Category: shell

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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The role of CRISPR in viral diagnostics

A comprehensive new review paper, published in the journal Virsues, explains in depth how CRISPR can be utilized as a reliable tool to investigate the viral life cycles – and especially how many new CRISPR systems can be repurposed for diagnostics. Study: CRISPR Tackles Emerging Viral Pathogens. Image Credit: Nathan…

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Australian Scientists Build DNA Nanostructures for Manipulating Synthetic Liposomes

Taking inspiration from the way that bacteria send messages to each other through electromagnetic waves, Dr. Matthew Baker and Dr. Shelley Wickham have developed a new way of creating and moving droplets of DNA-infused water. This process could make it possible to store and retrieve genetic information in a biological…

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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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Genome Spotlight: Mandarinfish (Synchiropus splendidus)

If any fish deserves the name spendidus, it is the mandarinfish. Its magnificent colors have made this fish popular in the aquarium industry despite the fact that it’s covered in poison, has notoriously picky eating habits, and smells terrible. The secrets of how it produces its vibrant hues and foul…

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California Condors Are Capable of ‘Virgin Birth’

When you get to be as endangered as the California condor, your sex life becomes a highly public affair. Since 1983, when the number of California condors in existence was a mere 22, biologists have been carefully breeding the birds in captivity. They kept track of who mated with whom,…

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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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Crocodilia in Malaysian waters

DNA sequencing has found the Malaysian gharial to be a descendent of the Crocodylidia order. – Photo by Fritz Geller-Grimm/Wikimedia Commons “OF all the reptiles in Borneo, by far the most important, when it is considered in relation to man, is the Crocodile” (Robert WC Shelford – ‘A Naturalist in…

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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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sperezconesa/electroporation_modeling: Bayesian survival analysis of electroporation times from coarse grained molecular dynamics simulations performed by Dr. Lea Rems.

Authors: Sergio Pérez-Conesa, Lea Rems and Lucie Delemotte. This project uses Bayesian Survival Analysis (PYMC3) to study the rate of membrane electroporation events. The first electroporation times are obtained from coarse-grained molecular dynamics simulations using realistic membrane compositions with a constant external electric field. The simulations were run by prof….

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Oct 20 | Command Line Basics – University of Pittsburgh

Event listing from University of Pittsburgh: Wednesday, October 20 from 1:00 PM to 3:00 PM This will be a flipped class â�� a prerecorded video and a hands-on workshop â�� which will cover the basics of command-line skills for data analysis. During this class, participants will learn how to:access Center…

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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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Bioinformatics Pipeline Development with Nextflow (only 3 seats left)

Bioinformatics Pipeline Development with Nextflow How to manage your own data analysis pipelines using workflow management systems When? November 22-25, 2021 9 am – 5 pm (CET) Where? Online Link? www.ecseq.com/workshops/workshop_2021-10-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course.html Streamline your research through the development of reproducible analysis pipelines In a nutshell Learn the fundamental best-practices of bioinformatic…

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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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An Honest Perspective Through the Eyes of Homeless Kalamazoo Man

When it comes to the topic of homelessness and the impact it has on not only the community but on the people themselves, we tend to hear a lot of opinions from different sources. Opinions from politicians, from the news, and, of course, opinions readily and hastily shared on social…

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10 critical nutrients and the plant-based foods packed with them

Brent Hofacker // Shutterstock 10 critical nutrients—and the plant-based foods packed with them Nutrition labels on the foods we buy have changed significantly over the years to keep pace with updates from the Food and Drug Administration (FDA) on recommended daily values for various nutrients. As of 2020, recommended daily…

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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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Bioconductor/EuroBioC2022: European Bioconductor conference website 2022

GitHub – Bioconductor/EuroBioC2022: European Bioconductor conference website 2022 Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time This repository contains material for the European Bioconductor annual conference. View the conference web site Make sure Hugo is installed. Check hugo version Clone the repository and…

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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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CrayLabs/smartsim-lammps: Examples of running LAMMPS with SmartSim

LAMMPS is a popular Molecular Dyanmics (MD) library written in C++. This repository integrates the SmartRedis C++ client into a fork (hopefully soon to be merged) of LAMMPS for online data analysis and visualization. An example of the interactive LAMMPS visualization with ipyvolume: Example: Lennard-Jones Melt Benchmark The melt/ directory…

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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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Mean Length Of Fasta Sequences

Erlang special golfing 213 chars version: -module(g). -export([s/0]). s()->open_port({fd,0,1},[in,binary,{line,256}]),r(0,0),halt(). r(C,L)->receive{_,{_,{_,<<$>:8,_/binary>>}}}->r(C+1,L);{_,{_,{_,Line}}}->r(C,L+size(Line));_->io:format(“~p~n”,[L/C])end. Readable but reliable version: -module(g). -export([s/0]). s()-> P = open_port({fd, 0, 1}, [in, binary, {line, 256}]), r(P, 0, 0), halt(). r(P, C, L) -> receive {P, {data, {eol, <<$>:8, _/binary>>}}} -> r(P, C+1, L); {P, {data, {eol, Line}}} -> r(P,…

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NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

General This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes. The pipeline can be deployed in cloud computing environment or in dedicated computing cluster. The tool extends the CHIC aligner gitlab.com/dvalenzu/CHIC with distributed and scalable features. DHPGIndex have been tested…

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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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The 2nd place solution of 2021 google landmark retrieval on kaggle.

