Tag: python

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: …

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Pytorch Foundation

pytorch yes Facebook Developed deep learning library . Details visible Official website . For the convenience of management , Usually in Anaconda or miniconda Create a new virtual environment installation in pytorch. New virtual environment (MacOS) Method 1 : direct Anaconda Navigator Install in stay Navigator>Environments Create a new environment…

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python – Scikit-learn LogisticRegression overparametrised? Option for setting one of the K coefficient vectors to zero?

Suppose we run logistic regression on K classes. Unsurprisingly, sklearn.linear_model.LogisticRegression gives you a set of coefficients (or weights, stored in the attribute LogisticRegression.coef_) that has shape (K, D) where D is the input dimensionality of the data. (Actually I would rather it had shape (D, K) but whatever.) However, we…

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Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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Postdoctoral Researcher in Computational Biology at Karolinska Institute, Sweden 2022

Postdoctoral Researcher in Computational Biology is available for doctoral degree candidates in Bioinformatics, Computer science, Mathematics, Biostatistics, Neuroscience, or similar field at the Department of Clinical Neuroscience, Karolinska Institute, Sweden 2022 Qualification Details Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent…

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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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Postdoctoral position in Bioinformatics at Uppsala, Sweden, Aug 2022

The postdoctoral fellow position in Bioinformatics is available for applicants with a doctoral degree at the Department of Cell and Molecular Biology, Uppsala University, Sweden, in August 2022. General Info Position: Postdoctoral FellowNo. of Positions: 1Research Field: Bioinformatics, Computational BiologyJoining Date: ASAPContract Period: 2 YearsSalary: Subject to norms Workplace: Department…

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Sr. Research Associate, Bioinformatics job with F. Hoffmann-La Roche AG

The Bioinformatics Senior Research Associate is responsible for designing and troubleshooting PCR-based assays for use with the GenMark Dx ePlex platform. The ideal candidate must be able to work in a collaborative research and IVD product development environment and demonstrate ability to analyze sequence data to drive assay development. The…

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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…

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Use the tool of your choice (e.g. RStudio, Excel, Python) to generate advanced graphs using given data sets

   Graphs to Produce:Bar Plot: (Use dataset_student_survey_data.csv)x=Smokefill=Exerposition=dodgefacet=Sexx-label=Smokery-label=Countstitle=The Exercise habits of Male and Female students that smokeHistogram: (Use dataset_us_car_price_data.csv)x=Pricefill=Typefacet=Typex-label=Pricey-label=Freqtitle=Car Price Distribution based on Car TypeBox Plot: (Use dataset_production_of_rice_in_india.csv)x=varietiesy=pricefill=bimasfacet=statusx-label=Rice Varietiesx-label=Pricetitle=India Rice Prices based on Varieties, Land Status, and Bimas ProgramScatter Plot: (Use dataset_production_of_rice_in_india.csv)x=pricey=wageshape=bimascol=bimasfacet=statusmethod=lmse=Fx-label=Rice Pricey=Wagetitle=India Rice Prices vs Wage broken down by Land…

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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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scikit learn – Create X train and Y Train for CSV dataset in Python

This seems a general question, but I can answer with: You can use following block to import these csv files in your env. import pandas as pd # for CSV file I/O operations train = pd.read_csv(‘../input/data_train.csv’) test = pd.read_csv(‘../input/data_test.csv’) I did not see your .csv files but it must be:…

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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…

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BAM – Job openings – Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable

Section S.3 – eScience To strengthen our team in the division “eScience” in Berlin-Steglitz, starting as soon as possible, we are looking for a Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable Salary…

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Bioinformatics Programmer I – 115257

UCSD Layoff from Career Appointment: Apply by 04/04/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 04/14/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Department of Medicine (DOM) is the largest department within the…

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St. Jude Children’s Research Hospital hiring Bioinformatics Analyst in Memphis, Tennessee, United States

The Chi Lab is seeking a Systems Immunology Specialist to work on exciting projects related to immune signaling and metabolism in the St. Jude Deparment of Immunology. One of the premier pediatric research institutions in the world, St. Jude Children’s Research Hospital provides exceptional resources, a collaborative environment, and access to…

