Tag: cluster

Leveraging Modern Electronics to Streamline CRISPR Workflows

By Kiana Aran, PhD The adoption of CRISPR-Cas systems in therapeutics development has led to the rapid emergence of several clinical candidates for treating rare and challenging diseases, including sickle-cell anemia, β-thalassemia, Duchenne muscular dystrophy, and ocular diseases. Translation into the clinic has been facilitated by a robust preclinical framework…

Continue Reading Leveraging Modern Electronics to Streamline CRISPR Workflows

[slurm-users] How to launch slurm services after installation

Hello, all supported build flags are available with “./configure –help” command. On of them is “–with-systemdsystemunitdir=DIR”, which will allow you to specify the directory for the systemd service files for all Slurm daemons. The most important of the flags is imho the “–prefix”, which sets the installation directory. I’ll describe my build setup shortly…

Continue Reading [slurm-users] How to launch slurm services after installation

Gromacs: nbnxn_sci Struct Reference

#include <gromacs/nbnxm/pairlist.h> Description Grouped pair-list i-unit. Public Member Functions int  numJClusterGroups () const   Returns the number of j-cluster groups in this entry.   Public Attributes int  sci   i-super-cluster   int  shift   Shift vector index plus possible flags.   int  cjPackedBegin   Start index into cjPacked.   int …

Continue Reading Gromacs: nbnxn_sci Struct Reference

Bioconductor – EasyCellType

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

Continue Reading Bioconductor – EasyCellType

Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

Changes of straw degradation characteristics at different culture stages Corn straw degradation ratio Corn straw weight loss in M44 at F1 reached 35.90% at 15 ℃ for 21 days, which was greater than that at F5, F8, and F11 by 2.33%, 3.01%, and 3.35%, respectively. There were no significant differences between…

Continue Reading Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

Continue Reading lazy loading failed, unable to load shared object rtracklayer.so

Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males

Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …

Continue Reading Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males

Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

Continue Reading Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

Bioinformatics Analyst II – Epigenetics & 3D Genomics Job in Texas

Summary The lab of Dr. Kyle Eagen (www.eagenlab.org) at Baylor College of Medicine focuses on elucidating how DNA folds within cells and how DNA misfolding relates to human disease. Baylor College of Medicine, one of the top ranked medical schools in the country, is well known for its exceptional,…

Continue Reading Bioinformatics Analyst II – Epigenetics & 3D Genomics Job in Texas

VIB hiring Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome in Leuven, Flemish Region, Belgium

The lab of Jeroen Raes (VIB, KU Leuven) is looking for a postdoctoral researcher in the computational analysis of microbiome data, with a particular emphasis on human-associated microbial communities in health and disease.Projects Will Focus On(i) bioinformatics/statistics method development for joint host and microbiota data analysis, multi-omics and clinical data…

Continue Reading VIB hiring Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome in Leuven, Flemish Region, Belgium

Bioinformatics Analyst Jobs

We have an exciting contract opportunity for a Bioinformatics analyst to support a collaboration between the Biologics Science and Technology group and Genomics Research Center, in which we are using genomics tools to optimize the development of better Chinese Hamster Ovary (CHO) cells for biologics manufacturing. The ideal candidate will…

Continue Reading Bioinformatics Analyst Jobs

Bioinformatics Analyst II (Remote) Position In North Chicago, IL

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: We have an exciting contract opportunity for a Bioinformatics analyst…

Continue Reading Bioinformatics Analyst II (Remote) Position In North Chicago, IL

Bioinformatics Analyst-Entry Level Position In North Chicago, IL

Description du poste Bioinformatics Analyst Supports a collaboration between the Biologics Science and Technology group and Genomics Research Center, in which we are using genomics tools to optimize the development of better Chinese Hamster Ovary (CHO) cells for biologics manufacturing. The ideal candidate will have broad experience in genomics data…

Continue Reading Bioinformatics Analyst-Entry Level Position In North Chicago, IL

Research Investigator – Dr. Karras’s Lab (Bioinformatics & Genetics) job with University of Texas MD Anderson Cancer Center

The University of Texas MD Anderson Cancer Center in Houston is one of the world’s most respected centers focused on cancer patient care, research, education and prevention. It was named the nation’s No. 1 hospital for cancer care in U.S. News & World Report’s 2022 rankings. It is one of…

Continue Reading Research Investigator – Dr. Karras’s Lab (Bioinformatics & Genetics) job with University of Texas MD Anderson Cancer Center

Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2

Cell isolation, reprogramming and culture Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written…

Continue Reading Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2

Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation.   Overview: Bioinformaticsand Integrative Genomics  …

Continue Reading Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster

Pseudo-bulk DEG analysis with Multi-tissue in scRNA-seq

Hi all, I have 4 datasets (Brain region A (Control & Disease), Brain region B (Control & Disease)) and performed scRNA-seq by integrating all data. And I want to compare Disease and Control in each brain region using pseudo-bulk DEG analysis. (ex. Region A Disease vs Region A Control) Even…

Continue Reading Pseudo-bulk DEG analysis with Multi-tissue in scRNA-seq

r – how to separate 3 different groups of y in a simple linear regression?

You appear to have data like this (which I quickly simulated). > str(dat[-3]) ‘data.frame’: 1000 obs. of 3 variables: $ age : num 61 62 31 57 48 42 53 24 49 51 … $ insurance: num 14786 1225 32650 2500 2043 … $ charges : num 28788 15386 37445…

Continue Reading r – how to separate 3 different groups of y in a simple linear regression?

Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…

Continue Reading Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

Researchers develop new machete technique to slice into cancer genome and study copy number alterations — ScienceDaily

MACHETE is a new CRISPR-based technique developed by researchers at the Sloan Kettering Institute (SKI) to study large-scale genetic deletions efficiently in laboratory models. People are already calling it the Machete Paper. Still, lead authors Francisco “Pancho” Barriga and Kaloyan Tsanov of the Sloan Kettering Institute don’t want the name…

Continue Reading Researchers develop new machete technique to slice into cancer genome and study copy number alterations — ScienceDaily

Scikit-Learn Cheat Sheet (2022), Python for Data Science

The absolute basics for beginners learning Scikit-Learn in 2022 Photo from Unsplash by Tim Stief Scikit-learn is a free software machine learning library for the Python programming language. It features various classification, regression, clustering algorithms, and efficient tools for data mining and data analysis. It’s built on NumPy, SciPy, and Matplotlib. Sections:1….

Continue Reading Scikit-Learn Cheat Sheet (2022), Python for Data Science

Sbatch How Submitted Location Using Jobid With Code Examples

Sbatch How Submitted Location Using Jobid With Code Examples With this piece, we’ll take a look at a few different examples of Sbatch How Submitted Location Using Jobid issues in the computer language. scontrol show job your_job_id_234533 We learned how to solve the Sbatch How Submitted Location Using Jobid by…

Continue Reading Sbatch How Submitted Location Using Jobid With Code Examples

java – I am unable to execute the fastqc command in HPC cluster

I am trying to run fastqc for fastq.gz files in RNA-seq Data analysis and I have written a PBS script. However, I am encountering the following error Can’t exec “java”: No such file or directory at /home/paksls/Atreya/software/FastQC/fastqc line 307 I have written the following script: #!/bin/bash #PBS -l nodes=1:ppn=6,pmem=10240MB,walltime=04:00:00 #PBS…

Continue Reading java – I am unable to execute the fastqc command in HPC cluster

Novel equi merozoite antigen (ema-1) gene heterogeneity in a geographically isolated Theileria equi population in Croatia | Parasites & Vectors

Richter S. Vrste haemosporidia u konja i goveda NR Hrvatskoj. Thesis: Veterinary faculty university of zagreb; 1954. Google Scholar  Rothschild CM. Equine piroplasmosis. J Equine Vet Sci. 2013;33:497–508. Article  Google Scholar  Ueti MW, Palmer GH, Scoles GA, Kappmeyer LS, Knowles DP. Persistently infected horses are reservoirs for intrastadial tick-borne transmission…

Continue Reading Novel equi merozoite antigen (ema-1) gene heterogeneity in a geographically isolated Theileria equi population in Croatia | Parasites & Vectors

Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

Continue Reading Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

Continue Reading Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Completed: Quarterly Cluster Maintenance Tuesday October 25 | crc.pitt.edu

Dear CRC User Community, We have completed our quarterly maintenance and have returned the clusters to production. The key changes to the CRC clusters are the following: Storage Systems updates – Improved performance of iX with cache upgrades SLURM Workload Manager –  Update to newest version (22.05) Due to incompatibility between…

Continue Reading Completed: Quarterly Cluster Maintenance Tuesday October 25 | crc.pitt.edu

