Tag: cluster

Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions

GROMACS version: 2024-dev-20240201-787d96c7a9-unknownGROMACS modification: YesI’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a single node. GROMACS build infoHere, GROMACS was built using GCC v11.4.0, uses OpenMP and OpenMPI v4.1.5, and builds its own FFTW v3.3.8. JUWELS Cluster…

Continue Reading Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions

What’s New in IntelliJ IDEA Ultimate 2023.3

Releases The Ultimate edition of IntelliJ IDEA goes beyond the basics, offering a comprehensive suite of features, including in-depth profiling capabilities, database tools, built-in support for many web and enterprise frameworks, and more. In this latest v2023.3 release, we’ve rolled out a suite of new features to enhance your coding…

Continue Reading What’s New in IntelliJ IDEA Ultimate 2023.3

GenomeFace: a deep learning-based metagenome binner trained on 43,000 microbial genomes

Abstract Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution…

Continue Reading GenomeFace: a deep learning-based metagenome binner trained on 43,000 microbial genomes

King’s College London hiring Research Associate in Translational Bioinformatics in London, England, United Kingdom

Job DescriptionThis is a Pre-Fellowship for early career researchers wanting to establish a career in MND translational research and become MND research leaders of the future. The postholder will have a leading role in an exciting new project funded by Motor Neurone Disease Association and MND Scotland. The project is…

Continue Reading King’s College London hiring Research Associate in Translational Bioinformatics in London, England, United Kingdom

Deploying OpenAPI Helm Chart on AWS EKS

To deploy the OpenAPI Helm chart on AWS Elastic Kubernetes Service (EKS), we’ll follow these steps: Create an EKS cluster. Configure Kubeconfig to interact with your cluster. Use the Pulumi Kubernetes provider to deploy the OpenAPI Helm chart using kubernetes.helm.v3.Chart. Before we begin, ensure you have the following prerequisites in…

Continue Reading Deploying OpenAPI Helm Chart on AWS EKS

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

Continue Reading A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

NYU High Performance Computing – HPC Projects

Depending on your role, you will see the corresponding interface at the Portal. HPC Project Owner You can register an HPC project if you are a full-time faculty and sponsoring a currently active HPC account for research or instruction. If you are a part-time faculty teaching a course, please get…

Continue Reading NYU High Performance Computing – HPC Projects

Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

Continue Reading Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration

Structure-guided discovery of anti-CRISPR and anti-phage defense proteins

Identification of putative anti-crispr proteins using structural features To identify Acrs in phage genomes, we began by retrieving ~66.5 million proteins from Integrated Microbial Genomes Virus database (IMG/VR)37. We excluded large proteins because over 90% of known Acrs contain less than 200 amino acids38 (Fig. 1A, Supplementary Data 1). To reduce computational…

Continue Reading Structure-guided discovery of anti-CRISPR and anti-phage defense proteins

504 gateway timeout rstudio ondemand – IFB Core Cluster

Hi, I’m trying to access rstudio via the ondemand portal but independently of how many resources I allocate to it I can’t connect to the rstudio and get error 504 gateway timeout when trying to access the instance. I can regularly access rstudio from the rstudio older portal but I’m…

Continue Reading 504 gateway timeout rstudio ondemand – IFB Core Cluster

Cluster Information – SLING user documentation

Slurm offers a range of commands for interacting with the cluster. In this section, we will explore some examples of using the sinfo, squeue, scontrol, and sacct commands, which provide valuable insights into the cluster’s configuration and status. For comprehensive information on all the commands supported by Slurm, please refer…

Continue Reading Cluster Information – SLING user documentation

UC San Diego’s Bioengineering Team Uses TSCC at SDSC for Bioinformatics Tool

Jan. 19, 2024 — Over 18 million people worldwide are annually diagnosed with cancer, with each case hiding many mutations in its genome. Understanding these mutations furthers cancer research, while also providing a deeper understanding to create possible cures, therapies and prevention strategies. The Triton Shared Computer Cluster at the…

Continue Reading UC San Diego’s Bioengineering Team Uses TSCC at SDSC for Bioinformatics Tool

Stochastic biological system-of-systems modelling for iPSC culture

Cell proliferation and aggregation dynamics modeling The aggregation process is characterized by the dynamic evolution of a density profile of aggregates. Let \(\phi (x,t)\) denote the average number of aggregates or clusters of size \(x\) (i.e., mass and volume) at time \(t\), where mass is equal to a buoyant density…

