Tag: python

Software Engineer – Python and Pytorch

Computer Vision Researcher / Research Scientist – 12 month contract This is a unique opportunity to snap up very quickly. Our client is a leading technology firm looking to hire a recent graduate / post doc graduate. An ideal role for a newly qualified individual looking to gain experience within…

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python – DeprecationWarning when importing Scikit-learn

I’m using JupyterLab. When importing some packages, or executing some functions from scikit-learn, very long list of deprecation warnings fill the screen. I googled about this problem and upgraded the packages (scikit-learn, numpy), but I still get the warnings. pip install scikit-learn –upgrade Requirement already satisfied: scikit-learn in c:users…appdatalocalprogramspythonpython39libsite-packages (1.0.2)…

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Senior Manager, Bioinformatics and Genomics Data Scientist

Job Description Do you want to be part of an inclusive team that works to develop innovative therapies for patients? Every day, we are driven to develop and deliver innovative and effective new medicines to patients and physicians. If you want to be part of this exciting work, you belong…

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Intern- Bioinformatics – Foster City

Gilead Sciences is continuing to hire for all open roles. Our interview process may be conducted virtually and some roles will be asked to temporarily work from home. Over the coming weeks and months, we will be implementing a phased approach to bringing employees back to site to ensure the…

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biopython – Help to create a dataframe in Python from a FASTA file

I want to create a dataframe in Python starting from a FASTA format file. Given the toy FASTA file that I am attaching, I built this program in Python that returns four colums corresponding to id, sequence length, sequence, animal name and rows corresponding to all the data available. However,…

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Bayesian Open Source Software for Biomedicine: Stan, ArviZ and PyMC3

Back to Proposal List Projects PyMC, ArviZ, Stan Lead Christopher Fonnesbeck (NumFOCUS) Funding Cycle 4 Proposal Summary To develop key infrastructure updates and collaboration resources for state-of-the-art Bayesian modeling software libraries. Project PyMC PyMC3 is the current version of the PyMC open source probabilistic programming framework for Python, having been…

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python – One Hot Encoding: Avoiding dummy variable trap and process unseen data with scikit learn

I’m building a model, pretty much similiar to the well known House Price Prediction. I got to the point that I need to encode my nominal categorical variables by using scikit-learns OneHotEncoder. The so called “Dummy Variable Trap” is clear to me so I need to drop one of my…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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Python For Machine Learning (ML) Course

Course Instructor: Fabio Mardero is a data scientist from Italy. He graduated in physics and statistical and actuarial sciences. He is currently working at a well-known Italian insurance company as a data scientist and Non-Life technical provisions evaluator.  Course Overview & Lectures Duration: 14+ hours Project Insurance Project Italian COVID dataset (official…

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Job Application for Director, Bioinformatics Applications at Recursion

Recursion is a clinical-stage biotechnology company decoding biology by integrating technological innovations across biology, chemistry, automation, data science and engineering to radically improve the lives of patients and industrialize drug discovery. Our team is working to solve some of the hardest, most meaningful problems facing human health today. Come join…

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Top Quantum Computing Jobs to Apply for in January 2022

Quantum computing has emerged as an interesting career option in recent years Experts believe that quantum computing can change the world. It possesses the capabilities of revolutionizing the drug discovery process, facilitating deciphering codes for security purposes, and so much more. Currently, it is safe to say that quantum computing…

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Bioinformatics Specialist Job Opening in Aliso Viejo, CA at Ambry Genetics

JOB OVERVIEW: The main role of this position is project coordination, timeline management, and requirement gathering. To this end, the Bioinformatics Specialist analyzes and refines business and user requirements, and coordinates with developers to facilitate bioinformatics solutions through the entire SDLC, from discovery, design, development, and validation. The Bioinformatics Specialist…

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Bound State of a Protein through kmeans (or GMVAE) Clustering : comp_chem

I am an undergraduate researching in a computational chem lab at UMD. I am done running many HMMM and then AA simulations via CHARMM and NAMD. So far HMMM simulations were converted to AA when the secondary structure seemed stable and the distance to the bilayer was minimal through visual…