Bioinformatics Training Project Manager at European Molecular Biology Laboratory (EMBL)

About the team/job Are you passionate about computational training in life sciences and wish to focus your career on the management and coordination of training programs? We are looking for a team member who will coordinate a new multi-organization project (BioNT) funded by the European Commission, embedded in the Data…

Continue Reading Bioinformatics Training Project Manager at European Molecular Biology Laboratory (EMBL)

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Overview of the viromes In all, 41 wild Qinghai voles were collected from pasture habitats located on the eastern Tibetan Plateau, China (Fig. 1). Tissue samples from liver, lung, spleen, small intestine (with content), and feces (large intestinal content) of each vole were disrupted, and viral RNA was extracted. The RNA…

Continue Reading Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Scientist, Discovery Bioinformatics Jobs in San Diego, CA

Scientist, Discovery Bioinformatics Jobs in San Diego, CA at Velia Title: Scientist, Discovery Bioinformatics Company: Velia Location: San Diego, CA Velia is a transformative biotech company with the ambitious goal to harness the therapeutic potential of a novel class of human peptides, also known as microproteins. Building upon our founders’…

Continue Reading Scientist, Discovery Bioinformatics Jobs in San Diego, CA

Bioconductor – clusterExperiment

DOI: 10.18129/B9.bioc.clusterExperiment     Compare Clusterings for Single-Cell Sequencing Bioconductor version: Release (3.5) Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets. Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb] Maintainer: Elizabeth Purdom <epurdom at…

Continue Reading Bioconductor – clusterExperiment

Three-dimensional in vitro model to reproduce COVID-19-induced endothelial dysfunction

In a recent study posted to the bioRxiv* preprint server, researchers developed a three-dimensional (3D) in vitro tissue model to assess the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the vascular endothelial cells. Study: SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks. Image Credit:…

Continue Reading Three-dimensional in vitro model to reproduce COVID-19-induced endothelial dysfunction

Inferring and perturbing cell fate regulomes in human brain organoids

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

Continue Reading Inferring and perturbing cell fate regulomes in human brain organoids

Install Sview On A Debian, Ubuntu, Kali, Fedora And Raspbian

sview GUI to view and modify SLURM state Maintainer: Debian HPC Team Section: admin Install sview Debian apt-get install sview Click to copy Ubuntu apt-get install sview Click to copy Kali Linux apt-get install sview Click to copy Fedora dnf install sview Click to copy Raspbian apt-get install sview Click…

Continue Reading Install Sview On A Debian, Ubuntu, Kali, Fedora And Raspbian

NCSU Job Openings – Full Professor – Bioinformatics

Posting Details Posting Information Posting Number PG191392EP Internal Recruitment No Working Title Assistant/Associate/Full Professor – Bioinformatics Anticipated Hiring Range Commensurate With Credentials, Qualifications, And Experience Work Schedule Academic position – schedule varies. Job Location Raleigh, NC Department Chancellor’s Faculty Excellence Program About The Department NC State University provides a vibrant…

Continue Reading NCSU Job Openings – Full Professor – Bioinformatics

Low number of nCount_RNA in single-cell RNAseq clusters?

Low number of nCount_RNA in single-cell RNAseq clusters? 0 Hello, after standard Seurat workflow, I checked the metrics of each cluster in the object. Please see the attached picture. How may I explain, in some of clusters, such as cluster 9 which has low nCount_RNA and nFeature_RNA but with an…

Continue Reading Low number of nCount_RNA in single-cell RNAseq clusters?

Grabled LOG-file after running 2e6 steps – LAMMPS General Discussion

Hello guys! Recently I ran an Equilibrium of my model(see attachment), and try to get density, energy and steps out of it. After running 2e6 steps, 2e5 lines of data should be output, but there are a lot of garbled characters in the obtained log file (see attachment) and only…

Continue Reading Grabled LOG-file after running 2e6 steps – LAMMPS General Discussion

Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

Continue Reading Genetic footprints of assortative mating in the Japanese population

How to use Scikit-Learn in Python [Complete Tutorial]

In this tutorial, we will focus on Scikit-Learn library usage in Python. Scikit-Learn is simple, fast and useful library used in python machine learning. It provides simple and efficient tools used in data analysis and data mining. Its free, easy to use and accessible to everyone. It is reusable in…

Continue Reading How to use Scikit-Learn in Python [Complete Tutorial]

