Tag: PASS

ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

hi,i am working on jetson Xavier NX box,i updated to jetpack 5.0.1 and deepstream6.1 right now.before i setup ARCH= -gencode arch=compute 72 for NX to train some models.but i cmake another file yesterday it detected arch-gencode 75!so i am confuse right now, should i setup 72 or 75 for jetson…

Continue Reading ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

Robotic Left Hepatectomy using Indocyanine Green Fluorescence Imaging for an Intrahepatic Complex Biliary Cyst

Robotic liver surgery has gained more acceptance as a feasible, safe, and effective procedure for the treatment of both benign and malignant indications. However, robotic left hepatectomy is still technically demanding. We describe our surgical technique of a robotic left hepatectomy using indocyanine green fluorescence imaging for a large biliary…

Continue Reading Robotic Left Hepatectomy using Indocyanine Green Fluorescence Imaging for an Intrahepatic Complex Biliary Cyst

Left and right DataArray objects are not close

Source: python-xarray Version: 2022.06.0~rc1-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of python-xarray the autopkgtest of python-xarray fails in testing when that autopkgtest is run with the binary packages of python-xarray from unstable. It passes when run with only packages from testing. In tabular form: …

Continue Reading Left and right DataArray objects are not close

Ubuntu Manpage: Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = Bio::Map::OrderedPosition->new(-order => 1, -positions…

Continue Reading Ubuntu Manpage: Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of

Issue with streamlit as dependency when deploying my package to Bioconda repository – Using Streamlit

Hello,I am opening an issue here for a problem that I don’t think you guys can solve, but you never know. I recently developped a Python tool, and I need to get it onto the Bioconda repository . To do this, I have created a recipe that I must know…

Continue Reading Issue with streamlit as dependency when deploying my package to Bioconda repository – Using Streamlit

autopkgtest regression with openssl 3

I raised the issue to the upstream developer, and he is working on it: github.com/grke/burp/issues/904 He is very responsive and gentle. On Tue, 24 May 2022 20:53:39 +0200 Sebastian Ramacher <sramac…@debian.org> wrote: > Source: burp > Version: 2.4.0-3 > Severity: serious > Tags: sid bookworm > > burp’s autopkgtest fail…

Continue Reading autopkgtest regression with openssl 3

python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

Continue Reading python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

Five basic functions dealing with tensors in pytorch

Every beginner of deep learning should know these five basic functions of pytoch. It is one of the most sought after skills for recruiters to build neural networks in an accurate and effective way. Pytorch is a python library mainly used for deep learning. One of the most basic and…

Continue Reading Five basic functions dealing with tensors in pytorch

React Query Codegen from OpenAPI

Rapini is a new tool that can generate custom React Query hooks using OpenAPI (Swagger) files. The Command Line Interface (CLI) tool will take a path to an Open API file and generate a package that includes react hooks, typescript types and axios http requests – and this package is…

Continue Reading React Query Codegen from OpenAPI

PyMC3 Normal with variance per column

One can pass an argument for the shape parameter to achieve this. To demonstrate this, let’s make some fake data to pass as observed, where we use fixed values for epsilon that we can compare against the inferred ones. import numpy as np import pymc3 as pm import arviz as…

Continue Reading PyMC3 Normal with variance per column

clustalw and muscle in Biopython

First, try installing Biopython 1.63 from here, it may solve some of your problems. Second, make sure you’re using the latest Python from python.org – you might want to run the installer again just to ensure that none of your files are corrupted, if you’re still getting the same error…

Continue Reading clustalw and muscle in Biopython

Mulugeta Metaferia – Academia.edu

Mulugeta Metaferia – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our…

Continue Reading Mulugeta Metaferia – Academia.edu

Special Issue : Methods and Tools in RNA Biology

A special issue of Non-Coding RNA (ISSN 2311-553X). Deadline for manuscript submissions: 30 November 2022 | Viewed by 9 Special Issue Editors Dr. Mirolyuba Ilieva E-Mail Website Guest Editor Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, DenmarkInterests: non-coding RNAs; stem cell biology; neuroscience Special…

Continue Reading Special Issue : Methods and Tools in RNA Biology

Blackrock Clinic launches new device to help combat AF

Electroporation systems being used to tackle a condition which one in four over-55s will develop THE Blackrock Clinic recently started its new program of electroporation for the treatment of patients with atrial fibrillation. Conventional catheter ablation for the treatment of cardiac arrhythmias uses tissue heating (radiofrequency current) to cauterize the…

Continue Reading Blackrock Clinic launches new device to help combat AF

Error in BAFFromGVCFs – GenotypeGVCFs

Bug Report Affected module(s) or script(s) Module00c/BAFFromGVCFs/GenotypeGVCFs Affected version(s) Description I’m running GATKSVPipelineBatch and I got the following error in the GenotypeGVCFs task: A USER ERROR has occurred: Input /tmp/scratch/bean-resources/broad-references/v0/Homo_sapiens_assembly38.dbsnp138.vcf must support random access to enable queries by interval. If it’s a file, please index it using the bundled tool…