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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…

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python – Scikit Learn IsolationForest: How to Fit Multiple Dataframes With Different Parameters (Not Using GridSearchCV)

I have a five separate pandas dataframes that I’ve put inside a dictionary. I want to run five separate IsolationForest models in scikit-learn with different sets of parameters for each model. However, I don’t want to run each model separtely. So my question is, how can I run these models…

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python – NotFittedError – Titanic Project Kaggle

I am trying different machine learning projects from Kaggle to make myself better. Here is the model that I am using: from sklearn.ensemble import RandomForestClassifier y = train_data[“Survived”] features = [“Pclass”, “Sex”, “SibSp”, “Parch”] X = pd.get_dummies(train_data[features]) X_test = pd.get_dummies(test_data[features]) model = RandomForestClassifier(n_estimators = 100, max_depth = 5, random_state =…

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Bioinformatics Analyst at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate…

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

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

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R programming language tutorials – Technical Ripon

Are you learning the R programming language? Want to learn how to do more tasks with R? Check out our Do More With R video tutorials below — most with accompanying text articles and code, almost all under 10 minutes. In the table below you can easily search all tutorials…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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python – ValueError: Unused step method arguments: {‘initvals’} in pymc3

I am trying to use Automated Recommendation Tool which utilizes pymc3 package but I am facing issues while executing the following code cell – %%time if run_art: art = RecommendationEngine(df, **art_params) else: with open(os.path.join(art_params[‘output_directory’], ‘art.pkl’), ‘rb’) as output: art = pickle.load(output) Following is the error that pops up – ValueError…

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python – Scikit optimize with objective function returning None

Can the expensive objective function that is being passed to scikit-optimize return None (NA/NaN/…) type? I would need to optimize simulation parameters and sometimes, the simulation can return a non-feasible result. I could theoretically return some artificially large number (1/ε), but that would probably break the scikit normality assumption. And…

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main-i386-default][science/cp2k] Failed for cp2k-9.1.0 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy17.nyi.freebsd.org/data/main-i386-default/p429f3de9bdcd_s2573e6ced9/logs/cp2k-9.1.0.log Build URL: beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p429f3de9bdcd_s2573e6ced9 Log: =>> Building science/cp2k build started at Sat Jun 4…

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python3.7 biopython, how to learn python3 and still use biopython

Firstly, check out this page: biopython.org/wiki/Download You don’t have to worry about biopython being bound to a specific version of python – you can use it with either v2.7 or v3.4/v3.5/v3.6. You can also have multiple version installed on your system but I recommend you to focus on digging deeper…

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python 3.x – No torchdyn library found in kaggle

I am trying to install torchdyn in my kaggle enviroment. However, when I try to install by following: pip install torchdyn I get the following error: ERROR: Ignored the following versions that require a different python version: 0.3.0 Requires-Python >=3.8,<4.0 ERROR: Could not find a version that satisfies the requirement…

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Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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Bioinformatics Specialist I — Cancer Computational Biology —- Cancer Center in Boston, MA for MGH Institute of Health Professions

Details Posted: 05-Jun-22 Location: Boston, Massachusetts Salary: Unpaid Internal Number: 3190190-3499_1654275737 URLs: www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/rheinbay-lab www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/lawrence-lab Unique opportunity to join an interdisciplinary team bridging the Harvard Medical School, the Massachusetts General Hospital, and the Broad Institute of Harvard and MIT. The Rheinbay Lab and Lawrence Lab at the Massachusetts General Hospital Cancer…

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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: Convert each CSV Row into XML File sepperate

You are overwriting the same file everytime in your loop. You need to change the file-name as well: pFile = ‘test.csv’ oFile = ‘test’ #add xml later if os.path.isfile(pFile) and pFile.endswith(ext): with open(pFile, ‘r’) as pData: reader = csv.reader(pData) pData = {} for i, row in enumerate(reader, 1): #count each…

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Abdullah_DS_Lab03.pdf – CSL-487: Introduction to Data Science Lab BS(CS) – Semester 06 (Spring 2022) Abdullah Abdul Wahid BS(CS) 6B 02-134192-015 Lab

