Tag: GUI

GPU support and installation – User discussions

tebg January 19, 2024, 8:51am 1 GROMACS version: 2023.3GROMACS modification: Yes (I think??) I’ve just started setting up a new PC with the main goal of running MD simulations, and I’m trying to test out a simple membrane simulation generated by CHARMM-GUI. I installed GROMACS with GPU support, but I…

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Accelerating Stable Diffusion Performance

“` OpenAI’s ChatGPT has brought AI technology like Stable Diffusion, an image-generating algorithm, into the mainstream, with advancements being made to improve its speed and efficiency. To enhance the speed of Stable Diffusion, users can employ techniques such as cross-attention optimization, which reduces memory usage and accelerates calculations, with tools…

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Current and Future Analysis of Data Mining Tools Market Types and Applications, Drivers, Ongoing Trends, Future Demand, Challenges, Top Companies & Forecast 2023-2030 |Oracle Corporation (U.S.), IBM Corporation (U.S.)

“Worldwide Market Reports offers a UP-TO 70% discount on Data Mining Tools Market Reports on Single User Access and Unlimited User Access“ The latest research study released by Worldwide Market Reports on “Data Mining Tools Market” with 100+ pages of analysis on business strategy taken up by emerging industry players, geographical scope,…

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Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions

GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….

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Whole-Lung 3D Reconstruction Using Medical Image Processing Technology

To begin, copy the patient’s digital imaging and communications in medicine, or DICOM data, to a defined working directory. Using the file browser, examine each file directory to identify the image sequence with the highest number of scanning layers for analysis. Employ the DICOM function within MATLAB by providing DICOM…

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Efficient Ways To Get Help On An R Package In RStudio

Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…

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Command to run gromacs in parallel – User discussions

cjbraz December 11, 2023, 5:06pm 1 GROMACS version: 2023.2GROMACS modification: Yes/NoHere post your question Hello all. I have used CHARMM-GUI solvent builder to print out a script I can use in a protein simulation. I am able to run the script successfully, but would like to run the full script…

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How to speed-up to contruct phylogenetic tree

How to speed-up to contruct phylogenetic tree 2 I have ~600 protein sequences from different species( same protein family) for which I wanted to contruct Maximum likelihhod with 1000 bootstrap. But in MEGA GUI (version 11.0.11), it’s took me about 1 month to contruct it. There is an option given…

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The most effective Schema-Driven Development using OpenAPI for Logistic Engineer

In web application development, your team use OpenAPI document in many cases When you separate backend and frontend. But, the API specification document based on OpenAPI is written in yaml or json format. Then it is a very stressful task. Also, writing up the API document doesn’t mean completing by…

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How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)?

How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)? 2 Does anyone know how display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)? Is this possible at all? The number of variants…

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LCA from BLAST output

LCA from BLAST output 1 I have a fairly large BLAST output from a metagenomics project with millions of lines per sample. The input sequences for the blast search were prodigal annotated proteins. I have been looking for a while now to find a suitable program that calculates the LCA…

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Error in StarDist groovy script for QuPath – Usage & Issues

I’m trying to adapt a StarDist groovy script to run StarDist on a dsDNA channel in a MIBI image stack. I’ve entered the path to the model and changed “DAPI” to “dsDNA”. When I run the script, I get the following error: ERROR: Mismatch of count of formal and actual…

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IDE & Compilers: best downloads for Windows

Fifsoft Open source C/C++ Integrated Development Environment. Free B.E.I.C. ELECTRONICS Utility to Encode/Decode File, Text, String, etc. Shareware 861.3 KB JetBrains s.r.o. Analyzes your code to provide code completion, formatting and refactorings. Shareware 155.85 MB AlterMedia, Inc. Offers an intuitive experience for managing the business of…

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Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis

Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef  CAS  PubMed  Google Scholar  Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef  PubMed Central  PubMed …

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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]

Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…

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Issue with Accessing Thermo Data in Pylammps – LAMMPS Installation

Dear members of the LAMMPS mailing list, I have been attempting to build and install the LAMMPS Python interface (Pylammps) to leverage the advantages of accessing thermos data. However, I am encountering the following error: Based on my understanding from the documentation, if I set up a simulation with a…