Global Fibroblast Growth Factor Receptor 2 market key industry players and their market scope 2022

Pune, Maharashtra, India, September 22 2022 (Wiredrelease) Marke.biz–:The research provides the Global Fibroblast Growth Factor Receptor 2 Market aims at leveraging the insights and perspectives derived based on both qualitative and quantitative data evaluations for the forecast period, 2022-2030. The use of the technology for malady wipeout through direct correction of disturbances…

Continue Reading Global Fibroblast Growth Factor Receptor 2 market key industry players and their market scope 2022

Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster at Cedars-Sinai

Responsibilities Requisition # 20002022A At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert faculty mentors, Cedars-Sinai supports the ongoing medical education process that continues…

Continue Reading Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster at Cedars-Sinai

Low expression of key transcripts in scRNAseq dataset after deeper sequencing

Low expression of key transcripts in scRNAseq dataset after deeper sequencing 1 I am having an issue with my single cell data set. This alert was shown after I requested additional reads per cell to be incorporated with the initial data we received. We have previously performed single cell on…

Continue Reading Low expression of key transcripts in scRNAseq dataset after deeper sequencing

Why is the wrong queue being selected when submitting a job to my cluster using a Slurm scheduler? – MATLAB Answers

My workflow consists of submitting jobs to my cluster which is using Slurm as the scheduler. I am trying to target a specific queue/partition on my Slurm scheduler. I have used ‘AdditionalProperties’ to set the queue to the desired one via the following: c = parcluster(‘<CLUSTER_NAME>’) c.AdditionalProperties.Partition = ‘<PARTITION>’ c.AdditionalProperties.QueueName…

Continue Reading Why is the wrong queue being selected when submitting a job to my cluster using a Slurm scheduler? – MATLAB Answers

Running lammps on a cluster – LAMMPS Installation

Hello all,I have created a Linux cluster with ssh and NFS. I have installed lammps in the NFS folder. I have verified that the cluster works properly with openmpi and the communication is good. But when I run lammps, after reading the data file it gets stuck on the first…

Continue Reading Running lammps on a cluster – LAMMPS Installation

05 Postdoctoral Fellowship at Lund University, Scania, Sweden

Lund University, Scania, Sweden invites online Application for various Postdoctoral Fellowship in their different Departments. We are providing a list of Postdoc Fellowship positions available at Lund University, Scania, Sweden. Eligible candidate may Apply as soon as possible.   (01) Postdoctoral Fellowship Position Postdoc Fellowship Position summary/title:  Postdoctoral researcher in…

Continue Reading 05 Postdoctoral Fellowship at Lund University, Scania, Sweden

Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

Continue Reading Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Isolation of Rat Adipose Tissue Mesenchymal Stem Cells for Differentiation into Insulin-producing Cells

Adipose tissue-derived mesenchymal stem cells (Ad-MSCs) can be a potential source of MSCs that differentiate into insulin-producing cells (IPCs). In this protocol, we provide detailed steps for the isolation and characterization of rat epididymal Ad-MSCs, followed by a simple, short protocol for the generation of IPCs from the same rat…

Continue Reading Isolation of Rat Adipose Tissue Mesenchymal Stem Cells for Differentiation into Insulin-producing Cells

The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Continue Reading The genus Serratia revisited by genomics

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

Continue Reading Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

Continue Reading NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

Continue Reading Acute phase of ischemia-reperfusion in rats

Setting root folder to shared folder – Zero to JupyterHub on Kubernetes

peppie August 23, 2022, 10:20am #1 I have a homemade Kubernetes Cluster with an NFS configured on each node + shared with developpers. It is used for shared storage of code and data. I configured JupyterHub using the Zero to JupyterHub tutorial with Helm chart, which is running correctly and…

Continue Reading Setting root folder to shared folder – Zero to JupyterHub on Kubernetes

Protocol for Human Blastoids Modeling Blastocyst Development and Implantation

A protocol outlining the formation of human blastoids that efficiently, timely, and sequentially generate blastocyst-like cells. Research on human embryos is limited by their low availability and ethical concerns, thus obtaining individual models that faithfully replicate early human development would support scientific and medical progress. The ability of this technique…

Continue Reading Protocol for Human Blastoids Modeling Blastocyst Development and Implantation

Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

Continue Reading Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Running parfor on SLURM limits cores to 1 – MATLAB Answers

Hello, I’m trying to run some parallelized code (through parfor) on a university high performance cluster. In order to make sure parallelization is working correctly, I set up a single node with 32 cores via “srun –pty -t 00:30:00 -n 32 -N 1 /bin/bash -l”, which I verify does start…

Continue Reading Running parfor on SLURM limits cores to 1 – MATLAB Answers

Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

Continue Reading Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

Continue Reading Live-seq enables temporal transcriptomic recording of single cells

uniprot – How to annotate list of proteins with KEGG orthology groups?

