Tag: Jupyter

‘info jupyterhub’ displays the manpage although it suggests ‘info’ to get the full doc

Package: jupyterhub Version: 2.0.0+ds1-2 Severity: normal X-Debbugs-Cc: gkni…@australdx.fr Dear Maintainer, ‘man jupyterhub’ ends with: > The full documentation for jupyterhub is maintained as a Texinfo manual. If the info and jupyterhub programs are properly installed at your site, the command > info jupyterhub > should give you access to the complete manual. although…

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

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

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Bioinformatics Programmer 2 – 118717

UCSD Layoff from Career Appointment: Apply by 09/09/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 09/21/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Bioinformatics Programmer will work with a multi-disciplinary group to adapt…

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

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

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python – module ‘pymc3.stats’ has no attribute ‘hpd’

I am trying to calculate highest posterior density (HPD) but it is giving this error. Also I already installed pymc3 using pip install pymc3 on jupyter notebook and the code will be ran on jupyter notebook. from statsmodels.stats.proportion import proportion_confint proportion_confint(814,1142,method=’jeffreys’) import pymc3 from scipy.stats import beta beta_dist=beta.rvs(size= 5000000, a=814.5,b=328.5)…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in WORLDWIDE

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. This opportunity is…

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JetBrains’ Big Data Tools 1.6 keeps track of Flink jobs

Big Data tools 1.6, a plug-in for accessing Zeppelin notebooks, can now also monitor Apache flink and integrate the Hive Metastore. jetbrains has updated the Big Data Tools. In version 1.6, the plug-in for the IDEs IntelliJ IDEA Ultimate, DataGrip, DataSpell and PyCharm Professional offers bug fixes and general improvements…

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS in Singapore, Singapore

The Laboratory of Cancer Epigenetic Regulation, helmed by GIS Executive Director Patrick Tan, is seeking a Bioinformatician to join a new multi-institutional effort targeting the genetic basis of cancer to create novel therapies and diagnostics. Led by an award-winning thought leader in the field of Asian gastrointestinal cancer research with…

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Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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Jupyter WebIO in binder – JupyterHub

I just learned how to run julia notebooks in binder. Now I want to use the PlotlyJS package in julia. Usually, when I need a package in julia on binder, I install it locally in a conda environment first and then copy Project.toml and Manifest.toml to my repository to start…

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Python for Bioinformatics Biopython | SerbianForum

Python for Bioinformatics: Biopython Published 05/2022 MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 Ch Genre: eLearning | Language: English + srt | Duration: 11 lectures (1h 43m) | Size: 744.7 MB​ Learn Biopython in Google Colab.​ What you’ll learn You will learn to handle Biological Data…

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Jupyter notebook not loading the correct virtual environment

We deployed Jupyterhub in Kubernetes using the helm chart , the chart version is 0.9.0 github.com/jupyterhub/zero-to-jupyterhub-k8s/tree/main/jupyterhub zero-to-jupyterhub.readthedocs.io/en/latest/jupyterhub/installation.html Users creating virtual environments using the terminal and created kernals as well, But when they accessing the jupyter notebook using the newly created kernal and run the command !conda info It is not…

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How to set NotebookApp.iopub_data_rate_limit and others NotebookApp settings in JupyterHub?

Open the command line and enter jupyter notebook –NotebookApp.iopub_data_rate_limit=1e10 This should start jupyter with the increased data rate. You have to create config file using this command $ jupyter notebook –generate-config, The answer in this link 04: “IOPUB data rate exceeded” problem of “jupyter low memory..” in windows: open cmd:…

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Description, Programming Languages, Similar Projects of Python-for-Text-Classification

Python for Text Classification with Machine Learning in Python 3.6. Installation Guide Start your environment by picking either pipenv (recommended) or virtualenv. Simple guides are below. Using pipenv Initialize pipenv (setup guide): cd path/to/your/dev/folder mkdir text-classify cd text-classify pipenv install –three After installation of pipenv works, just activate it (same…

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handle VPN drops for long-running notebooks : JupyterNotebooks

Summary of my needs Retail supply-chain data from relational databases. Data sets are usually 1 – 100 GB in size. All data is on-prem in my employer’s data center, not cloud based. Pandas or Dask and scikit-learn for clustering, classification, and regression Models often take several hours to train. Pandas…

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difficulty filtering vcf file with vcftools

difficulty filtering vcf file with vcftools 1 I had a large VCF file named “common_known_variants.vcf ” which contains all known human variants downloaded from ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz -O common_known_variants.vcf.gz I’m trying to extract the known variants from only chromosomes 1,2,3,9,22, and X and write them in a new vcf file with the…

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Utilizing Kaggle in Machine Studying Tasks

You’ve in all probability heard of Kaggle knowledge science competitions, however do you know that Kaggle has many different options that may allow you to together with your subsequent machine studying challenge? For folks on the lookout for datasets for his or her subsequent machine studying challenge, Kaggle means that…

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python – Pymc3 install issues on windows 10

So I downloaded pymc3 (uninstalled and reinstalled a few times) and every time I try to import pymc3 into a jupyter notebook I get some kind of error. I am guessing that I am having an issue with how I am installing Pymc3, I followed this tutorial: github.com/pymc-devs/pymc/wiki/Installation-Guide-(Windows). After my…

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An argument against using Jupyter Notebook for Machine Learning

Joel Grus, an Allen Institute for Artificial Intelligence researcher, addressed a Jupyter developers’ conference where he gave a presentation titled ‘I don’t like notebooks’. He said, “One hand, you have this idea that no books are great for iterative development, but then you also have this idea that notebooks are…

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docker compose – How to enable authentication via openLDAP on JupyterHub without SSL certificate?

I am trying to create a JupyterHub that uses an LDAP to authenticate users. The JupyterHub is working but when I am trying log on the web page show a Error 500. I must clarify that when I tried it with the PAM method it worked without problems, but when…

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How to install SageMath in Ubuntu Linux?

SageMath is a free and open-source software for mathematical computation. It is built on top of many existing open-source libraries which include NumPy, SciPy, Matplotlib, SymPy, Maxima, etc. SageMath provides a command-line interface, browser-based notebooks, and tools for embedding formulas in other documents. Its syntax is similar to Python. In…

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What’s new in DataSpell 2022.1

JupyterHub, a platform that provides multi-user access to remote Jupyter servers, received a major upgrade with version 2.0, which introduced roles and scopes. DataSpell 2022.1 has adopted the API changes of the new version and allows connections to JupyterHub 2.0 by URL, the same way connections work for Jupyter and…

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Filtering outgoing container traffic – General Discussions

melhayany (Melhayany) April 12, 2022, 10:12pm #1 Hello Docker Community, I am facing a networking issue with my application to run JupyterHub using Docker containers. To give you a bit of context. I created a virtual machine, on it: port 2022 (ssh) served by my server, port 443 (https) served…

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