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Bioconductor – epivizrChart

DOI: 10.18129/B9.bioc.epivizrChart     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see epivizrChart. R interface to epiviz web components Bioconductor version: 3.14 This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used…

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A Modular Parallel Pipeline Architecture for GWAS Applications in a Cluster Environment

Abstract A Genome Wide Association Study (GWAS) is an important bioinformatics method to associate variants with traits, identify causes of diseases and increase plant and crop production. There are several optimizations for improving GWAS performance, including running applications in parallel. However, it can be difficult for researchers to utilize different…

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140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build

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: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/cytoscape-3.6.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building biology/cytoscape build started at Sat Dec 2…

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The Top 5 Alternatives to GitHub for Data Science Projects

Image by Author   GitHub has long been the go-to platform for developers, including those in the data science community. It offers robust version control and collaboration features. However, data scientists often have unique requirements, such as handling large datasets, complex workflows, and specific collaboration needs that GitHub may not…

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Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

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20 Best Neural Network Software for 2024

Image: Siarhei/Adobe Stock eWEEK content and product recommendations are editorially independent. We may make money when you click on links to our partners. Learn More. Neural network software enables the implementation, deployment and training of artificial neural networks. These networks are designed to mimic the behavior of the human brain…

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Help! RStudio starts to a blank screen after update; clean install worked, but not after time machine backup. – RStudio IDE

Error Information: Description of issue – After updating to OS Sonoma, RStudio is a blank window. I only see the name of the toolbar. There are no options in the toolbar either, it says empty. R app works fine. Attempted steps taken to fix –Reinstalled appsReinstalled OS system sonoma (didn’t…

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Testing an OpenAPI specification in PHP

Introduction OpenAPI has become the de facto standard for API specifications. According to its description, “It is a specification language for HTTP APIs that defines structure and syntax in a way that is not wedded to the programming language the API is created in”. The specification is independent of the…

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Awesome List Updates on Nov 29, 2023

7 awesome lists updated today. 🏠 Home · 🔍 Search · 🔥 Feed · 📮 Subscribe · ❤️ Sponsor Projects / API Management WSO2 API Manager (⭐778) (⭐778) – A fully open-source API management platform that provides comprehensive API management capabilities and allows you to manage APIs with ease. Projects…

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Interrogating ligand-receptor interactions using highly sensitive cellular biosensors

Dimitrov, D. S. Virus entry: molecular mechanisms and biomedical applications. Nat. Rev. Microbiol. 2004 22 2, 109–122 (2004). Google Scholar  Chen, W., Zarnitsyna, V. I., Sarangapani, K. K., Huang, J. & Zhu, C. Measuring Receptor-Ligand Binding Kinetics on Cell Surfaces: From Adhesion Frequency to Thermal Fluctuation Methods. Cell. Mol. Bioeng….

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Visualize and explore eventalign data against reference

Visualize and explore eventalign data against reference 0 Hi all, Is anyone aware of a tool (GUI or python/R/bash package) to explore eventalign nanopore data (or fast5 raw data) with the corresponding alignment to a reference genome? Kind of like viewing how reads in a bam file align against a…

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MinKNOW software installation doubt for MinION Nanopore sequencing

MinKNOW software installation doubt for MinION Nanopore sequencing 0 Hi good people, Recently in lab we have received a Nanopore MinION device and currently trying to figure out installation and other details. I am seeking a few suggestions from users and experts. The running machine spec is AMD Ryzen 9…

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Awesome List Updates on Nov 22, 2023

6 awesome lists updated today. 🏠 Home · 🔍 Search · 🔥 Feed · 📮 Subscribe · ❤️ Sponsor CI / Tools & Plugins Lightning – Framework to integrate JMeter non-functional tests with CI/CD server. Tools / Utilities Hamster (⭐9) – Swiftly launch your JMeter test plans from Mac menubar….

