Tag: shell

130releng-armv7-quarterly][math/py-pymc3] Failed for py38-pymc3-3.11.4 in fetch

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/130releng-armv7-quarterly/46aef99be2ae/logs/py38-pymc3-3.11.4.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=46aef99be2ae Log: =>> Building math/py-pymc3 build started at Sat Nov 27…

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M1provm-lammps Performance – OpenBenchmarking.org

Apple M1 Pro vmware testing on Debian 11 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 2111259-TJ-M1PROVMLA17 Unknown – EFI VGA – VMware VBSA v1 (VEFI BIOS) Processor: Unknown (8 Cores), Motherboard: VMware VBSA…

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7713-gromacs Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a Inspur 4.02.06 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 2111266-HOWE-7713GRO09 2 x AMD EPYC 7713 64-Core – ASPEED…

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R-Studio 8.17 Build 180955

R-Studio is a family of powerful and cost-effective data recovery and undelete utilities. Empowered by the new unique data recovery technologies, it is the most comprehensive solution for data recovery from FAT12/16/32, NTFS, NTFS5 (created or updated by Windows 2000), and Ext2FS (LINUX file system) partitions. It functions on local…

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7713-lammps Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a Inspur 4.02.06 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 2111256-HOWE-7713LAM91 2 x AMD EPYC 7713 64-Core Processor: 2…

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Snakemake: MissingInputException

Snakemake: MissingInputException 0 Hello, I am trying to create a simple Snakemake workflow and I am having some issues. My file looks like this: ——————– ARCHIVE_FILE = ‘output.tar.gz’ **a single output file** OUTPUT_FILE = ‘output/{species}.out’ **a single input file** INPUT_FILE = ‘proteins/{species}.fasta’ **Build the list of input files.** INP =…

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Using the Slurm REST API to integrate with distributed architectures on AWS

The Slurm Workload Manager by SchedMD is a popular HPC scheduler and is supported by AWS ParallelCluster, an elastic HPC cluster management service offered by AWS. Traditional HPC workflows involve logging into a head node and running shell commands to submit jobs to a scheduler and check job status. Modern…

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Problem with installing python-gi-cairo on Linux

Problem with installing python-gi-cairo on Linux 0 When I’m trying to install python-gi-cairo with Bash on Linux, I get the following message: “Some packages could not be installed. This may mean that you have requested an impossible situation, or if you are using an unstable distribution that some required packages…

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Unix and shell scripting for bioinformatics

News:Unix and shell scripting for bioinformatics 0 Physalia-course: UNIX and shell scripting for bioinformatics ONLINE, 10-14 January 2022 In this course, students will be introduced to the most powerful Unix commands and they will learn how to connect to external resources/servers, install specialist tools, and ultimately to combine commands into…

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RStudio Platform Support Engineer | Job Ohio

Position Description: CGI is hiring a RStudio Platform Support Engineer to join our dynamic team. At CGI, you get to build solutions as a full time consultant with a world-class IT company. You will be involved in a mission critical project, working with a team of smart, dedicated people like…

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Bioinformatics Computing Consultant

Bioinformatics Computing Consultant – 94306 Organization: JG-Joint Genome Institute U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab) has an opening for a Bioinformatics Computing Consultant to join the team. In this exciting role, you…

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Bioinformatics Postdoc in Microbial Ecology: France

We are seeking a highly motivated post-doc who will develop computing solutions in support of microbial ecology and molecular ecology research in our group in Lyon France. Our group focuses on the microbial adaptation to environmental perturbations with a range of model ecosystems from polluted soil to antibiotic resistance dispersion…

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QIAGEN hiring Bioinformatics Scientist in United States

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

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Bioinformatics Postdoctoral Research Associate, Bioinformatics Group

Job Description Benaroya Research Institute at Virginia Mason (BRI) is an internationally recognized non-profit medical research institute affiliated with the Virginia Mason Health System. BRI works to advance the science that will predict, prevent, reverse and cure diseases of the immune system, to achieve its vision of a healthy immune…