Unformatted text preview: CSL-487: Introduction to Data Science Lab BS(CS) – Semester 06 (Spring 2022) Abdullah Abdul Wahid BS(CS) 6B 02-134192-015 Lab 03: Installation & Introduction to RStudio and Basics 1. Access R Studio Cloud 2. R verses Python Debate 3. R Studio Desktop Installation 4. The R Studio Interface…

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#1012224 – python-tornado: autopkgtest regression in testing

#1012224 – python-tornado: autopkgtest regression in testing – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, Debian Python Team <team+python@tracker.debian.org>:Bug#1012224; Package src:python-tornado. (Wed, 01 Jun 2022 18:00:03 GMT) (full text, mbox, link). Acknowledgement sent to Graham Inggs <ginggs@debian.org>:New Bug report received…

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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…

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Bioinformatics Remote Jobs – Find popular part time/ full time remote Bioinformatics jobs

Explore 2 recent remote Bioinformatics jobs & apply for free. Biology Breed new fish for sportfishing Hourly – Posted at 5 hours ago $19.43Hourly Jun 20, 2022Expiry We need help creating a new species of fish to the Sportfishing industries. The fish is to be stocked & produced by a…

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RegEx: Listing all possibilities to build sample code in python

itertools.product() is the way to go here. If your proteins are all single characters then for each position in your “regex”, just put a string representing the valid proteins for that position into the itertools.product() arguments. For example [IG]…D.SG would become the following: p = ‘ABCDEFGHIJKLMNOPQRST’ # or whatever the…

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How do I find all Sequence Lengths in a FASTA Dataset without using the Biopython

You really don’t need regular expressions for this. header = None length = 0 with open(‘file.fasta’) as fasta: for line in fasta: # Trim newline line = line.rstrip() if line.startswith(‘>’): # If we captured one before, print it now if header is not None: print(header, length) length = 0 header…

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Unable to install bioconda packages in conda environments

From your command line it appears you are on windows. There are several veresions of pybedtools on bioconda, however, if I grep through them, they are all for the linux platform. If you’re on Windows 10, you could consider setting up the ‘windows subsystem for linux’ (and possibly Xming), installing…

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Python scikit-learn: prediction on dataset with text and numeric variables

The issue is you use TfidfTransformer which transforms a count matrix to a normalized tf or tf-idf representation instead of TfidfVectorizer which converts a collection of raw documents to a matrix of TF-IDF features from sklearn.feature_extraction.text import TfidfVectorizer X = pd.DataFrame({‘Project Title’: [‘hello stackoverflow’, ‘text column’, ‘scikit learn’, ‘machine learning…

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python – Getting error while using the H2o AutoML model for h2o stacking

I tried using the 2 best models from AutoML and used one of them as Meta learner for stacking. Named the new model stack_test. Code that I used is: stack_test = H2OStackedEnsembleEstimator(base_models=[model1_xg, model2_xg], metalearner_algorithm=model1_xg) stack_test.train(x=x, y=y, training_frame=h2o_train) stack_test.model_performance(h2o_test).auc() Error I am getting: NameError: name ‘stack_test’ is not defined What am…

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Learning how to write script for lammps in python – LAMMPS Beginners

Good day to all,I am trying to apply Monte Carlo method within the intervals of MD simulation.Specifically, I am trying to write python code that could be invoked from lammps(or vice versa) so that I could add a new calculation method. To begin with, I am currently running Lammps on…

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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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python – How can I get Pandas 1.4.2 on Kaggle

# Making a group with the age and the Survived age_survived = titanic_df.groupby(“Survived”, as_index=False)[“Age”].value_counts() #Filtering Values survived_over_30 = age_survived [age_survived.Age > 30] #People with age more than 30 survived_under_30 = age_survived [age_survived.Age < 30] #People with age less than 30 survived_over_30 = survived_over_30 [survived_over_30.Survived == 1] #Getting only the values…

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Bioinformatics Jobs : Latest 251 Bioinformatics Openings & Vacancies in Singapore

