Tag: docker

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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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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