The 2nd place solution of 2021 google landmark retrieval on kaggle. Environment We use cuda 11.1/python 3.7/torch 1.9.1/torchvision 0.8.1 for training and testing. Download imagenet pretrained model ResNeXt101ibn and SEResNet101ibn from IBN-Net. ResNest101 and ResNeSt269 can be found in ResNest. Prepare data Download GLDv2 full version from the official site….

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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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A Tool for Rapid Sequence Comparison

MinHash Sketch is a method of rapidly comparing large strings or sets. In genomics, you can use it like this: 1) Gather all the kmers in a genome. 2) Apply a hash function to them. 3) Keep the 10000 smallest hashcodes and call this set a “sketch”. If you do…

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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 Pipeline Development with Nextflow (November 22-25, 2021)

Bioinformatics Pipeline Development with Nextflow How to manage your own data analysis pipelines using workflow management systems When? November 22-25, 2021 9 am – 5 pm (CET) Where? Online Link? www.ecseq.com/workshops/workshop_2021-10-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course.html Streamline your research through the development of reproducible analysis pipelines In a nutshell Learn the fundamental best-practices of bioinformatic…

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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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Using `Directory` as an output type

Using `Directory` as an output type 0 I’m creating a pipeline and one of my tools (let’s call it Tool 2) accepts Directory as an input, like so: “inputs”: [ { “id”: “analysis_inputs_id”, “type”: “Directory”, “inputBinding”: { “position”: 11, “shellQuote”: true } } ], My preceding tool (Tool 1) performs…

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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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40th Anniversary Recollections & Predictions

To help celebrate GEN’s 40th Anniversary with this special October issue, we asked scientists and business professionals in academia and industry to give us their reflections, impressions, and insights on the biotechnology industry and the life sciences. We also queried them on what they believe the future might look like…

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ML Kaggle Titanic Problem using LogisticRegrission

here you will find the solution for the titanic problem on kaggle with comments and step by step coding Problem Overview The sinking of the Titanic is one of the most infamous shipwrecks in history. On April 15, 1912, during her maiden voyage, the widely considered “unsinkable” RMS Titanic sank…

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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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Kaggle G2Net Gravitational Wave Detection : 2nd place solution

Solution writeup: www.kaggle.com/c/g2net-gravitational-wave-detection/discussion/275341 Instructions 1. Download data You have to download the competition dataset from competition website,and place the files in input/ directory. ┣ input/ ┃ ┣ training_labels.csv ┃ ┣ sample_submission.csv ┃ ┣ train/ ┃ ┣ test/ ┃ ┣ configs.py ┣ … (Optional:) Add your hardware configurations # configs.py HW_CFG…

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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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biopython write fasta

Step 1 − Create a file named blast_example.fasta in the Biopython directory and give the below sequence information as input. 3. “””Bio.SeqIO support for the “fasta” (aka FastA or Pearson) file format. Then we save this line of text to the output file: Now we have finished all the genes,…

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Bioinformatics Scientist in Diagenode – GrabJobs

Job Description Diagenode (a Hologic company) is an international biotech company that develops and commercializes innovative instruments and reagents systems for the life science research and molecular diagnostics. Founded in 2003, the Group is headquartered in Liège (Belgium), with subsidiaries in Denville (NJ, USA), in Toyama (Japan) and in Santiago…

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Associate Bioinformatician in Phoenix, AZ

Job:Associate Bioinformatician in Phoenix, AZ 0 TGen is a non-profit research institute located in Phoenix, Arizona. We are focused on translational science – and have been since our formation in 2002. Our immediate goal is to make a difference in the lives of patients suffering from disease. We are moderately…

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Job vacancy in Global Worldwide: Bioinformatics Analyst II – Remote at Geisinger

Job details Job type full-time Full job description 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 researchPerforms and supervises complex data extraction,…

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genbank database slideshare

Found inside – Page iiThis book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome … If you continue browsing the site, you agree to the use of…

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Lab Officer

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

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Bioinformatics Specialist – jobRxiv

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 population, but…

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Cool Bioinformatics Scripts With Python

