Tag: docker

Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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R programming language tutorials – Technical Ripon

Are you learning the R programming language? Want to learn how to do more tasks with R? Check out our Do More With R video tutorials below — most with accompanying text articles and code, almost all under 10 minutes. In the table below you can easily search all tutorials…

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Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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Go Echo API Server for openapi

A hello world service. Overview This server was generated by the openapi-generator project. By using the OpenAPI-Spec from a remote server, you can easily generate a server stub. To see how to make this your own, look here: README API version: 1.0 Build date: 2022-05-28T21:42:12.319613+10:00[Australia/Sydney] export GO_POST_PROCESS_FILE=”/usr/local/bin/gofmt -w” openapi-generator generate…

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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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Recent questions tagged fasta – Q&A

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

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nf-core presentation – HackMD

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

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

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docker compose – How to enable authentication via openLDAP on JupyterHub without SSL certificate?

I am trying to create a JupyterHub that uses an LDAP to authenticate users. The JupyterHub is working but when I am trying log on the web page show a Error 500. I must clarify that when I tried it with the PAM method it worked without problems, but when…

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

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

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Two polynomials multiply incorrectly only on my computer

I am using Docker Desktop on Windows 11 to run Sagemath with Macaulay package. The polynomials “F[0]” and “xd” below multiply into “dat” incorrectly (when compared to the correct result on another computer.) I tried to obtain a minimal example illustrating my problem: Source Code import numpy as np import…

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Filtering outgoing container traffic – General Discussions

melhayany (Melhayany) April 12, 2022, 10:12pm #1 Hello Docker Community, I am facing a networking issue with my application to run JupyterHub using Docker containers. To give you a bit of context. I created a virtual machine, on it: port 2022 (ssh) served by my server, port 443 (https) served…

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

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

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Push DaPars2 Docker image to APAeval Dockerhub

Following up on comments in PR review and #158, I need to push the Docker image to the APAeval instead of my personal account. It builds locally (and workflow works with it). 132341b425d1bbe0b1307bc50e8c0adcf1f7d68b on branch DaPars2-snakemake is the specific commit adding the Dockerfile (at execution_workflows/DaPars2/Dapars2_snakemake/workflow/envs/Dockerfile). @yuukiiwa @uniqueg could one of…

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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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Python JupyterHub Developer at Pachyderm

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

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

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

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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

The protocol presented here describes a complete pipeline to analyze RNA-sequencing transcriptome data from raw reads to functional analysis, including quality control and preprocessing steps to advanced statistical analytical approaches. Welcome to the protocol of high-throughput transcriptome analysis for investigating host-pathogen interactions. This protocol is divided in the following steps….

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CORS issues behind nginx ingress after updating to JupyterHub 2.1.1 – JupyterHub

Hi there, I noticed multiple issues after upgrading to JupyterHub 2.1.1 from 2.0.0. I stopped seeing spawn progress when starting the singleuser server. Logs: [I 2022-03-04 20:57:47.436 JupyterHub log:189] 302 GET /hub/spawn -> /hub/spawn-pending/konstantin.taletskiy@labshare.org (konstantin.taletskiy@labshare.org@192.168.15.108) 1006.02ms [I 2022-03-04 20:57:47.524 JupyterHub pages:405] konstantin.taletskiy@labshare.org is pending spawn [I 2022-03-04 20:57:47.528 JupyterHub log:189]…

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

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

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Senior Bioinformatics Engineer, remote in Marlborough, MA at 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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JupyterLab Installation and Configuration – HEAVY.AI Docs

container_name: omnisciserver image: omnisci/omnisci-ee-cuda:v5.9.0 – /var/lib/omnisci:/omnisci-storage – /var/lib/omnisci/data/omnisci_import/jhub_omnisci_dropbox:/jhub_omnisci_dropbox # If using binary encryption, uncomment the below line to override the default # command that uses startomnisci, noting that you must have an existing OmniSci # data directory and run initdb before making this change. # command: /bin/bash -c “/omnisci/bin/omnisci_web_server –config…