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Python Install Scikit Learn – January 2022

Learning Model Building in Scikit-learn : A Python Machine … Posted: (4 days ago) Feb 17, 2017  · Pre-requisite: Getting started with machine learning scikit-learn is an open-source Python library that implements a range of machine learning, pre-processing, cross-validation, and visualization algorithms using a unified interface.. Important features of scikit-learn:…

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a Rust-backed Python library for DNA translation that is up to 100x faster than Biopython : bioinformatics

Background: I work at SecureDNA1, where we use Biopython pretty extensively. It’s a great library, but often quite slow, and we’ve run into bottlenecks in our processing pipelines around Biopython’s translation speed. I wrote this library to augment Biopython — you can read your sequences out of FASTA files with…

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Extracting organism and seq from fasta

Extracting organism and seq from fasta 0 Hi, I am trying to extract sequences from a fasta file from a database with a specific organism species keyword from a .txt file containing the relevant headers. Do you know how I can do this in python as the biopython guide I’ve…

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Bioconda faststructure – gitmetadata

I am using the conda env of faststructure from bioconda channel. Got this error messages. Could it be that the bioconda package needs to be updated? Best regards: python structure.py structure.py:3: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 import fastStructure structure.py:4: RuntimeWarning: numpy.dtype size changed,…

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python xarray – PyMC3/Arviz: CDF value from trace

I have a sample from PyMC3 and I’m trying to get a cumulative probability from it, e.g. P(X < 0). I currently use this: trace = pymc3.sample(return_inferencedata=True) prob_x_lt_zero = (trace.posterior.X < 0).sum() / trace.posterior.X.size Is there a better way to do this, either with some helper function from Arviz or…

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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…

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Fasta file reading python

Answer by Aidan Golden I think you can just use Biopython,It is indeed wrong today. I edited the answer since it has been possible to use str(sequence) for a long time now.,Very useful answer from 7 years ago! FYI, in current version of biopython(1.69), fasta.seq.tostring() is obsolete, use str(fasta.seq) instead.,Nicely…

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Python through jupyterhub. Simple animation with Xarray data

I’m working on a project where I will try to do an animation of the mixed layer depth for 12 months. My current concern is that I want to do an animation where I only show the current month with data in the plot, but they keep showing vertically in…

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Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research

Job title: Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research Company: Workscout Job description Job beskrivelse We are looking for a highly motivated and dynamic Assistant Professor for a 4-year position to commence on the 1st of April 2022 or soon hereafter. The position…

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ImportError: cannot import name _aligners [biopython]

I had a problem with this when biopython (as a dependency) was installed during the installation of another package. Solution: pip uninstall biopython pip install biopython This can occur on Biopython version >= 1.72 and has been discussed on the biopython mailing list here. This error occurs when you try…

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Genomics and Bioinformatics in Ames, IA for Iowa State University

Details Posted: 08-Jan-22 Location: Ames, Iowa Salary: Open Categories: Academic/Faculty Position Title: Postdoctoral – Genomics and Bioinformatics Appointment Type: Post Doc/Trainee Job Description: Summary of Duties and Responsibilities: Contribute to the Functional Annotation of Animal Genomes (FAANG) project in developing and testing of pipelines for the analysis of high-throughput genomics…

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python – Where to upload the image files to JupyterHub server (ltjh)

I would like to create a jupyter notebook that displays some images like this. In the case of my computer, the image files are stored in the local device. So I wrote one-line tag to show the image. <img src=”images/python_with_Birds.gif” width=”400″/> But if I want to share my created jupyter…

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Description, Programming Languages, Similar Projects of Gpt 2 Pytorch

GPT2-Pytorch with Text-Generator Better Language Models and Their Implications Our model, called GPT-2 (a successor to GPT), was trained simply to predict the next word in 40GB of Internet text. Due to our concerns about malicious applications of the technology, we are not releasing the trained model. As an experiment…

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Python scikit learn multi-class multi-label performance metrics?