Continue Reading Stochastic biological system-of-systems modelling for iPSC culture

[slurm-users] GPU devices mapping with job’s cgroup in cgroups v2 using eBPF

Hello all, Happy new year! We have recently upgraded the cgroups on our SLURM cluster to v2. In cgroups v1, the interface `/devices.list` used to have the information of which device has been attached to that particular cgroup. From my understanding, cgroups v2 use eBPF to manage devices and so…

Continue Reading [slurm-users] GPU devices mapping with job’s cgroup in cgroups v2 using eBPF

Sox2 Gene Enhancers: Unraveling Cancer’s Genetic Secrets

Unveiling Cancer’s Genetic Mechanisms: Role of Sox2 Gene Enhancers In a groundbreaking study led by Professor Jennifer Mitchell at the University of Toronto’s Department of Cell and Systems Biology, vital insights were garnered on the role of ‘enhancer’ regions in gene expression and their implications for cancer growth. Enhancers, non-coding…

Continue Reading Sox2 Gene Enhancers: Unraveling Cancer’s Genetic Secrets

CRISPR Therapeutics Highlights Strategic Priorities and

ZUG, Switzerland and BOSTON, Jan. 08, 2024 (GLOBE NEWSWIRE) — CRISPR Therapeutics (Nasdaq: CRSP), a biopharmaceutical company focused on creating transformative gene-based medicines for serious diseases, today highlighted its strategic priorities and 2024 outlook as the Company enters its next phase of growth. “We had a landmark year in 2023, marked…

Continue Reading CRISPR Therapeutics Highlights Strategic Priorities and

The best countries for biotech according to the OECD

The OECD recently published an update on key biotechnology indicators, an opportunity for us to delve into the top-performing countries in the field. With the highest number of active biotech companies (2,840) and an R&D intensity added value of 17%, the U.S. remains a strong leader in the industry. But…

Continue Reading The best countries for biotech according to the OECD

Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control

Isolate characteristics From June 2020 to October 2021, our analysis included a total of 28 isolates from patient and environmental samples, all subjected to Whole Genome Sequencing (WGS) (refer to Table 1). To ensure robustness and minimize the influence of sequencing errors on our findings, all 28 WGS datasets maintained a…

Continue Reading Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control

hpc – For SLURM clusters why do we need to specify memory allocation for jobs?

It’s not so much a problem of allocating memory, but of knowing the shape of the workload to place it optimally (or at least non-problematically) in the cluster. The point is so that jobs can be placed on nodes with sufficient memory to handle the task. This avoids problems that…

Continue Reading hpc – For SLURM clusters why do we need to specify memory allocation for jobs?

Assistant Professor of Biology – Bioinformatics Job in Georgia

Assistant Professor of Biology – BioinformaticsGeorgia Southern University – Statesboro, GAAbout Us Join Our Team at Georgia Southern! Georgia Southern is a dynamic university with three vibrant campuses in Hinesville, Savannah and Statesboro serving the communities in Southeast Georgia. As a Carnegie Doctoral/R2 institution, our world-class scholars…

Continue Reading Assistant Professor of Biology – Bioinformatics Job in Georgia

Mozambique – Food Security Outlook Update, December 2023 – Mozambique

Attachments El Niño impacts likely to increase humanitarian needs in 2024 Key Messages Crisis (IPC Phase 3) and Stressed (IPC Phase 2) outcomes are present in southern and central areas most impacted by climate shocks in 2023, where very poor households have already depleted their food stocks earlier than usual.Household…

Continue Reading Mozambique – Food Security Outlook Update, December 2023 – Mozambique

Top 20 Hadoop Competitors and Alternatives

Hadoop is an open-source big data analytics platform headquartered in Baltimore, Maryland. The solution evolved from the Google File System paper published by Doug Cutting and Mike Cafarella in October 2003 as part of the Apache Nutch project. The co-founders moved the platform to the Hadoop subproject in 2006. In…

Continue Reading Top 20 Hadoop Competitors and Alternatives

Solved You are expected to visit data repositories such as

You are expected to visit data repositories such as Kaggle, UCI Machine learning repository, PROMISE, etc. and extract three different datasets in the areas of classification, clustering and regression respectively. Note that the dataset for classification should be unbalanced [3 marks]. • Preprocess the datasets based on the following issues…

