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Some small fixes #43

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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
## Galaxy

[The Galaxy team](https://github.com/orgs/galaxyproject/people) is a community that develops software infrastructure for deploying Galaxy instances. There are three major Galaxy instances in the US ([https://usegaxy.org](https://usegaxy.org)), Europe ([https://usegalaxy.eu](https://usegalaxy.eu)), and Australia ([https://usegalaxy.au.org](https://usegalaxy.au.org)) and many regional instances. Galaxy is an application that allows users to run a wide variety of command-line, web-based, or interactive tools on any type of compatible data. Galaxy can be accessed either through a web-browser, or programmatically via application programming interface (API). A Galaxy instance can be configured to manage local or remote computational resources, and schedule tool runs on any modern computational infrastructure including local hardware, conventional clusters, commercial or public clouds, and beyond. The Galaxy team also operates and maintains the Galaxy ToolShed—a growing repository of >8,500 analysis tools available for use in Galaxy. The ToolShed is closely aligned with the [BioConda](https://bioconda.github.io) and [BioContainers](https://biocontainers.pro) communities that package and have become the standard distribution channels for bioinformatics tools. The Galaxy software ecosystem also includes scheduling components, tool development utilities, training infrastructure, and many other features (e.g., [Planemo](https://planemo.readthedocs.io, [Pulsar](https://github.com/galaxyproject/pulsar, [TPV](https://github.com/galaxyproject/total-perspective-vortex)). The main public [https://usegalaxy.org](https://usegalaxy.org) site is an example of a Galaxy instance. Usegalaxy.org supports 10s of thousands of active users running 100s of thousands jobs per month and manages over 4 petabytes of user data. [The Galaxy Training Network](https://training.galaxyproject.org) (GTN) contains a comprehensive collection of tutorials covering all aspects of Galaxy from basic functionality to advanced analyses—it is a widely used community-curated resource.
[The Galaxy team](https://github.com/orgs/galaxyproject/people) is a community that develops software infrastructure for deploying Galaxy instances. There are three major Galaxy instances in the US ([https://usegaxy.org](https://usegaxy.org)), Europe ([https://usegalaxy.eu](https://usegalaxy.eu)), and Australia ([https://usegalaxy.au.org](https://usegalaxy.au.org)) and many regional instances. Galaxy is an application that allows users to run a wide variety of command-line, web-based, or interactive tools on any type of compatible data. Galaxy can be accessed either through a web-browser, or programmatically via application programming interface (API). A Galaxy instance can be configured to manage local or remote computational resources, and schedule tool runs on any modern computational infrastructure including local hardware, conventional clusters, commercial or public clouds, and beyond. The Galaxy team also operates and maintains the Galaxy [ToolShed](https://testtoolshed.g2.bx.psu.edu/)—a growing repository of >8,500 analysis tools available for use in Galaxy. The ToolShed is closely aligned with the [BioConda](https://bioconda.github.io) and [BioContainers](https://biocontainers.pro) communities that package and have become the standard distribution channels for bioinformatics tools. The Galaxy software ecosystem also includes scheduling components, tool development utilities, training infrastructure, and many other features (e.g., [Planemo](https://planemo.readthedocs.io), [Pulsar](https://github.com/galaxyproject/pulsar), [TPV](https://github.com/galaxyproject/total-perspective-vortex)). The main public [https://usegalaxy.org](https://usegalaxy.org) site is an example of a Galaxy instance. Usegalaxy.org supports 10s of thousands of active users running 100s of thousands jobs per month and manages over 4 petabytes of user data. [The Galaxy Training Network](https://training.galaxyproject.org) (GTN) contains a comprehensive collection of tutorials covering all aspects of Galaxy from basic functionality to advanced analyses—it is a widely used community-curated resource.

## UCSC Genome Browser

[The UCSC Genome Browser](https://genome.ucsc.edu, maintained by the University of California, Santa Cruz (UCSC)), is a widely used and highly regarded online tool for visualizing and exploring genomic information. It is one of the most widely used sources of genomic data in the world, with more than 150,000 monthly users, spread over 200 countries and the majority of usage coming from outside the United States. The Browser team has been generating and distributing multiple alignments for genomes distributed on the site.
[The UCSC Genome Browser](https://genome.ucsc.edu), maintained by the University of California, Santa Cruz (UCSC), is a widely used and highly regarded online tool for visualizing and exploring genomic information. It is one of the most widely used sources of genomic data in the world, with more than 150,000 monthly users, spread over 200 countries and the majority of usage coming from outside the United States. The Browser team has been generating and distributing multiple alignments for genomes distributed on the site.

## HyPhy

Expand All @@ -16,8 +16,8 @@ Key tools for the analysis of pathogen evolution and dynamics are contained with

## Collaborative strategy

The research team responsible for implementing this work is headed by five PI with complementary research expertise domains, and a long history of collaboration. It includes Dr. Nekrutenko (Penn State), the original co-developer and PI of the Galaxy Project for the past 15 years. Dr. Pond (Temple) a computational evolutionary biologist whose core expertise is methodology development (including the HyPhy package) and two decades of experience in viral and pathogen evolution (HIV, IAV, and more recently SARS-CoV2). Dr. Schatz (Johns Hopkins) is a computational biologist who developed widely used algorithms for de-novo genome assembly and variant detection as well as pioneered the use of computational clouds in life sciences. Dr. Haeussler (UCSC) a software engineer and the PI of the Browser Project. Dr. John Fonner, a biomedical engineer who serves as the Director of Special Projects at TACC. Importantly, the team consists of highly experienced and skilled software developers and engineers who worked on the project for many years [1]. Just in the past three years this group has published over 40 papers on pathogen genomics including recent high profile publications on SARS-CoV2 genomics in [Cell](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8421097), [Nature Biotechnology](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8845060), [Nature Reviews Genetics](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447121), [Nature Genetics](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016453) and others. A high level overview of dependencies among these components is shown below:
The research team responsible for implementing this work is headed by five PI with complementary research expertise domains, and a long history of collaboration. It includes Anton Nekrutenko (Penn State), the original co-developer and PI of the Galaxy Project for the past 15 years. Sergei Kosakovsky Pond (Temple) a computational evolutionary biologist whose core expertise is methodology development (including the HyPhy package) and two decades of experience in viral and pathogen evolution (HIV, IAV, and more recently SARS-CoV2). Michael Schatz (Johns Hopkins) is a computational biologist who developed widely used algorithms for de-novo genome assembly and variant detection as well as pioneered the use of computational clouds in life sciences. Maximilian Haeussler (UCSC) a software engineer and the PI of the Browser Project. John Fonner, a biomedical engineer who serves as the Director of Special Projects at TACC. Importantly, the team consists of highly experienced and skilled software developers and engineers who worked on the project for many years. Just in the past three years this group has published over 40 papers on pathogen genomics including recent high profile publications on SARS-CoV2 genomics in [Cell](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8421097), [Nature Biotechnology](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8845060), [Nature Reviews Genetics](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447121), [Nature Genetics](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016453) and others. A high level overview of dependencies among these components is shown below:

![Platforms together](/about/platforms-together.svg)

Dependencies between the four projects involved in the design of BRC.Analytics. The TACC will form an infrastructural layer by providing computational and storage resources. Galaxy will serve as an analysis environment allowing users to run tools and workflows (such as HyPhy) on a dataset that can be obtained from existing resources or our integrated source of BRC data (BRC.data). Results of analyses can then be displayed in external applications such as the UCSC Genome Browser.
Dependencies between the four projects involved in the design of BRC-Analytics. The TACC forms an infrastructural layer by providing computational and storage resources. Galaxy serves as an analysis environment allowing users to run tools and workflows (such as HyPhy) on a datasets that can be obtained from existing resources or our integrated source of BRC data (BRC.data). Results of analyses can then be displayed in external applications such as the UCSC Genome Browser.
Original file line number Diff line number Diff line change
Expand Up @@ -154,9 +154,8 @@ export const buildOrganismListHero = (): ComponentProps<
> => {
return {
children:
"The list of currently available taxa was generated by comparing the list maintained by VeuPathDb against official NCBI genome builds. The three buttons adjacent to each taxon direct you to a page listing available analytical workflows as well as direct links to genomic data (NCBI Datasets) and a genome browser (UCSC). A comprehensive search functionality will be developed to allow complex queries.",
icon: false,
severity: "info",
"If you do not see your organism in this list: it will be there! We are in the process of ingesting sequences and annotations for all 785 taxa from VEuPathDb. The table below is generated by comparing the list maintained by VeuPathDb against official NCBI genome builds. The three buttons adjacent to each taxon direct you to a page listing available analytical workflows as well as direct links to genomic data (NCBI Datasets) and a genome browser (UCSC). A comprehensive search functionality will be developed to allow complex queries.",
severity: "warning",
};
};

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