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you have…

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GitHub – Zilong-Li/BioScripts: Cool Bioinformatics Scripts

You can use make a QQ plot in the following ways. one-liner for reading tons of millions of P values from the pipe # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia (recommand to run it in the REPL) zcat pval.txt.gz | qqplot.jl…

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PM wraps up whirlwind US visit: 20 meeting in 65 hours

During the whirlwind visit, Modi held bilateral meetings with US President Joe Biden, Vice-President Kamala Harris, Australian Prime Minister Scott Morrison and Japan Prime Minister Yoshihide Suga. Modi said it is absolutely essential to ensure that Afghanistan territory is not used to spread, terrorism, and terrorist attacks Wrapping up his…

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Cool Bioinformatics Scripts | PythonRepo

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you…

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NYU Langone Health hiring Bioinformatics Programmer in New York, New York, United States

Job ID: 1080691_RR00048323 NYU Grossman School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral…

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Tools or Method for batch analysis of Paired end WES data in a queue way.

Tools or Method for batch analysis of Paired end WES data in a queue way. 0 Hello Everyone, Hope you are doing well. So the thing is I have a Exome Analysis Script pipeline which I have written in shell. Currently it does analysis of paired end samples one by…

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New biostar-tools metaport for FreeBSD

FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running pkg install biostar-tools bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the…

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NASA Space Station On-Orbit Status 23 September, 2021 – How Space Affects Skin Processes

The Expedition 65 astronauts are moving full speed ahead today studying how living in space affects skin processes. The International Space Station is also gearing up for a busy period of spaceship activities. Rodents continue to be observed aboard the orbiting lab today so scientists can identify genes and observe…

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Rockefeller New York Science Jobs

Job: IRC26953 Description Job Title Bioinformatics Assistant Laboratory / Department Human Genetics of Infectious Disease Department Description The Laboratory of Human Genetics of Infectious Diseases studies the genetics of human predisposition to pediatric infectious diseases, particularly mycobacterial diseases, invasive pneumococcal diseases and herpes simplex encephalitis. It aims to identify Mendelian…

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Early Humans Dabbled With Fashion a Hundred Thousand Years Ago, Indicate Clues from Moroccan Cave | The Weather Channel – Articles from The Weather Channel

Carnivores were skinned for fur and bone tools were then used to prepare the furs into pelts. (Jacopo Niccolò Cerasoni, 2021) You know what they say: fashion always finds a way back—the return of bootcut jeans from the groovy 60s is a recent example. But we bet it never occurred…

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Kaggle Kaggle-Api Statistics & Issues

Issue Title State Comments Created Date Updated Date Closed Date Where is the kaggle kernel .ipynb stored? closed 1 2021-09-11 2021-09-16 2021-09-15 Bug during kernel-metadata.json generation (“competition_sources”) closed 2 2021-09-02 2021-09-16 2021-09-08 when I upload dataset I get stuck open 0 2021-08-25 2021-09-16 – Leaderboard download fails if leaderboard only…

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Linux for Biologists e-book (free to read online)

News:Linux for Biologists e-book (free to read online) 1 Hi all, I wrote this book for students and researchers in biological sciences who are new to Linux. I believe some topics discussed might be useful for beginners in Bioinformatics as well. Outline of contents: Getting started with Linux What is…

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Bioinformatics Analyst II – Remote job in Danville at Geisinger

Job Title Bioinformatics Analyst II – Remote Location Work from Home Job Category Information Technology Support Services Schedule Days Work Type Full time Department Research Informatics Department Date posted 09/22/2021 Job ID R-15599 Job Summary Primary accountability is to leverage the organization’s…

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Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome

Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome 2 Hi, I am looking for a way to download the fasta sequence of all protein coding mRNA in the escherichia coli genome. Does anyone know a simple way to do this. I would be most comfortable…

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Flavivirus-GLUE by giffordlabcvr

Overview The flaviviruses (family Flaviviridae) are a group of enveloped, positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Arthropod-borne flaviviruses such as Zika virus (ZIKV), Dengue virus (DENV), and yellow fever virus (YFV) are the causative agents of large-scale outbreaks that result…

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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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Linux for Biologists e-book is free for one more week

News:Linux for Biologists e-book is free for one more week 1 Hi all, I wrote this book for students and researchers in biological sciences who are new to Linux. I believe some topics discussed might be useful for beginners in Bioinformatics as well. Free download (on Leanpub, ends June 6)…

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Epistasis shapes the fitness landscape of an allosteric specificity switch

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

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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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Selection of DNA Aptamers Recognizing EpCAM-Positive Prostate Cancer b

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

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Affinia Therapeutics hiring Senior Scientist, Bioinformatics/Computational Biology in Waltham, MA, US

