Tag: HPC

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

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…

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ？, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

OSTHUS brings innovative scientific informatics applications to many of the world’s largest pharmaceutical, Crop Sciences and Life Sciences companies. We provide both software solutions as well as consulting expertise to help guide your business strategy in adopting valuable technologies. With teams of unique interdisciplinary experts, we help our clients solve…

<!– .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/) — ##…

This position may be based out of Santa Clara, California, USA, with remote work locations possible in The United States.Impact HealthcareRoche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools,…

Reference-based alignment using MUSKET 1 I’m running MUSKET on my dataset trimmed_data.tar.gz using 1000 threads, 2000 threads, and 4000 threads on a HPC. I’ve been unable to obtain any results because the software seems to be running for a long time. ./../musket-1.1/musket -k 90 600000000 -p 1000 -zlib 9 -ino…

Singapore, April 22, 2022 — Two collaborations were signed today between APBioNET and NSCC as well as between AMBIS and NSCC to strengthen cooperation to develop and upskill the field of bioinformatics in Singapore. The proposed activities include developing high-performance computing (HPC) capability and talent development for bioinformatics, education and…

I have a workstation with 4 GPUs. I’ve setup my machine as a single-node slurm instance. I use slurm to automate complex job pipelines in the background while I work in the foreground. So I’m not doing much HPC, I’m just using SLURM to handle job DAGs. I have a…

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 22 Mar 2022 21:59:40 +0100 Source: slurm-wlm Architecture: source Version: 21.08.6-1 Distribution: unstable Urgency: medium Maintainer: Debian HPC Team <debian-…@lists.debian.org> Changed-By: Gennaro Oliva <oliv…@na.icar.cnr.it> Changes: slurm-wlm (21.08.6-1) unstable; urgency=medium . * New upstream release * Remove fix-typos patch included upstream…

The largest AI models can require months to train on today’s computing platforms. That’s too slow for businesses. AI, high performance computing and data analytics are growing in complexity with some models, like large language ones, reaching trillions of parameters. The NVIDIA Hopper architecture is built from the ground up…

DeepMind’s AlphaFold 2 grabbed headlines last year by leveraging a transformer-based model architecture to achieve atomic accuracy in protein structure prediction. While the development of deep neural networks (DNNs) has enabled significant performance improvements across a variety of natural language processing and computer vision tasks, AlphaFold’s success showed that DNNs…

Hello, I’m trying to setup my first CycleCloud cluster, but I keep getting error in the initialization phase. In particular, it complains about not finding nodes for “nodearray hpc”. The full error message: CycleCloud Version: 8.2.0-1616 Cluster: Test2 (version 8.2.x) ============================== Status: Error [Software Configuration] (retrying) Start Time: 2022-03-13T17:31:29.377Z Description:…

please have a look if you might be interested – I’ll post directly below here as well. Timescale, as ever, is tight. Do send emails if you might be interested. Subject: Extended deadline – computational scientist positions at STFC (UK) Senior Computational Scientists – Accelerator Development and Multiscale Workflows Science…

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…

Here are the most common types of dependencies you can specify: after:job_id[:jobid…]                      This job can begin execution after the specified jobs have begun execution. afterany:job_id[:jobid…]                      This job can begin execution…

Hi there, I am recently want to try running an oxidation process.Here is my codes and report from the cluster.it can run the minimize part. After the minimization,it seems that it stop after printing” setting up verlet run”.Can you help me? Thank you So much!package omp 4 neigh no#newton onunits…

Research Associate Dr. Brent Richards is seeking a Research Associate to assist in the creation and management of a research program to improve clinical care through the use of computational genomics. The job will take place at the Lady Davis Institute of the Jewish General Hospital, a McGill University teaching…

Example: how to create temporary folders in a slurm script hpc script #!/bin/bash #SBATCH –job-name=sand_min #SBATCH -N 1 #SBATCH -n 1 ##SBATCH –gres=gpu:1 #SBATCH –partition=shortq7 #SBATCH –exclude=node[007,041,046],nodeamd[010-014],nodeeng[009-010],nodegpu001,nodenviv[100001-100002,100004-100015] #SBATCH –mail-type=ALL #SBATCH –time=6:00:00 echo “NODE NAMES = “$SLURM_NODELIST echo “CUDA_VISIBLE_DEVICES = “$CUDA_VISIBLE_DEVICES date # # Load the necessary modules, etc… # module…

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

Cloud computing and digital transformation have been powerful enablers for genomics. Genomics is expected to be an exabase-scale big data domain by 2025, posing data acquisition and storage challenges on par with other major generators of big data. Embracing digital transformation offers a practically limitless ability to meet the genomic…

I am trying to create an automatic chain of commands for analyzing biological data. For this I am using Samtools in Slurm cluster. This line below is one of the commands I run for the analysis: samtools view -h file.sam | awk ‘$6 ~ /N/ || $1 ~ /^@/’ |…

#114267 Sr. Bioinformatics Scientist-Project Manager Filing Deadline: Mon 2/14/2022 UCSD Layoff from Career Appointment: Apply by 02/02/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 02/14/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The UCSD…