MiRXES is a Singapore-headquartered molecular diagnostic company with R&D, manufacturing, and clinical lab operations in Singapore, USA, Japan, and China. We specialize in microRNA technologies and th Skills : Genomics , NGS , Data Analysis , Pipelines , Interpersonal Skills , assay development , workflow management , Bioinformatics , sequencing…

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Kaggle Archives | Fire Forty Six

It took me a while to finally complete all 17 modules, but knowing that there was a clear outcome helped motivate me to keep taking the next step, and the step after that. So, if you’re interested in getting a taste of what the world of machine learning has to…

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Research Engineer – AlphaFold Improvements at DeepMind – London, UK

At DeepMind, we value diversity of experience, knowledge, backgrounds and perspectives and harness these qualities to create extraordinary impact. We are committed to equal employment opportunity regardless of sex, race, religion or belief, ethnic or national origin, disability, age, citizenship, marital, domestic or civil partnership status, sexual orientation, gender identity,…

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(Senior) Consultant – Bioinformatics (m/f/x) – OSTHUS GmbH – Pharmaceutics

OSTHUS brings innovative scientific informatics applications to many of the world’s largest pharmaceutical, Crop Sciences and Life Sciences companies. We provide both software solutions as well as consulting expertise to help guide your business strategy in adopting valuable technologies. With teams of unique interdisciplinary experts, we help our clients solve…

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Pose Residual Network Pytorch – Python Repo

This repository contains a PyTorch implementation of the Pose Residual Network (PRN) presented in our ECCV 2018 paper: Muhammed Kocabas, Salih Karagoz, Emre Akbas. MultiPoseNet: Fast Multi-Person Pose Estimation using Pose Residual Network. In ECCV, 2018. arxiv PRN is described in Section 3.2 of the paper. Results on COCO val2017…

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Parse a file of strings in python separated by newline into a json array

I don’t see where you’re actually reading from the file in the first place. You have to actually read your path_text.txt before you can format it correctly right? with open(‘path_text.txt’,’r’,encoding=’utf-8′) as myfile: content = myfiel.read().splitlines() Which will give you [‘/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam’, ‘/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam’] in content. Now if you want to write this…

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Sweeps while using MPI and SLURM – W&B Support

Hello! I am attempting to perform a hyperparameter search on my project, which uses MPI under the hood to aggregate the results of multiple agents. I have 63 agents that run an episode, returning a total reward at the end. At the end, each worker node sends their results to…

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genetic epidemiology postdoc

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

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Assistant Project Scientist, Bioinformatics in Los Angeles, CA for University of California Los Angeles

Details Posted: 15-May-22 Location: Los Angeles, California Type: Full-time Salary: Open Categories: Academic/Faculty Physical Sciences Assistant Project Scientist, BioinformaticsUniversity of California Los Angeles Requisition Number: JPF07378 The Department of Molecular and Medical Pharmacology is recruiting for a bioinformatics Project Scientist at the Assistant level. The candidate will investigate the human…

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Database Administrator at European Molecular Biology Laboratory (EMBL)

About the team/job In this role you will join an established Database team of database administrators in order to support the ongoing database operations. The main duties for this post are: DBA of MySQL and MongoDB.The Database Team provides day-to-day Database Administration support , database performance tuning and query optimization…

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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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Senior Research Associate, Bioinformatics at Kite Pharma

Job details Job type full-time Full job description Job description At kite pharma we are revolutionizing the treatment for cancers through immunotherapy through novel breakthrough technologyWe have developed and launched best in class car-t therapy yescarta, currently curing patients from previously intractable b-cell malignanciesWe are using our expertise to apply…

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Bioinformatics Jobs in Lausanne, Vaud

3.1 Data Manager Our client will be looking for a candidate with Data Management experience and experience in a previous Data Manager role.… 3.8 4.3 4.3 PhD Student in Gene Regulation There are regular possibilities to present and participate in local or international conferences and workshops. A copy of your…

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Associate Bioinformatics Scientist at Flagship Pioneering, Inc.