To calculate the unsupported hamming loss for multiclass / multilabel, you could: import numpy as np y_true = np.array([[1, 1], [2, 3]]) y_pred = np.array([[0, 1], [1, 2]]) np.sum(np.not_equal(y_true, y_pred))/float(y_true.size) 0.75 You can also get the confusion_matrix for each of the two labels like so: from sklearn.metrics import confusion_matrix, precision_score…

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Roche hiring Sr Bioinformatics Scientist in Cambridge, Massachusetts, United States

SUMMARY We are seeking a talented and motivated Senior Bioinformatics Scientist who will be an integral member of the Sequencing team contributing to the support and development of ground-breaking next-generation sequencing (NGS) products. As a member of Roche’s Sequencing and Life Science (SLS), Scientific Support and Applications team, you will…

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Assistant Professor Job – Bioinformatics and Metagenomics, UCPH, Denmark, Jan 2022

The University of Copenhagen invites applications for an Assistant Professor position will be in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research, Denmark – Jan 2022 Qualification Details Six overall criteria apply for Assistant Professor appointments at the University of Copenhagen. The six criteria…

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The Evolution of scRNA-seq Analysis

By Jane CookNovember 29, 2021 What Can scRNA-seq Data Tell Us? Single cell sequencing technologies have exploded in popularity for biological research over the last five years. The appeal of scRNA-seq lies in its specificity and scalability compared to older research techniques like Western blotting. Researchers can use scRNA-seq to…

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genbank – Github Help

7 1 4 genbank,MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from…

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make Pyspark working inside jupyterhub

You need to configure the pyspark kernel. On my server jupyter kernels are located at: /usr/local/share/jupyter/kernels/ You can create a new kernel by making a new directory: mkdir /usr/local/share/jupyter/kernels/pyspark Then create the kernel.json file – I paste my as a reference: { “display_name”: “pySpark (Spark 1.6.0)”, “language”: “python”, “argv”: […

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Installation issues with PyMC3 – Stackify

Just had this problem and found a solution. When searching (with Bing or Google) for conda install of pymc3, several links come up. The first is with conda-forge: conda install -c conda-forge pymc3 DO NOT USE THIS or you will get the error messages in the above posts. I have…

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Mle Application With Gekko In Python

The true power of the state space model is to allow the creation and estimation of custom models.This notebook shows various statespace models that subclass sm. That means your MAGeCK python module is installed in /home/john/.pyenv/versions/2.7.13/lib/python2.7/sitepackages.I use conda to install the latest version of. This twovolume set Diseases and Pathology…

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python – Creating batches of sequences for pytorch LSTM

I’m currently working on a LSTM Autoencoder using pytorch. I have a big amount of samples. Each sample contains 120 features. For now, I’m creating sequences of length 1, batch_size is equal to 1 and everything is working fine. I first convert my data array to a list and then…

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[lh3/minimap2] Memory leak when using Python and threads

The program align.py uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to climb steadily through 40Gb an beyond. This issue was first discovered in bonito and isolated to mappy. The data flow…

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[PATCH 0/3] Add Optuna.

* gnu/packages/machine-learning.scm (python-optuna): New variable. gnu/packages/machine-learning.scm | 96 +++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) Toggle diff (116 lines) diff –git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fd3e6b2090..3b6f709c4e 100644 — a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) #:use-module (gnu packages parallel) + #:use-module (gnu packages openstack) #:use-module (gnu packages perl)…

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The Kaggle Way to Tune Hyperparameters with Optuna

Optimize fetching data from Neo4j with Apache Arrow High-performance data retrieval from Neo4j with Apache Arrow. The year is 2022, and graph machine learning is one of the rising trends in data analytics. While Neo4j has a Graph Data Science library that supports multiple graph algorithms and machine learning workflows,…

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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biopython – Github Help

1 1 0 biopython,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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cry from hellman – Github Help

This repository contains a bunch of various crypto-related algorithms implemented in Python 3 and SageMath. Pure Python code is located in cry/py package and can be imported from python code. The other modules must be imported from the SageMath interpreter. The most significant part is formed by S-Box analysis algorithms,…

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fairtracks/fairtracks_validator_python: FAIRification of Genomic Data Tracks JSON Schema validator, Python edition

GitHub – fairtracks/fairtracks_validator_python: FAIRification of Genomic Data Tracks JSON Schema validator, Python edition You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here:…

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Kaggle-titanic – A tutorial for Kaggle’s Titanic: Machine Learning from Disaster competition. Demonstrates basic data munging, analysis, and visualization techniques. Shows examples of supervised machine learning techniques.