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a free and open source electronic lab notebook

Tool:eLabFTW: a free and open source electronic lab notebook 0 Hello everyone, The last time I was here was 5 years ago (see post), and since then eLabFTW grew tremendously! So I wanted to present this tool that I made with love to this community again (I believe I’m being…

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nf-core/circrna

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

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Materials Science Community Discourse

Sign Up Log In Log In Popular FireworksFireWorks Using fix GCMC to plot adsorption isothermsLAMMPS General Discussion Topic of the Month: What are your favorite pre- and postprocessing toolsLAMMPS Why is My lattice size increasing during the initial NPT run for equilibrating Si diamond crystal?LAMMPS General Discussion About fix smdLAMMPS…

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Bioconductor on Microsoft Azure – Microsoft Tech Community

Co-authored by: Nitesh Turaga – Scientist at Dana Farber/Harvard, Bioconductor Core Team Erdal Cosgun – Sr. Data Scientist at Microsoft Biomedical Platforms and Genomics team Vincent Carey – Professor at Harvard Medical School, Bioconductor Core Team   Introduction   The Bioconductor project promotes the statistical analysis and comprehension of current and emerging…

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Petabase-scale sequence alignment catalyses viral discovery

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

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CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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Mle Application With Gekko In Python

The true power of the state space model is to allow the creation and estimation of custom models.This notebook shows various statespace models that subclass sm. That means your MAGeCK python module is installed in /home/john/.pyenv/versions/2.7.13/lib/python2.7/sitepackages.I use conda to install the latest version of. This twovolume set Diseases and Pathology…

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okay to run docker build test only on changes to Dockerfiles ?

I’d like to see a quicker response from the CI system when we make a pull request etc. I’ve opened this issue to ask if you agree to only run the job testing the build of the Dockerfiles when we change the Dockerfiles. Would that be reasonable? If so, I’ll…

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‘dataspell’ tag wiki – Stack Overflow

JetBrains DataSpell is an IDE for data science with intelligent Jupyter notebooks, interactive Python scripts, and lots of other built-in tools. The IDE for Professional Data Scientists DataSpell is an Integrated Development Environment (IDE) that is dedicated to specific tasks for exploratory data analysis and prototyping ML (machine learning)…

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Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant – C samtools

Thanks for getting back to me Valeriu. As you suggested, I used the latest commit from the develop branch in my pipeline, and the results look good. I was able to replicate the numbers from samtools v1.10.2 and v1.11 for both variant callers. FYI $ docker run scilifelabram/htslib:dev_proper /opt/samtools/samtools version…

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deseq2 machine sizing best practices for very large data set

deseq2 machine sizing best practices for very large data set 0 @aa611017 Last seen 8 hours ago United States I want to perform differential expression analysis on a data set containing 17,000 samples. The salmon quant.sf files are about 1.5 Tb. based on my naive understanding of R and R…

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Sr. Research Scientist I, Bioinformatics job with Gilead Sciences, Inc.

Sr. Research Scientist I, BioinformaticsUnited States – California – Foster City Gilead Sciences, Inc. is a research-based bio-pharmaceutical company that discovers, develops and commercializes innovative medicines in areas of unmet medical need. With each new discovery and investigational drug candidate, we seek to improve the care of patients living with…

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Biopython Contact Us | Contact Information Finder

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

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Ensembl vep singularity

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

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Full Stack DevOps Software Developer Jobs in Grenoble (38) at European Molecular Biology Laboratory –

EMBL Grenoble is looking for a Full-Stack Software Developer to join the Crystallographic Information Management System (CRIMS) project. The Marquez Team operates the High Throughput Crystallization Laboratory (HTX Lab), one of the largest facilities of its kind in Europe and has developed automated pipelines for macromolecular crystallography and fragment screening…

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deepmind alphafold github

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

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Associate Director, Computational Biology/Bioinformatics Job Opening in Cambridge, MA at Obsidian Therapeutics

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. We’re proud of our diverse talented team and committed to…

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Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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Bioinformatics Scientist Job Opening in Iowa City, IA at Jones Microbiology Institute Inc

Description: JMI Laboratories is a mid-sized company based in North Liberty, IA. A global leader for twenty years in anti-infectives research, JMI monitors annual changes in antibiotic resistance patterns through the SENTRY Antimicrobial Surveillance Program, serves as a clinical and reference laboratory in support of new drug development, and conducts…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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Invitae hiring Bioinformatics Scientist/Engineer in San Francisco, California, United States

Invitae is dedicated to bringing comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Our team is driven to make a difference for the patients we serve. We are leading the transformation of the genetics industry, by making genetic testing affordable and accessible for everyone to…

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Alphafold News – DeepMind and EMBL release the most complete database of,

Jul 22, 2021Jul 22, 2021Jul 22, 2021Dec 03, 2018 · “The AlphaFold database is a perfect example of the virtuous circle of open science,” said EMBL Director General Edith Heard. “AlphaFold was trained using data from public resources built by the …Jul 15, 2021 · reply. pjfin123 32 minutes ago [–]…

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R Bioconductor Courses

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

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Trimmomatic error: cannot execute binary file: Exec format error

Trimmomatic error: cannot execute binary file: Exec format error 1 I am trying to run Trimmomatic from a docker container using this piece of command: docker run -v ~:/home -v /data:/data quay.io/biocontainers/trimmomatic:0.36–6 trimmomatic PE -trimlog /usr/local/share/trimmomatic-0.36-6/adapters/NexteraPE-PE.fa:2:30:10 | /data/Sample1_R1.fastq.gz /data/Sample1_R2.fastq.gz | Sample1_R1_paired.fastq.gz Sample1_R1_unpaired.fastq.gz Sample1_R2_paired.fastq.gz Sample1_R2_unpaired.fastq.gz this is the error I recieve…

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How to build and run a docker container with multiple conda envs – General Discussions

As a novice to this community (and technology) I have only a basic knowledge regarding how to build and deploy a docker so i was hoping someone could provide some help. The situation is the following: I wanna create a docker container with two conda environments and I wanna call…

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Serotiny hiring Data Scientist / Bioinformatics Scientist

About Serotiny Serotiny is a company that is engaged in the discovery of proteins for cell therapies. It focuses on such proteins as CARs (chimeric antigen receptors) for the treatment of cancers and genetic disorders. Job Description Description Serotiny invents multi-domain proteins for gene and cell therapies including genome editors…

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ARACNE-AP output for Viper R package

ARACNE-AP output for Viper R package 1 Hello, I am using ARACNE-AP via Docker to generate networks from my gene matrix. As an input, I am using a text file, with genes on rows and samples on columns and a gene list( the ones that I am mostly interested in…

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Research Scientist Bioinformatics at Exscientia

We are looking to hire an experienced bioinformatician who specializes in the analysis of human NGS data. The Research Scientist Bioinformatics will lead the development and expansion of our in-house NGS capabilities together with data managers and software developers, while also carrying out project-specific analyses. Exscientia GmbH is a company…

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Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

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

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Solvuu hiring Bioinformatics Engineer in United States

Summary At Solvuu, we are building technology to revolutionize bioinformatics and data science. We are seeking an accomplished, self-motivated and ambitious bioinformatics engineer with a strong track record in developing, executing, and maintaining bioinformatics pipelines on AWS for biotech R&D. The successful candidate will have the opportunity to drive and…

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Setup my Github repo in a Kaggle environment | Python

I would like step by step instructions to: 1. Set up Git so that commands like “git pull” work within the provided linux environment 2. Create a Conda environment (or overwrite the existing one) in this Kaggle environment, generated from my own [login to view URL] file 3. Preserve all…