Continue Reading Solved You are expected to visit data repositories such as

Help getting the right blob mount permissions – Zero to JupyterHub on Kubernetes

Hello,I have a cluster running on AKS after following the guideI am trying to mount a static Azure Blob Storage (bring your own storage) shared by all of the singleuser pods (I have a custom spawner that mounts subdirectories of the blob). I have setup an SC, PV, and PVC…

Continue Reading Help getting the right blob mount permissions – Zero to JupyterHub on Kubernetes

Problem getting GPU solving to work with our Azure CycleCloud / Slurm HPC cluster System

I am using the Azure CycleCloud 8.4 Marketplace image and it is fully updated, along with Slurm version 22.05.8-1. I have configured a GPU Enabled Slurm Partition consisting of some NC24sv3 VMs (which have 4x Nvidia Tesla V100 GPUS in each), but the Slurm Scheduler is showing the Partition as…

Continue Reading Problem getting GPU solving to work with our Azure CycleCloud / Slurm HPC cluster System

GPATCH4 regulates rRNA and snRNA 2′-O-methylation in both DHX15-dependent and DHX15-independent manners

doi: 10.1093/nar/gkad1202. Online ahead of print. Nidhi Kanwal  1 , Nicolai Krogh  2 , Indira Memet  1 , Nicolas Lemus-Diaz  1 , Chairini C Thomé  1 , Luisa M Welp  3   4 , Athanasia Mizi  5 , Philipp Hackert  1 , Argyris Papantonis  5 , Henning Urlaub  3   4   6   7 , Henrik Nielsen  2 , Katherine…

Continue Reading GPATCH4 regulates rRNA and snRNA 2′-O-methylation in both DHX15-dependent and DHX15-independent manners

2024 Ford Kuga facelift spied in new rugged Active trim

We’ve been patient but now it looks like the facelifted Ford Kuga’s arrival in the UK is imminent with specifications unveiled on CAP’s automotive data site. We expect Ford’s refreshed family SUV to go on sale here in early 2024.  As ever, the Kuga’s competition will be stiff. There’s the…

Continue Reading 2024 Ford Kuga facelift spied in new rugged Active trim

ML Pipelines on GCP with Vertex AI

20 Nov 2023 by dzlab Vertex AI Pipelines are a platform for building and running machine learning workflows on Google Cloud Platform. They allow the orchestration of machine learning tasks using pre-built or custom components, and leverage the serverless and scalable infrastructure of Vertex AI. Vertex AI Pipelines is based…

Continue Reading ML Pipelines on GCP with Vertex AI

cluster analysis – The enrichWP function is no longer recognized in `comparecluster()` (clusterProfiler R package)

I have been using clusterProfiler for quite a while, specifically the compareCluster() function. I have used enrichKEGG()and enrichWP()for my workflow since January 2023. But now fun = “enrichWP” isn’t recognized in the comparecluster() function. Indeed when checking the R doc, it does now state for the fun argument : One…

Continue Reading cluster analysis – The enrichWP function is no longer recognized in `comparecluster()` (clusterProfiler R package)

Seroprevalence and Molecular Characterization of B. abortus

Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…

Continue Reading Seroprevalence and Molecular Characterization of B. abortus

Bwa-mem2 indexing not working down stream

Bwa-mem2 indexing not working down stream 0 I am using bwa-mem2 to create my index and to map my reads to the reference genome. This is my indexing code #!/bin/bash #SBATCH -J index #SBATCH -A gts-rro3 #SBATCH -N 1 –ntasks-per-node=24 #SBATCH –mem-per-cpu=8G #SBATCH -t 1:00:00 #SBATCH -o index.out cd $SLURM_SUBMIT_DIR…

Continue Reading Bwa-mem2 indexing not working down stream

Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

Continue Reading Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

The year in Google Cloud: Top news of 2023

In the world of technology and cloud computing, the news comes fast and furious. Blink and you’ll miss it. As we wind down the final days of 2023, here’s a look at the top stories of the year that we published on the Google Cloud blog — the product launches,…

Continue Reading The year in Google Cloud: Top news of 2023

Characteristics of Amorphophallus konjac as indicated by its genome

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

Continue Reading Characteristics of Amorphophallus konjac as indicated by its genome