The Bioinformatics Scientist will take lab-generated data and create computational models that allow further manipulation and experimentation, perform incremental analysis required to process large amounts of data generated in a high-throughput Next Generation Sequencing (NGS) laboratory devoted to analysis of genomics data with a focus on long- and short-read sequencing…

Hello, I have some questions about adding nodes in configless mode. My version of SLURM is 21.08.5. I gave logs below to ease the read of the message. First, is “scontrol reconfigure” equal to “scontrol reconfig” ? Then, I have a strange behaviour at node addition. I have an healthy…

New Job opportunity posted by European Bioinformatics Institute (EMBL-EBI): 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…

Dear LAMMPS users, I want to run a LAMMPS simulation using HPC that include the Linux version of LAMMPS (14 Dec 2021), but I face the below error just after running the simulation: ERROR: Unrecognized atom style ‘full’ is part of the MOLECULE package which is not enabled in this…

Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage? 1 I am using a SLURM HPC to run jobs and have ran into issues with storage. I have 3TB storage, and want to run over 1000 publicly available RNAseq data through my pipeline, which includes…

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

Hi, I was relatively recently told about slurm, however, as usual, I did not have time to go into details and had to quickly write scripts and subsample them “to not waste time”. Well, since recently, constantly goes out of timeout and scripts “do not finish” as simply not enough…

Optical computing startup Lightelligence has developed a new GPU that outstrips the very best GPUs on the planet — at least in the most challenging mathematical problems — with the introduction of the Photonic Arithmetic Computing Engine (PACE). VIEW GALLERY – 2 IMAGES Lightelligence’s new Photonic Arithmetic Computing Engine (PACE)…

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

Welcome to join another exciting community workshop with Juju and related projects! This time @mmrezaie will take us through an interesting deployment of Slurm charms to build a HPC cluster with juju and lxd. Meeting link: meet.google.com/ceh-zber-jnf Date: Fri 2021-12-17 09:00 – 10:00 (UTC) Abstract In this workshop we will…

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

I ran an HF calculation in Gaussian with the option formchk, and I’d like to take a look at the output orbitals. Usually I would use Gaussview, but our HPC system’s interactive desktop is down right now. The Gaussian documentation states:” formchk converts the data in a Gaussian checkpoint file…

Reports to: Samra Turajlic [C] Job Description: Project summary An exciting opportunity to be part of a pioneering biomedical research institute, dedicated to innovation and science, in the laboratory of Samra Turajlic (Cancer Dynamics, www.crick.ac.uk/research/labs/samra-turajlic). We are seeking a highly collaborative and self-motivated post-doctoral bioinformatician to work within our comprehensive…

Macbook Pro or PC laptop for bioinformatics? 3 I would like to be able to run most any of the typical ChIP-seq and RNA-seq tools (e.g. MACS2) from a home laptop computer; in other words, without access to HPC. I will be working with data from the relatively small eukaryotic…

Unable to download fastq files in parallel / SOS 0 Hi! Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language. I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:…

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:…

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….

Illumina’s Customer Collaboration & Innovation (CCI) team transforms the relationship between top-tier customers and our Product Development organization, and we are looking for a select individual to join the team as a Bioinformatics Software Engineer 2. The team works externally with a small number of Illumina’s top customers to design…

We are looking for an enthusiastic and ambitious postdoctoral fellow to study the pathophysiological bases of vascular anomalies via an integrated analysis of “omics” data (incl. single cell and bulk transcriptome, methylome, genome). The postdoctoral fellow will participate in all the omic aspects of the studies, from data analysis and…

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 part of , the Grossman School of Medicine…

Illumina’s Customer Collaboration & Innovation (CCI) team transforms the relationship between top-tier customers and our Product Development organization, and we are looking for a select individual to join the team as a Bioinformatics Software Engineer 2.  The team works externally with a small number of Illumina’s top customers to design…

Suggestions for Alternate Assembly Resources to Trinity 0 As far as I can tell, Galaxy no longer seems to support Trinity as an assembler – or at least, I have not been able to assemble any read data using Trinity for the past several months. Initially, I had had success…

Bioinformatics Analyst 40%-60%, Zurich, fixed-term 40%-60%, Zurich, fixed-term The ETH Zurich core facility NEXUS Personalized Health Technologies enables discovery and translational research for personalized health. We are recruiting a part-time Bioinformatics Analyst for the Clinical Bioinformatics Unit in Zurich to commence immediately or by mutual agreement. Job description The mission of…

Principal Bioinformatics Scientist – Cell and Gene Therapy Germany – Pharma The global Computational Biology and Digital Sciences (gCBDS) department is engaged in target discovery research and the application of innovative methods to resolve causative factors in disease progression. This is a great opportunity to lead computational projects in a…

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…

Bioinformatics / Pipeline Developer – Post DocCambridge This is a fantastic opportunity for a Post-Doc/PhD Graduate to join the R&D computational biology group as a Bioinformatics pipeline developer. This exciting company aim to transform the lives of cancer patients and their families through the development of precision treatments and ground-breaking…

