues when running r8s for an ultrametric tree

Hi all, I have been working on a comparative genomic analysis of 15 species with their peptide sequence files. r8s is being employed to obtain an ultrametric tree for the Expansion/Contraction gene families. I have used the Orthofinder software and the online website named timetree to generate the input file…

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Error with file guillaumeKUnitigsAtLeast32bases_all.fasta, kUnitigLengths.txt is of size 0, must be at least of size 1.

Hello, I am trying running an assembly with MaSuRCa but am getting an error at the step: “Computing super reads from PE”. here’s the output with the error: [xxxx@vic Bovidae]$ cd Assembly_test/ [xxxx@vic Assembly_test]$ ls assemble.sh guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 meanAndStdevByPrefix.pe.txt pe_data.tmp quorum_mer_db.jf work1 environment.sh guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352…

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[moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

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bedops bedmap operation in python

bedops bedmap operation in python 1 I noticed there is a conda version of bedops bedmap function available. I’ve been struggling to use it though. Could someone refer me to any documentation of it’s usage in a python script please. Have a great day. Thanks in advance. python bedops bedmap…

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analysis of multi-omics biological data in novel populations of Brachypodium

Applications are invited for a PhD fellowship/scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Quantitative Genetics and Genomics programme. The position is available from 1 July 2022 or later. Title: PhD position in statistical genetics and computational biology: analysis of multi-omics biological data in novel populations…

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RStudio AI Weblog: Coaching ImageNet with R

ImageNet (Deng et al. 2009) is a picture database organized in keeping with the WordNet (Miller 1995) hierarchy which, traditionally, has been utilized in pc imaginative and prescient benchmarks and analysis. Nonetheless, it was not till AlexNet (Krizhevsky, Sutskever, and Hinton 2012) demonstrated the effectivity of deep studying utilizing convolutional…

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European Bioinformatics Institute | EMBL-EBI hiring Software Engineer in Hinxton, England, United Kingdom

In this role you will analyse data, develop production software, create technical documents, take part in the daily Scrum meeting, as well as communicate with other teams at EMBL-EBI and/or with our international collaboration partners. Scalability will be an important feature of your clear, concise, well tested and documented code….

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Install pytorch in jetson nano

install pytorch in jetson nano Done! Getting Started with Jetson Nano In this tutorial, you will learn how to set up the NVIDIA ® Jetson ™ Nano and install everything you need to use the full power of the tiny embedded board. Git – Version Contol…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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main-arm64-default][devel/RStudio] Failed for RStudio-2021.09.1+372 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

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jupyter lab – How do I set logo and launchers in Jupyterlab and Jupyterhub?

For the logo, I am not sure about JupyterHub-specific solutions, but you could see how Elyra does that for their JupyterLab distribution with Elyra theme extension here (under Apache License, so it should not be pasted in here). In short they first locate the icon in the “top” area of…

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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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The Role Of Process Integration

Article | By Ahmed Besheer, Lonza As the field of biologics increases its focus on identifying new diseases to target and novel constructs to treat them, innovative administration devices are once again in the spotlight. Article | By Bruce C. Simpson, Thermo Fisher Scientific Due to the complexity and temperature sensitivity…

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Devember project, From The Depths PyTorch – Gaming

So anyone familiar with From The Depths (FTD) would know that the difference between a weapon system that works and one that is optimized is pretty night and day. However the characteristics of the custom ammunition and advanced cannon configurations are terrifyingly hard to find definitive solutions. In particular the…

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How To Compute Transformer Architecture Model Accuracy — Visual Studio Magazine

The Data Science Lab How To Compute Transformer Architecture Model Accuracy Dr. James McCaffrey of Microsoft Research uses the Hugging Face library to simplify the implementation of NLP systems using Transformer Architecture (TA) models. By James McCaffrey 12/07/2021 This article explains how to compute the accuracy of a…

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[slurm-users] Enforce shell options for job environment when submitting job?

Hi, does anybody know a simple way to enforce certain shell options such as set -o errexit (a.k.a. set -e) set -o pipefail and maybe also set -o nounset (a.k.a. set -u) for the job environment at job submission time (without modifying the batch scripts themselves)? Background of…

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Re: [lammps-users] Postprocessing Software/Codes – LAMMPS Mailing List Mirror

Hi RajOVITO has the ability to make really beautiful ray traced images, but they charge money for some of the ray-tracing features. (For what it’s worth, I support them for doing that. It’s hard to get funding to feed yourself when writing software like this.) Don’t feel bad if you…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Boston, Massachusetts, United States

IDT is the leading manufacturer of custom oligonucleotides and proprietary technologies for genomics applications. Our work is complex and cutting-edge, and our team members are curious, creative thinkers who understand that good data drives smart decisions. At IDT, we realize that although science may be uniform, people are unique. We…