Continue Reading Error in BAFFromGVCFs – GenotypeGVCFs

Environmental Factor – May 2022: Scientific moonshot: Now is the time to sequence RNA, expert says

Rick Woychik, Ph.D., directs NIEHS and the National Toxicology Program. (Image courtesy of NIEHS) Almost two decades have passed since the first sequence of a complete set of DNA was released as part of the Human Genome Project. That initiative expanded understanding of certain cancers, boosted the effectiveness of some…

Continue Reading Environmental Factor – May 2022: Scientific moonshot: Now is the time to sequence RNA, expert says

Missing data per site

Hi, I want to calculate statistics of missing data per each site in my vcf file. Using vcftools –missing-site gives wrong stats for several sites. Is there is any other way to calculate it? Thank you! I have 36 samples and here is an example of the vcftools –missing-site output…

Continue Reading Missing data per site

AIM brings innovations from labs to hospitals and masses

Human body like the Space is an endless frontier made even more complex by the irreversibility of life by the arrow of time. Similar to the mystery of origin of the Universe some problems in the human body are so complex, for example, the problem of qualia or the Hard…

Continue Reading AIM brings innovations from labs to hospitals and masses

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

Continue Reading Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Microsoft Store Web

Skip to main content Microsoft Windows Apps Software Microsoft 365 Office Windows Software for Mac Business Software Software support Games & Entertainment Xbox consoles Xbox games Xbox Game Pass Ultimate Xbox Live Gold PC games Movies & TV All Microsoft Software Software Windows Apps OneDrive Outlook Skype OneNote Teams…

Continue Reading Microsoft Store Web

Reproduce incorrect goa generation of MapOf in OpenAPI body

goa version 3.7.2 Design The field name anyobject with Attribute MapOf(String, Any) should describe a map of string to any unknown value. For HTTP requests, the field anyobject can be sent like the following (i.e. any json object): { “anyobject”: { “testkey”: 10, “test1”: “testval”, “myarr”: [ { “nestedk”: {…

Continue Reading Reproduce incorrect goa generation of MapOf in OpenAPI body

Stacey Dash Bio, Age, Height, Career , Family, Salary, And Net Worth

Stacey Dash Biography Stacey Dash is a native American actress and former talk show host. In the 1995 feature picture clueless and its television series of the same name, she portrayed Dionne Marie Davenport. She appeared on television in the NBC 1982 drama pilot Farrell: For the people, that got…

Continue Reading Stacey Dash Bio, Age, Height, Career , Family, Salary, And Net Worth

Limit Fragment Duration Polymorphisms (RFLP) Style of DNA Profiling

Limit Fragment Duration Polymorphisms (RFLP) Style of DNA Profiling Conceptual The amazing strength regarding DNA technical as the a recognition product got lead a tremendous change in crimnal fairness . DNA studies legs is an information capital into forensic DNA typing neighborhood having informative data on popular quick tandem repeat…

Continue Reading Limit Fragment Duration Polymorphisms (RFLP) Style of DNA Profiling

Bioinformatics Specialist (Pathology and Laboratory Medicine) at University of Pennsylvania in Philadelphia, Pennsylvania

Job Description: Bioinformatics Specialist (Pathology and Laboratory Medicine) University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey….

Continue Reading Bioinformatics Specialist (Pathology and Laboratory Medicine) at University of Pennsylvania in Philadelphia, Pennsylvania

Kaggle Machine Learning

In this article, we’ll learn step by step an entire process of machine learning to solve a challenge in Kaggle Competition and make a submission. We’ll explore through Kaggle Competition joining, Data Exploration, Feature Engineering, Model Training, Testing, Scoring, and Evaluation. Then, we’ll go ahead and submit our result to…

Continue Reading Kaggle Machine Learning

No rule to make target ‘/usr/lib/x86_64-linux-gnu/libpython3.10.so’

Source: opm-grid Version: 2021.10-3 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of opm-grid the autopkgtest of opm-grid fails in testing when that autopkgtest is run with the binary packages of opm-grid from unstable. It passes when run with only packages from testing. In tabular form:…

Continue Reading No rule to make target ‘/usr/lib/x86_64-linux-gnu/libpython3.10.so’

python – Creating a phylogenetic tree with domain annotations using BioPython

You could use ETE3 to implement this as well – it can load the tree as a newick, and then you can set it up with the motifs – from how I understand the documentation you’ll have to have a list of lists for each organism, like so: motifs =…

Continue Reading python – Creating a phylogenetic tree with domain annotations using BioPython

Issues with searching Swissprot #25

Eddykay310 Hi @cruizperez Please help me understand the problem here and how I can fix it. I have successfully generated my DBs but I get this error during analysis. The .dmnd files do not exist in the folders as the error says but I don’t know how I can generate…