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes.  We’re treating cancer, one patient at a time. Join us and make a…

Job Summary We have an exciting opportunity in our US office for an experienced bioinformatician who is interested in working at the forefront of the gene editing (CRISPR knock-out, HDR, base editing) and gene modulation (CRISPRa, CRISPRi, RNAi) fields. As a Bioinformatics Scientist 2, you will have the opportunity to…

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…

HaplotypeCaller Memory Optimization 0 When using HaplotypeCaller on GATK, is there a fixed amount of memory that works well for for the java -Xmx input, or does it scale with the size of the input bam? eg if I have a 50 GB file do I need to set -Xmx…

Job details Salary $125,001 – $135,000 a year job type full-time Full job description Job id: 2112092 Location: college park , md , us Date posted: 2021-08-12 Category: engineering and sciences Subcategory: systems engineer Schedule: full-time Shift: day job Travel: no Minimum clearance required: public trust Clearance level must be…

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

6500 – The number of associates in the Novartis Institutes for BioMedical Research (NIBR). This division is the innovation engine of Novartis, focusing on powerful new technologies that have the potential to help produce therapeutic breakthroughs for patients. We are seeking a bioinformatics scientist to coordinate the processing and…

The Bioinformatics and Whole Genome Sequencing (WGS) Software Development unit is part of Data Analytical Sciences within PHE’s National Infection Service Division. The unit is globally pre-eminent in the design, construction, validation and deployment of bioinformatics pipelines for the automated analysis of Next Generation Sequencing (NGS) whole Genome Sequence (WGS)…

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

Job Information Role Overview We are currently looking for a Bioinformatics Pipeline Developer to join a leading Biotech company based in the Cambridgeshire area. As the Bioinformatics Pipeline Developer you will be working on early cancer detection technology by supporting software developers and bioinformaticians Key Duties and Responsibilities 1. The…

JOB DESCRIPTION: The Human Genetics Department is currently offering an temporary employee position for students or working professionals in Bioinformatics/Computational Biology to join its Bioinformatics Team. The successful candidate will be actively engaged in mining the human genetics and genomics data to identify and prioritize targets. The successful candidate will be…

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…

Northumbria University is a member of the COVID-19 Genomics UK Consortium (COG-UK).  COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. We seeking to…

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

Genmab is focused on the creation and development of innovative and differentiated antibody products, with the aim of improving the lives of cancer patients. The Role The successful candidate will lead the global bioinformatics function and be responsible for many aspects of data including architecture, access, classification, standards, integration, pipelines…

The role We are looking for an experienced bioinformatician to provide support for academic users of the University of Bristol Genomics facility and to teach on our Bioinformatics Masters course. What will you be doing? The role holder will be working as part of the Genomics Facility team, a core…

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…

You will have: • B.S./M.S. in Computer Science or Bioinformatics, with 2-4 years of related professional experience• Domain knowledge in bioinformatics and experience in working with omics data• Experience with a combination of Python, R• Experience working in Linux environment and proven knowledge of Linux command line utilities• Experience with…

Description Purpose: The UPMC Genome Center is a clinical grade, full-service, high-throughput genome center with sequencing options designed for both clinical and research needs. We are looking for members to join our Bioinformatics team for analysis of a wide spectrum (Whole Exome/Genome Germline and Somatic, RNAseq, scRNAseq) of NGS data…

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…

Job Description6,000 people dedicated to discovery – 6 research campuses across the globe – 1 purpose…to reimagine medicine! Novartis Institutes for BioMedical Research (NIBR) is the innovation engine of Novartis, focusing on powerful new technologies that have the potential to help produce therapeutic breakthroughs for patients. We are seeking a…

I am having some trouble with REditools2 (HPC-Reditools). In the original version of reditools there was a python script for de-novo prediction of editing sites from RNAseq data using a strategy outlined in Picardi et al 2012. I assumed reditools2 would have this same feature. However, after inputting the appropriate…

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…

In KisSplice, I already set “ulimit -s unlimited”, but I am still getting stack limit error. Is there a work around this? 1 Objective: I am trying to use kissplice to obtain SNPs from my RNA-seq (fastq) data. Problem: Even after setting the stack limit to unlimited, I am still…

  Job Seekers, Welcome to HERC Jobs Senior Programmer Analyst/Bioinformatics Columbia University Columbia University Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range: Commensurate with experience  …

The Gene Expression Team analyses expression data sets at tissue or single cell level and develops Expression Atlas, a resource that provides information about the expression of genes and proteins in different cells, tissues, developmental stages and conditions. Your role We are looking for a data production service bioinformatician to…

About the team/job EMBL is Europe’s flagship research organization for the life sciences – an intergovernmental organization with more than 80 independent research groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its approx. 2000 employees of more than 80 nationalities, operate across six sites…

Error when Phasing with Beagle 5.2 0 I’m having trouble phasing a multi-sample (9-samples) vcf file produced by gatk HaplotypeCaller with Beagle 5.2. I do not have a genetic map or reference panel. I am working with a very heterozygous group of organisms (sea urchins). When I run beagle with…

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…