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Setting PATH environment variable in Rprofile – RStudio IDE

This is related to:community.rstudio.com/t/how-to-make-rstudio-use-the-right-system-path/119880/4 I want to use an executable installed with Homebrew (macOS 13.5.2), but the necessary path (/opt/homebrew/bin) is not in the PATH environment variable of an R Studio session. I can add it within a session using a command like this: Sys.setenv(PATH=paste(“/opt/homebrew/bin”, Sys.getenv(“PATH”), sep=”:”)) But I don’t…

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[slurm-users] Usage of particular GPU out of 4 GPUs while submitting

Hi Daniel Letai Thanks for the quick response and guidance. I have done the changes as mentioned in gres.conf and slurm.conf and now I am able to submit the jobs to a particular GPU. Regarding MIG, it was just a thought came in m mind, in case studentA wants to…

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How to solve the GROMACS error “One or more water molecules can not be settled” during SMD? – User discussions

mari November 19, 2023, 6:17pm 1 GROMACS version:2019.6GROMACS modification: NoHow to solve the GROMACS error “One or more water molecules can not be settled” during SMD?I hope this message finds you well. I’m currently conducting research involving simulating a membrane protein system using GROMACS 2019.6. I have encountered an issue…

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[slurm-users] SLURM new user query, does SLURM has GUI /Web based management version also

On 19-11-2023 09:11, Joseph John wrote: > I am new user, trying out SLURM > > Like to check if the SLURM has a GUI/web based management tool also Did you read the Quick Start Administrator Guide at slurm.schedmd.com/quickstart_admin.html ? I don’t believe there are any Slurm management tools as…

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Exited with exit code 255 “Display Warning”

Dear Slurm Users,   May I have your suggestion/recommendation to solve the issue,   We have 2 servers Platinum and Cerium,  when I launch the job in Platinum the tool launches successfully, and the job is complete. But when I try to launch a job in cerium from platinum,…

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Release notes Indicium 2023.3.12 | Thinkwise Community

Hello everyone, In this sprint, we have added the possibility to filter within the open API document. We have also made Indicium more robust against missing decryption keys. You can read more about Indicium’s features in the Indicium user manual. We will keep you updated regularly about Indicium’s progress.  …

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GGPLOT2

Somsak Chanim 🤓 Internation College of Digital Innnovation, CMU 2023-09-16 ggplot2 package Created by Hadley Wickham in 2005 and released in 2007, ggplot2 is a crucial data visualization package for the R programming language. ggplot2 can serve as a replacement for the base graphics in R(ggplot2 is the one part…

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Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

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How To Install R Packages: Steps For Efficient Integration

Installing R packages is a fundamental skill for every programmer and developer working with R. This guide provides straightforward steps to ensure a smooth installation process. Whether you’re a beginner or an experienced user, these instructions will help you efficiently integrate new packages into your R environment. Understanding R Package…

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Scientists discover key to a potential natural cancer treatment’s potency

Within the glass vials of the Natural Products Discovery Center at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, scientists have discovered two useful new enzymes which may help them create medicines for cancer and other conditions. Credit: Scott Wiseman Slumbering among thousands of bacterial strains in…

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Bioconductor – AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub     Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…

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Mechanism and therapeutic potential of targeting cGAS-STING signaling in neurological disorders | Molecular Neurodegeneration

Hemmi H, et al. A toll-like receptor recognizes bacterial DNA. Nature. 2000;408(6813):740–5. Article  CAS  PubMed  Google Scholar  Unterholzner L, et al. IFI16 is an innate immune sensor for intracellular DNA. Nat Immunol. 2010;11(11):997–1004. Article  CAS  PubMed  PubMed Central  Google Scholar  Chiu YH, Macmillan JB, Chen ZJ. RNA polymerase III detects…

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RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics

Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…

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A Flexible, Modular and Scalable Approach for Building Production ML Models

Transcript Rajpal: I’m going to be talking about declarative machine learning systems, a new paradigm for flexible, modular, and scalable machine learning development. My name is Shreya. I’m a Senior Machine Learning Engineer and the Domain Lead for Machine Learning Infrastructure at Predibase. Previously, I’d spend some time at Apple…

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Restrains positions issue of metal ions in protein active site – User discussions

GROMACS version:2021GROMACS modification: Yes/NoHere post your questionHi all,I have prepared my metalloprotein-inhibitor model with CHARMM-GUI and need to restrains positions of Zn atoms. I have tried two different methods and got the same error for both of them: Adding these lines into ZN2.itp file in toppar folder:#ifdef POSRES_ZN[ position_restraints ];…

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Using Homer3 Software to Perform the Pre-Processing of the fNIRS Hyperscanning Data

To begin open MATLAB, then navigate to the folder where the raw and irs files are saved. Select and open the folder. Type Homer3 into the command window of MATLAB to launch the Homer3 GUI. Homer3 will detect the nirs files and ask to convert them to snirf format to…

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Synergistic effects of Azithromycin and DMXAA

Kanoktip Petcharat,1 Narongsuk Munkong,2 Rungthip Thongboontho,1 Widsanusan Chartarrayawadee,3 Arthid Thim-Uam1 1Division of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, 56000, Thailand; 2Department of Pathology, School of Medicine, University of Phayao, Phayao, 56000, Thailand; 3Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand Correspondence: Arthid Thim-Uam,…

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Uses of Interface org.biojava.bio.gui.sequence.ImageMap (BioJava-1.7 API)

Constructors in org.biojava.bio.gui.sequence with parameters of type ImageMap BasicImapRenderer(BasicFeatureRenderer renderer, ImageMap imageMap, URLFactory urlFactory)           Creates a new BasicImapRenderer. RectangularImapRenderer(RectangularBeadRenderer renderer, ImageMap imageMap, URLFactory urlFactory)           Creates a new RectangularImapRenderer. ZiggyImapRenderer(ZiggyFeatureRenderer renderer, ImageMap imageMap, URLFactory urlFactory)           Creates a new ZiggyImapRenderer. Read more here: Source link

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Phase separation in cGAS-STING signaling

Sun L, Wu J, Du F, Chen X, Chen ZJ. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 2013; 339(6121): 786–791 Article  CAS  PubMed  Google Scholar  Wu J, Sun L, Chen X, Du F, Shi H, Chen C, Chen ZJ. Cyclic GMP-AMP…

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Unlocking the genetic potential of poplars: A

The Populus genus, commonly known as poplars, cottonwoods, and aspens, consists of approximately 30 tree species native to the northern hemisphere. Because of their diverse usages in landscape, agriculture, bioenergy, and industry, Populus species have been the focus of many tree breeding and genetic improvement programs. Modern biotechnologies, including both genomics and genetic…

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Unlocking the Power of Kubeflow Pipelines v2 for ML Efficiency | by Vishnu Adithyan | SquareShift | Oct, 2023

In today’s tech-driven world, machine learning is a vital tool for businesses of all sizes. However, getting from concept to reality with ML models can be a challenging journey. That’s where Kubeflow Pipelines (KFP) v2 comes in, promising to make this journey smoother. Let’s explore what’s new and exciting in…

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Bioconductor – GNOSIS (development version)

DOI: 10.18129/B9.bioc.GNOSIS   This is the development version of GNOSIS; to use it, please install the devel version of Bioconductor. Genomics explorer using statistical and survival analysis in R Bioconductor version: Development (3.18) GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic…

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Maven Central: org.biojava:gui

<dependency> <groupId>org.biojava</groupId> <artifactId>gui</artifactId> <version>1.9.7</version> </dependency> <?xml version=”1.0″ encoding=”UTF-8″?> <project xmlns=”http://maven.apache.org/POM/4.0.0″ xmlns:xsi=”http://www.w3.org/2001/XMLSchema-instance” xsi:schemaLocation=”http://maven.apache.org/POM/4.0.0 maven.apache.org/maven-v4_0_0.xsd“> <modelVersion>4.0.0</modelVersion> <parent> <artifactId>biojava-legacy</artifactId> <groupId>org.biojava</groupId> <version>1.9.7</version> </parent> <artifactId>gui</artifactId> <packaging>jar</packaging> <version>1.9.7</version> <name>gui</name> <description>BioJava gui module</description> <dependencies> <dependency> <groupId>junit</groupId> <artifactId>junit</artifactId> <scope>test</scope> </dependency> <dependency> <groupId>org.biojava</groupId> <artifactId>core</artifactId> <version>${project.version}</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.biojava</groupId> <artifactId>sequencing</artifactId> <version>${project.version}</version> <scope>compile</scope> </dependency> </dependencies> </project> Read more here: Source…

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Associate Engineer Bioinformatics, Biopharma Libraries – Twist Bioscience

  Programmable DNA, the software of Life, is finally here! Twist Bioscience is developing a disruptive Synthetic DNA technology that will change the world, enabling widespread health and sustainability. Synthetic biologists use our products to engineer how organisms produce cures to diseases; everyday chemicals are made using the atmosphere as…

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Uses of Package org.biojava.bio.structure.jama (BioJava-1.7 API)

Packages that use org.biojava.bio.structure.jama org.biojava.bio.structure Interfaces and classes for protein structure (PDB).  org.biojava.bio.structure.align Classes for the super-imposition of structures.  org.biojava.bio.structure.align.helper Helper classes for structural alignment.  org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures.  org.biojava.bio.structure.gui A few convenience classes to view protein structures with Jmol (if it is on the classpath),…

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GSEA error 1005 The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub

I am using the GUI version of GSEA. The samples are of mice. I prepared the required files (.gct) and phenotypelabel (.cls), as required. Expression dataset (partial, feature used are normalized counts) 409 5 NAME description CF355 CF328 WT316 WT351 WT354 ENSMUSG00000025902.14 NA 77 61 110 76 54 ENSMUSG00000102269.2 NA…

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Force fields – User discussions

GROMACS version:GROMACS modification: Yes/NoHere post your questionI have created my pdb with lipids triglycerides using CHARMM gui , now I run pdb2gmx using gromacs selecting CHARMM forcefeilds, However I get the error “Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain…

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Transcriptional regulation and overexpression of GST cluster enhances pesticide resistance in the cotton bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae)

Bras, A., Roy, A., Heckel, D. G., Anderson, P. & Green, K. K. Pesticide resistance in arthropods: ecology matters too. Ecol. Lett. 25, 1746–1759 (2022). Article  PubMed  PubMed Central  Google Scholar  Chen, Y. H. & Schoville, S. D. Editorial overview: ecology: ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary…

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rstudio – Setting the working directory in R when you’ve tried everything and it still won’t work

I know you said you have tried some stuff but I’ll spell everything out here for clarity and reference of others. The procedure you typed out is the correct one and RStudio should be setting your working directory. If you aren’t getting error messages, it is likely working and just…

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R OpenStreetMap package functions — EndMemo

R OpenStreetMap package Access to Open Street Map Raster Images. Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported, including Apple, Mapnik, Bing, and stamen. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted…

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HK2 contributes to the proliferation, migration, and invasion of diffuse large B-cell lymphoma cells by enhancing the ERK1/2 signaling pathway

References [1] Thandra KC, Barsouk A, Saginala K, Padala SA, Barsouk A, Rawla P. Epidemiology of Non-Hodgkin’s Lymphoma. Med Sci (Basel). 2021 Jan 30;9(1):5.10.3390/medsci9010005Search in Google Scholar PubMed PubMed Central [2] Mafra A, Laversanne M, Gospodarowicz M, Klinger P, De Paula Silva N, Piñeros M, et al. Global patterns of…

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Molecular classification of hormone receptor-positive HER2-negative breast cancer

Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 70, 7–30 (2020). Article  PubMed  Google Scholar  Huppert, L. A., Gumusay, O., Idossa, D. & Rugo, H. S. Systemic therapy for hormone receptor-positive/human epidermal growth factor receptor 2-negative early stage and metastatic breast cancer….

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Docking protocol – In silico Molecular Docking Protocol Using AutoDock Vina Prepared by: Jessa A.

In silico Molecular Docking Protocol Using AutoDock Vina Prepared by: Jessa A. Payusan Organic Synthesis Chemistry/Drug Design and Development Related Research Laboratory, Premier Research of Science and Mathematics, MSU-Iligan institute of Technology Iligan City, Philippines May 2020 Docking Protocol ii Table of Contents Page Title Page……………………………………………………………………………………………………………………… i – Introduction……………………………………………………………………………………………………… Table…

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Twist Bioscience hiring Associate Engineer Bioinformatics, Biopharma Libraries in South San Francisco, CA

Programmable DNA, the software of Life, is finally here! Twist Bioscience is developing a disruptive Synthetic DNA technology that will change the world, enabling widespread health and sustainability. Synthetic biologists use our products to engineer how organisms produce cures to diseases; everyday chemicals are made using the atmosphere as the…

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The Biostar Herald for Tuesday, September 26, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, Shred, and was edited by…

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Bioconductor – wpm

DOI: 10.18129/B9.bioc.wpm   Well Plate Maker Bioconductor version: Release (3.17) The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of…

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Awesome List Updates on Sep 20, 2023

7 awesome lists updated today. 🏠 Home · 🔍 Search · 🔥 Feed · 📮 Subscribe · ❤️ Sponsor Learn / Notebooks Other LLM Frameworks / Videos Playlists LangStream (⭐105): Framework for building and running event-driven LLM applications using no-code and Python (including LangChain-based) agents. Compilers and interpreters Projects /…

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autodock tools (adt) on catilina and newer

Hi, anyone is able to use adt from MGLtools (ccsb.scripps.edu/mgltools/) on catilina and newer? Since in documentation is reported that it does not run properly on Catilina and newer, seems to me the right moment to begin using docker, but when I exec adt command I get this error: docker…

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DNA sequencing at the picogram level to investigate life on Mars and Earth

All the extractions, dilutions and library preparation for sequencing were carried out inside the clean room environment of ISO (International Organization for Standardization) level 5 (ECSS-Q-ST-70-55C standard)32. An ISO 5 Class clean room is a semi-closed ultra clean environment that utilises High Efficiently Particle Air (HEPA) filtration systems to maintain…

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Research and describe the different applications.docx – Research and describe the different applications for each tool: RStudio: Before knowing about

Research and describe the different applications for each tool: RStudio: Before knowing about RStudio, let us understand R Programming. It is a Programming language used for statistics and graphics. It is a great data analysis. RStduio is the integrated development environment (IDE) for R Programming. RStudio comes in 2 flavors,…

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Get Started with Google’s Vertex AI and Gen AI Studio | by Varinderjot | Sep, 2023

Are you curious about generative AI? With Vertex AI and Gen AI Studio, you can explore the possibilities of this powerful technology without having to build any models yourself. Vertex AI is a managed machine learning platform that provides a unified experience for managing all aspects of the machine learning…

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Free Course: How to Do SDXL Training For FREE with Kohya LoRA – Kaggle – NO GPU Required – Pwns Google Colab from Software Engineering Courses – SE Courses

Introduction to how to do amazing FREE training of Stable Diffusion XL without owning a GPUHow to register Kaggle to get a free account to do free trainingHow to verify your phone number in Kaggle to be able to use cloud GPUs for freeHow to generate a Kaggle notebook and…

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3 Ways to Optimize It

Stable Diffusion, a state-of-the-art algorithm in the realm of artificial intelligence (AI) image generation, has revolutionized the way we create images. However, just like many cutting-edge technologies, it comes with its own set of challenges. One of the primary hurdles faced by developers and researchers alike is the latency issue…

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Houston Methodist hiring Bioinformatician – Urology – Chan lab in Houston, Texas, United States

Job SummaryAt Houston Methodist, the Bioinformatician position is responsible for managing all aspects of data analysis, data storage and bioinformatics support. This position specifically performs bioinformatics and statistical analysis for Next Generation Sequencing (NGS) experiments as well as develops pipelines, application tools for laboratory scientists, and administrating local and remote…

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choose.dir() results in NA in RStudio IDE but not in R gui – RStudio IDE

I would like to share my findings, in case they can help identifying the source of the problem. I am using the latest version of RStudio (just downloaded it), on Windows 10:RStudio 2023.06.2+561 “Mountain Hydrangea” Release (de44a3118f7963972e24a78b7a1ad48b4be8a217, 2023-08-25) for windowsMozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.06.2+561…

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Role of the cGAS-STING pathway in radiotherapy for non-small cell lung cancer | Radiation Oncology

Sung H, Ferlay J, Siegel RL, et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and Mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660 Article  PubMed  Google Scholar  Duma N, Santana-Davila R, Molina JR. Non-Small Cell Lung Cancer: Epidemiology, Screening, diagnosis, and treatment….