Ford Kuga facelift to go back to basics with new entry-level Active trim

We’ve been patient but now it looks like the facelifted Ford Kuga’s arrival in the UK is imminent with specifications unveiled on CAP’s automotive data site. We expect Ford’s refreshed family SUV to go on sale here in early 2024.  As ever, the Kuga’s competition will be stiff. There’s the…

Continue Reading Ford Kuga facelift to go back to basics with new entry-level Active trim

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

Continue Reading Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach

Bacterial profile variations in mock communities at the genus level While 16S rRNA metabarcoding only identified bacteria and archaea, Saccharomyces cerevisiae and Cryptosporidium were only identified by a shotgun metagenomics approach. Only three metabarcoding partners (P1, P4, and P5), out of six, detected all eight bacterial species present in the…

Continue Reading Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach

Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185…

Continue Reading Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer

Confusion about “Top Features table” in cellranger web summary output for CITE-Seq libraries

Confusion about “Top Features table” in cellranger web summary output for CITE-Seq libraries 0 I am reviewing the Web Summary (count) documentation on the 10X genomics website and became confused as to what is being displayed in the Top Features by Cluster table under the Antibody tab (see screenshot below)….

Continue Reading Confusion about “Top Features table” in cellranger web summary output for CITE-Seq libraries

Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

Continue Reading Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Dihedral atom missing error on lammps – LAMMPS

Dear All, I have a linear coarse-grained polymer system, with nonbonded, bond, angle, and dihedral interactions as a tabulated potential. My simulations consist of 1000 polymer chains, each chain has 200 monomers. The simulations sometimes crash because of dihedral atom missing errors in some processors. I am running the latest…

Continue Reading Dihedral atom missing error on lammps – LAMMPS

Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

Continue Reading Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Ray on Vertex AI: Let’s get it started | by Ivan Nardini | Google Cloud – Community | Dec, 2023

Figure 1 — Image from author At Next 2023, Google Cloud announced Ray on Vertex AI, a managed service that provides scalability for AI and Python applications using Ray.As a Vertex AI developer, you may be wondering: As a Vertex AI developer, you may be wondering: What is Ray? Why…

Continue Reading Ray on Vertex AI: Let’s get it started | by Ivan Nardini | Google Cloud – Community | Dec, 2023

bwa-mem reproducibility

bwa-mem reproducibility 1 I have a set of paired end fastq files, and I run bwa-mem (v0.7.17-r1188) on the files with the same exact parameters, including the same number of threads, in two different computing clusters. I compare the BAM file produced via samtools stats. and the outputs are different…

Continue Reading bwa-mem reproducibility

Gut Microbiome and Bifidobacterium Research in Zimbabwe

Introduction The Infant Gut Microbiome Untangling what constitutes a healthy gut microbiome is timely, particularly in low- and middle-income (LMIC) settings where problems of infant nutrition, chronic diarrhea, and failure to thrive are high priority.1,2 Studying the infant gut microbiome is also crucial as many of the events capable of…

Continue Reading Gut Microbiome and Bifidobacterium Research in Zimbabwe

Binning the rare biosphere

Hello everyone. I would like to start a discussion here. Recently, I responded to a question on Seqanswers regarding the binning of rare microbes from shotgun metagenomes (www.seqanswers.com/forum/applications-forums/metagenomics/324515-software-recommendation-for-metagenome-assembly-for-low-abundance-bacteria). I suggested an idea for an appropriate pipeline for this task, but unfortunately, it did not gain much attention. Nevertheless, I tried…

Continue Reading Binning the rare biosphere

Single-cell RNA-seq workflow

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

Continue Reading Single-cell RNA-seq workflow

Phylogenomic analysis of 343 Xanthomonas citri pv. citri strains unravels introduction history and dispersal paths

. 2023 Dec 15;19(12):e1011876. doi: 10.1371/journal.ppat.1011876. Online ahead of print. Jin Xu  1 , Yanan Zhang  1 , Jinyun Li  1 , Doron Teper  1 , Xiaoan Sun  2 , Debra Jones  2 , Yayu Wang  3 , Jin Tao  4 , Erica M Goss  5   6 , Jeffrey B Jones  5 , Nian Wang  1 Affiliations Expand Affiliations…

Continue Reading Phylogenomic analysis of 343 Xanthomonas citri pv. citri strains unravels introduction history and dispersal paths

Obtain satellite DNA monomer from dot plot

Obtain satellite DNA monomer from dot plot 1 I have come across numerous articles in which researchers extract monomers of satellite DNA, creating dot plots from contigs that contain this satellite. For instance, in the article linked doi: 10.3390/ijms22116052 the process is described as follows: ‘For each candidate cluster, we…