Company Summary: Who Are We? Founded by Flagship Pioneering, Empress pioneers the future of small molecule drugs through the discovery of pharmacologic loci. The company’s product platform leverages AI and multi’omic data from thousands of humans around the globe to discover novel, important small molecules inside of humans and their cognate mechanisms…

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Cepheid hiring Staff Bioinformatics Scientist – Remote in Atlanta, Georgia, United States

At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex health challenges. Our associates are involved in every stage of molecular diagnostics, from ideation to…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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Anthony Nolan hiring Bioinformatics Developer in Swiss Cottage, England, United Kingdom

We’re Anthony Nolan and we save the lives of people with blood cancer who need a stem cell transplant. We’re unique. Thanks to the incredible donors on our register, our pioneering research and our passionate fundraisers, we give the chance of life to three people a day. But we won’t…

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Recent questions tagged fasta – Q&A

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

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scRNAseq analysis – h5ad file conversion to Seurat format

scRNAseq analysis – h5ad file conversion to Seurat format 0 Hi all. I have a single .h5ad file that contains scRNAseq data from several samples. I would like to convert it so that I can open it in Seurat (I am comfortable with R, but not with Python). I have…

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Multiplexed genome regulation in vivo with hyper-efficient Cas12a

. 2022 Apr;24(4):590-600. doi: 10.1038/s41556-022-00870-7. Epub 2022 Apr 12. Lucie Y Guo #  1   2 , Jing Bian #  3 , Alexander E Davis  4 , Pingting Liu  4 , Hannah R Kempton  3 , Xiaowei Zhang  3 , Augustine Chemparathy  3 , Baokun Gu  3 , Xueqiu Lin  3 , Draven A Rane  3 , Xiaoshu Xu  3 , Ryan M…

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[Solved] How can I translate this SageMath code to run in Python?

The first error is RuntimeError: Use ** for exponentiation, not ‘^’, which means xor in Python, and has the wrong precedence. Once that is fixed, there are various missing imports. Find each of them with Sage’s import_statements function. sage: import_statements(x) from sage.calculus.predefined import x sage: import_statements(sum) from sage.misc.functional import symbolic_sum…

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python – Install autodock vina via pip in Windows

I trying to install vina using pip and get this error: C:\Users\chase>pip install vina Collecting vina Using cached vina-1.2.3.tar.gz (95 kB) Installing build dependencies … done Getting requirements to build wheel … error ERROR: Command errored out with exit status 1: command: ‘D:\Anaconda\python.exe’ ‘D:\Anaconda\lib\site- packages\pip\_vendor\pep517\in_process\_in_process.py’ get_requires_for_build_wheel ‘C:\Users\chase\AppData\Local\Temp\tmpo4147jnr’ cwd: C:\Users\chase\AppData\Local\Temp\pip-install- x0_x1cyl\vina_418ca6103711445caf359fdf3574d54b…

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Director of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

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Programmer or Software Developer in Bioinformatics

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

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Scientist, Bioinformatics – Urgent Hiring at Tonix Pharmaceuticals Inc

Job Description We are searching for a capable Scientist, Bioinformatics to join our high calibre team at Tonix Pharmaceuticals Inc in Chatham, NJ 07928.Growing your career as a Full Time Scientist, Bioinformatics is a fantastic opportunity to develop exceptional skills.If you are strong in presentation, adaptability and have the right…

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BenchSci hiring Bioinformatics Engineer (Remote) in Toronto, Ontario, Canada

BenchSci’s vision is to bring novel medicine to patients 50% faster by 2025. We’re achieving it by empowering scientists with the world’s most advanced biomedical artificial intelligence. Backed by F-Prime, Gradient Ventures (Google’s AI fund), and Inovia Capital, our platform accelerates science at 15 top-20 pharmaceutical companies and over 4,300…

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ERROR_ non-ACGTN characters in genome

ERROR_ non-ACGTN characters in genome 0 Hi, I am trying to run quast and i encountered this error, please help me. **quast /home/bvs/neelam/complete_genome/complete.fna -o ./outdir1 Version: 5.0.2 System information: OS: Linux-5.8.0-59-generic-x86_64-with-debian-bullseye-sid (linux_64) Python version: 3.7.12 CPUs number: 96 Started: 2022-05-02 12:30:13 Logging to /home/bvs/neelam/complete_genome/outdir1/quast.log NOTICE: Maximum number of threads is…