Continue Reading Issues with searching Swissprot #25

filtering host and gut material #340

Pdawyndt Pierre Rouzé yesterday hinted on a possible application of the Unipept Shotgun Metagenomics/Metaproteomics Analysis Pipeline. They are sequencing a marine organism (forgot about the name), but after DNA extraction and sequencing, they end up both with DNA reads and transcript data from the marine organism they want to sequence…

Continue Reading filtering host and gut material #340

Cardior Appoints Dr. Russell Greig as Independent Chairman of the Board

HANOVER, Germany–(BUSINESS WIRE)–Cardior Pharmaceuticals, a clinical-stage biotech company developing non-coding RNA (ncRNA)-based therapeutics for patients with cardiac diseases, today announced the appointment of Dr. Russell Greig, as independent Chairman of its Board of Directors. Dr. Greig brings more than 35 years of experience in the pharmaceutical industry from GlaxoSmithKline, with…

Continue Reading Cardior Appoints Dr. Russell Greig as Independent Chairman of the Board

Python scikit learn pipelines (no transformation on features)

Yes, you can simply do pipe = Pipeline(steps=[(‘clf’, RandomForestClassifier())]) Also, if you had some custom base transformation you almost always wanted, and it also had certain hyperparameters or added functionality you could also do something like (somewhat lame example, but just for ideas..) from sklearn.base import TransformerMixin class Transform(TransformerMixin): def…

Continue Reading Python scikit learn pipelines (no transformation on features)

Establishment of a Mouse Severe Acute Pancreatitis Model using Retrograde Injection of Sodium Taurocholate into the Biliopancreatic Duct

A mouse model of severe acute pancreatitis is described herein. The procedure presented here is very rapid, simple, and accessible, thereby potentially allowing the study of the molecular mechanisms and different therapeutic interventions in acute pancreatitis in a convenient way. The overall goal of this video is to establish a…

Continue Reading Establishment of a Mouse Severe Acute Pancreatitis Model using Retrograde Injection of Sodium Taurocholate into the Biliopancreatic Duct

Solved Question 14 1 pts Hirschsprung disease (aka

Transcribed image text: Question 14 1 pts Hirschsprung disease (aka congenital aganglionic megacolon) stems from a failure of enteric nervous system (ENS) innervation of the distal colon resulting in the inability to pass stool. Scientists studying this disease are interested in modeling the ENS in culture beginning with human iPSCs….

Continue Reading Solved Question 14 1 pts Hirschsprung disease (aka

dx: error: unrecognized arguments: running swiss army knife plink2

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

Continue Reading dx: error: unrecognized arguments: running swiss army knife plink2

What is genetic engineering and how can it benefit healthcare?

Have you heard of purple tomatoes? Or golden rice? If you haven’t, you might be surprised to know that these have actually been created by scientists via genetic engineering. These are genetically modified foods, with purple tomatoes containing 10 times more antioxidants than a normal red tomato. On the other…

Continue Reading What is genetic engineering and how can it benefit healthcare?

golang-github-albenik-go-serial: autopkgtest regression on ppc64el: undefined: unix.TCGETS2

Source: golang-github-albenik-go-serial Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of golang-github-albenik-go-serial the autopkgtest of golang-github-albenik-go-serial fails in testing when that autopkgtest is run with the binary packages of golang-github-albenik-go-serial from unstable. It passes when run with only packages from testing. In tabular form:…

Continue Reading golang-github-albenik-go-serial: autopkgtest regression on ppc64el: undefined: unix.TCGETS2

[Kernel-packages] [Bug 1966093] Autopkgtest regression report (nvidia-graphics-drivers-390/390.147-0ubuntu0.18.04.1)

All autopkgtests for the newly accepted nvidia-graphics-drivers-390 (390.147-0ubuntu0.18.04.1) for bionic have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-390/390.147-0ubuntu0.18.04.1 (i386) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

Continue Reading [Kernel-packages] [Bug 1966093] Autopkgtest regression report (nvidia-graphics-drivers-390/390.147-0ubuntu0.18.04.1)

#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’

#1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’ – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Joel Rosdahl <joel@debian.org>:Bug#1007732; Package src:ccache. (Tue, 15 Mar 2022 20:27:05 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers <elbrus@debian.org>:New Bug report received…

Continue Reading #1007732 – ccache: autopkgtest regression: cannot execute ‘cc1plus’

python – using scikit-learn preprocesser to select subset of rows in pandas dataframe

You can use a FunctionTransformer to do that. To a FunctionTransformer, you can pass any Callable that exposes the same interface as standard scikitlearn transform calls have. In code import pandas as pd from sklearn.preprocessing import FunctionTransformer class RowSelector: def __init__(self, rows:list[int]): self._rows = rows def __call__(self, X:pd.DataFrame, y=None) ->…