I’ve got a list of proteins, complete with Uniprot IDs. I’d like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column with KEGG groups. I’ve tried poking around in the documentation for UniProt, but all I can find…

Continue Reading uniprot – How to annotate list of proteins with KEGG orthology groups?

mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

Continue Reading mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

Stifel Raises Price Target for CRISPR Therapeutics (CRSP) to $69

Benjamin Burnett, an analyst at Stifel, increased his price objective for CRISPR Therapeutics (NASDAQ: CRSP) to $69.00 (from $55.00) while keeping a Hold rating on the stock. Jay Olson, an analyst at Oppenheimer, reduced his price objective for CRISPR Therapeutics (NASDAQ: CRSP) on November 4, 2021, from $185.00 to $172.00…

Continue Reading Stifel Raises Price Target for CRISPR Therapeutics (CRSP) to $69

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

Continue Reading In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Multidrug resistance microbial therapy | VMRR

Introduction Antimicrobials are the most important and useful therapeutic discovery in the history of medicine. It allows living beings to survive the microbial disease, enhances invasive surgical procedures, ensures animal health, and protects the food chain since 1928 after the discovery of penicillin. However, the indiscriminate use of antibiotics and…

Continue Reading Multidrug resistance microbial therapy | VMRR

Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…

Continue Reading Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Centre to Delhi and 6 states amid rise in Covid cases

As Covid cases are rising in some parts of the country, the Centre has asked Delhi and six states to ensure adequate testing, promote Covid-appropriate behaviour and increase the pace of vaccination to contain the surge. Union Health Secretary Rajesh Bhushan has written a letter to Delhi, Kerala, Karnataka,…

Continue Reading Centre to Delhi and 6 states amid rise in Covid cases

r – ggtree setting height scale

I’m doing microssatellite analysis to understand genetic relationship between fungal isolates. For that I first calculated the Jaccard’s coefficient and then want to generate a dendrogram using UPGMA cluster analysis. I did the following: jacc_coef <- vegdist(HC_df, method = “jaccard”) *100 (HC_df is my data frame) afu_clin.hc <- hclust(d =…

Continue Reading r – ggtree setting height scale

Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

Continue Reading Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Pre-existing anti-SARS-CoV-2 immunity decreases viral spread but increase SARS-CoV-2 Omicron competitiveness in hamsters

In a recent study posted to the bioRxiv* preprint server, researchers assessed the impact of pre-existing immunity against severe acute respiratory coronavirus 2 (SARS-CoV-2) acquired by previous infections (PI) or coronavirus disease 2019 (COVID-19) vaccination on the transmission of SARS-CoV-2 variants of concern (VOCs) such as Delta and Omicron. Study:…

Continue Reading Pre-existing anti-SARS-CoV-2 immunity decreases viral spread but increase SARS-CoV-2 Omicron competitiveness in hamsters

GROMACS Installation Problem in The Grid Computer – User discussions

GROMACS version: 2021.2GROMACS modification: No Hello all, I am new to GROMACS. I wanted to install it on a grid computer servers supported by the government and I’ve done step by step instructions in the following link (The language of the instructions is in Turkish but you may find the…

Continue Reading GROMACS Installation Problem in The Grid Computer – User discussions

Postdoc in Computational method development for precision medicine in

Area of research: Scientific / postdoctoral posts Job description: : Discover personalized medical solutions for environmentally triggered diseases to promote a healthier society in a rapidly changing world. The Institute of Computational Biology (ICB) is globally recognised for its innovations in data analysis and modelling of biological systems and diseases,…

Continue Reading Postdoc in Computational method development for precision medicine in

Postdoc in Applied bioinformatics (m/f/d)

The Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) in Jena is a federal and state government-funded research institute and member of the Leibniz Association. FLI’ s internationally visible and highly competitive research is focused on understanding the mechanisms of aging and associated age-related diseases. Scientists from over 40…

Continue Reading Postdoc in Applied bioinformatics (m/f/d)

RSCH DATA ANALYST I BIOINFORMATICS

Job Description Position Highlights: The Research Data Analyst I (Bioinformatics) will be responsible for conducting bioinformatics or statistical analyses in R, Python, SAS, or some other statistical software package under supervision of Principal Investigators from the Gastrointestinal Oncology (GI) Program. The Ideal Candidate: Familiarity with Next Generation sequencing Familiarity with…

Continue Reading RSCH DATA ANALYST I BIOINFORMATICS

Development of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis

Cui, B., Smooker, P. M., Rouch, D. A., Daley, A. J. & Deighton, M. A. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling. J. Clin. Microbiol. 51, 9–14 (2013). CAS  PubMed  PubMed Central  Article  Google Scholar  Tevell, S., Hellmark, B.,…

Continue Reading Development of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis

(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData

(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData 0 I have a question regarding re-clustering after removing cells using SubsetData (R – Seurat package). I am in the process of analyzing a relatively large single-cell dataset (16 separate samples of ~5-10k cells each). In our first…

Continue Reading (Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData

Bioinformatics Engineer job with Simons Foundation

POSITION SUMMARY The Simons Foundation is seeking a Bioinformatics/Senior Bioinformatics Engineer (dependant upon experience) to develop and support whole exome and genome sequence data analysis pipelines in both research and operational modalities. This position will report to the Director of Data and Analytics in the informatics group and will work…

Continue Reading Bioinformatics Engineer job with Simons Foundation

Researchers assess the evolution and diversity of monkeypox virus genomes using phylogenomic analysis

In a recent study published in Travel Medicine and Infectious Disease, researchers phylogenomically analyzed the monkeypox virus (MPXV). Study: Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage? Image Credit: ART-ur/Shutterstock Background Since May 2022, there have been various reports of increasing MPVX infections…

Continue Reading Researchers assess the evolution and diversity of monkeypox virus genomes using phylogenomic analysis

2 PhD candidates in Bioinformatics Stem Cells-Based Therapies Development

The Faculty of Science and the Leiden Academic Centre for Drug Research are looking for a:  2 PhD candidates in Bioinformatics Stem Cells-Based Therapies DevelopmentVacancy number: 22-435 Key responsibilities The research group of Prof. M. Drukker focuses on stem cell based therapeutics, and novel models for human disease and drug development….

Continue Reading 2 PhD candidates in Bioinformatics Stem Cells-Based Therapies Development

Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

Continue Reading Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

Jupyterhub on AWS EKS – Classic Load Balancer retiring – Zero to JupyterHub on Kubernetes

Per AWS blog, the classic networking model is retiring on Aug 15. As I understand it, the official Helm chart uses CLB. Is there a plan to add support for ELB in the official chart? Thanks much! manics July 8, 2022, 3:56pm #2 Z2JH uses whatever LoadBalancer is provided by…

Continue Reading Jupyterhub on AWS EKS – Classic Load Balancer retiring – Zero to JupyterHub on Kubernetes

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

Continue Reading Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

Continue Reading Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

scikit learn – python clustering package that can cluster based in distance matrix but also predict new row (without new clustering/distance matrix)

I am aware of various (sklearn) clustering algorithm that work with distance matrices – e.g. produced via a proximity matrix coming from a random forest (some clumsy reproducible code below). Is there any clustering algorithm (working with distance matrix), where the fitted cluster model (e.g. cluster_model below) can produce the…

Continue Reading scikit learn – python clustering package that can cluster based in distance matrix but also predict new row (without new clustering/distance matrix)

[slurm-users] “Plugin is corrupted” message when using drmaa / debugging libslurm

On 28/06/2022 23:14, Chris Samuel wrote: > On 28/6/22 12:19 pm, Jean-Christophe HAESSIG wrote: Hi, Yes I also found it and that’s where I saw the detailed debug3 & debug4 calls. > it’s when it’s checking it can load the plugin and not hit any > unresolved library symbols. The…

Continue Reading [slurm-users] “Plugin is corrupted” message when using drmaa / debugging libslurm

Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

Continue Reading Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Hubble captures a galactic menagerie

Credit: ESA/Hubble & NASA, H. Ebeling; Acknowledgment: L. Shatz The NASA/ESA Hubble Space Telescope captured this massive galaxy cluster, called Abell 1351, with its Wide Field Camera 3 and Advanced Camera for Surveys. Abell 1351 lies in the constellation Ursa Major in the northern hemisphere. This image is filled with…

Continue Reading Hubble captures a galactic menagerie

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

Continue Reading Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

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…

Continue Reading parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

Senior Scientist – Clinical Bioinformatics and Data Science (m/w/d)

OUR COMPANY At Boehringer Ingelheim we develop breakthrough therapies and innovative healthcare solutions in areas of unmet medical need for both humans and animals. As a family owned company, we focus on long-term performance. We believe that if we have talented and ambitious people who are passionate about innovation, there is no…

Continue Reading Senior Scientist – Clinical Bioinformatics and Data Science (m/w/d)

SARS-CoV-2 ORF8 protein binds to dendritic cells and induces a hyper-inflammatory cytokine storm

In a recent study posted to the bioRxiv* pre-print server, researchers examined how the interaction of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 8 (ORF8) protein with host dendritic cells (DCs) induced cytokine storm. ​​​​​​​Study: The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells…

Continue Reading SARS-CoV-2 ORF8 protein binds to dendritic cells and induces a hyper-inflammatory cytokine storm

Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP – Feature Requests

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

Continue Reading Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP – Feature Requests

A few resources to help enable using Distributed.jl on a SLURM cluster – Specific Domains

jmair May 30, 2022, 11:38am #1 I created some resources for a few colleagues new to Julia, to enable them to use our SLURM cluster effectively, using existing packages like Distributed.jl and ClusterManagers.jl. These scripts and resources do nothing novel or imaginative, and are more of an example of how…

Continue Reading A few resources to help enable using Distributed.jl on a SLURM cluster – Specific Domains

Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions

The heat-shock response is represented by a small set of genes in C. elegans We initially aimed at identifying those HSE-containing promoters that are most strongly upregulated under heat-stress conditions. Given that the HSR is complex in nematodes we used data from several heat-shock studies based on microarray and RNAseq…

Continue Reading Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions

Microsoft (MSFT) Azure Selected by Meta to Boost AI Innovation

Microsoft MSFT, over the past few years, has almost doubled down on the cloud computing opportunity. Growing demand for the company’s cloud solutions is expected to strengthen its competitive position in the cloud computing market. In the last reported quarter, Microsoft Cloud revenues were up 32% year-over-year, at $23 billion….

Continue Reading Microsoft (MSFT) Azure Selected by Meta to Boost AI Innovation

minimum number of protein sequences for a sequence logo

minimum number of protein sequences for a sequence logo 1 Hi, I’m interested in generating sequence logo of a series of defensin related proteins I’ve clustered using CD-Hit. There are aproximately 7600 sequences with about 2500 clusters, but many of them have few sequences per cluster. Which is the minimum…

Continue Reading minimum number of protein sequences for a sequence logo

MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

Continue Reading MND1 Expression as a Predictor of Breast Cancer Survival

RPostgreSQL connections are expired as soon as they are initiated with doParallel clusterEvalQ

I was able to reproduce your problem locally. I am not entirely sure but I think the problem is related to the way clusterEvalQ works internally. For example, you say that dbGetQuery(con, “select inet_client_port()) gave you the client port output. If the query was actually evaluated/executed on the cluster nodes…

Continue Reading RPostgreSQL connections are expired as soon as they are initiated with doParallel clusterEvalQ

Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

Continue Reading Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Problem on R when creating a PCA plot

Problem on R when creating a PCA plot 0 A very weird thing is happening to me on R, the first time i installed “ggfortify” pacakage to create a PCA plot, the result was an Rplots.pdf file, it worked perfectly. The second time i used it, with the same exact…

Continue Reading Problem on R when creating a PCA plot

Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites

Van Treuren, W. & Dodd, D. Microbial contribution to the human metabolome: implications for health and disease. Annu. Rev. Pathol. 15, 345–369 (2020). PubMed  Article  CAS  Google Scholar  Russell, W. R. et al. Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol. Nutr. Food…

Continue Reading Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites

Programmer or Software Developer in Bioinformatics

Job:Programmer or Software Developer in Bioinformatics 0 Dr. Vikas Bansal’s research group (bansal-lab.github.io) in the School of Medicine at the University of California San Diego is looking for a programmer or software developer to advance the development of computational tools and methods for human genome analysis. Research in the group…

Continue Reading Programmer or Software Developer in Bioinformatics

Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

Continue Reading Error in SummarizedExperiment