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Analysis of drug-resistance characteristics of MDR-TB

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), continues to pose a significant global public health challenge.1–3 In 2021, there were 10.6 million new TB cases worldwide, with China accounting for 780,000 cases, making it the third highest burden country for TB globally.4 The World Health Organization (WHO) estimates that…

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Civitai | How to Do SDXL Training For FREE with Kohya LoRA – Kaggle – NO GPU Required

If you don’t have a strong GPU for Stable Diffusion XL training then this is the tutorial you are looking for. We will use Kaggle free notebook to do Kohya SDXL LoRA training. In this tutorial you will master Kohya SDXL with Kaggle! 🚀 Curious about training Kohya SDXL? Learn…

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The Two Most Popular Stable Diffusion UIs Just Got Major Upgrades

This week brought big news in the world of AI art, with two of the most popular user interfaces (UIs) for Stable Diffusion announcing major upgrades. Automatic 1111 and InvokeAI, leading tools for running the open-source Stable Diffusion models SD 1.5, SD 2.1 and the brand new SDXL, released significant…

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Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate

Kagi, D., Ledermann, B., Burki, K., Zinkernagel, R. M. & Hengartner, H. Molecular mechanisms of lymphocyte-mediated cytotoxicity and their role in immunological protection and pathogenesis in vivo. Annu. Rev. Immunol. 14, 207–232 (1996). Article  CAS  PubMed  Google Scholar  Prager, I. & Watzl, C. Mechanisms of natural killer cell-mediated cellular cytotoxicity….

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Awesome List Updates on Aug 30, 2023

5 awesome lists updated today. 🏠 Home · 🔍 Search · 🔥 Feed · 📮 Subscribe · ❤️ Sponsor Photoshop / Illustrator Projects / API Management WSO2 API Manager (⭐755) (⭐750) – A fully open-source API management platform that provides comprehensive API management capabilities and allows you to manage APIs…

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Using tool of charmm2gmx – User discussions

Brief description of tools/files:Charmm2gmx 1.0.2J. Chem. Inf. Model. 2023, 63, 14, 4246–4252awacha.gitlab.io/charmm2gmx/index.html Link:Contact person (JieChen and chenjiedlpu@163.com): How the work has been tested/reviewed:Hi Proffessor Justin, I found good tool for convert CHARMM stream files produced by CGenFF to GROMACS topologies, named Charmm2gmx. It likes the python file of charmm2gmx.py. But…

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Scale Biosciences and Basepair to Democratize Single Cell Sequencing Data Analysis

SAN DIEGO–(BUSINESS WIRE)–Scale Biosciences, Inc. (aka ScaleBio), a pioneer in single-cell sequencing technology, today announced a new collaboration with Basepair to provide point and click bioinformatic analysis of single-cell data produced with its patented and disruptive combinatorial indexing technology. As a result of this collaboration, scientists will be able to…

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How does having -DEFLEXIBLE versus -DPOSRES defined in an the mdp file affect the equilibration? – User discussions

GROMACS version: 2016.3GROMACS modification: NoI’ve been trying to get this CG simulation of two vesicles of 1000 lipids each in water and I’ve been having difficulty going from the minimization step to equilibration step. I was getting these errors saying pressure scaling was too high which as I learned indicates…

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Running Gromacs on CCAST Clusters

Introduction This document describes basic usage of GROMACS on CCAST clusters. Far more information about GROMACS is available in the GROMACS manual, which is available online and is maintained by the GROMACS developers. GROMACS is a free and open-source high-performance molecular dynamics package, mainly designed for simulations of proteins, lipids,…

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Problem with small molecule MM

Dear CP2K users, I am trying to run a MM geometry optimization for a small molecule using CP2K. I have prepared the pdb and psf files for the molecule using Charmm-Gui and I am using the cgenff forcefield. For some reason, I am getting this strange error:  A string type…

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Ulcerative Colitis Treatment by CLP loaded with NLRP3 siRNA

Introduction Since the 20th century, tThe incidence of ulcerative colitis (UC) has been increasing over time, negatively affecting peoples’ health.1,2 UC is a multifactorial induced inflammatory bowel disease (IBD) characterized by chronic recurrent and remitting mucosal inflammation.3,4 It originates in the rectum and then extends to the proximal segments of…

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R Esquisse: How to Explore Data in R Through a Tableau-like Drag-and-Drop Interface

R Esquisse is an R package that provides an intuitive GUI for creating data visualizations using ggplot2. This package is particularly valuable for stakeholders seeking quick interactive analysis and insights gathering from data sources, whether they are new to R or prefer a more visual approach to creating plots. With…

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Submitting jobs (to a postgre database) through django webpage, using slurm