Continue Reading python – using scikit-learn preprocesser to select subset of rows in pandas dataframe

python – Pytorch: Which class weights I need to pass to BCELoss

I’m trying to build a Resnet model with Sigmoid with BCELoss lose. Since my data is imbalance, I guess I need to use “class weights” as an argument for the “BCELoss“. But which weight I should pass, is it for the positive (with 1) or negative (with 0). Of course,…

Continue Reading python – Pytorch: Which class weights I need to pass to BCELoss

bedtools -u not giving unique files

bedtools -u not giving unique files 1 The following are the steps Im following: First step to extract sample using bed file is this (here the bedfile is input bedfile converted to Hg38): tabix -h -R Hg19_to_Hg38_sorted.bed.gz gnomad.genomes.v{g_version}.hgdp_tgp.chr{chr}.vcf.bgz | perl {vcftools} -c {sample_name} > {sample_name}_out.vcf’ output({sample_name}_out.vcf’) chr2 113982416 rs56177103 TATAAAATAAAATAAA…

Continue Reading bedtools -u not giving unique files

#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error

#1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>:Bug#1007013; Package src:freecad. (Thu, 10 Mar 2022 14:21:07 GMT) (full text, mbox, link). Acknowledgement sent to Paul Gevers…

Continue Reading #1007013 – freecad: autopkgtest regression on arm64 and armhf: syntax error

Function plot in ggplot incorrectly displayed as constant line-Tech Notes

Technical otaku 2022-03-08 I want to plot a high degree polynomial function with given coefficients.I created this functionf_erzeuger() is for writing a polynomial functionf to be able to use ggplot2 and stat_function(fun=f).coef is the coefficient vector of the polynomial function. f_erzeuger <- function(coef) { f <- function(x) { x_vec <-…

Continue Reading Function plot in ggplot incorrectly displayed as constant line-Tech Notes

AlphaFold, GPT-3 and How to Augment Intelligence with AI

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

Continue Reading AlphaFold, GPT-3 and How to Augment Intelligence with AI

A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

Continue Reading A Comprehensive Guide on ggplot2 in R

CORS issues behind nginx ingress after updating to JupyterHub 2.1.1 – JupyterHub

Hi there, I noticed multiple issues after upgrading to JupyterHub 2.1.1 from 2.0.0. I stopped seeing spawn progress when starting the singleuser server. Logs: [I 2022-03-04 20:57:47.436 JupyterHub log:189] 302 GET /hub/spawn -> /hub/spawn-pending/konstantin.taletskiy@labshare.org (konstantin.taletskiy@labshare.org@192.168.15.108) 1006.02ms [I 2022-03-04 20:57:47.524 JupyterHub pages:405] konstantin.taletskiy@labshare.org is pending spawn [I 2022-03-04 20:57:47.528 JupyterHub log:189]…

Continue Reading CORS issues behind nginx ingress after updating to JupyterHub 2.1.1 – JupyterHub

Demystifying RNAi and creating experimental myths

Transfection with siRNA is unstable, and symptoms disappear after a few passages of cells, so protein should be extracted and analyzed immediately after a few days (1-3) of transfection. The shRNA in the plasmid is used for transfection. If the plasmid contains antibiotic sites, it can be screened to obtain…

Continue Reading Demystifying RNAi and creating experimental myths

Bug#1006850: python-munch: autopkgtest regression: No module named ‘pkg_resources’

Source: python-munch Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of python-munch the autopkgtest of python-munch fails in testing when that autopkgtest is run with the binary packages of python-munch from unstable. It passes when run with only packages from testing. In tabular form:…

Continue Reading Bug#1006850: python-munch: autopkgtest regression: No module named ‘pkg_resources’

Mechanisms involved in the transmission of genetic diseases from mother to child

Mitochondria are the organelles that produce most of the chemical energy needed by the cell. Mitochondrial DNA (mtDNA) contains 16,569 nucleotides that can be mutated. Some of these mutations can lead to the development of mitochondrial diseases. While nuclear DNA (the well-known double helix, which encodes most of the genome)…

Continue Reading Mechanisms involved in the transmission of genetic diseases from mother to child

LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Published: 4 March 2022| Version 1 | DOI: 10.17632/2289cnrdtz.1 Contributors: Description The first version of this code (Mackay et al., 2013) [10] implemented long-range hydrodynamic interactions into the open-source molecular dynamics package LAMMPS. This was done through the creation of a fix, lb/fluid which was subsequently included as a user-package…

Continue Reading LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

Continue Reading Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…

Continue Reading Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

Continue Reading Transcriptional kinetics and molecular functions of long noncoding RNAs

The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill. — ScienceDaily

Imagine Bach’s “Cello Suite No. 1” played on a strand of DNA. This scenario is not as impossible as it seems. Too small to withstand a rhythmic strum or sliding bowstring, DNA is a powerhouse for storing audio files and all kinds of other media. “DNA is nature’s original data…

