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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<title>Grassroots Infrastructure</title>
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<div class="container">
<a class="navbar-brand js-scroll-trigger" href="#page-top"
style="text-transform: none ! important;">Grassroots
Infrastructure</a>
<button class="navbar-toggler navbar-toggler-right" type="button" data-toggle="collapse"
data-target="#navbarResponsive" aria-controls="navbarResponsive" aria-expanded="false"
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Menu
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<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="navbar-nav ml-auto">
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#services">Services</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#data">Data</a>
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<a class="nav-link js-scroll-trigger" href="docs/">Docs</a>
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<a class="nav-link js-scroll-trigger" href="dfw">DFW</a>
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<a class="nav-link js-scroll-trigger" href="service/search">Search</a>
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<div class="explanatory-text" style="margin-bottom: 20px; color: #2C3E50;">
<p>Grassroots is a data sharing platform for the wheat community. Use the search box below to find resources, or scroll down to read more about the project.</p>
<!-- Search Box -->
<div class="search-box" style="border: 2px solid #2C3E50; padding: 20px; border-radius: 5px; background-color: rgba(255, 255, 255, 0.9); box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);">
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<h4 style="margin: 0; color: #2C3E50;">Grassroots Search</h4>
<p style="margin: 0; color: #2C3E50; font-size: 14px;">Explore our system</p>
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<option value="All">All</option>
<option value="Dataset">Dataset</option>
<option value="Service">Service</option>
<option value="Field Trial">Field Trial</option>
<option value="Study">Study</option>
<option value="Location">Location</option>
<option value="MARTi Sample">MARTi Sample</option>
<option value="Programme">Programme</option>
<option value="Publication">Publication</option>
</select>
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<button onclick="sendSearchRequest()" class="btn btn-primary btn-xl js-scroll-trigger" style="margin-top: 10px; background-color: #2C3E50; border: none;">Search</button>
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</section>
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<script>
function sendSearchRequest() {
var keyword = document.getElementById('searchInput').value.trim(); // Trim to remove any leading/trailing white spaces
var category = document.getElementById('categorySelect').value;
if (keyword === "") {
// Display an alert or message on the page that a search term is required.
alert("Please enter a search term.");
} else {
// Construct the URL for results.html with query parameters for keyword and category
var resultsUrl = `results.html?keyword=${encodeURIComponent(keyword)}&category=${encodeURIComponent(category)}`;
// Redirect the browser to the results page
window.location.href = resultsUrl;
}
}
</script>
<!-- Portfolio Grid Section -->
<section class="success" id="services">
<div class="container">
<h2 class="text-center">Services</h2>
<hr class="star-light">
<p style="text-align: justify;">
<p>The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected.
With the data-generative approaches that are increasingly common in modern life
science research, it is
vital
that the data and metadata produced by these efforts can be shared and reused. The Grassroots
Infrastructure
project wraps up industry-standard software tools with a consistent API that can be federated on a
number of
levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local
data, connect up any existing data services, and federate their instance of the Grassroots with others
out-of-the-box.</p>
<p> The Grassroots Infrastructure has been developed to expose a number of important
and powerful technologies
that can benefit
researchers and developers to realise their data management needs.</p>
<p>Existing services:</p>
<ul>
<li><a class="darker" href="service/search" target="_blank">Search Grassroots</a></li>
<li><a class="darker" href="fieldtrial" target="_blank">Field Trials</a></li>
<li><a class="darker" href="docs/user/services/field_trial/" target="_blank">Submitting Field Trials</a></li>
<li><a class="darker" href="service/blast-blastn" target="_blank">Blast searches</a>
</li>
<li><a class="darker" href="https://opendata.earlham.ac.uk/wheat/under_license/toronto/" target="_blank">Grassroots Data Portal</a></li>
<li><a class="darker" href="yellowrust-map/" target="_blank">Yellow Rust Field Pathogenomics</a></li>
<li><a class="darker" href="service/" target="_blank">List of all public services</a></li>
</ul>
</div>
</section>
<!-- Portfolio Grid Section -->
<section id="data">
<div class="container">
<h2 class="text-center">Data</h2>
<hr class="star-primary">
<p style="text-align: justify;">As well as providing services, the Grassroots infrastructure also has the
ability to host data. Building upon <a href="https://irods.org/" target="_blank">iRODS</a> as a data
management solution, we have added a number of features
such as a search service and a fully featured web interface, using <a
href="https://github.com/billyfish/eirods-dav">mod_eirods_dav</a>, for accessing the data
and metadata. Currently it is used to host the <a href="https://opendata.earlham.ac.uk/wheat">Designing
Future Wheat Data Portal</a>.</p>
</div>
</section>
<!-- About Section -->
<section class="success" id="about">
<div class="container">
<h2 class="text-center">About</h2>
<hr class="star-light">
<h3>Designing Future Wheat:</h3>
<p style="text-align: justify;">Grassroots has traditionally been the result of an effort to produce an
interoperable data sharing platform
for the wheat community. Whilst Grassroots is by no means organism-specific, our main use cases come
from
the wheat community. We get most of our community feedback from plant researchers at the EI, JIC,
Bristol
University, and other UK institutions, as well as from various international wheat working groups such
as
the <a class="darker" href="https://www.rd-alliance.org/groups/wheat-data-interoperability-wg.html"