Continue Reading Obtain satellite DNA monomer from dot plot

Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry

To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…

Continue Reading Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry

Bioinformatics Scientist – Job at Spectraforce Technologies in Cambridge, MA

Title: Bioinformatics Scientist Location: Cambridge, MA 02141 Duration: 12 Months Pay rate starts from $70/hr. Note: * Shift: M-F(9am-6pm)EST * Work location: Cambridge, MA-Hybrid (2 days/week) or Remote (ideally, eastern time zone) Qualifications: Education Minimum Requirement: * Ph.D. (or 5+ years of relevant experience) in Bioinformatics, Biostatistics, Computational…

Continue Reading Bioinformatics Scientist – Job at Spectraforce Technologies in Cambridge, MA

Error in calculating inter-individual divergence / spread

Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…

Continue Reading Error in calculating inter-individual divergence / spread

X-Line trim in a detailed walkaround video

Kia India has finally revealed the Sonet facelift in India. The bookings for this all-new updated model will commence from the 20th of December, and the price reveal will be done next year. Currently, the company has shown the vehicle in the flesh, and walkaround videos of this sub-compact SUV…

Continue Reading X-Line trim in a detailed walkaround video

Upcoming Google Event Highlights & Insights

The recently held Google Cloud Next event in San Francisco was a major highlight of the year, featuring keynotes from Google’s top management, 161 announcements, and thousands of attendees. The event emphasized the importance of artificial intelligence (AI) in driving innovation across various industries and highlighted the latest developments in…

Continue Reading Upcoming Google Event Highlights & Insights

Condition specific marker detection and problem with the distribution of cells from different samples

Condition specific marker detection and problem with the distribution of cells from different samples 1 I have 6 scRNAseq samples and made a umap using all cells from all 6 samples and in the UMAP every sample has a different color (in total 6 colors) and the goal was to…

Continue Reading Condition specific marker detection and problem with the distribution of cells from different samples

Gadolinium Oxide Nanoparticles reinforce immune response

Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…

Continue Reading Gadolinium Oxide Nanoparticles reinforce immune response

Jupyterhub z2jh ingress not working – Zero to JupyterHub on Kubernetes

bpfrd December 15, 2023, 6:54pm 1 Hi, I deployed z2jh on a single-node microk8s cluster on a server and it is supposed to be used in production. The problem is ingress address is missing. here is some details: # config.yaml ingress part ingress: annotations: kubernetes.io/tls-acme: “true” enabled: true hosts: -…

Continue Reading Jupyterhub z2jh ingress not working – Zero to JupyterHub on Kubernetes

Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

Continue Reading Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

Slurm job submisson script: assigning gpus to separate processes when asking for multiple nodes

I’m trying to submit a slurm job that requires 8 gpus. The cluster I am submitting to has 2 gpus per node and therefore I request 4 nodes. I was wondering how can I construct my job submission script so that 32 processes are split amongst the 8 gpus (4…

Continue Reading Slurm job submisson script: assigning gpus to separate processes when asking for multiple nodes

Whole-Lung 3D Reconstruction Using Medical Image Processing Technology

To begin, copy the patient’s digital imaging and communications in medicine, or DICOM data, to a defined working directory. Using the file browser, examine each file directory to identify the image sequence with the highest number of scanning layers for analysis. Employ the DICOM function within MATLAB by providing DICOM…

Continue Reading Whole-Lung 3D Reconstruction Using Medical Image Processing Technology

Page not found at /mature/MIMAT0027893?acc=MIMAT0027893

Page not found at /mature/MIMAT0027893?acc=MIMAT0027893 Using the URLconf defined in mirbase_new.urls, Django tried these URL patterns, in this order: __debug__/ admin/ [name=”home”] __debug__/ ajax/draw_reads_plot/<slug:accession> [name=”ajax_draw_reads_plot”] ajax/draw_reads_plot_mismatch/<slug:accession> [name=”ajax_draw_reads_plot_mismatch”] ajax/load-chromosomes/ [name=”ajax_load_chromosomes”] ajax/load-tissues/ [name=”ajax_load_tissues”] ajax/load-experiments/ [name=”ajax_load_experiments”] ajax/load-hairpins-for-mature/ [name=”ajax_load_hairpins_for_mature”] ajax/load-papers/ [name=”ajax_load_papers”] ajax/page-clusters/ [name=”ajax_page_clusters”] ajax/load-clusters/ [name=”ajax_load_clusters”] ajax/load-sentences/ [name=”ajax_load_sentences”] ajax/load-reads/ [name=”ajax_load_reads”] ajax/load-reads-mismatches/ [name=”ajax_load_reads_mismatches”] ajax/load-results/ [name=”ajax_load_results”] ajax/get-sequences/…