Continue Reading The Information Age needs a new data storage powerhouse. With an expanded molecular alphabet and a 21st century twist, DNA may just fit the bill. — ScienceDaily

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy. The overall goal of the following method article is to demonstrate a protocol useful to study RNA interactions with proteins or…

Continue Reading Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Linear Transformation to incoming data in Pytorch

We could apply linear transformation to the incoming data using the torch.nn.Linear() module in PyTorch. This module is designed to create a Linear Layer in the neural networks. A linear layer computes the linear transformation as below-   Where Please note that weights  and biases  are initialized randomly. Stepwise Implementation Below are…

Continue Reading Linear Transformation to incoming data in Pytorch

Passing a parameter into a slurm script (matlab)

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter: function test(variable_1) and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file, but I would like…

Continue Reading Passing a parameter into a slurm script (matlab)

File “sage/symbolic/pynac_impl.pxi”, Exception. Unhandled SIGSEGV: A segmentation fault occurred

I am not sure if this is a bug in Python or sagemath. Using sagemath 9.5 on Linux Arch. I’ll describe the problem in words, then given MWE to reproduce it. I have an integrand integrand = “F(x)*(-x^2+x)^(1/2)” as string. I pass it to a subprocess using multiprocessing. When I…

Continue Reading File “sage/symbolic/pynac_impl.pxi”, Exception. Unhandled SIGSEGV: A segmentation fault occurred

Validea Motley Fool Strategy Daily Upgrade Report – 2/26/2022

The following are today’s upgrades for Validea’s Small-Cap Growth Investor model based on the published strategy of Motley Fool. This strategy looks for small cap growth stocks with solid fundamentals and strong price performance. EXLSERVICE HOLDINGS, INC. (EXLS) is a mid-cap growth stock in the Business Services industry. The rating…

Continue Reading Validea Motley Fool Strategy Daily Upgrade Report – 2/26/2022

u-net deployment based on tensorrt

The code used in this project is pytorch-Unet, Link to :GitHub – milesial/Pytorch-UNet: PyTorch implementation of the U-Net for image semantic segmentation with high quality images. The project is based on the scale of the original image as the final input , This for data If the size of the…

Continue Reading u-net deployment based on tensorrt

[slurm-users] mps on A100 only zero-index GPU was used when there is four GPUs

Hi threre, I was testing the MPS on Slurm19.05.5 with 4 A100 in compute node. In my opinion, the 4 A100 will be used.  But I found that only the first GPU was used. like below: the job script: #!/bin/bash #SBATCH -J date #SBATCH -p NVIDIAA100-PCIE-40GB #SBATCH -n 1 #SBATCH…

Continue Reading [slurm-users] mps on A100 only zero-index GPU was used when there is four GPUs

Help regarding LAMMPS HMC using C – LAMMPS Development

Hello I am working on creating a Hybrid Monte Carlo (HMC) code in LAMMPS using C programming language for running a NPT system.I have a working HMC code for a NVT system. I am trying to make it into a NPT system but am facing difficulty in passing the changed…

Continue Reading Help regarding LAMMPS HMC using C – LAMMPS Development

API for NCBI Accession ID (GenBank or RefSeq) generation from a list of species names? : bioinformatics

TL;DR: How can I convert a list of species names (common or scientific) into a corresponding list of NCBI database accession IDs to download the respective species’ reference genome from NCBI. The NCBI urls’ are not common or scientific name compatible so a regular python script for web scrapping that…

Continue Reading API for NCBI Accession ID (GenBank or RefSeq) generation from a list of species names? : bioinformatics

How to Build a Code Search Tool Using PyTorch Transformers and Annoy | by Youness Mansar | Feb, 2022

Leveraging joint text and code embeddings for search. Modified from Photo by Markus Winkler on Unsplash Did you ever look for a code snippet on google because you were too lazy to write it yourself? Most of us did! Then how about building your own code search tool from scratch?…

Continue Reading How to Build a Code Search Tool Using PyTorch Transformers and Annoy | by Youness Mansar | Feb, 2022

How to define a matrix using if and for loops in sagemath?

When constructing a matrix in Sagemath, you can pass in a function that computes its entries, which eliminates the need for explicit (and generally inefficient) loops. This function is defined below as xentries: I used the same conditionals as in your post, but grouped them for readability. def xentries(i, j,…

Continue Reading How to define a matrix using if and for loops in sagemath?

A mammalian methylation array for profiling methylation levels at conserved sequences

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

Continue Reading A mammalian methylation array for profiling methylation levels at conserved sequences

In Focus: electroporation – RegMedNet

Transfection is the process of introducing foreign material – generally nucleic acids (DNA or RNA) – into cells. This allows for the study of gene function and protein expression in the context of the cell, or transformation of the cell into a potential cell therapy product such as a CAR-T….

Continue Reading In Focus: electroporation – RegMedNet

autopkgtest regression on armhf and i386

Source: django-q Version: 1.3.9-2 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of django-q the autopkgtest of django-q fails in testing when that autopkgtest is run with the binary packages of django-q from unstable. It passes when run with only packages from testing. In…

Continue Reading autopkgtest regression on armhf and i386

Bug#1004512: autodock-vina: autopkgtest regression on armhf: warning on stderr

Source: autodock-vina Version: 1.2.3-1 X-Debbugs-CC: debi…@lists.debian.org Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of autodock-vina the autopkgtest of autodock-vina fails in testing when that autopkgtest is run with the binary packages of autodock-vina from unstable. It passes when run with only packages from testing. In…

Continue Reading Bug#1004512: autodock-vina: autopkgtest regression on armhf: warning on stderr

Split multiallelic SNPs to biallelic from vcf

Dear all, I have a particular vcf file like this, chrX 29 . G A,T . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:4839:0.003,0.001:0.002,0.0:0.005,0.003:14;0,4;2 I tried various tools to split this, but I get the following results, so the FORMAT and INFO lines are identical. chrX 29 . G A . PASS AC=1,1;AN=3;OLD_MULTIALLELIC=chrM:899:G/A/T GT:DP:HF:CILOW:CIUP:SDP…

Continue Reading Split multiallelic SNPs to biallelic from vcf

Install CUDA on NVIDIA Jetson Nano

Hardware Pre-requisite Jetson Nano A 5V 4Ampere Charger 64GB SD card Software Preparing Your Raspberry Pi Flashing Jetson SD Card Image Unzip the SD card image Insert SD card into your system. Bring up Etcher tool and select the target SD card to which you want to flash the image….

Continue Reading Install CUDA on NVIDIA Jetson Nano

log repeats until it times out)

Your message dated Sat, 22 Jan 2022 21:52:05 +0100 with message-id <f98ce279-5828-d2b5-8b7c-88287a3ab…@debian.org> and subject line Re: Bug#997845: bug 997845 has caused the Debian Bug report #997845, regarding growlight: autopkgtest regression: log repeats until it times out to be marked as done. This means that you claim that the problem has…

Continue Reading log repeats until it times out)

Python – canvas selection – Developer Questions

Hi from krita import * def selectRGB(node, red, green, blue, selectionLevel=255): # get pixels data from node projection # for RGBA/8bit, pixel data format: Blue, Green, Red, Alpha pdata=node.projectionPixelData(node.bounds().left(), node.bounds().top(), node.bounds().width(), node.bounds().height()) bred=red.to_bytes(1, ‘big’) bgreen=green.to_bytes(1, ‘big’) bblue=blue.to_bytes(1, ‘big’) # prepare selection (0=no selection, 255=full selection) selectionPixels=[0]*(node.bounds().width()*node.bounds().height()) offset=0 for index in…

Continue Reading Python – canvas selection – Developer Questions

Tutorial on Box Plot in ggplot2 with Examples – MLK

Introduction Boxplots are a useful visualization technique to understand the distribution and outliers in a dataset. In this article, we will go through the tutorial for box plot in ggplot2 function of R which is a popular visualization package. We will first understand the syntax of ggplot2 function geom_boxplot() for…

Continue Reading Tutorial on Box Plot in ggplot2 with Examples – MLK

Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

There is a need to determine which atherosclerotic lesions will progress in the coronary vasculature to guide intervention before myocardial infarction occurs. This article outlines the biomechanical modeling of arteries from Optical Coherence Tomography using fluid-structure interaction techniques in a commercial finite element solver to help predict this progression. Atherosclerosis…

Continue Reading Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma

Interrogation of cell-free DNA (cfDNA) represents an emerging approach to non-invasively estimate disease burden in multiple myeloma (MM). Here, we examined low-pass whole genome sequencing (LPWGS) of cfDNA for its predictive value in relapsed/ refractory MM (RRMM). We observed that cfDNA positivity, defined as ≥10% tumor fraction by LPWGS, was…

Continue Reading Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma

Process Development for the Production and Purification of Adeno-Associated Virus (AAV)2 Vector using Baculovirus-Insect Cell Culture System

In this protocol, AAV2 vector is produced by co-culturing Spodoptera frugiperda (Sf9) insect cells with baculovirus (BV)-AAV2-green fluorescent protein (GFP) or therapeutic gene and BV-AAV2-rep-cap infected Sf9 cells in suspension culture. AAV particles are released from the cells using detergent, clarified, purified by affinity column chromatography, and concentrated by tangential…

Continue Reading Process Development for the Production and Purification of Adeno-Associated Virus (AAV)2 Vector using Baculovirus-Insect Cell Culture System

Plink Alternative Phenotype File Columns not being Read

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

Continue Reading Plink Alternative Phenotype File Columns not being Read

Bug#1003563: aide: autopkgtest regression: unexpected character: ‘@’ in /etc/aide/aide.conf.d/31_aide_spamassassin

Source: aide Version: 0.17.3-6 X-Debbugs-CC: debi…@lists.debian.org Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of aide the autopkgtest of aide fails in testing when that autopkgtest is run with the binary packages of aide from unstable. It passes when run with only packages from testing. In…

Continue Reading Bug#1003563: aide: autopkgtest regression: unexpected character: ‘@’ in /etc/aide/aide.conf.d/31_aide_spamassassin

Getting number of arguments error with scikit rfe ( Python, Scikit Learn )

Problem : ( Scroll to solution ) I am learning machine learning and came across this error. I think it is an issue with my local setup. # Importing RFE and LinearRegression from sklearn.feature_selection import RFE from sklearn.linear_model import LinearRegression # Running RFE with the output number of the variable…

Continue Reading Getting number of arguments error with scikit rfe ( Python, Scikit Learn )

Microtubule Plus-End Dynamics Visualization in Huntington’s Disease Model based on Human Primary Skin Fibroblasts

This protocol is dedicated to the microtubule plus-end visualization by EB3 protein transfection to study their dynamic properties in primary cell culture. The protocol was implemented on human primary skin fibroblasts obtained from Huntington’s disease patients. The Huntington’s disease, HD, is an incurable, neurodegenerative pathology caused by a mutation in…

Continue Reading Microtubule Plus-End Dynamics Visualization in Huntington’s Disease Model based on Human Primary Skin Fibroblasts

swagger – How to define this array of objects in OpenAPI?

How to write an OpenAPI definition for the following JSON? Bazically it is an array consisting of two objects with similar attributes but different fields. [ { “studentname”: “somename”, “studentrollno”: “somerollno”, “studentsubjects”: [ { “level”: “third”, “physics”: “xyz”, “maths”: “somevalue” }, { “level”: “second”, “physics”: “abc”, “maths”: “somevalue11” } ],…

Continue Reading swagger – How to define this array of objects in OpenAPI?

Bug#1003017: dulwich: autopkgtest regression: src/debian/tests/testsuite3: 10: -m: not found

Source: dulwich Version: 0.20.26-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of dulwich the autopkgtest of dulwich fails in testing when that autopkgtest is run with the binary packages of dulwich from unstable. It passes when run with only packages from testing. In…

Continue Reading Bug#1003017: dulwich: autopkgtest regression: src/debian/tests/testsuite3: 10: -m: not found

Stan vs PyMC3 vs Bean Machine

I have been a light user of Stan and RStan for some time and while there are a lot of things I really like about the language (such as the awesome community you can turn to for support and ShinyStan for inspecting Stan output) there are also a few things…

Continue Reading Stan vs PyMC3 vs Bean Machine

Columntransformer & pipeline with ohe – is the ohe encoded field retained or removed after ct is performed? ( Python, Scikit Learn )

Problem : ( Scroll to solution ) Doc on CT: remainder{‘drop’, ‘passthrough’} or estimator, default=’drop’ By default, only the specified columns in transformers are transformed and combined in the output, and the non-specified columns are dropped. (default of ‘drop’). By specifying remainder=”passthrough”, all remaining columns that were not specified in…

Continue Reading Columntransformer & pipeline with ohe – is the ohe encoded field retained or removed after ct is performed? ( Python, Scikit Learn )

Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn.

Live webpage Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn. Running locally Setup a virtual environment. Install requirements pip install -r requirements Create a personal access token and set it to GITHUB_TOKEN. Run the following to call the GitHub API for repo information and cache the results…

Continue Reading Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn.

clusterExport, environment and variable scoping

You’re getting the error when calling clusterExport(cl, list(“a”, “b”, “data”)) because clusterExport is trying to find the variables in .GlobalEnv, but fn1 isn’t setting them in .GlobalEnv but in its own local environment. An alternative is to pass the local environment of fn1 to fn2, and specify that environment to…

Continue Reading clusterExport, environment and variable scoping

Bug#1002588: wurlitzer: autopkgtest regression on ppc64el: AssertionError: assert 65536 == 32768

Source: wurlitzer Version: 3.0.2-3 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of wurlitzer the autopkgtest of wurlitzer fails in testing when that autopkgtest is run with the binary packages of wurlitzer from unstable on ppc64el. It passes when run with only packages from…

Continue Reading Bug#1002588: wurlitzer: autopkgtest regression on ppc64el: AssertionError: assert 65536 == 32768

Delightful code generation for OpenAPI specs for Swift written in Swift

Delightful code generation for OpenAPI specs for Swift written in Swift. Fast: processes specs with 100K lines of YAML in less than a second Smart: generates Swift code that looks like it’s written by hand Reliable: tested on 500K lines of publically available OpenAPI specs producing correct code every time…