I’m looking for advice on how to proceed, assuming at all this could be a viable course of action. I have coded a web-based interface (Django) to access some data stored on (an external) database. The role of the webpage is to serve as GUI to show the user what…

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How to save a RStudio Script File from a Shiny GUI? – shiny

We are currently working on our first attempt at QCA for a comparative study of governance structures in city regions. As beginners, we are not yet familiar with RStudio, so we are glad that the QCA package includes a graphical user interface. We would like to create the script file…

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A genome visualization python package for comparative genomics

Tool:pyGenomeViz – A genome visualization python package for comparative genomics 0 pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib. This package is developed for the purpose of easily and beautifully plotting genomic features and sequence similarity comparison links between multiple genomes. It supports genome…

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Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores

DNA-nanostructure barcodes To observe that the CRISPR–dCas9 system is specific enough to detect the single base pair, DNA constructs with different ‘barcodes’ plus an overhang sequence for dCas9 was created. The DNA construct was synthesized from pairing a linearized 7.2 kbp single-stranded (ss) M13mp18 DNA (GuildBiosciences) with 190 complementary oligonucleotides via…

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No trajectory .trr file produced – User discussions

GROMACS version: 2018.4 and 2022.3GROMACS modification: No Hi! new user here.I have tried to use 2018.4 and 2022.3 for running NVT on my system and it sucessfully finishes the simulation and outputs my .xtc, .edr and my .log file but not my .trr file. However, my energy minimization does output…

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A Quick and Simple Tutorial

In this tutorial, we will guide you on how to check the version of R in RStudio. Knowing your R version is crucial for compatibility with packages and ensuring smooth data analysis. In this post, we will cover step-by-step instructions to find your R version using easy-to-follow methods. You can…

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How to create a basic GUI for rna seq pipeline

Please do not reinvent the wheel – for your own sanity, because if you want to write that from the bottom up, you need a team of software engineers and at least (!) a year of time*. So rather check what is already out there in the Bioinfo world: Galaxy…

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Flat-bottom potential renders an unstable system – User discussions

GROMACS version: 2022GROMACS modification: No I’m trying to equilibrate a membrane generated with CHARMM-GUI for the Martini forcefield. My membrane contains 512 lipids per monolayer and I’m using 28000 water beads (equivalent to 110 waters per lipid), this membrane as pre-equilibrated using CHARMM-GUI’s protocol. I want to make a pore…

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Oracle Corporation (U.S.), IBM Corporation (U.S.)

The “Global Data Mining Tools Market” research report represents major insights on the current growth dynamics as well as the primary revenue generation elements that are available in the Data Mining Tools industry along with various other factors over the predicted period 2023-2030. The report on the Data Mining Tools…

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Pytorch does not work in JupyterLab desktop version – JupyterLab

JupyPt July 31, 2023, 8:57pm 1 Hi. I would like to ask if somebody could help me with installing Pytorch for JupyterLab desktop version (Windows 10). I’ve installed Pytorch via command line (“python” > “import torch” = works in command line). When I write “import torch” to JupyterLab line, it…

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Zhejiang Nonglin reveals a new mechanism of cell wall xylan acetylation affecting the biomass energy conversion efficiency of poplar

Recently, the research team of Professor Zhang Jin from Zhejiang A&F University published a research paper entitled Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus online in Plant Physiology . Plant lignocellulosic biomass, the secondary cell walls of plants, is an important alternative source…

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Error starting RStudio 2023.06.01 on Macbook M1 2020 – RStudio IDE

System details RStudio Edition : Desktop RStudio Version : RStudio 2023.06.01 “Mountain Hydrangea” 547dcf86, 2023-07-06) for macOS OS Version : Ventura 13.4.1 – macOS – Apple Macbook Pro 13-inch M1, 2020 R Version : 4.3.1 (2023-06-16) — “Beagle Scouts”, Platform: x86_64-apple-darwin20 (64-bit) Steps to reproduce the problem I just downloaded…

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integrated development environment (IDE) for R (Free software)

RStudio is the integrated development environment (IDE) for R programming language, It was built to ease and automate the workflow of R with a user-friendly interface. Many people are not comfortable working with terminals, RStudio was built to make R easier for them. It has a built-in package manager, session…

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