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4 Use Cases of OpenAPI Which Are Good to Know | by Na’aman Hirschfeld | Dec, 2021

An introduction to OpenAPI with use cases Photo by Gertrūda Valasevičiūtė on Unsplash In this article I offer an introduction to OpenAPI (OA) and some of its more interesting use cases. If you are already familiar with what OA is, you can skip ahead to the use-cases part of this…

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Synthesis and Characterization of Multi-Modal Phase-Change Porphyrin Droplets

In this protocol, methods for synthesizing and characterizing multi-modal phase-change porphyrin droplets are outlined. This protocol is significant because it provides the complete procedure for creating droplets from the lipid film to lipid solution to microbubbles and then to droplets. The main advantage of this technique is the simplicity for…

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Development of a Lateral Flow Immunochromatographic Strip for Rapid and Quantitative Detection of Small Molecule Compounds

The procedure describes the preparation of colloidal gold and assembly of the immunochromatographic strips. Firstly, chloroauric acid and sodium citrate were used for the synthesis of colloidal gold. Sodium citrate was added to chloroauric acid solution and boiled to obtain colloidal gold with appropriate particle size. Synthesis, the colloidal gold…

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PyTorch core developer soul asks: Why are we becoming more and more like Julia?

There is a voice in the PyTorch community recently: the next version should abandon Python and switch to Julia. Now even the PyTorch team makes a joke about this statement. To this question, Edward Yang, one of the core development members, has made some responses on the forum. He believes…

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Multiprocess sampling with SMC fails on linux cluster – theano

Hi there, I am using the SMC sampler with pymc version 3.11.2 and theano-pymc version 1.1.2 in a conda environment. I am working on a linux cluster with several CPUs. I tried the multiprocess sampling on multiple cores with multiple SMC chains. For testing, I used the example (without gradient)…

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How to Install RStudio IDE on Fedora 35 / Fedora 34

RStudio IDE provides a software development environment that enables you to run R commands, inspect variables, visualize output, and manage your project files. RStudio makes it easier to write Python, Shell, SQL scripts with syntax highlighting, code completion, and smart indentation. In this post, we will see how to install…

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DNA inside conch shell leads to suspect in 2001 homicide

NEW BEDFORD, Mass. (AP) — DNA recovered from the interior of a conch shell thought to have been used as a weapon in the 2001 killing of a Massachusetts woman has led to the indictment on a murder charge of the victim’s half-brother, prosecutors said. David Reed, 53, formerly of…

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Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS

Job:Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS – Research Triangle Park, NC 0 Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. We are seeking an individual to work as a Ph.D. Bioinformatics Specialist at the National Institutes of Health in…

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BioSpace hiring Associate Bioinformatics Scientist in Cambridge, Massachusetts, United States

About Us…Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s programs apply our CytoDriveTM technology in Cell and Gene therapy products to control expression of proteins for enhanced therapeutic efficacy and safety. Obsidian’s lead program is currently in preclinical development for the treatment…

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Bioinformatics Postdoctoral Research Associate, Long Lab job with Benaroya Research Institute at Virginia Mason

Benaroya Research Institute at Virginia Mason (BRI) has a bold mission: Predict, prevent, reverse and cure immune system diseases, from autoimmune disease to cancer to COVID-19. We examine the immune system in both health and disease to understand how disorders start and how to rebalance the immune system back to…

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Postdoc (3 years) in Bioinformatics and 3D genome modeling

Position as Postdoctoral Research Fellow available at the Department of Biosciences. The appointment is a fulltime position and is made for a period of three years, and devoted to carrying out a project entitled URGE-3D, funded by the Norwegian Research Council. No one can be appointed for more than one…

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Quest Diagnostics Bioinformatics and Computational Biology Staff Scientist – remote in San juan capistrano, CA | 685400906

Job Description Look for more than answers. At Quest, we are on a continuous journey of discovery and development. Its this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you…

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130i386-default][biology/minimap2] Failed for minimap2-2.23 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: j…@freebsd.org Log URL: beefy15.nyi.freebsd.org/data/130i386-default/b8c4bfe660b3/logs/minimap2-2.23.log Build URL: beefy15.nyi.freebsd.org/build.html?mastername=130i386-default&build=b8c4bfe660b3 Log: =>> Building biology/minimap2 build started at Thu Dec 2…

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7643-gromacs-tyan-s8252 Benchmarks – OpenBenchmarking.org

2 x AMD EPYC 7643 48-Core testing with a TYAN S8252GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2112014-HOWE-7643GRO17 2 x AMD EPYC 7643 48-Core…

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7643-lammps-tyans8252 Benchmarks – OpenBenchmarking.org

2 x AMD EPYC 7643 48-Core testing with a TYAN S8252GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2112015-HOWE-7643LAM13 2 x AMD EPYC 7643 48-Core…

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