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Research Associate II, Bioinformatics at Sherlock Biosciences

Job details Salary $65,546 – $106,525 a year job type full-time Full job description Job description:Summary/objective: As part of this role, you will support the bioinformatics team in building a comprehensive bioinformatics software that informs the design of next generation molecular diagnosticsTogether with your mentor, you will refine and expand…

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Senior Research Associate/Principal Research Associate, Bioinformatics job with Vedanta Biosciences

Title: Senior Research Associate/Principal Research Associate, Bioinformatics Location: Cambridge, MA, or up to 100% remote Reports to: Scientist I, Bioinformatics The Role: We are looking for a bioinformatician/computational biologist to support the Research and Development team in the maintenance and querying of an existing laboratory information management system (LIMS), construction…

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How to upgrade Kernel version? – JupyterHub

I have.a JupyterHub running in a local K8s cluster, deployed via KubeApps. It works like.a charm, except for the fact that it is running Python 3.7. I would like to upgrade it to Python 3.10. I tried to run conda update python and conda install -y python=3.10 from the notebook,…

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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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Mbedtls Application On Tcp

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

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installation of qiime2 on pycharm with anaconda interperter

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

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which of the following are the prerequisite packages for scikit-learn?

Mohammed Guys, does anyone know the answer? get which of the following are the prerequisite packages for scikit-learn? from screen. Installing scikit There are different ways to install scikit-learn: Install the latest official release. This is the best approach for most users. It will provide a stable version and pre-built…

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Distributed training on slurm cluster – distributed

chinmay5 (Chinmay5) April 29, 2022, 12:48pm #1 Sorry for the naive question but I am confused about the integration of distributed training in a slurm cluster. Do we need to explicitly call the distributed.launch when invoking the python script or is this taken care of automatically? In other words, is…

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DNA sequencing with Python | Python | GitHub | Bioinformatics

Hello, i need to add a step into a script (find attached). The step is DNA sequencing with a Python library, for example: [login to view URL] [login to view URL] [login to view URL] You can find many on Github. Thanks Skills: Python, GitHub, Bioinformatics See more: need classified…

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python – How can I respond to a CLI prompt in Kaggle?

I’m using Kaggle to generate poetry samples with GPT-2. My notebook uses datasets from Gwern’s poetry generator and uses nshepperd’s GPT-2 model. This all works fine with my notebook when generating unconditional samples. !python src/generate_unconditional_samples.py –top_k 40 –nsamples 1 –temperature 0.9 –model_name=1.5b-model –length=300 However, I want to generate samples with…

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How can I validate the results by the software package, I have recently developed using python for genomic data?

How can I validate the results by the software package, I have recently developed using python for genomic data? 1 I have developed a software package for the analysis of genomic data, in which, I have implemented a variety of functions like normalization, clustering etc (from already available tools i.e.,…

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Principal Bioinformatics Scientist I (REMOTE) job with F. Hoffmann-La Roche AG

Job Description We are seeking a committed and driven Principal Bioinformatics Scientist for our Computational Bioinformatics Research and Early Development team. We have a team of skilled bioinformatics researchers working in a highly collaborative environment with multiple internal and external teams. The work will be focused on developing novel methods…

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Research Fellow in Health and Biomedical Data Sciences job with UNIVERSITY OF SURREY

Health Sciences Research Location: Guildford Salary: £33,309 to £40,927 Post Type: Full Time Closing Date: 23.59 hours BST on Tuesday 10 May 2022 Reference: 027322 This is a rare opportunity for a talented, motivated postdoctoral fellow to work on a number of exciting health data-sciences and biomedical informatic studies. You will…

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Euro-BioImaging Bio-Hub – FAIR Image Data Steward at European Molecular Biology Laboratory (EMBL)

About the team/job Euro-BioImaging ERIC (www.eurobioimaging.eu) is a leading pan-European research infrastructure that provides the research community open access to cutting-edge imaging services. The Euro-BioImaging Bio-Hub hosted by European Molecular Biology Laboratory (EMBL) is looking for a highly motivated FAIR Image Data Steward to develop general guidelines and technically support…