Continue Reading Page not found at /mature/MIMAT0027893?acc=MIMAT0027893

Formononetin | FGFR2 inhibitor | Axon 4067

All All Products Enzymes Receptors Ion Channels Research Areas Oxidoreductases Transferases Lyases Isomerases Ligases Nuclear Receptors Ligand-gated ATP-Sensitive Angiogenesis Apoptosis Cardiovascular Cell Cycle Regulation Cell Signaling & Oncology CNS Diabetes & Metabolism Epigenetics Immunology Miscellaneous Pain & Inflammation Stem Cell Oxidases MAO Cys-loop, cationic Cis-Trans Isomerase CypA DNA Topoisomerase Synthetases…

Continue Reading Formononetin | FGFR2 inhibitor | Axon 4067

Genetic basis of osteogenesis imperfecta from a single tertiary centre in South Africa

We used ES, gene panel testing, and a single variant test to achieve a diagnostic yield of 100% for patients with OI in this study. The patient demographic is representative of the Western Cape Province, with Tygerberg Hospital being the largest tertiary referral centre in the province. Since it is…

Continue Reading Genetic basis of osteogenesis imperfecta from a single tertiary centre in South Africa

Study uncovers unique genetic diversity in Australian Indigenous populations

Scientists at the Australian National University (ANU) have comprehensively analyzed the genomes of Australian Indigenous communities and found a rich genetic diversity. Their study is published in the journal Nature. Study: Indigenous Australian genomes show deep structure and rich novel variation. Image Credit: ChameleonsEye / Shutterstock Background Genetic structures of Australian Indigenous…

Continue Reading Study uncovers unique genetic diversity in Australian Indigenous populations

Senior R Studio Administrator – Remote – EPAM Systems

If you are looking for a high-impact Senior R Studio Administrator with a global leader in digital transformation, EPAM is the perfect next step in your career! As an EPAMer, you’ll have the opportunity to work with a supportive team, on a variety of interesting projects for some of the…

Continue Reading Senior R Studio Administrator – Remote – EPAM Systems

Wrangling And Analyzing Data In RStudio

Article Summary Box Efficient data preparation in RStudio hinges on automated data cleaning techniques, significantly reducing manual errors and streamlining the initial stages of analysis. Vectorized operations and the apply() family functions in RStudio dramatically enhance data manipulation efficiency, especially for large datasets. Utilizing multiple linear regression and PCA in…

Continue Reading Wrangling And Analyzing Data In RStudio

A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…

Continue Reading A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…

Continue Reading A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus

Dynamic mRNA signatures in the early phase of epileptogenesis after Pilocarpine-induced SE To decipher transcriptional changes early after pilocarpine-induced SE in the hippocampal CA1 subfield, we compared mRNA expression profiles of pilocarpine-induced SE animals and non-SE controls in hippocampal CA1 at five different time points, i.e. 6, 12, 24, 36…

Continue Reading Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus

Conserved and divergent gene regulatory programs of the mammalian neocortex

Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…

Continue Reading Conserved and divergent gene regulatory programs of the mammalian neocortex

2024 Chevelle 70/SS: Every Trim Compared

The Chevrolet Chevelle is one of the most iconic muscle cars from the golden era of America’s motor industry. Fast-forward to today and the legendary Chevelle costs upwards of $100,000 in good condition, and thanks to the immense rarity of the model, these prices aren’t likely to soften any time…

Continue Reading 2024 Chevelle 70/SS: Every Trim Compared

Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

Continue Reading Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023

docs.stackable.tech/home/stable/demos/jupyterhub-pyspark-hdfs-anomaly-detection-taxi-data So, this is an article in an ongoing series where I investigate the deployment tools of Stackable.tech This firm supplies supported versions of many open source data engineering tools to easily build data platforms on Kubernetes (k8s) clusters. These can be on your own premises, in a data centre,…

