Search Results for "hiv"

...There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is a 3D virtual reality version of cellPAINT, with molecular building blocks for a red blood cell cytoskeleton --cellPAINT_2D is the initial alpha release of cellPAINT, with building blocks for HIV, blood plasma, and a human T-cell. For more information and tutorials, see our website at https://ccsb.scripps.edu/cellpaint Please submit any bug or feature requests to our ticket page.

This code has been used in the study: Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa; PLoS Pathogens 2019 https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007976 Please note that the code includes test input data that does not necessarily reproduce the results included in the manuscript.

...This is not an R-package (although there are plans to extend the code and eventually make it into an R-package). Please read the PDF file supplied for further instructions on how to use this code. [1] HBV vaccination and PMTCT as elimination tools in the presence of HIV: insights from a clinical cohort and dynamic model https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-019-1269-x

This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population.

ISDTool is developed to predict ISD of retroviruses, including HERV, HTLV-1, HIV-1, STLV and SIV.

This provides the source code for reproducing the mathematical model and analysis presented in the manuscript: Eaton JW, Hallett TB. Why transmission during early-stage HIV infection does not predict the long-term impact of HIV treatment-as-prevention. (submitted.)

...The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and tested by applying to reads obtained from experimental HIV samples.

...Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. Full details can be found in our paper titled "Application of a new informatics tool for contamination screening in the HIV sequencing laboratory" The code provided is a simple user interface to the underlying algorithm. We provide it as a convenience but it comes with absolutely no warranty as stated in the Apache License, Version 2.0.

Program for predicting HIV-1 coreceptor usage using logistic regression: input is a HIV-1 genotypic sequence spanning the V3 loop of the envelope region.

HIVM, An Application for Prediction of HIV Drug Resistance using Support Vector Machine Algorithms

A project to create an interactive, scientifically-accurate 3D model of the HIV virus. Particularly intended for use in education.