target="_blank">RDA Wheat Data
Interoperability maintenance group</a> and the <a class="darker"
href="http://www.wheatinitiative.org/activities/expert-working-groups/wheat-information-system"
target="_blank">Wheat
Initiative Wheat Information
System expert working group</a>. The newly awarded cross-institute programme grant,
Designing Future Wheat (DFW), is the first flagship project of its kind to bring the UK’s wheat
researchers
together to deliver new varieties relevant to the international stage, through the coordinated effort of
biologists, breeders, and informaticians. As such, Grassroots is funded by the DFW programme, enabling
us to
build a platform that can meet the needs of not only this ambitious programme, but the wider UK and
international wheat community that needs fast and openly-licenced unfettered access to the data and
experimental information arising from DFW.</p>
<h3>How to cite us:</h3>
<p style="text-align: justify;">If you have used any of the services that Grassroots provides in your own
research, we would very much
appreciate that you let us know and cite us in any publications, as follows:</p>
<p>Bian. X, Tyrrell. S, Davey R.P. <i>The Grassroots life science data infrastructure (2017).</i>
https://grassroots.tools</p>
</div>
</section>
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<h2 class="text-center">Contact us</h2>
<hr class="star-primary">
<p>If you have any queries, please email the <a href="mailto:[email protected]">Grassroots
Helpdesk</a></p>
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<h3>Earlham Institute</h3>
<p>Norwich Research Park<br />
Norwich<br />
NR4 7UZ<br />
UK</p>
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<div class="footer-col col-md-4">
<h3>Project Code</h3>
<p>The project is fully open source and the source code is available on <a
href="https://github.com/TGAC?q=grassroots" target="_blank">GitHub</a>:</p>
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<h3>Funding</h3>
<p>The Grassroots project is strategically funded through the BBSRC Designing Future Wheat
programme
grant, BB/P016855/1, and aims to develop a lightweight reusable set of open source software
tools
to allow researchers to share and federate life science datasets.</p>
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© 2017 - 2019 Brought to you by <a href="http://www.earlham.ac.uk/" target="_blank">Earlham
Institute</a>, powered by <a href="http://cyverseuk.org" target="_blank">CyVerse UK</a>
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<h2>Robert Davey</h2>
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<img class="img-fluid img-centered" src="img/rob-davey-web.jpg" alt="">
<p>Earlham Institute</p>
<p style="text-align: left ! important;">Rob leads the <a
href="http://www.earlham.ac.uk/davey-group">Data Infrastructure
group</a> at the Earlham Institute and is the PI for the
Grassroots project. He has a PhD in Computer Science from the University of East
Anglia,
undertaken at the Roberts lab in the <a href="http://www.ncyc.co.uk"
target="_blank">National
Collection
of Yeast Cultures</a>. Rob leads a
number of large computing infrastructure development and deployment projects, is a
certified <a href="https://software-carpentry.org" target="_blank">Software
Carpentry</a> Instructor and
Trainer, an editorial board member for
Nature Scientific Data, and a <a href="https://www.software.ac.uk">Software
Sustainability Institute</a> Fellow.</p>
<a href="https://orcid.org/0000-0002-5589-7754" target="orcid.widget"
rel="noopener noreferrer" style="vertical-align:top;"><img
src="https://orcid.org/sites/default/files/images/orcid_16x16.png"
style="width:1em;margin-right:.5em;"
alt="ORCID iD icon">orcid.org/0000-0002-5589-7754</a>
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<h2>Xingdong Bian</h2>
<hr class="star-primary">
<img class="img-fluid img-centered" src="img/xingdong-bian-web.jpg" alt="">
<p>Research Software Engineer, Earlham Institute</p>
<p style="text-align: left ! important;">Xingdong is a member of the Data Infrastructure
group, he joined the Earlham Institute in
January 2010 and was involved in the development of EI's Laboratory Information
Management System (MISO) and the TGAC Browser. He has worked on solutions for data
visualisation, managing servers, genomic databases and bioinformatics tools.
Xingdong is
now working mainly on the Grassroots project as a research software engineer. He has
a
BSc in Computer Science from the University of Sheffield and a MSc in Software
Engineering from the University of York.</p>
<a href="https://orcid.org/0000-0002-4719-3220" target="orcid.widget"
rel="noopener noreferrer" style="vertical-align:top;"><img
src="https://orcid.org/sites/default/files/images/orcid_16x16.png"
style="width:1em;margin-right:.5em;"
alt="ORCID iD icon">orcid.org/0000-0002-4719-3220</a>
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<h2>Simon Tyrrell</h2>
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<p>Research Software Engineer, Earlham Institute</p>
<p style="text-align: left ! important;">Simon is a research software engineer and a
member
of the Data Infrastructure group,
joining the Earlham Institute in June 2014. He has a PhD in Cheminformatics from the
University of Sheffield. He has worked on a variety of molecular modelling, data
mining
and visualisation projects in different scientific disciplines.
</p>
<a href="https://orcid.org/0000-0002-7789-6875" target="orcid.widget"
rel="noopener noreferrer" style="vertical-align:top;"><img
src="https://orcid.org/sites/default/files/images/orcid_16x16.png"
style="width:1em;margin-right:.5em;"
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<h2>Daniel Olvera</h2>
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<p>Research Software Engineer, Earlham Institute</p>
<p style="text-align: left ! important;">Daniel is a research software engineer and a
member
of the Data Infrastructure group,
joining the Earlham Institute in 2022. He obtained his PhD from the School of
Mathematics at the University of Bristol, working on turbulence and optimization
techniques.
He continued working in fluid mechanics at Coventry University and
later moved to Barcelona as a postdoctoral researcher working at the
Catalan Institute of Nanoscience and Nanotechnology. He is interested in
code development, numerical simulations, optimisation, high performance computing
and data visualisation.
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