Continue Reading Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023

Lightning AI’s new platform is a one-stop shop for developers

Lightning AI, the vendor behind the popular open source Python library Pytorch Lightning, is out with a new AI studio that makes it easier for developers to build, train and develop AI models on the cloud. Unveiled on Dec. 13, Lightning AI Studios is an all-in-one platform that unites…

Continue Reading Lightning AI’s new platform is a one-stop shop for developers

Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

Continue Reading Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer

How To Install slurm-doc on Rocky Linux 8

In this tutorial we learn how to install slurm-doc on Rocky Linux 8. slurm-doc is Slurm documentation Introduction In this tutorial we learn how to install slurm-doc on Rocky Linux 8. What is slurm-doc Documentation package for Slurm. Includes documentation and html-based configuration tools for Slurm. We can use yum…

Continue Reading How To Install slurm-doc on Rocky Linux 8

R ComplexHeatmap – Adujusting the cell size in heatmap

I think the main thing is not to use “width = width/2” in cell_fun1. Using ComplexHeatmap 2.14.0 on R 4.2.1 i was able to modify cell width and height via width and height params in call to Heatmap. I tried a few different widths and heights and each time the…

Continue Reading R ComplexHeatmap – Adujusting the cell size in heatmap

Lightning AI Unveils Lightning AI Studios to Advance the AI Development Landscape

NEW YORK, Dec. 13, 2023 — Lightning AI, the company behind PyTorch Lightning, with over 91 million downloads, today announced the introduction of Lightning AI Studios, the culmination of three years of research into the next-generation development paradigm for the age of AI. Software 1.0 such as web apps, servers, etc.,…

Continue Reading Lightning AI Unveils Lightning AI Studios to Advance the AI Development Landscape

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Prediction with AlphaFold2 and AlphaFold-Multimer For each PDB the release date in the Protein Data Bank34 was recorded. AlphaFold 2 (2.2.2) was run setting the –max_template_date flag to be the day before the release date of the PDB and the –model_preset to be either monomer for AF or multimer for…

Continue Reading Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

[slurm-users] Slurm versions 23.11.1, 23.02.7, 22.05.11 are now available (CVE-2023-49933 through CVE-2023-49938)

Slurm versions 23.11.1, 23.02.7, 22.05.11 are now available and address a number of recently-discovered security issues. They’ve been assigned CVE-2023-49933 through CVE-2023-49938. SchedMD customers were informed on November 29th and provided a patch on request; this process is documented in our security policy. [1] There are no mitigations available for…

Continue Reading [slurm-users] Slurm versions 23.11.1, 23.02.7, 22.05.11 are now available (CVE-2023-49933 through CVE-2023-49938)

Single-cell analysis of chromatin accessibility in the adult mouse brain

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

Continue Reading Single-cell analysis of chromatin accessibility in the adult mouse brain

A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception

Identification of novel TAS1R family members We identified homologues of TAS1R genes that are included in public genome/transcriptome databases for diverse taxa of jawed vertebrates (Supplementary Table 1). Except for jawed vertebrates, TAS1R genes were not identified in any Deuterostomia reference genomes (lampreys, hagfishes, tunicates, lancelets, sea urchins, starfish, hemichordate,…

Continue Reading A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception

Indigenous Australian genomes show deep structure and rich novel variation

Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…

Continue Reading Indigenous Australian genomes show deep structure and rich novel variation

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

Continue Reading Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Bioactive glycans in a microbiome-directed food for children with malnutrition

Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…

Continue Reading Bioactive glycans in a microbiome-directed food for children with malnutrition

The landscape of genomic structural variation in Indigenous Australians

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Continue Reading The landscape of genomic structural variation in Indigenous Australians

Lightning AI Introduces Lightning AI Studios; its Enterprise-Grade Platform for Rapid-prototyping, and Deploying AI Products

Article content The ‘Operating System’ for AI Development; Lightning AI Studios is The Enterprise-Grade Platform that Allows AI Developers to Code on Cloud GPUs from the Browser or their Laptops with Zero Setup NEW YORK — Lightning AI, the company behind PyTorch Lightning, with over 91 million downloads, today announced…

Continue Reading Lightning AI Introduces Lightning AI Studios; its Enterprise-Grade Platform for Rapid-prototyping, and Deploying AI Products