About Affinia Therapeutics Affinia Therapeutics is working to transform gene therapy through a methodically designed proprietary platform. By engineering vectors and gene constructs, Affinia is building toward revolutionary treatments for devastating diseases. Job Description Scientist/Senior Scientist, Bioinformatics/Computational Biology Affinia Therapeutics is an innovative gene therapy company with a proprietary platform…

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Obsidian Therapeutics hiring Associate Director, Computational Biology/Bioinformatics in Cambridge, MA, US

About Obsidian Therapeutics Obsidian Therapeutics is a biotechnology company using its proprietary cytoDRiVE™ technology to pioneer a new generation of controllable cell and gene therapies to treat diseases like cancer. Job Description About Us… Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s…

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Presence of male mitochondria in somatic tissues and their functional importance at the whole animal level in the marine bivalve Arctica islandica

1. Karnkowska, A. et al. A eukaryote without a mitochondrial organelle. Curr. Biol. 26, 1274–1284 (2016). CAS  PubMed  Article  Google Scholar  2. John, U. et al. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci. Adv. 5, 1–12 (2019). Article  CAS  Google Scholar  3. Breton,…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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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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python – snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

I have written a rule for CombineGVCFs in gatk4. The rule is as follow all_gvcf = get_all_gvcf_list() rule cohort: input: all_gvcf_list = all_gvcf, ref=”/data/refgenome/hg38.fa”, interval_list = prefix+”/bedfiles/hg38.interval_list”, params: extra = “–variant”, output: prefix+”/vcf/cohort.g.vcf”, shell: “gatk CombineGVCFs -R {input.ref} {params.extra} {input.all_gvcf_list} -O {output} –tmp-dir=/data/tmp -L {input.interval_list}” all_gvcf is the dataset for…

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Evidence of Fur and Leather Clothing, Among World’s Oldest, Found in Moroccan Cave | Science

A bone tool from Contrebandiers Cave likely used for making clothes out of the skin of predators. Jacopo Niccolò Cerasoni Fur is a controversial fashion statement these days. But stepping out in a wildcat cape or jackal wrap was de rigueur for Pleistocene humans, according to the recent discovery of…

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Bioinformatics Postdoctoral Research Associate job in Seattle, WA | Benaroya Research

Overview COMBATING IMMUNE DISEASE THROUGH GENOMICS ANALYSIS Come join our team and improve human health We need individuals to apply cutting edge big data approaches to study of the human immune system. We believe that understanding how the immune system is broken in diseases like cancer and autoimmunity will lead…

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Use BLAST Command Line Applications on combined FASTA files

Use BLAST Command Line Applications on combined FASTA files 1 Hi, I have been having some difficulties with blasts I am running on several species of fish. I have been trying to combine the FASTA files as it will make my blasts much easier but have noticied some oddities. If…

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Dnaman software manual

Dnaman software manual DNADynamo DNA Sequence Analysis SoftwareCLC Genomics Workbench – Qiagen They have sent a man to locate the key. He was making notes with a slim gold pen on a Gucci pad? When I married my husband, that all…

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Difficulty installing Bioperl for use with GUIDANCE

Difficulty installing Bioperl for use with GUIDANCE 0 Hi, I am trying to use the Guidance software to analyze a set of 427 sequences. I have the software downloaded and installed the modules indicated in the Guidance user guide (Perl/BioPerl/Ruby), but when I attempt to run Guidance with the following…

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Online Workshop – Bioinformatics Pipeline Development with Nextflow (November 22-25, 2021)

Bioinformatics Pipeline Development with Nextflow How to manage your own data analysis pipelines using workflow management systems When? November 22-25, 2021 9 am – 5 pm (CET) Where? Online Link? www.ecseq.com/workshops/workshop_2021-10-Bioinformatics-Pipeline-Development-with-Nextflow-Online-Course.html Streamline your research through the development of reproducible analysis pipelines In a nutshell Learn the fundamental best-practices of bioinformatic…

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Sql Server Import From Excel With Sql, Duplicate Column Names

Explore LabKey Server’s specialized tools for assay data management below and read additional documentation on the LabKey support and documentation portal. Flow. Using SQL Search you can search for the column name and find all the stored procedures where it is used. Work faster. Finding anything in the Object Explorer….

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Quest Diagnostics hiring Staff Scientist – Bioinformatics and Computational Biology in Marlborough, Massachusetts, United States

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 change…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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Regeneron hiring Associate Scientist-Bioinformatics in Tarrytown, New York, United States

SummaryThe Molecular Profiling and Data Science group is seeking a bioinformatics data scientist with experiences in OMICS data analytics and algorithm development. In this role, you will analyze preclinical and clinical data to identify novel therapeutic targets and biomarkers, as well as to develop cutting-edge algorithms and statistically sound methodologies…

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