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autopkgtest failing on Testing after updating mbedtls

Source: shadowsocks-libev Version: 3.3.5+ds-6 Severity: normal —–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Hi, I’ve recently updated the mbedtls package to the latest LTS version, and it seems that it has caused a regression for shadowsocks-libev. In fact, debci reports one failed test in autopkgtest. The failure is quite strange though, since I can’t reproduce…

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122arm64-quarterly][math/py-pymc3] Failed for py38-pymc3-3.11.4 in fetch

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: ampere1.nyi.freebsd.org/data/122arm64-quarterly/f5532da8b875/logs/py38-pymc3-3.11.4.log Build URL: ampere1.nyi.freebsd.org/build.html?mastername=122arm64-quarterly&build=f5532da8b875 Log: =>> Building math/py-pymc3 build started at Sat Nov 20…

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Research Asst/Associate Bioinformatics

  We are a world class research-intensive university. We deliver teaching and learning of the highest quality. We play a leading role in economic, social and cultural development of the North East of England. Attracting and retaining high-calibre people is fundamental to our continued success.  …

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Permanent error in installing GenomeInfoDb

Permanent error in installing GenomeInfoDb 1 @fereshteh-15803 Last seen 1 hour ago United Kingdom Hello I am not able to install GenomeInfoDb Can you help me please? > remotes::install_github(“Bioconductor/GenomeInfoDb”) Downloading GitHub repo Bioconductor/GenomeInfoDb@HEAD ✓ checking for file ‘/tmp/Rtmp4he3Nm/remotese273c245ce2/Bioconductor-GenomeInfoDb-d4604b1/DESCRIPTION’ … ─ preparing ‘GenomeInfoDb’: ✓ checking DESCRIPTION meta-information … ─ checking for…

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Natera hiring Senior Bioinformatics Scientist in United States

Successful applicants for this position must be fully vaccinated against COVID-19 as a condition of employment. Vaccine verification will be required.Position SummaryNatera is currently seeking a Senior Bioinformatics Scientist to join our computational oncology team to make the vision of cancer early detection a reality. The ideal candidate should have…

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EMDB

Field: Choose…EMDB IDTitleAuthorEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular WeightRecombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA structure SerotypeSerocomplexCategoryIsolateEnvelopedEmptyNatural host organismNatural host organism (NCBI code)Host recombinant organismHost recombinant…

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SpongebBob – Github Help

包梦蛟’s Projects ajvm A hobby jvm, just want to know how a java virtual machine works. AndriodGroupNotifcation Project CRM Group Notifcation Modle Android_Statics project_crm AutoML-startingkit AutoML-startingkit for NIPS 2018 BDC2017 basic version BiliBiliTool .Net 5 编写的跨平台的B站(哔哩哔哩)任务工具,通过GitHub Actions实现每日线上自动运行任务:每日自动登录、观看、分享、投币视频,获取每日任务的满额经验,轻松升级Level 6,实现自动领取大会员权益、月底自动为自己充电等功能。 bilm-tf Tensorflow implementation of contextualized word representations from bi-directional language models BUAAthesis…

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SpongebBob – Github Help

包梦蛟’s Projects ajvm A hobby jvm, just want to know how a java virtual machine works. AndriodGroupNotifcation Project CRM Group Notifcation Modle Android_Statics project_crm AutoML-startingkit AutoML-startingkit for NIPS 2018 BDC2017 basic version BiliBiliTool .Net 5 编写的跨平台的B站(哔哩哔哩)任务工具,通过GitHub Actions实现每日线上自动运行任务:每日自动登录、观看、分享、投币视频,获取每日任务的满额经验,轻松升级Level 6,实现自动领取大会员权益、月底自动为自己充电等功能。 bilm-tf Tensorflow implementation of contextualized word representations from bi-directional language models BUAAthesis…

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Assistant/Associate Teaching Professor job with Northeastern University

