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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

David Seide November 23, 2020

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

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Cloud Blast and Cloud Units: How to use resources wisely

Stefan Götz September 30, 2020

This article describes how to run CloudBlast wisely. OmicsBox allows you to perform NCBI Blast searches using a cloud system for high-performance computing. This system runs jobs in parallel and autoscales depending on demand. To control usage we use so-called CloudUnits. These units represent computation time (cpu seconds) on the AWS infrastructure. At the moment only Blast and InterProScan consume

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OmicsBox Update Version 1.4

OmicsBox Update Version 1.4

Stefan Götz September 24, 2020

We are happy to announce the latest version of OmicsBox 1.4, a very technical release of the OmicsBox base platform. We upgraded many internal libraries and updated to the latest version of many underlying software packages. These changes required a lot of code-refactoring and software testing to comply with all our internal security and quality standards. OmicsBox is now more

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courtship song Laupala crickets

Zeroing in on genes involved in courtship song variation in Laupala crickets

Mariana Monteiro June 9, 2020

OmicsBox Supported Project. Researchers: Hayden Waller, Cornell University, USA Background and Project Overview: One of the primary outcomes of speciation – the formation of new species – is the generation of pre-mating barriers that prevent or greatly reduce gene flow. Behavioral changes are perhaps the most potent in the early stages of speciation. In particular, the divergent evolution of sexual

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Clustering redundant transcripts in OmicsBox with CD-HIT

Carlos Menor May 8, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. However, with the advancement of next-generation sequencing technologies, the amount of available sequencing data is growing exponentially. Because of this, assembly algorithms often generate a large number of transcripts. Removing redundancy from such data could be crucial for reducing storage space,

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Long-Reads Assembly with OmicsBox

Carlos Menor May 6, 2020

Third-generation DNA sequencing technologies allows scientist to generate longer sequence reads, which can be used in whole-genome sequencing projects to yield better repeat resolution and more contiguous genome assemblies. However, although long-read sequencing technologies can produce genomes with long contiguity, the relatively high error rate of long reads has made it challenging to generate highly accurate final sequences. OmicsBox now

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