Kaggle-titanic This is a tutorial in an IPython Notebook for the Kaggle competition, Titanic Machine Learning From Disaster. The goal of this repository is to provide an example of a competitive analysis for those interested in getting into the field of data analytics or using python for Kaggle’s Data Science…

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‘dataspell’ tag wiki – Stack Overflow

JetBrains DataSpell is an IDE for data science with intelligent Jupyter notebooks, interactive Python scripts, and lots of other built-in tools. The IDE for Professional Data Scientists DataSpell is an Integrated Development Environment (IDE) that is dedicated to specific tasks for exploratory data analysis and prototyping ML (machine learning)…

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python error :Conda channels

conda channels what is conda channels ? Conda channels are the locations where packages are stored. They serve as the base for hosting and managing packages. Conda packages are downloaded from remote channels, which are URLs to directories containing conda packages set up channels The conda-forge channel contains many general-purpose…

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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…

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Single cell RNAseq data analysis

Github repository  02-04 February 2022  SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours)…

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kegg – Github Help

1 1 0 kegg,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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Introduction to Generative Adversarial Networks with PyTorch

Introduction to Generative Adversarial Networks with PyTorch. A comprehensive course on GANs including state of the art methods, recent techniques, and step-by-step hands-on projects What you’ll learn How Generative Adversarial Networks work internally How to implement state of the art GANs techniques and methods using PyTorch How to improve the…

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ValueError while using linear SVM of scikit-learn python

The error message ValueError: X.shape[1] = 1199847 should be equal to 1199830, the number of features at training time explains itself: the number of features in the testing data is different compared to the training data, which has been used to train the model. That is, X_train.shape[1] is not equal…

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sagemath/sage-windows – githubmate

Build files and instructions for the Cygwin-compatible build of Sage and its executable installer and auxiliary files. You can find the latest release (for now) at github.com/sagemath/sage-windows/releases Occasionally new versions of SageMath for Windows are released independently of the Sage version (e.g. to make improvements with the Windows installer itself)….

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Why is the plot generated from ggplot not showing up?

The line plt = ggplot(…. is not right, for a few reasons. plt is the name you’ve given the pylab module. plt = will delete it! data=df is a keyword argument (because of the data= part). They have to go after positional arguments. See the keyword entry of the Python…

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python – NameError: name ‘Seq’ is not defined

I want to fill null value with Average. data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) data2.display() This error I got: ————————————————————————— NameError Traceback (most recent call last) <command-1060196488305723> in <module> —-> 1 data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) 2 data2.display() NameError: name ‘Seq’ is not defined Read more here: Source link

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Job Opportunity: HPC Engineer at European Bioinformatics Institute (EMBL-EBI) (Hinxton, UK)

New Job opportunity posted by European Bioinformatics Institute (EMBL-EBI): We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with…

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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…

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Running on CUDA 10.X – Python alphafold

Hi! It looks like our server’s GPU nodes only support up to CUDA 10.2. With the downgraded versions of tensorflow and other modules/packages, will be output consistent with those produced from the default set-up? Thanks! Asked Jul 25 ’21 at 22:21 skyungyong 1 Answer: Hi, Looking at storage.googleapis.com/jax-releases/jax_releases.html it appears…

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Gilead Sciences hiring Intern – Bioinformatics in Foster City, California, United States

Gilead Sciences is continuing to hire for all open roles. Our interview process may be conducted virtually and some roles will be asked to temporarily work from home. Over the coming weeks and months, we will be implementing a phased approach to bringing employees back to site to ensure the…

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Data Visualization using Plotnine and ggplot2 in Python

  Data Visualization is the technique of presenting data in the form of graphs, charts, or plots. Visualizing data makes it easier for the data analysts to analyze the trends or patterns that may be present in the data as it summarizes the huge amount of data in a simple…

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How To Install RStudio IDE on Fedora 35

In this tutorial, we will show you how to install RStudio IDE on Fedora 35. For those of you who didn’t know, RStudio provides free and open-source tools for R and enterprise-ready professional software for data science teams to develop and share their work at scale. RStudio makes it easier…

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Pytorch YoloV2 implementation from scratch

This repository is simple implementation of YOLOv2 algorithm for better understanding and use it for more object detection usage. This project based on Pytorch. The code of project is so easy and clear. Dataset Pretrained weights in this implemetation are based on training yolo team on COCO trainval dataset Usage…

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makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version of BLAST (Version 2.11.0+) and downloaded the refseq_protein database from NCBI using the following code wget ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz The database gets downloaded…

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Python scikit learn n_jobs – Stackify

what is the point of using n-jobs (and joblib) if the the library uses all cores anyway? It does not, if you specify n_jobs to -1, it will use all cores. If it is set to 1 or 2, it will use one or two cores only (test done scikit-learn…

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htseq-count python tutorial attribute counts error

Hello, I’m following the htseq-count tutorial for RNA-seq (counting the overlapping genes and exons) here htseq.readthedocs.io/en/master/tour.html. However, when I get to the point where I need to find the overlaps in the .sam file and .gtf file, I get an error. This is the code I ran originally that gave…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

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

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La Jolla Institute for Immunology hiring Bioinformatics Postdoc – Systems Immunology of Infectious Diseases in San Diego, California, United States

The Peters Lab at the La Jolla Institute for Immunology (LJI) is looking for a bioinformatics postdoc to join our efforts in profiling immune system responses to a variety of infectious agents, such as M. tuberculosis and B. Pertussis, as well as various cancers. Qualified applicants will have the opportunity…

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Elucidata Corporation hiring Bioinformatics Scientist in Remote

About Elucidata Corporation Provider of cloud-based data analytics platform designed to analyze omics datasets to understand the molecular basis of cellular phenotypes. Job Description About Elucidata:    Elucidata has assembled an elite group of scientists, engineers, and business development professionals to create technologies and products that will shape the future…

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Associate Scientist, Bioinformatics – jobRxiv

Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center?  This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University…

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Visualisation for MD simulations data : comp_chem

I’m a second year phd student running mostly orca calculations on a range of MOFs and quantifying their properties (mostly reaction free energies of adsorption for small molecules). However, from next year I’ll be running some MD simulations to track diffusion of ions through MOF pores. I’m already familiar with…

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The Hot Topic In Probabilistic Programming

One of the biggest challenges of this decade is solving uncertainty, ethical and explainable problems in the thousands of machine learning models we interact with daily. Meta, formerly Facebook, announced the release of their supplement to aid this developing sphere. Bean Machine, Meta’s probabilistic programming system, is a PyTorch-based model…

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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…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology

DepartmentDepartment of Histology and Embryology  – Faculty of MedicineDeadline 28 Feb 2022Start date Jully 2022Job type full-timeJob field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of Histology and Embryology is…

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how do you connect a javascript app to a jupyterhub kernel? – Python jupyterhub

We want to embed a notebook type thing in our app but @nteract/notebook-app-component is not finished, jupyterlab is heavy and takes over the whole screen, thebelab is also heavy (1.6Mb) … these solutions don’t work for a simple web app to embed a notebook kernel right now How do you…

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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…

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Bioinformatics Engineer/Senior Engineer – Cambridge Massachusetts

Flagship Pioneering has launched a privately held, biotechnology company that is pioneering novel diagnostics for cancer. This new company, Harbinger Oncology, is a highly dynamic, entrepreneurial, and innovation-driven organization seeking to hire a Bioinformatics Engineer/Senior Engineer to join our team. Flagship Pioneering conceives, creates, resources, and grows first-in-category life sciences…

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Moodle Authentication for JupyterHub Docker image | Moodle | Docker | Python | GitLab | OAuth

I have a JupyterHub installation managed within Docker. Also, I have a Moodle installation. I need a freelancer who is competent in both JupyterHub configuration and Moodle configuration. The task is to take my GitLab repository of the JupyterHub Docker file as a basis, create a new branch and do…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology job with MASARYK UNIVERSITY

Department Department of Histology and Embryology – Faculty of Medicine Deadline 28 Feb 2022 Start date Jully 2022 Job type full-time Job field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of…

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CSIRO Postdoctoral Fellowship in Pathogen Genomics and Bioinformatics

CSIRO Postdoctoral Fellowship in Pathogen Genomics and Bioinformatics – Job posted on PostdocJobs.com CONNECT WITH US :    CSIRO Postdoctoral Fellowship in Pathogen Genomics and Bioinformatics Job Number: Date Posted: Dec 23, 2021 Application Deadline: Open Until Filled Job Description Acknowledgment of Country   CSIRO acknowledges the Traditional Owners of the…

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Bioinformatics Analyst in Evanston, IL for Northwestern University

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

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Bioinformatician – qPCR and annotation directions Jobs at Nalagenetics, Jakarta

We are hiring a bioinformatics specialist interested in developing a clinical decision support for implementation of genetics in clinical settings. The person will be responsible of building analytical pipelines forpatients’ genomic, demographic, and individual data, as well as working with our senior software engineer tointegrate our knowledge base with existing…

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Machine Learning Engineer Pipeline (Cape Town or Johannesburg) at Capitec

Purpose Statement To build, implement, improve and support the AI platform which will support delivery of the Capitec AI strategy. To collaborate in creating and delivering the AI strategy to ensure Capitec is able to compete in a fast changing landscape. The effective use of AI technologies will be a…

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Error reporting of scikit learn (sklearn)

Record some scikit learn errors The questions are as follows: ModuleNotFoundError: No module named ‘sklearn. utils. linear_ assignment_’ Solution: the scikit learn version here is too high (it was 1.0.1 before, and it should be made into 0.19. X or before). Refer to the blogger to solve modulnotfounderror: no module…

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End-to-End AutoML Pipeline with H2O AutoML, MLflow, FastAPI, and Streamlit | by Kenneth Leung | Dec, 2021

Now that we have selected our best model, it is time to deploy it as a FastAPI endpoint. The goal is to create a backend server where our model is loaded and served to make real-time predictions through HTTP requests. Inside a new Python script main.py , we create a…

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AutoDock Vina 1.2.0 | Macs in Chemistry

  A new publication describes and update to AutoDock Vina “AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings” DOI. AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it…

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Kaggle Certification 2021 | Kaggle Python Machine learning Deep learning DataScience Certification Courses

Hey Readers Looking for the Certification in Machine learning , Deep Learning , Data Science SL and more So the Kaggle and Google       is  Gaving this Free  today for limited time only . Read Following instruction and details before applying.  Course List Of Certification : Python Learn the…

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Clinical Bioinformatics Analyst (m/w/d) – Foundation Medicine GmbH – Biology & Life Sciences

Clinical Bioinformatics Analyst (m/w/d) PENZBERG, GERMANY Foundation Medicine is leading a transformation in cancer care, where each patient’s treatment is informed by a deep understanding of the molecular changes that contribute to their disease. As a molecular information company, we are focused on fundamentally changing the way in which patients…

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Principal Scientist, Disease Strategy (Translational bioinformatics) on beHired.in

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change. We…

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Bioinformatics, Computer Science, Biology – Transcriptomic, Genomic Assays (f/m/d) – Evotec International GmbH – Biologie & Life Sciences

Evotec is a life science company with a unique business model focused on delivering highly effective new therapeutics to the patients. The Company leverages its multimodality platform, the “Data-driven R&D Autobahn to Cures”, for proprietary projects and within a network of partners including Pharma, Biotech, academics, and other healthcare stakeholders….

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python – How to implement Bayesian Inference correctly with pymc3?

I have been working with pymc3 for a while and I was observing the several tutorials with examples. However, I am not sure if I am approaching the Bayesian InFerence method correctly. Find below my approach: from pymc3.distributions import Interpolated import numpy as np # import warnings # import sys…

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Implement of homography net by pytorch

Implement of homography net by pytorch Brief Introduction This project is based on the work Homography-Net: @article{detone2016deep, title={Deep image homography estimation}, author={DeTone, Daniel and Malisiewicz, Tomasz and Rabinovich, Andrew}, journal={arXiv preprint arXiv:1606.03798},c year={2016} } Dependencies OpenCV pytroch 1.8.1 numpy pandas tqdm Running the code Before you run the code,confirm all…

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Top 10 AutoML Libraries for Implementing in Your Machine Learning Projects

by Disha Sinha December 19, 2021 Learn about AutoML libraries to get access to thousands of machine learning models AutoML libraries are also known as Automated Machine Learning libraries in the field of machine learning, programming languages, and data science. It is now an emerging domain to build multiple machine…

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[biopython/biopython] local pairwise alignment using pairwise2

Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01) [GCC 9.3.0] CPython Linux-5.11.0-41-generic-x86_64-with-debian-bullseye-sid 1.78 # also tested on windows-subsystem 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] CPython Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.31 1.78 Expected behaviour…

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BioSpace hiring Bioinformatics Scientist in Bethesda, Maryland, United States

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the Center for Alzheimer’s and Related Dementias, National Institute on Aging. The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it…

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r – Avoiding eval-parse or do.call

I am trying to select a theme from ggplot2 based on some string given. For demo purposes, consider the following code: library(dplyr); library(ggplot2) mtcars %>% ggplot(aes(mpg, wt))+ geom_point() -> p all_ggplot2_funs <- getNamespaceExports(“ggplot2”) p + eval(parse(text=paste0(all_ggplot2_funs[grep(“theme_”, all_ggplot2_funs)][15], “()”))) This works fine and would allow me to use theme_minimal. However, from…

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make PyPI package that does not include NUPACK or ViennaRNA

Before figuring out #12, an easier thing to implement would be a PyPI package that does not include NUPACK or ViennaRNA. This would slightly simplify the instructions for installation, even though it would remain necessary to install NUPACK and ViennaRNA to use most pre-packaged constraints. I recall that NUPACK has…

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Python Sklearn Preprocessing – December 2021

An Introduction to Scikit-Learn: Machine Learning in Python Posted: (2 days ago) Sep 16, 2021  · Python is one of the most popular choices for machine learning. It has a low entry point, as well as precise and efficient syntax that makes it easy to use. It is open-source, portable,…

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Bioinformatics Engineer – Idealist

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…

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Average Read length

Average Read length 3 Hello Everyone! Is there a standard tool commonly used to calculate the average read length of fastq files? If yes please mention it here because I want to know the size of average reads of my fastq files so that I can decide the cutoff for…

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[Bug 1951032] Autopkgtest regression report (glibc/2.31-0ubuntu9.4)

All autopkgtests for the newly accepted glibc (2.31-0ubuntu9.4) for focal have finished running. The following regressions have been reported in tests triggered by the package: snapd-glib/1.58-0ubuntu0.20.04.0 (armhf) apt/2.0.6 (armhf) libmath-mpfr-perl/4.13-1 (armhf) art-nextgen-simulation-tools/20160605+dfsg-4 (armhf) ruby-nokogiri/1.10.7+dfsg1-2build1 (armhf) r-cran-rgdal/1.4-8-1build2 (armhf) arrayfire/3.3.2+dfsg1-4ubuntu4 (armhf) libpango-perl/1.227-3build1 (armhf) libimage-sane-perl/5-1 (s390x) ruby-bootsnap/1.4.6-1 (arm64) mle/1.4.3-1 (ppc64el, arm64) libsyntax-keyword-try-perl/0.11-1build1 (armhf)…

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