Assistant/Associate Teaching Professor About Northeastern Founded in 1898, Northeastern is a global research university and the recognized leader in experience-driven lifelong learning. Our world-renowned experiential approach empowers our students, faculty, alumni, and partners to create impact far beyond the confines of discipline, degree, and campus. Our locations—in Boston; Charlotte, North…

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Assistant/Associate Teaching Professor job with Northeastern University

Assistant/Associate Teaching Professor About Northeastern Founded in 1898, Northeastern is a global research university and the recognized leader in experience-driven lifelong learning. Our world-renowned experiential approach empowers our students, faculty, alumni, and partners to create impact far beyond the confines of discipline, degree, and campus. Our locations—in Boston; Charlotte, North…

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Natera hiring Senior Bioinformatics Scientist in San Carlos, California, United States

Successful applicants for this position must be fully vaccinated against COVID-19 as a condition of employment. Vaccine verification will be required. Position Summary Natera is currently seeking a Senior Bioinformatics Scientist to join our Bioinformatics Research & Development team with a focus on cancer early detection. Natera’s mission is to…

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SLURM batch spawner failing with client process running, config issue – JupyterHub

I am running a slurm cluster and running batchspawner, but the spawned server does not communicate with the frontend server and keeps getting killed off. c = get_config() import batchspawner import wrapspawner c.JupyterHub.ip = ‘0.0.0.0’ c.JupyterHub.hub_ip = ‘0.0.0.0’ c.JupyterHub.hub_connect_ip = ‘server_ip’ c.JupyterHub.spawner_class=”wrapspawner.ProfilesSpawner” c.Spawner.http_timeout = 60 c.BatchSpawnerBase.req_nprocs=”1″ c.BatchSpawnerBase.ip = ‘server_ip’ c.BatchSpawnerBase.req_runtime=”12:00:00″…

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SLURM batch spawner failing with client process running, config issue – JupyterHub

I am running a slurm cluster and running batchspawner, but the spawned server does not communicate with the frontend server and keeps getting killed off. c = get_config() import batchspawner import wrapspawner c.JupyterHub.ip = ‘0.0.0.0’ c.JupyterHub.hub_ip = ‘0.0.0.0’ c.JupyterHub.hub_connect_ip = ‘server_ip’ c.JupyterHub.spawner_class=”wrapspawner.ProfilesSpawner” c.Spawner.http_timeout = 60 c.BatchSpawnerBase.req_nprocs=”1″ c.BatchSpawnerBase.ip = ‘server_ip’ c.BatchSpawnerBase.req_runtime=”12:00:00″…

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SLURM: After allocating all GPUs no more cpu job can be submitted

Jobs Programming & related technical career opportunities , Stack Overflow Public questions & answers ,Thanks for contributing an answer to Stack Overflow!, Stack Overflow for Teams Where developers & technologists share private knowledge with coworkers Make sure that SelectType in your configuration is CR_CPU or CR_Core and that the shared…

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Emulating SLURM on Ubuntu 16.04

I would still prefer to run SLURM natively, but I caved and spun up a Debian 9.2 VM. See here for my efforts to troubleshoot a native installation. The directions here worked smoothly, but I needed to make the following changes to slurm.conf. Below, Debian64 is the hostname, and wlandau…

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Paragon Genomics hiring Bioinformatics Scientist in United States

Paragon Genomics is seeking a bioinformatics scientist who is passionate about making real differences in the field of molecular diagnostics and is enthusiastic about working in an exciting startup environment. This position will report to the head of bioinformatics and will be involved in improving and developing targeted sequencing panel…

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Missing Input files Error with snakemake pipeline

Hello hive mind, I am having issues with a snakemake script. What I want it to do is use abricate to look for AMR and resistance genes for each of my samples and then make a summary file for AMR, virulence factors, and plasmids. What is happening is the script…

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Downgrade R version and R package Bioconductor [duplicate]