Continue Reading Delightful code generation for OpenAPI specs for Swift written in Swift

Science snapshots from Berkeley Lab

image: 3D image of melanin in a zebrafish sample captured by micro-computed tomography. view more  Credit: Spencer R. Katz and Daniel J. Vanselow, Penn State College of Medicine) Adapted from a UC Berkeley news release To date, CRISPR enzymes have been used to edit the genomes of one type of cell…

Continue Reading Science snapshots from Berkeley Lab

Harvard University hiring Bioinformatics Engineer in Boston, Massachusetts, United States

Job-Specific ResponsibilitiesWe are looking for a motivated bioinformatics engineer to join the Department of Biomedical Informatics at Harvard Medical School, to build platforms for genome analysis. Genome sequencing is becoming a routine approach for diagnosing genetic diseases. As the number of patients referred to genetic screening is increasing, there is…

Continue Reading Harvard University hiring Bioinformatics Engineer in Boston, Massachusetts, United States

Bug#1001735: node-trust-keyto: autopkgtest regression: Cannot find module ‘@trust/keyto’

Source: node-trust-keyto Version: 2.0.0~alpha1-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of node-trust-keyto the autopkgtest of node-trust-keyto fails in testing when that autopkgtest is run with the binary packages of node-trust-keyto from unstable. It passes when run with only packages from testing. In…

Continue Reading Bug#1001735: node-trust-keyto: autopkgtest regression: Cannot find module ‘@trust/keyto’

bcftools merge of over 9000+ vcf files

Hi all, I have around 9000+ vcf files that I’m trying to merge using bcftools merge. They are all located in their own folder so essentially I have a folder containing 9000+ separate folders, each containing one vcf.gz file. I have tried out the following code via this tutorial bcftools…

Continue Reading bcftools merge of over 9000+ vcf files

How does the new SageMaker Studio Lab compare to Colab and Kaggle?

Taken from benjaminwarner.dev Machine Heart Compilation SageMaker Studio Lab will be a strong competitor in the field of free computing resources. A week ago, Amazon launched the free simplified version of SageMaker Studio SageMaker Studio Lab, providing a CPU instance with a time limit of 12 hours and a GPU…

Continue Reading How does the new SageMaker Studio Lab compare to Colab and Kaggle?

[BUG] (python-fastapi) OneOf class not generated

Bug Report Checklist Description For oneOf fields, the python-fastapi server generator creates a function that returns a OneOf* class, but that class itself is not generated. For example, for an API like /status: get: summary: Get the status of the upstream server responses: 200: description: successful operation content: application/json: schema:…

Continue Reading [BUG] (python-fastapi) OneOf class not generated

Pytorch implementation of Bert (super detailed)

B Station video explanation This article mainly introduces how to use PyTorch Reappear BERT. Please spend it first 10 Minutes to read my article BERT Detailed explanation ( Incidental ELMo、GPT Introduce ), Let’s look at this article , In order to achieve enlightenment , Get twice the result with half…

Continue Reading Pytorch implementation of Bert (super detailed)

Swagger Routes Express – Open Source Agenda

Connect Express route controllers to restful paths using a Swagger v2 or OpenAPI v3 definition file. Assumptions This library assumes you are using: NodeJS version 6.4.0 or better, expressjs any version, and swagger version 2, or OpenAPI version 3. Install Add swagger-routes-express as a dependency: npm i swagger-routes-express Examples A…

Continue Reading Swagger Routes Express – Open Source Agenda

Fairring (FAIR + Herring) is a plug-in for PyTorch that provides a process group for distributed training that outperforms NCCL at large scales

TL;DR: Using a variation on Amazon’s “Herring” technique, which leverages reduction servers, we can perform the all-reduce collective faster than NCCL: up to 2x as fast as NCCL in microbenchmarks up to 50% speedup in end-to-end training workloads You can use it right away in your project, with no code…

Continue Reading Fairring (FAIR + Herring) is a plug-in for PyTorch that provides a process group for distributed training that outperforms NCCL at large scales

Easy OpenAPI specs and Swagger UI for your Flask API

Easy Swagger UI for your Flask API Flasgger is a Flask extension to extract OpenAPI-Specification from all Flask views registered in your API. Flasgger also comes with SwaggerUI embedded so you can access localhost:5000/apidocs and visualize and interact with your API resources. Flasgger also provides validation of the incoming data,…

Continue Reading Easy OpenAPI specs and Swagger UI for your Flask API

How to clear Cuda memory in PyTorch

Hello Guys, How are you all? Hope You all Are Fine. Today We Are Going To learn about How to clear Cuda memory in PyTorch in Python. So Here I am Explain to you all the possible Methods here. Without wasting your time, Let’s start This Article. How to clear Cuda…

Continue Reading How to clear Cuda memory in PyTorch