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Building Docker images

If you wonder what an image and a container is, please see : Building an image starts from a Dockerfile which is a plain text file with instructions. Here an example which we are going to build: It is based on the mambaforge image, so mamba is already installed which…

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Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health

Job:Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health 0 You will be part of a team of molecular biologists, medical geneticists, and bioinformaticians working together to analyze new and archival clinical cases using high throughput sequencing. As one of a newer team of software engineers, you will have the unique opportunity…

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Twist Bioscience hiring Bioinformatics Scientist, Production Bioinformatics in South San Francisco, California, United States

Twist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better…

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Senior Bioinformatics Scientist (Remote) – Torre

Description Basepair develops SaaS to manage, analyze and interpret next generation sequencing (NGS) data. Scientists and physicians working in molecular diagnostics, biopharma, assay development at top universities like Harvard, Stanford, NYU, UCSD, etc. use Basepair to make breakthrough medical discoveries and provide better medical care to patients. Founded by a…

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Bioinformatics Software Engineer – jobRxiv

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents, and…

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Asuragen hiring Advanced/ Senior Bioinformatics Analyst in Austin, Texas, United States

The Opportunity Asuragen, a Bio-Techne brand, is a global molecular diagnostics product and solutions company, and we use our unique combination of proprietary chemistry and bioinformatics to develop products that address unmet needs for both clinical research and diagnostic laboratories. Our product portfolio is comprised of reagent kits and software…

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HPC Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with technical users across EMBL-EBI, playing an…

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cannot write to FASTA lockfile

Ensembl VEP Docker: cannot write to FASTA lockfile 0 Hello, I am trying to use the Ensembl VEP tool to annotate a database after liftover. For ease of use (or so I thought) I followed all the necessary steps decribed in the official documentation. I want to use local cache…

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Senior Research Scientist, BioInformatics job with Gilead Sciences, Inc.

Senior Research Scientist, BioInformaticsUnited States – California – Foster City Gilead Sciences, Inc. is a research-based bio-pharmaceutical company that discovers, develops and commercializes innovative medicines in areas of unmet medical need. With each new discovery and investigational drug candidate, we seek to improve the care of patients living with life-threatening…

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Head of Bioinformatics & Data Mining at HUMMINGBIRD BIOSCIENCE PTE. LTD. Singapore

About Hummingbird Bioscience Hummingbird Bioscience is an innovative clinical-stage biotech company focused on developing precision therapies against hard-to-drug targets to improve treatment outcomes. We harness the latest advances in systems biology and data science to better understand and solve the underlying causes of disease and guide development of our therapeutics. Enabled…

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Gritstone bio hiring Scientist, bioinformatics in Cambridge, Massachusetts, United States

Gritstone bio is a public, next-generation immuno-oncology and infectious disease focused company. The company is leveraging its antigen discovery machine learning platform EDGETM to define targets for personalized and shared immuno-oncology therapies, as well as for developing vaccines for infectious diseases such as COVID-19. Gritstone bio is seeking a Bioinformatics…

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Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

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Answer: alphafold online availability and use case

1. There is no need for heavy-duty methods such as AlphaFold2 (AF2) in all cases. It is very unlikely that you have 1500 sequences that only have domains of unknown function, and even if you do, there were successful structure prediction servers in existence before AF2. So even though what…

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Comment: alphafold online availability and use case

Not my area of expertise particularly but; 1. I don’t think you can use a structure prediction tool to really ‘validate’ HMMER predictions. I’m pretty sure most structure predictors are relying on HMMER or similar HMM based approaches (Martin told me AlphaFold leans on HHBlits API calls for example). I…

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BUSCO installation and run

BUSCO installation and run 2 That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity: Download the image: singularity pull Run the image with example genome.fasta, assuming it’s a genome and a plant: singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l…

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