If my Bioconductor packages were installed in the R home directory, then I’d remove.packages() instead of setting .libPaths(), or I’d run BiocInstaller::biocValid() and follow the directions for reverting “too new” packages.,Generally, Bioconductor is designed to work with specific versions of R, so there are no guarantees associated with using older…

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Forcing Rstudio to use a specific version of R on linux

Meta Stack Overflow ,Stack Overflow en español,Stack Overflow em Português, Stack Overflow Public questions & answers load more v I have installed an older R version using the source on a mac, but I am finding it difficult to get Rstudio to see this version. Is there an easy way…

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Use slurm job id – Pretag

1 Note, using –parsable flag you might get a comma separated list. From the man page of sbatch: –parsable Outputs only the job id number and the cluster name if present. The values are separated by a semicolon. Errors will still be displayed. – Stefan Aug 7 ’20 at 9:56 ,The…

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GitHub Actions workflows for Shiny and related packages

🚩 🚩 🚩 This repo is intended for internal use only. Sweeping changes will be made without notice. 🚩 🚩 🚩 A reusable workflow is a workflow that is defined in a single location but can be executed from another location as if it was locally defined. Link: docs.github.com/en/actions/learn-github-actions/reusing-workflows Usage:…

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Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

1. Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010). CAS  PubMed  Google Scholar  2. Chou, C. et al. Increase in the range between wet and dry season precipitation. Nat. Geosci. 6, 263–267 (2013). CAS  Google Scholar  3. Li,…

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[lammps-users] Problem with Reax – LAMMPS Mailing List Mirror

Hi everyone, I hope you are fine. I’m using lammps-29Sep2021 on Linux Bash Shell in Windows 10. I want to use the Reax force field, so installed the ReaxFF package, but I got this error: ERROR**:** Unrecognized pair style ‘reax/c’ is part of the USER-REAXC package, which is not enabled…

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Snakemake Megahit error

Snakemake Megahit error 0 Hello everyone! A few days ago I started using Snakemake for the first time. I am having an issue when I am trying to run the megahit rule in my pipeline. It gives me the following error “Outputs of incorrect type (directories when expecting files or…

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rna seq – Snakemake Fastqc: “SyntaxError in line [#] of [working directory]/Snakefile: Multiple run or shell keywords in rule run_fastqc.”

I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error “Multiple run or shell keywords in rule run_fastqc”. Snakefile: rule run_fastqc: input: “/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz” output: “./[out path]/well01_S001_L001_R1_001.fastqc.html”, “./[out path]/well01_S001_L001_R1_001.fastqc.zip” wrapper: “0.79.0/bio/fastqc” shell: “fastqc {input}…

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Quadram Institute keeps food safe using genome sequencing

Published: 8:45 AM November 11, 2021 Researchers from the Quadram Institute at Norwich Research Park have used genome sequencing to discover that a significant amount of uncooked prawns bought from UK retailers have been contaminated with bacteria called Vibrio. Though not harmful in the vast majority of cases, it means that…

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README – DeepDeblur-PyTorch

2021-11-11 09:04:40  阅读:6  来源: 互联网 标签:— py dataset python PyTorch DeepDeblur README GPUs main This is a pytorch implementation of our research. Please refer to our CVPR 2017 paper for details: Deep Multi-scale Convolutional Neural Network for Dynamic Scene Deblurring[paper][supplementary][slide] If you find our work useful in your research or publication, please cite our work: @InProceedings{Nah_2017_CVPR, author…

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How can I load numerous files from a config file in Snakemake? Is it worth it ?