Lightning AI debuts ‘iPhone approach’ to new AI dev platform

Are you ready to bring more awareness to your brand? Consider becoming a sponsor for The AI Impact Tour. Learn more about the opportunities here. Lightning AI, the company behind popular open source framework PyTorch Lightning, has launched Lightning AI Studios, an enterprise-grade, all-in-one cloud-based platform for building and deploying…

Continue Reading Lightning AI debuts ‘iPhone approach’ to new AI dev platform

Topological structures and syntenic conservation in sea anemone genomes

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

Continue Reading Topological structures and syntenic conservation in sea anemone genomes

Galaxy Macau officially launches the newest phase of its resort

Galaxy Entertainment Group (GEG) held a formal ceremony today to mark the completion of its Phase 3 expansion project, almost two years after it announced the end of construction in February 2022.  Phase 3 consists of three buildings – the 700-room Andaz hotel, the 450-suite Raffles hotel and the 40,000-square-metre…

Continue Reading Galaxy Macau officially launches the newest phase of its resort

Top 10 Kaggle ML Projects To Work On In 2024 To Become Data Scientists

ML projects are the first steps in becoming a Data Scientist in the field of Machine Learning. These projects give them hands-on experience dealing with real-world datasets, which helps them improve their data science abilities. In addition to learning how to handle big information, working on these projects helps data…

Continue Reading Top 10 Kaggle ML Projects To Work On In 2024 To Become Data Scientists

Query about Atom Index Ordering in GROMACS 2021.0 and 2023.3 – Developers discussions

Lorien December 12, 2023, 10:55am 1 Hello. I am developing a constraint algorithm and primarily working with GROMACS 2021.0. In executions without domain decomposition and with constraints set to all-bonds, the atom indices appear to follow an order similar to that in the PDB file. For instance, in simulations involving…

Continue Reading Query about Atom Index Ordering in GROMACS 2021.0 and 2023.3 – Developers discussions

Comprehensive Review of Small Interfering RNAs (siRNAs)

Introduction Cancer, also called malignancy, is a group of diseases caused by the rapid multiplication and spread of malignant cells.1,2 According to statistics from the National Cancer Center, more than 100 types of cancer have been identified.3 The ability of malignant tumor cells to metastasize via the blood-lymphatic system and…

Continue Reading Comprehensive Review of Small Interfering RNAs (siRNAs)

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

Continue Reading An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

How to remove center population from seurat cluster

How to remove center population from seurat cluster 0 Dear all, apologize for many posts. I have done my clustering, but there is weird tidy population (in red circle) that is not stay close to its assigned cluster (kindly see attach). In the attached imaged, that cluster has been assigned…

Continue Reading How to remove center population from seurat cluster

Methylation Analysis Tutorial in R_part1

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

Continue Reading Methylation Analysis Tutorial in R_part1

Phylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China

Phylogenetic analysis of lineage IIb C.1 containing all ten local MPXV from Guangdong To rapidly characterize the phylogeny of the MPXVs involved in the outbreak in Guangdong, we constructed a phylogenetic tree by integrating 10 MPXV sequences from Guangdong into the global MPXV genetic diversity sequences derived from GISAID (Fig. 1a,…

Continue Reading Phylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China

2024 Genesis Electrified G80 Gets Sub-$80,000 Entry-Level Trim

When we tested the Genesis Electrified G80 in February, we said that it feels like good value for folks who prioritize quality construction, a smooth ride, and an enjoyable driving experience. That said, the electric sedan fell short in the pricing department, lowering its total score to (a still impressive)…

Continue Reading 2024 Genesis Electrified G80 Gets Sub-$80,000 Entry-Level Trim

2024 Genesis G80 Electrified new base trim lowers price by $5,580

Another entry in the automaker trend of putting updated vehicles on sale without announcement, Genesis has played a little presto-change-o with the 2024 Electrified G80. The battery-electric version of the traditional G80 went on sale last year with a single trim, the loaded Prestige that started at $80,950 after the…

Continue Reading 2024 Genesis G80 Electrified new base trim lowers price by $5,580

Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia

Rasche M, Zimmermann M, Borschel L, Bourquin J, Dworzak M, Klingebiel T, et al. Successes and challenges in the treatment of pediatric acute myeloid leukemia: a retrospective analysis of the AML-BFM trials from 1987 to 2012. Leukemia. 2018;32:2167–77. Article  PubMed  PubMed Central  Google Scholar  Manola KN. Cytogenetics of pediatric acute…

Continue Reading Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia