Tag: Monterey

r – RStudio JavaScript Schema Error on opening and when selecting Global Options

RStudio Edition : Desktop RStudio Version : 2023.09 OS Version : Platform: x86_64-apple-darwin20 (64-bit), macOS Monterey 12.7 R Version : 4.3.2 (2023-10-31) I believe this started when I attempted to render a very large mapview object. RStudio crashed and then when I tried to re-open the application, this error popped…

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Bioinformatics Analyst – Charlottesville, Virginia, United States

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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]

Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…

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R freezing when I create a simple plot – General

Hello! My issue is similar than the one discussed: Running even a simple plot command triggers never-ending stop sign. Only resolution is hitting the stop button several times to abort. The following freezes the session: x <- c(1,2,3) y <- c(1,2,3) plot(x,y) > sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0…

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r – ggplot2: Display per Months using Stacked Bar Chart with

With ggplot, I want to create an overview that shows what kind of tasks have to be done on three (agricultural) fields over the course of a year (per month). I want to use a stacked bar chart to create a chart that looks like this: Months on the x-axis,…

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R-Studio 7.3.191246 download free | macOS

R-Studio for Mac is specially designed for the Mac OS environment, including the Apple M1/M2 chip. It recovers files from APFS/HFS+/HFS (Macintosh), FAT/NTFS/ReFS (Windows), UFS1/UFS2 (FreeBSD/OpenBSD/NetBSD/Solaris) and XFS/Ext2/Ext3/Ext4 FS (Linux) partitions. In addition, raw file recovery (scan for known file types) can be used for heavily damaged or unknown file…

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Problems installing RMarkdown for R v2023.06.1 on a Mac – R Markdown

I’m having troubles installing RMarkdown for using knitr and publish my work, I’m using R Studio v2023.06.1 on a Mac with a macOS Monterey version 12.6.3. This is what I’m getting: install.packages(“knitr”)also installing the dependency ‘xfun’ There are binary versions available but the source versions are later:binary source needs_compilationxfun 0.30…

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Precision issue after converting to CoreML

bcxiao September 26, 2023, 7:02pm 1 Hello, I am trying to convert my Pytorch model to CoreML format. However, the outputs of pytorch model and the converted CoreML model do not match well. Here is the code of a minimal example: import numpy as np import torch import torch.nn as…

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Covid helped China secure the DNA of millions, spurring arms race fears

BELGRADE — Most of Europe was in lockdown in April 2020 when a plane arrived in the Serbian capital bearing a well-timed gift from the People’s Republic of China. Inside was a Chinese invention called the Fire-Eye, a sophisticated portable lab that could detect coronavirus infections from tiny genetic fragments…

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Comb jelly likely descended from ‘sister of all animals’

We still don’t know what the world’s first animal looked like, but scientists say it arose roughly 700 million years ago from a soup of single-celled organisms floating in the ocean. The multi-celled creature thrived, multiplied and evolved, at some point splitting into two distinct species. One species kept evolving,…

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View() shows blank pane in RStudio Desktop Pro 2023.06.2 – RStudio IDE

I installed RStudio Desktop Pro version 2023.06.2 yesterday, and now when I use View() I get a blank pane. Anyone else experiencing this? To repro: Open RStudio, run > x<-data.frame(x=runif(50)) > View(x) … observe that you get a blank pane showing no data. The same thing happens if I click…

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Research Scientist in Bioinformatics and Computational Genomics

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‘syscall’ is deprecated during installing jellyfish kmer counting

‘syscall’ is deprecated during installing jellyfish kmer counting 0 I have zero knowledge in bioinformatics. I’m using MacOS monterey and bash terminal for bioinformatics. Trying to install jellyfish to count kmer prior to DNA assembly. I’m using www.cs.cmu.edu/~ckingsf/software/jellyfish/README to help me install the tool. Can only do ./configure and already…

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Linda Rae Jacobs & Ida Florence Jacobs are now Identified

Summary In February 2014, the Monterey Police Department (MPD) responded to the death of a woman in the 1100 block of Fourth Street in Monterey, California. The woman, identified by her California Driver’s license as Francesca Linda Jacobs with a birth date in 1955, had died from starvation. No foul…

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CRISPR Crops Are Here – proto.life

Had it been coined intentionally for the purpose of marketing fresh produce, the acronym CRISPR would have been a stroke of advertising genius. After all, who wouldn’t want their salad to be crisper?  But the true genius of this gene-editing technology could be its ability to jump straight to consumer…

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12 new species of sea sponges found off Monterey California

Marine biologists have discovered a dozen new species of sea sponges at the Monterey Bay National Marine Sanctuary off California. Thomas Turner They were practically hiding in plain sight. Marine biologist Thomas Turner said he couldn’t believe what he saw on a research dive in the stunning Carmel Pinnacles State…

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Tutustu 63+ imagen r studio mac os

Jaa kuvia r studio mac os. RStudio Settings in Mac OS Catalina – General – Posit Community Getting Setup with R and RStudio (Mac) – YouTube Install R and RStudio on Mac. Download R from the following link… | by Michael Galarnyk | Medium Brief introduction to running Rstudio on…

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Error in RStudio startup – RStudio IDE

Hello all, I am experiencing following issue while trying to open RStudio. I am using macOS Monterey Version 12.5.1 (MacBook Air (M1, 2020)). I am using R base version 4.3.1. I made sure that R starts correctly outside RStudio (terminal), fully uninstalled all versions of R and reinstalled again, made…

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Samtools Failing to Install through Conda

Samtools Failing to Install through Conda 2 Hi all, I just got a new laptop and am trying to work on some sequencing data and need to install samtools. On my old laptop, I was able to do this through conda using: conda install -c bioconda samtools However, when I…

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Scientists hope to tech the heck out of eDNA sampling with drones, robots

The collection of DNA samples with the assistance of drones and robots was a recurring theme at the semifinals of a $10 million competition to identify automated rainforest conservation solutions. At least half of the 13 teams used drones and robots to retrieve genetic samples left behind by wildlife on…

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Bioconductor/SparseArray source: tests/testthat/test-SparseArray-Math-methods.R

.IS_INTEL_MAC <- Sys.info()[[“sysname”]] == “Darwin” && Sys.info()[[“machine”]] == “x86_64” .test_Math_op <- function(a, svt, op) { FUN <- match.fun(op) ## Catch the warning if any. Unfortunately ‘FUN(a)’ is called twice. ## According to ## stackoverflow.com/questions/3903157/how-can-i-check-whether-a-function-call-results-in-a-warning ## it’s possible to avoid this by using handlers but I didn’t try it. ## The…

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Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

Fungal genomic DNA DNA extracted from Aspergillus niger (kindly provided by Dr. Takamitsu Imoto, Medical Research Institute, Kitano Hospital, Osaka, Japan) and a mock community DNA standard (Mycobiome Genomic DNA Mix, MSA-1010; ATCC, Manassas, VA, USA) were used to evaluate the validity of the sequencing methodology. The mock community standard…

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Research Associate – Dept. of Microbiology and Immunology

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samtools installed but error message: Library not loaded: @rpath/libcrypto.1.0.0.dylib

samtools installed but error message: Library not loaded: @rpath/libcrypto.1.0.0.dylib 1 I would like to convert input.sam to output.bam but I get following error message: kk$ samtools view -bS input.sam > output.bam dyld[88970]: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/kk/opt/anaconda3/bin/samtools Reason: tried: ‘/Users/kk/opt/anaconda3/bin/../lib/libcrypto.1.0.0.dylib’ (no such file), ‘/Users/kk/opt/anaconda3/bin/../lib/libcrypto.1.0.0.dylib’ (no such file), ‘/usr/local/lib/libcrypto.1.0.0.dylib’…

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Rstan not working after RStudio update – RStan

Hi everyone, Today I updated RStudio to its latest version (2023.03.1+446) on my two Macbook Pro laptops (one with an Intel chip running macOS Monterey and the other with an Apple m1 chip running macOS Ventura), and now I have been getting this error every time I try to use…

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Install r rstudio – Downloading and installing R and RStudio: Mac Follow these instructions if you

Downloading and installing R and RStudio: Mac Follow these instructions if you have a Mac. The last pages have a FAQ with troubleshooting tips so if you have any problems check there first! To determine which OS you have, go to the little apple in the upper left-hand corner of…

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The earliest animals were primitive

Biologists have been looking for the earliest animals for over a century, narrowing the options to two groups: sponges and comb jellies. Sponges spend their whole adult lives filtering food from saltwater; and comb jellies, ferocious predators that scull their way across the world’s oceans looking for food. According to…

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What Did the Earliest Animals Look Like? Chromosomal Clues Unearth the Origins of Animal Evolution

A new study used a unique approach based on chromosome structure to determine that comb jellies, also known as ctenophores, were the first lineage to diverge from the animal tree of life, with sponges following as the next branch. Previously, it was unclear whether sponges or comb jellies were the…

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What did the earliest animals look like?

Scientists have long debated whether comb jellies (left) or sponges (right) are the sister group to all other animals. A detailed comparison of the chromosomes of these and other animals to the chromosomes of three single-celled non-animal groups finally resolves the question. (Photos courtesy of MBARI) For more than a…

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What did Earth’s first animal look like? Scientists solve 700-million-year-old puzzle

BERKELEY, Calif. — Scientists believe they’ve identified the first animal to appear on Earth: a peculiar jellyfish-like creature. Researchers say all species evolved from a single common ancestor that lived as far back as 700 million years ago. These include creatures as diverse as sponges, insects, sharks, and humans. “The…

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PostDoc Research Associate – Dept. of Anatomy and Neurobiology

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Cannot connect to Postgres database from RStudio but can connect from DBeaver and psql

Can connect to the database from psql and DBeaver but when using RpostgreSQL package in RSudio I receive the following error: RPosgreSQL error: could not connect user@hostname on dbname “database”: FATAL: no pg_hba.conf entry for host “”, user “user_name”, database “databse”, SSL off Macbook Pro ’21, M1, macOS Monterey Here…

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Ucsc.Edu Login – EnewResult

UCSC.edu is the official website of one of the top public research universities in the United States, the University of California, Santa Cruz (UCSC). Established in 1965, UCSC is known for its strikingly beautiful campus situated on 2,000 acres of rolling hills and redwood groves overlooking the Monterey Bay. The…

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Download and Install R and RStudio for Mac OS Monterey(for Intel Processor and Apple M1 chip)

In this tutorial session, we will learn to Install R and RStudio on Mac OS Monterey. I have explained the installation process that will work with other previous Mac OS versions.Step 1: First we need to download and install the ‘R’ package for Mac OS.link: please check whether your Mac…

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Start up error after updating R and RStudio – RStudio IDE

Error Information: Description of issue –I updated R to 4.3.0 and RStudio to 2023.03.0+386 today. When I opened RStudio I immediately got the popup error message: “R encountered a fatal error.The session was terminated.” I then have to force quit RStudio to close it. R seems to be functioning as…

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Advanced Analytics Manager – Lookout Local Santa Cruz

Location: Merced; Salinas; Scotts Valley, California; Remote in California We have an opportunity to join the Alliance as the Advanced Analytics Manager in the Data Analytics Services Department. *There is one position which can be filled in any of our 3 offices (Scotts Valley, Merced or Salinas, California) or remotely…

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Cannot set locale in Rstudio

## — The problem: — I’m trying to run Rstudio, but whenever I start up I see these messages: During startup – Warning messages: 1: Setting LC_CTYPE failed, using “C” 2: Setting LC_COLLATE failed, using “C” 3: Setting LC_TIME failed, using “C” 4: Setting LC_MONETARY failed, using “C” Which I…

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Gene duplicate

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

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Stunning Diversity of Comb Jellies Revealed Through Genetic Probes

Researchers from the Monterey Bay Aquarium Research Institute (MBARI) have used genetics to study the comb jellies, or ctenophores, and have discovered new diversity within the species. Comb jellies—known to scientists as ctenophores (pronounced “teen-oh-fours”)—mesmerize with their beauty, but these captivating creatures remain poorly studied due to their delicate nature….

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r – RStudio problems on Mac: opening files, saving Data

I have an older Mac so I am running “Elsbeth Geranium” Release (7d165dcf, 2022-12-03) for macOS on MacOS Monterey version 12.6.3 The first problem: Having used a script and then closing it makes it unavailable to open via RStudio. The file is greyed out and cannot be selected for opening….