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Scientific Database Curator at European Molecular Biology Laboratory (EMBL)

About the team/job Metabolomics is the study of small molecule metabolites in the metabolome, which is the complete set of metabolites in a biological sample. By studying these metabolites, we can observe changes in cellular networks and biochemical pathways. This allows us to detect disease states and their progression, monitor…

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Unit Manager – Bioinformatics and Genomic Epidemiology

MPHI is a Michigan-based and nationally engaged, non-profit public health institute.  We are a team of teams, process and content experts, dedicated to building A world where tomorrow is healthier than today!   Title:                              Unit Manager – Bioinformatics and Genomic Epidemiology                                        $66,100 – $97,200 / Posted Thru:  4-28-22   Location: …

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All vs All blast not self hit? Orthogroup clustering and single copy genome?

Hey guys Self hit I have this actually a bit weird question about blast. I’ve been doing some work around single copy genome construction using Reciprocal best blast hit (RBBH) method. As I have something like 100+ annotated genome, I concatenated all annotated CDS into one fasta and makeblastdb with…

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Biomedical/BioInformatics Intern in Rockville, MD

Description Job Description: The Government Health and Safety Solutions Group within the Health group has an opening for a  Biomedical/Bioinformatics Intern. The intern will work alongside data scientists and managers and use biomedical or genomics data to inform health-related research questions. Primary Responsibilities: Under the guidance of Leidos staff, the…

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R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

[This article was first published on R | Ben Johnston, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. R For SEO Part 3:…

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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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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

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Summer Intern – Bioinformatics Jobs – VacancyPaper.com

Job Summary Illumina, is currently hiring on a vacant job post of Summer Intern – Bioinformatics based in Cambridge England United Kingdom. Please read the job detail carefully before applying. Job Title: Summer Intern – Bioinformatics Company Name: Illumina Job Type: Full Time Job Location: Cambridge England United Kingdom Salary:…

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Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 22-Apr-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Leads a team of bioinformaticians and provides technical guidance for the team to follow best practices and deliver data production timely. Collaborates cross-functionally with our user services, software engineering,…

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Optical Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job The Prevedel group in Heidelberg is seeking an optical engineer with an applied physics and/or engineering background to work on advanced spectroscopic imaging techniques for applications in biology and medicine. In particular, the candidate will work on the development of new optical instrumentation with a particular emphasis…

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TF differentiation of hiPSCs at Wellcome Sanger Institute

Salary per annum: c.£33,900 Contract Length: 2 years Here at the world-famous and internationally respected Wellcome Sanger Institute, we have an exciting opportunity for a postdoctoral researcher to perform high throughput screening for transcription factor-driven differentiation in human pluripotent stem cells (hiPSCs) in order to create better in vitro differentiated cells that more faithfully…

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pytorch – Is this a correct way to training U-Net using different GPUs

U-Net code: class UNet(nn.Module): def __init__(self): super(UNet, self).__init__() self.c1 = convBlock(1, 64).to(‘cuda:0’) self.d1 = downSample(64).to(‘cuda:0’) self.c2 = convBlock(64, 128).to(‘cuda:0’) self.d2 = downSample(128).to(‘cuda:0’) self.c3 = convBlock(128, 256).to(‘cuda:0’) self.d3 = downSample(256).to(‘cuda:1’) self.c4 = convBlock(256, 512).to(‘cuda:1’) self.d4 = downSample(512).to(‘cuda:1’) self.c5 = convBlock(512, 1024).to(‘cuda:1’) self.u1 = upSample(1024).to(‘cuda:1’) self.c6 = convBlock(1024, 512).to(‘cuda:1’) self.u2 = upSample(512).to(‘cuda:1’)…

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Using Scikit Learn – April 2022

Python Machine Learning From Scratch Step By Step Guide … Posted: (7 days ago) Using Scikit-Learn, Keras, And TensorFlow with PYTHON GUI In this book, implement deep learning-based image classification on detecting face mask, classifying weather, and recognizing flower using TensorFlow, Keras, Scikit-Learn, OpenCV, Pandas, NumPy and other libraries. In…

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