Tag: GUI

TDF to bed graph — IGV on command line

TDF to bed graph — IGV on command line 0 Hi all, I’m trying to convert some TDF files to bedgraph files so that I can do a genomic leftover on them (as far as I can tell, I can’t lift over TDF files). This google group answer here (groups.google.com/g/igv-help/c/RcZw5YB5SOQ)…

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Problem to open autodock

Problem to open autodock 0 Hey everyone, I need to do a torturial for docking for my study. I want to try it via autodock but I get every time after installing this following window from phython when I want to open AutodockTools. Type “copyright”, “credits” or “license()” for more…

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Thermostat and barostat in equilibration phase in a membrane-protein system – User discussions

Davidb November 9, 2022, 10:50am #1 GROMACS version: gromacs-2022GROMACS modification: Yes/No Hi, I am using CHARMM-GUI generated system of a transporter protein in a membrane bilayer. In the equilibration phase, the recommended workflow from CHARMM-GUI is to use Berendsen for both temperature and pressure (semi-isotropic). However, gromacs highly discourage it,…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

International Diabetes Federation (IDF). Diabetes Atlas 8th Edition 2017. www.idf.org/our-network/regions-members/africa/welcome.html. Accessed 15 July 2018 (2018). Singh, S., Usman, K. & Banerjee, M. Pharmacogenetic studies update in type 2 diabetes mellitus. World J. Diabetes. 7, 302. doi.org/10.4239/wjd.v7.i15.302 (2016). Article  PubMed  PubMed Central  Google Scholar  Inzucchi, S. E. et al. Management of…

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Emerging role of STING signalling in CNS injury: inflammation, autophagy, necroptosis, ferroptosis and pyroptosis | Journal of Neuroinflammation

Langlois JA, Rutland-Brown W, Wald MM. The epidemiology and impact of traumatic brain injury: a brief overview. J Head Trauma Rehabil. 2006;21:375–8. doi.org/10.1097/00001199-200609000-00001. Article  PubMed  Google Scholar  Cao HQ, Dong ED. An update on spinal cord injury research. Neurosci Bull. 2013;29:94–102. doi.org/10.1007/s12264-012-1277-8. Article  PubMed  Google Scholar  O’Donnell MJ, Xavier D,…

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Install Sview On A Debian, Ubuntu, Kali, Fedora And Raspbian

sview GUI to view and modify SLURM state Maintainer: Debian HPC Team Section: admin Install sview Debian apt-get install sview Click to copy Ubuntu apt-get install sview Click to copy Kali Linux apt-get install sview Click to copy Fedora dnf install sview Click to copy Raspbian apt-get install sview Click…

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Ggplot Save Plot With Code Examples

Ggplot Save Plot With Code Examples This article will demonstrate via examples how to resolve the Ggplot Save Plot error . ggsave(“filename.png”) We were able to fix the Ggplot Save Plot problem by looking at a number of different examples. How do I save a Ggplot plot? You can either…

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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Retrosynthesis from target to chassis Typically, the target compound, also named “source compound” is the compound of interest one wishes to produce, while the precursors are usually compounds that are natively present in a chassis strain. In the present implementation, the target can be any chemical that could be described…

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Data Communication Based on MQTT in a Polymer Extrusion Process

This work proposes a flexible method for data communication between a film extrusion system and monitoring devices based on a message protocol called Message Queuing Telemetry Transport (MQTT). The protocol in this work allows building a flexible data communication structure for a Polymer processing machine by employing a publisher subscriber…

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Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

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tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

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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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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Activation of STING by targeting a pocket in the transmembrane domain

Zhang, X., Bai, XC & Chen, ZJ Structures and mechanisms of the cGAS-STING innate immunity pathway. Immunity 5343–53 (2020). CAS PubMed Google Scholar Article Ishikawa, H. & Barber, GN STING is an endoplasmic reticulum adapter that facilitates innate immune signaling. Nature 455674–678 (2008). ADS CAS PubMed PubMed Central Article Google…

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Bioconductor – neaGUI

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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Using pyplot to plot and continue to work in terminal

I suppose that you are doing something like : import matplotlib.pyplot as plt myplot = plt.plot(yadda, yadda, yadda) plt.show(myplot) The help for plt.show (available by typing plt.show?) states, among other not unintersing things : Signature: plt.show(*, block=None) Docstring: Display all open figures. block : bool, optional Whether to wait for…

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ABAP OpenAPI UI v2, a long overdue update!

It’s already been two years since I first released ABAP OpenAPI v1. The past two years I’ve mainly been focusing on SAP BTP-related projects, but a few weeks ago, I stubbled upon a few customers that were still using my initial release. So I thought to myself, time for a…

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Need help from a math quant. Must know R/Rstudio – Freelance Job in AI & Machine Learning – Less than 30 hrs/week – undefined

Part 1) Need help analyzing data and coming up with the most profitable portfolio possible Part 2) I need to get some simulations running as fast as possible. I have the code completely finished so I just need suggestions on how to make it better. Video available if needed. I…

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Gromacs performance on GPU – User discussions

GROMACS version: 2022GROMACS modification: Yes/No Hi! I am checking the performance of my fresh Gromacs installation on a new PC. I have the newest Gromcas compiled (Linux Mint) using the basic scheme from the manual with added support for Nvidia GPU (CUDA, 11.60). CPU is AMD Ryzen 9 5950X (16…

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How To Plot The Log Of Somethin Gin Rstudio?

R’s log() function returns the logarithm of a value and is formatted as log(value, base). You can also use the logy() function to do a log in R. The natural logarithm of the value is the default output of this function. How Do I Create A Log In R? set…

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Install SageMath in Ubuntu 22.04

In this article, we would discuss how to install SageMath in Ubuntu 22.04 release. It is basically a free and open-source mathematics application. It combines the functionality of different open-source packages. The application is written in Python and Cython. It was first released on February 24, 2005. And, at the…

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Unable to install RStudio on Mac OSX 10.10

I was able to solve this problem by deleting all R/RStudio resources which remained from installing them manually from .dmg: Uninstall CRAN R GUI app (drag it into the trash) Uninstall RStudio app (drag it into the trash) From Terminal: $ rm -rf ~/.rstudio-desktop/ $ rm -rf /Library/Frameworks/R.framework /Applications/R.app /usr/bin/R…

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Bioconductor – pRolocGUI

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see pRolocGUI. Interactive visualisation of spatial proteomics data Bioconductor version: 3.4 The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny. Author: Lisa M…

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Example usage for com.intellij.openapi.options ConfigurationException ConfigurationException

Introduction In this page you can find the example usage for com.intellij.openapi.options ConfigurationException ConfigurationException. Prototype public ConfigurationException(String message, String title) Source Link Usage From source file:com.microsoftopentechnologies.intellij.ui.azureroles.ComponentsPanel.java License:Apache License @Override public void apply() throws ConfigurationException { try {/* w w w . j a v a 2 s . c o…

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SCHNAPPs – Single Cell sHiNy APPlication(s)

Abstract : Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed…

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List of software for nanostructures modeling

Three dimensional molecular model of an all-carbon tubular fullerene. This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics[1] and quantum mechanics. Ascalaph Designer Atomistix ToolKit and Virtual NanoLab[2] CST Studio Suite[3] CoNTub Deneb[4] – graphical user interface (GUI) for SIESTA,…

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Add module descriptors for javadoc

$ mvn javadoc:aggregate … [INFO] — maven-javadoc-plugin:3.0.1:aggregate (default-cli) @ biojava-legacy — [ERROR] no module descriptor for org.biojava:biojava-legacy [ERROR] no module descriptor for org.biojava:bytecode [ERROR] no module descriptor for org.biojava:core [ERROR] no module descriptor for org.biojava:alignment [ERROR] no module descriptor for org.biojava:biosql [ERROR] no module descriptor for org.biojava:blast [ERROR] no module…

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Updating scikit-learn to latest version with Anaconda environment fails with http error 000

I use Anaconda3 installed on my pc Win10 64bits. I noticed it runs with an outdated scikit learn version (0.21.3), and I am trying to update it (0.24.1 available on repo.anaconda.com/pkgs/main/win-64/) I do this: cmd I go in the script directory D:ProgramDataAnaconda3Scripts conda update scikit-learn it fails with this error…

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a Burp Suite extension for automating OpenAPI-based APIs security assessments

Swurg is a Burp Suite extension designed for OpenAPI testing. The OpenAPI Specification (OAS) defines a standard, programming language-agnostic interface description for REST APIs, which allows both humans and computers to discover and understand the capabilities of a service without requiring access to source code, additional documentation, or inspection of…

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How to use the Interactive Desktop on Open OnDemand

The Interactive Desktop app provides a grapical user interface that runs as a batch job on pronto. Any module that can be loaded in a normal Pronto batch job can be loaded within the interactive desktop. In addition, the following modules have easy-to-use launcher shortcuts. Matlab Mathematica RStudio Getting Started…

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New biosensors shine a light on CRISPR gene editing — ScienceDaily

Detecting the activity of CRISPR gene editing tools in organisms with the naked eye and an ultraviolet flashlight is now possible using technology developed at the Department of Energy’s Oak Ridge National Laboratory. Scientists demonstrated these real-time detection tools in plants and anticipate their use in animals, bacteria and fungi…

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Index of /~psgendb/birchhomedir/doc/local/pkg/PathVisio2.0.11/modules

Name Last modified Size Description Parent Directory   –   org.pathvisio.core.jar 2012-03-08 16:50 1.4M   org.pathvisio.core/ 2012-03-08 16:50 –   org.pathvisio.deskto..> 2012-03-08 16:50 238K   org.pathvisio.desktop/ 2012-03-08 16:50 –   org.pathvisio.gex/ 2012-03-08 16:50 –   org.pathvisio.gexplu..> 2012-03-08 16:50 53K   org.pathvisio.gui.jar 2012-03-08 16:50 208K   org.pathvisio.gui/ 2012-03-08 16:50 –  …

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[slurm-users] smap on Centos7

Hi, This is my first post. :-) Where can I find the ‘smap’ gui for Cenos7 ? I can’t seem to locate the package that provides this. I didn’t get any results with ‘yum whatprovides smap’. In contrast, ‘yum whatprovides sview’ gives me ‘slurm-gui’. Shouldn’t smap be part of…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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Repo template to use a Linux Desktop Application on a binder / jupyterhub

Generate a Git repository that can run any Linux GUI application in the browser via mybinder.org or any JupyterHub from this template repository! Uses jupyter-remote-desktop-proxy to work. How to use this reop 1. Create a new repo using this as a template Use the Use this template button on GitHub….

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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bioinformatics scientist – Besto

Bioinformatics Scientist Agexplorer Com . Learning Bioinformatics The Scientist Magazine . Bioinformatics Scientist . Bioinformatics Scientist . Learning Bioinformatics The Scientist Magazine . What Does A Bioinformatics Scientist Do . Bioinformatics Understanding Of Living Systems Through . Next Generation Bioinformatics Advaita Bioinformatics . Bioinformatics Scientist Science Engineering Career . Bioinformatics…

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Bioconductor – MSGFgui

DOI: 10.18129/B9.bioc.MSGFgui     A shiny GUI for MSGFplus Bioconductor version: Release (3.5) This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current…

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Bioconductor – HilbertVis

Hilbert curve visualization Bioconductor version: 2.6 Functions to visualize long vectors of integer data by means of Hilbert curves Author: Simon Anders <anders at fs.tum.de> Maintainer: Simon Anders <anders at fs.tum.de> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“HilbertVis”) To cite this package in a publication, start R…

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See AI Training at Google Developer Student Clubs Islamic University of Gaza

يعطيكم العافية أصدقاءنا في GDSC 👋 .. حيكون عنا في الفترة القادمة Course متخصص في الذكاء الاصطناعي: 💬 التعريف بالـ Course: هو تدريب مختص بالذكاء الاصطناعي مقدم من نادي الطلبة المطورين في الجامعة الإسلامية بغزة ،حيث سيتناول التدريب مجموعة من المواضيع العملية المختلفة مثل: – Machine Learning – Data Processing…

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how to install packages in r

In classic R you will have to press the tab button to show the functions on the screen, although it should be noted that if the package contains many functions not all will be shown, as is the case with the ggplot2 package: Sometimes it can be interesting to inspect…

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Error while running MEGAX

Error while running MEGAX 0 I am running the latest version of MEGA i.e MEGAX. I am trying to run the command megacc but it is throwing an error. My sequences.fas file contains the trimmed multiple sequence alignment (MSA) of 16S rRNA sequences of 1403 organisms in a fasta format….

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Pybedtools error sans

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

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biopython | DelphiFeeds.com

biopython | DelphiFeeds.com Story Category: biopython Hands-On Bioinformatics With These 6 Powerful Python Libs Muhammad Azizul Hakim Are you looking for tools to work in Bioinformatics…

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Output Polar Contacts Between Chains to Text File

  PYMOL: Output Polar Contacts Between Chains to Text File 0   I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A…

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