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macOS problems with files and pushing, RStudio and Push – RStudio IDE

Hi all, I posted this question on StackOverflow and had a suggestion to post it here: r – RStudio problems on Mac: opening files, saving Data – Stack Overflow I have an older Mac so I am running “Elsbeth Geranium” Release (7d165dcf, 2022-12-03) for macOS on MacOS Monterey version 12.6.3…

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HTSeqGenie run error

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

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Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

1. Introduction Soil harbors high abundance and diversity of prokaryotic microorganisms, with 1 g of soil containing up to 10 billion microbial cells (Torsvik and Øvreås, 2002) and 103–106 phylotypes (Bickel and Or, 2020), including many microorganisms that play critical biogeochemical roles (Crowther et al., 2019). With continuous expansion of prokaryotic…

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Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling

Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009). Article  CAS  PubMed  Google Scholar  Graham, E. B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7, 214 (2016). Article  PubMed  PubMed Central  Google Scholar …

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RStudio could not connect with R (MacOS, after upgrade to Monterey 12.6.3) – RStudio IDE

After upgrading to MacOS Monterey 12.6.3, a screen appeared stating thatRStudio could not connect with R, and suggesting various remedies, noneof which were clearly going to work. I then rebooted. This time, the Rcommand line appeared (directory name started with underscore), with an errormessage. I was then able, somewhat to…

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World’s deadliest mushroom conquered California with a clone army, study reveals

The world’s deadliest mushroom has been invading California by cloning itself, new research finds.  The poisonous “death cap” mushroom (Amanita phalloides) is an invasive fungus whose fatal amatoxin accounts for more than 90% of deaths from mushrooms worldwide, but how it spread from its European origins to colonize every continent…

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Studio not detecting R – RStudio IDE

Hi, I updated R to 4.2.2 and RStudio to 2022.12.0+353. My OS is MacOS Monterey (version 12.6.2) with Apple M1 chip. I didn’t have any errors during the installation of the packages and I am able to open R. However, when I try to open Rstudio, I get the following…

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Error Accessing Values in Snakemake Config File

Error Accessing Values in Snakemake Config File 0 Hello, I am trying to load some files from a config file in snakemake. I’m using snakemake 7.22 on MacOS Monterey with M1 chip. My config file is: files: A: file1.txt B: file2.txt My Snakemake file is: configfile: “config.yaml” rule all: input:…

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STR-based feature extraction and selection for genetic feature discovery in neurological disease genes

Analyze statistical results Descriptive statistics The summary of mean, maximum, minimum, and standard deviation of RSs, can be found as Supplementary Table S1 online. Based on the results, we conclude that generally, the neurological disease family genes have a larger mean of RSs than human genes. Moreover, variation in the…

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Unable to imports files to qiime2 – Technical Support

Hira_Hira (Hira Abid) February 3, 2023, 5:51pm 1 Hi, I have been trying to import my files into qiime2 but keep on getting error messages. I have tried different suggestions from forums and I have also tried all steps as given on qiime2 website tutorial but nothing works for me….

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r – monocle3 installation issues

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey. I am trying to install monocle3 using the following : BiocManager::install(‘monocle3’) I get a really long error message BiocManager::install(“monocle3”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Bioconductor installation problems

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

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python – Biopython cannot export numpy

I am trying to use Biopython using anaconda and the Jupiter notebook with Python3. However, simply import numpy gives the following error: ————————————————————————— ImportError Traceback (most recent call last) File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/__init__.py:23, in <module> 22 try: —> 23 from . import multiarray 24 except ImportError as exc: File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/multiarray.py:10, in <module>…

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Illumina Begins Climate Week by Highlighting How Sequencing Supports Resilient Responses to Climate Change

How Southern California scientists are working to stay ahead of dangerous outbreaks Northampton, MA –News Direct– Illumina The use of genomics is critical to help build strategies of resilience in our global response to climate change. In honor of Climate Week, we’re highlighting the important work of algae biologists at…

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Computational Scientist-Bioinformatics in Chicago, IL for University of Chicago (UC)

  UPDATE: We are in process of fixing some issues with our job board search function. If you are experiencing any problems, we apologize for the inconvenience and thank you for your patience. Job Seekers, Welcome to HERC Jobs…

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Toxic Algae Blooms Are on the Rise. Sequencing Can Help Manage Them.

This was a summer of unprecedented heat and runaway algae. At hundreds of beaches, lakes, and rivers across the US, the public was greeted by signs like this one at Hensley Lake in northern California: “Harmful algae may be present in this water.” Although blue-green algae, known as cyanobacteria, occur…

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Taking the Pulse of the Ocean’s Comb Jellies

The enormousness of the global sea has, over ages of exploration, made the appraisals of prime inhabitants more like rough sketches than detailed portraits. Now, scientists have devised a precise way of detecting one of the ocean’s more exotic creatures. Estimates of its global abundance, they say, will likely soar….

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