How can I load numerous files from a config file in Snakemake? Is it worth it ? 0 Hello there! A few days ago I started using Snakemake for the first time. Mainly I want to use fasterq-dump to download a big number of files from NCBI and I do…

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Conda activate not working : kaggle

Hi everyone, I’m new to Kaggle and I’m trying to use it for my Bachelor’s degree thesis. However when I try to activate my conda environment it runs into an error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

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Script for chromosome features

Script for chromosome features 0 Hi, I’m looking for any shell script which may provide the Y chromosome structure information, gene names, number of repeated/duplicated genes, STRs list, etc. via Terminal. Can anybody help me with that? Chromosome • 143 views Login before adding your answer. Read more here: Source…

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How do I activate a conda environment in Kaggle? : deeplearning

Hi everyone, I’m pretty new at this stuff, especially with Kaggle, and I’m trying to activate a conda environment with the conda activate command. However, it comes out with this error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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Job Opening – Bioinformatics Analyst

job summary: As the world’s largest staffing and recruitment agency in the world, we can commit to find you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network…

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Help installing Bioawk

Help installing Bioawk 1 Hello I’ve been trying to install bioawk on my ubuntu system however I’ve come into a few issues. in my user/bin directory which I’ve cloned the directory into sudo git clone github.com/lh3/bioawk.git cd bioawk/ sudo make ./bioawk ./bioawk returns usage: ./bioawk [-F fs] [-v var=value] [-c…

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Bioinformatics Scientist (Pacific Biosciences Data) in Bethesda, MD

Provide services as a Bioinformatics Scientist in support of the overall functions of the Viral Persistence and Dynamics Section (VPDS) within the National Institute of Allergy and Infectious Diseases (NIAID). Duties and Responsibilities: Perform computational analysis of Pacific Biosciences HiFi sequencing data: Standard/pre-packaged analyses Sequence data quality control and trimming…

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Bioinformatics Scientist – Job at DAWSON in Bethesda, MD

Bioinformatics Scientist Full Time Prof-Entry Bethesda, MD, US DAWSON is a Native Hawaiian Organization 8(a) small business that brings the Spirit of Aloha to our employees. As part of the DAWSON “Ohana”, you will be provided a best-in-class benefits program that strives to ensure our great people have peace of…

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Cp2k Xeon Benchmarks – OpenBenchmarking.org

1 Kernel Notes: Transparent Huge Pages: madviseProcessor Notes: Scaling Governor: intel_pstate powersave – CPU Microcode: 0xde – Thermald 2.3Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + l1tf: Not affected + mds: Not affected + meltdown: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1:…

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Recent activity – OStack Q&A-Knowledge Sharing Community

Recent activity – OStack Q&A-Knowledge Sharing Community     I have 2 samples Mocha web tests which I’m trying to run using Velocity. For some reason, client-side tests under the /tests/mocha/client … lib packages server tests mocha client server Thoughts ? See Question&Answers more detail:os…     I’m trying to find a way to…

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Synectics Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Contract: 3 months Pay: $22.91/hr ONSITE Description Perform bulk differential gene (ideally microarray and RNA-seq) and enrichment analysis in the R programming language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene (limma/varianceParition dream or other R method) and single-sample…

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Spectraforce Technologies hiring Bioinformatics analyst in Waukegan, Illinois, United States

Job Title: Bioinformatics analystLocation: Lake County, IL; 100% remoteDuration: 6 months Payrate: $24/hr on W2 DescriptionWe have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or…

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How To Run An R Script From Within Rstudio’S Built-In R Console?

2.1 Starting RStudio on the university network. Click on the Windows 10 icon in the bottom left corner of the screen then search the list of programs and click. Some Examples on basic concepts of R programming. We have provided working source code on all these examples listed below. However…

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DSSOPC) at National Cancer Centre Singapore Pte Ltd Singapore

We are looking for a post-doctoral fellow position in computational cancer biology. Your responsibilities will include the following: – Work as part of an established and nationally funded multi-disciplinary research group that focuses on hepatocellular carcinoma and other cancers.  – Involve in a large-scale international translational and clinical study on…

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Dir, Bioinfo & Comp Biology

Dir, Bioinfo & Comp Biology Back Apply Share Requisition no: 520104 Work type: Full Time Location: Medical Center School/Department: Center for Infection and Immunity Grade: Grade 106 Categories: Research (Lab and Non-Lab) Job Type: Officer of…

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Bam file depth of coverage and statstics

Bam file depth of coverage and statstics 0 I am looking for a tool that can provide a high level summary of coverage statistics of genomes used in an alignment. The only tools I have found that can provide summary statistics for the entire genome are bamdst, bamstats. However for…

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Biopython Seqio.Index() And Seqio.Index_Db() Very Slow For Large Sequence

Before switching to Biopython, I thought there are similar indexing features in biopython as in bioperl. However, the biopython SeqIO.index_db() and SeqIO.index() methods are so inefficient that it’s almost impossible to random access a segment of genomic sequence using biopython. I tested the performance of biopython and bioperl in retrieving…

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Bioinformatics Software Engineer at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and…

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Bioinformatics Analyst position in North Chicago, Illinois

Open for discussion of Remote  We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene?ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential…

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Advanced Bioinformatics Data Scientist job at BenevolentAI, November 2021

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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Bioinformatics Scientist – Job at University of North Carolina

Primary Purpose of Organizational Unit The UNC School of Medicine has a rich tradition of excellence and care. Our mission is to improve the health and wellbeing of North Carolinians, and others whom we serve. We accomplish this by providing leadership and excellence in the interrelated areas of patient care,…

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Jobot hiring Senior Bioinformatics Scientist in Boston, Massachusetts, United States

This Jobot Job is hosted by Emily Olinger Are you a fit? Easy Apply now by clicking the “Apply” button and sending us your resume. Salary $100,000 – $150,000 per year A Bit About Us We are a leading cloud based SaaS startup in the biotech industry. Our platforms leads…

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main-armv6-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: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/cp2k-data-7.1.0.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building science/cp2k-data build started at Fri Oct 29…

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main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 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: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

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shell — while

shell — while 1 when I do something like this,I got a question: yi@yi:~$ cat ids.txt CDS chromosome exon five_prime_UTR gene mRNA scaffold three_prime_UTR # this way has a result yi@yi:~$ while read line; do arr1[++i]=$line;done < ids.txt yi@yi:~$ echo ${arr1[@]} CDS chromosome exon five_prime_UTR gene mRNA scaffold three_prime_UTR #…

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shell –array in while loop

shell –array in while loop 0 first I have a file which have some gene_IDs: ZM011,ZD012,ZF033,….. Then I want to convert these gene id to different numbers. Like ZM011 -> 1, ZD012 -> 2,…. I try use shell script like this: i=1 cat ids.txt | while read id; do arr[$id]=$i…

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Bioinformatics Analyst II – Remote at Geisinger Health System

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. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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Help writing this shell for salmon quantification?

Noob: Help writing this shell for salmon quantification? 0 I am a total noob here trying to analyze my RNA seq data. I’ve just started trying to use Salmon for my quantifications, and wanted to use their suggested script for running all of the samples in a loop instead of…

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OPINION | Technological advances helping in the fight against emerging infections

Within a few weeks after SARS Coronavirus 2 (SARS-CoV-2), the virus causing Covid-19, was discovered, scientists characterised its full genome, meaning that they obtained all its genetic information. They managed to pull this off in such a short period thanks to rapid developments in the science of nucleic acid (information-carrying…

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Bioinformatics Scientist with Security Clearance job in Bethesda at Dawson

Company Description Dawson is a Staffing & Recruiting agency that was founded in 1946 and headquartered in Columbus, OH. They have the vision to help the small as well as large corporations and businesses to recruit the talent that can help them to provide the best customer service with exceptional…

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Staff Scientist – Bioinformatics and Computational Biology job with Quest Diagnostics

Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s 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 can affect…

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Scikitlearn In R With Reticulate

The goal of the package is to allow you to joyfully build with new building blocks that are scikitlearn compatible. Installation. Install scikitlego via pip. Python and R are two of the main programming languages used for data science. Both are great they are very used and they both have…

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Sensorium Therapeutics hiring Bioinformatics Scientist in Boston, Massachusetts, United States

We are seeking a Bioinformatics Scientist to partner with some of the world’s leading researchers from Harvard and MGH in the naturals space to develop a platform for a novel set of therapies to improve mental health. You will report directly to our Vice President of Scientific Strategy and Operations…

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The Definition of Gene Therapy Has Changed

Three decades after its first, faltering steps in humans, gene therapy is emerging as a treatment option for a small but growing number of diseases. Although the concept faced scientific and ethical uncertainty when it was floated in the 1970s, the foundation of the approach—replacing or fixing a single, disease-causing…

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[Solved] tatements are true about the commands used in mothur during the process of generating contigs, filtering and merging the contigs and countin…

Which of the following statements are true about the commands used… in mothur during the process of generating contigs, filtering and merging the contigs and counting contigs?Question 17 options: The make.contigs command will extract the sequence and quality score data from your fastq files, create the reverse complement of the…

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What is bigwig file?

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

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What is the best gun mod for GMOD?

[Top 10] Garrys Mod Best Weapon Addons Every Player Needs Customizable weaponry 2.0 – Khris’s Weapons – Full Package. No. Air To Surface Missile. RAMIREZ! … [TFA] Dead Space 2 Weapons. They’re coming out of the walls! … Tactical Baby Weapons. … WW2 Weapons Part 2. … Some throwable weapons….

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Is it possible to integrate shell scripts in snakemake

Is it possible to integrate shell scripts in snakemake 0 Hello, I need to integrate as inputs/outputs scripts written in python, R as well as shell scripts. I also would like to add to this list jupyter notebooks in constructing modular pipelines. While I found in the documentation about snakemake…

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how to convert output of bash script to .csv ?

how to convert output of bash script to .csv ? 0 I want to convert the output of the below mariamscript.sh shell script to csv, so that I can get the information in column format : #!/bin/bash Name=”mariam moahmed” Email=mariamdarwish880@gmail.com slack=mariamdarwish0 biostack=”transcriptomics/machinelearning and datascince” for i in {Name,Email,slack,biostack} do echo…

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Gmod E2 Portal – LoginWave

If you are looking for gmod e2 portal, simply check out our links below : steamcommunity.com/sharedfiles/filedetails/?id=571740596Store Page. Garry’s Mod … portal gun expression 2 (e2). Description … it’s a portal gun, right click or left click with a gravity gun to use it, reload to remove portals steamcommunity.com/sharedfiles/filedetails/?id=70749011 Steam Community:…

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post-link.sh | searchcode

post-link.sh | searchcode PageRenderTime 15ms CodeModel.GetById 8ms app.highlight 4ms RepoModel.GetById 1ms app.codeStats 0ms /recipes/bioconductor-hgu133afrmavecs/post-link.sh github.com/bioconda/bioconda-recipes Shell |…

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Research Associate – Bioinformatics at USC

A Research Associate position is available in the lab of Dr. Serghei Mangul in the Titus Department of Clinical Pharmacy, School of Pharmacy at the University of Southern California. The Mangul lab aims to improve the techniques of bioinformatics in order to better understand the mechanisms of disease. This includes…

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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

Alfaro-Nunez A, Bertelsen MF, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Olsen MT et al. (2014) Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 14:206 PubMed  PubMed Central  Article  Google Scholar  Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C et al….

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error in metagenemark

error in metagenemark 0 I have install the metagenemark on linux64, and I have done cp gm_key ~/.gm_key. It still have a error when run the shell. And I search online didn’t find the similar situation. The shell codes is: gmhmmp -m MetaGeneMark_v1.mod -a -k -f G -o gene.gff ./04_metaSPAdes/contigs.fasta…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Coralville, Iowa, 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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A Surprising New Lighting Collection Combines Ostrich Eggs and NFTs

DNA sequencing, computer-generated identity, and digital provenance might not come to mind when you think of a typical lighting collection. But for Franco-American architect Elliott Barnes, all are rife for exploration in his intriguing new lighting collection Iqanda. “The idea came to me at dinner, as most things do in…

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Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG

GROMACS, a simulation package for biomolecular systems, is one of the most highly used scientific software applications worldwide, and a key tool in understanding important biological processes including those underlying the current COVID-19 pandemic. In a previous post, we showcased recent optimizations, performed in collaboration with the core development team,…

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command not found, in IMPUTE2

Edit June 7, 2020: The code below is for phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs. For the initial pre-phasing process with SHAPEIT2, see my answer here: Phasing with SHAPEIT So, the steps are usually: pre-phasing into pre-existing haplotypes available from HERE ( Phasing…

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Bioinformatics Scientist Job Opening in Huntsville, AL at Discovery Life Sciences

Discovery Life Sciences are the Biospecimen and Biomarker Specialists™ serving thousands of scientists across the U.S. and around the world. We’re looking for a standout Bioinforatics Scientist for the HudsonAlpha Discovery sequencing lab in Huntsville, Alabama. The Bioinformatics Scientist contributes to our mission by taking lab-generated data and creating computational…

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Bioinformatics Specialist, Lab of Human Genomics, GIS at Agency for Science, Technology and Research Singapore

Job Description Bioinformatics Specialist We are inviting applications for a bioinformatics specialist position at the Genome Institute of Singapore. Successful candidate will join the research program on generating a human pangenome reference for Asian populations. The current reference (hg37/38) plays an essential role in large-scale genome sequencing analysis of human…

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Survey uncovers diversity of Vibrio in prawns bought in the UK

Vibrio alginolyticus. Credit: Quadram Institute Quadram Institute researchers have carried out a survey of prawns in the UK for Vibrio bacteria, in an effort to understand the bacterium’s potential contribution to human disease and its resistance to antibiotics. They found that whilst 46 percent of prawns were contaminated with Vibrio,…

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CyberCoders hiring REMOTE Sr Bioinformatician – $200k (DNA Sequencing) in Canton, Massachusetts, United States

Permanently Remote, Boston, MA and San Diego, CA Candidates are ideal!Job Title: REMOTE Sr Bioinformatician – $200k (DNA Sequencing) Salary: $150-$200k Base + Equity, 401k, Benefits, Vacation Requirements: 5+ Years Bioinformatician, DNA Sequencing Based in beautiful Boston, MA, we are a rapid growth long-read DNA sequencing org. We’ve been in…

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How to give explicitly input and output to Snakemake file?

How to give explicitly input and output to Snakemake file? 0 So I have a pipeline written in shell which loops over three folders and then an inside loop which loops over files inside the folder. For next step, I have a snakemake file, which takes an input folder and…

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Unable to locate package cuda-command-line-tools – TensorRT

Description Hi! I would like to get some help while building the docker file in AlphaFold2. when I execute the command following sudo docker build -f docker/Dockerfile -t alphafold . I got the following error. Get:22 archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [2668 B] Fetched 19.7 MB in 6s (3575 kB/s) Reading…

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Old, goopy museum specimens can tell fascinating stories of wildlife history

As the climate crisis threatens millions of species worldwide, biodiversity conservation is now an all-hands-on-deck operation. Natural history collections play a critical role in this effort as repositories holding records of historical biodiversity shifts, like libraries made of biological specimens. In response to the extinction crisis, the call is out…

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Index error list index out of range autodock 4

Index error list index out of range autodock 4 30-09-2021 apologise, but does not of index range 4 list index error range autodock not out try all successively IndexError: list index out of range…

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Boohoo drags on retail, as Q3 draws to a close

After starting on the front foot today, markets in Europe have seen the morning gains slowly slip away in a manner that has pretty much reflective of the wider uncertainty that has been characteristic of sentiment for most of this quarter.  Europe We’ve seen swings in both directions as we…

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Data Scientist job with University of California, San Francisco

Job Code and Payroll Title009401 BIOINFORMATICS PROGR 3 Job SummaryThe Data Scientist uses professional bioinformatics concepts. He/she applies computational procedures to resolve a variety of analysis and research issues. Works on assignments of moderate to extended scope where analysis of data requires a review of a variety of factors. He/she…

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