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<!DOCTYPE html>
<!--[if lt IE 7 ]>
<html class="ie ie6" lang="en"> <![endif]-->
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<title>COPO - Collaborative Open Plant Omics</title>
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<ul class="nav navbar-nav pull-right">
<li><a href="#about">Project</a>
</li>
<li><a href="#news-sec">News</a>
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<li><a href="#work-sec">People</a>
</li>
<li><a href="#contact-sec">Contact</a>
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<!--Header section -->
<div class="container" id="home">
<div class="row text-center">
<div class="col-md-12 col-md-12 col-sm-12">
<h1>
<img class="header-img" src="assets/img/logo8_white_trans.png">
</h1>
<h2 class="sub-head" id="carousel_text">describe   deposit   discover</h2>
<!--
<div class="head-sub-main">
<p id="carousel_text" class="text-center">Publications, data, images, and other ‘research objects’ can
be submitted through COPO to remote long-term
storage repositories, with a helpful graphical user interface (GUI) relieving much of the
eye-watering
formatting burden required for preparing the information that goes alongside the research data.</p>
</div>
-->
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</div>
<!--End Header section -->
<!--About Section-->
<section class="color-white" id="about">
<!-- <div class="container"> -->
<div class="row">
<div class="col-lg-2 col-md-2 col-sm-2"></div>
<div class="col-lg-8 col-md-8 col-sm-8">
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<div class="col-lg-4 col-md-4 col-sm-12 info-wrap">
<div id="pub-panel" class="info-panel">
<div class="info-panel-header">
<!-- <i class="fa fa-book fa-2x" aria-hidden="true"></i> -->
<span class="icon-text">Publication</span>
</div>
<div id="pub-panel-inner">
COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.
</div>
</div>
</div>
<div class="col-lg-4 col-md-4 col-sm-12 info-wrap">
<div id="cit-panel" class="info-panel">
<div class="info-panel-header">
<!-- <i class="fa fa-retweet fa-2x" aria-hidden="true"></i> -->
<span class="icon-text">Citation</span>
</div>
<div id="cit-panel-inner">
By tracking unique identifiers and DOIs, COPO can provide a way to monitor usage and get credit for your work, such as source code or research data, which still are not typically cited in the majority of scientific papers.
</div>
</div>
</div>
<div class="col-lg-4 col-md-4 col-sm-12 info-wrap">
<div id="auto-panel" class="info-panel">
<div class="info-panel-header">
<!--<i class="fa fa-magic fa-2x" aria-hidden="true"></i>-->
<span class="icon-text">Automation</span>
</div>
<div id="auto-panel-inner">
COPO Wizards allow metadata to be added to your research objects with guided help and natural workflows. COPO can suggest metadata that might be appropriate for your data based on past submissions and similar workflows.
</div>
</div>
</div>
</div>
</div>
<div class="col-lg-2 col-md-2 col-sm-2"></div>
</div>
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</section>
<!--End About Section-->
<section class="color-green" id="news-sec">
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<div class="col-lg-10 col-md-10 col-sm-10">
<div class="news-item">
<!-- CONTENT HERE -->
<h2 class="project-para">COPO 2nd Workshop <span
class="small">13th-14th December</span></h2>
<div class="news-item-text">We are pleased to announce the 2nd COPO Workshop / User group will be
held in mid December. The purpose of this workshop is to demonstrate progress so far, gauge
user opinion as the usability of the current COPO implementation and to discuss features and
functionality the community would like to see implemented in the near future.
<br/><br/>
Please find the <a href="agenda_workshop2.html">agenda</a> for the meeting here.
</div>
</div>
</div>
<div class="col-lg-1 col-md-1 col-sm-1"></div>
</div>
</div>
</section>
<section class="color-white" id="work-sec">
<div class="container">
<div class="row">
<h2>Organisations</h2>
<div class="col-md-3 col-md-3 col-sm-3 organisation">
<div class="o_img">
<img class="org_img" src="assets/img/ei.png"/>
</div>
<div class="o_bio">
<h4>Earlham Institute</h4>
The Data Infrastructure and Algorithms group focuses on research into understanding how best to
manage, represent and analyse
data for open science, as well as exploring new hardware, algorithms and methodologies to develop
tools to push the boundaries of data-driven informatics in the life sciences. The team applies their
research expertise to develop infrastructure platforms for data and software dissemination and
publication,
assembly algorithms for viral and microbial metagenomics, large-scale data visualisation, and best
practice and training in bioinformatics.
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 organisation">
<div class="o_img">
<img class="org_img" src="assets/img/oerc-logo.jpg"/>
</div>
<div class="o_bio">
<h4>Oxford e-Research Centre</h4>
The Oxford team mainly contributes elements of the open source metadata tracking framework
<a href="http://isa-tools.org">ISA Tools</a>, which is supported by an international
community (<a href="http://www.isacommons.org/">ISA Commons</a>). The team develops
the metadata representation, providing the model and configurations that enable standards-compliant
reporting, metadata deposition APIs and services, as well as conversion and validation services.
These functionalities are being developed within and incorporated into the wider ISA-API project
<a href="https://github.com/ISA-tools/isa-api">https://github.com/ISA-tools/isa-api</a>.
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 organisation">
<div class="o_img">
<img class="org_img" src="assets/img/york.png"/>
</div>
<div class="o_bio">
<h4>University of York</h4>
The York team deals with community liaison and provides a connection to key user groups of the COPO platform, assists with user testing and usability via the <a href="http://www.garnetcommunity.org.uk/">GARNet Network</a> and the <a href="http://globalplantcouncil.org/">Global Plant Council</a>.
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 organisation">
<div class="o_img">
<img class="org_img" src="assets/img/ebi.png"/>
</div>
<div class="o_bio">
<h4>EMBL-EBI</h4>
The role of EMBL-EBI in COPO is to support data from COPO to the public archives, and to
disseminate integrated data sets prepared through the COPO infrastructure through Ensembl Plants and
other public resources.
</div>
</div>
</div>
<div class="row">
<h2>People</h2>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/rob.jpg"/>
<div class="p_bio">
<h4>Robert Davey</h4>
<p class="p_position">Earlham Institute</p>
Rob leads the <a href="http://www.earlham.ac.uk/davey-group">Data Infrastructure and Algorithms
group</a> at the Earlham Institute and is the PI for the COPO 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">National Collection of Yeast Cultures</a>. Rob leads a number of
large computing infrastructure development and deployment projects, is a certified <a
href="http://software-carpentry.org">Software Carpentry</a> instructor, an editorial board
member for Nature Scientific Data, and a <a href="https://www.software.ac.uk">Software
Sustainability Institute</a> Fellow.
<p class="p_orcid"><img src="assets/img/orcid.png"><a href="http://orcid.org/0000-0002-5589-7754">orcid.org/0000-0002-5589-7754</a>
</p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/toni.jpg"/>
<div class="p_bio">
<h4>Toni Etuk</h4>
<p class="p_position">Earlham Institute</p>
Toni is a Research Software Engineer at the Earlham Institute. He has a PhD in
Computer Science from the University of Aberdeen. His area of interest was multi-agent systems, with
a focus on computational models of Trust and Reputation. He continues to explore these techniques,
and a number of techniques from Machine Learning and statistics, in contexts of Open Science and
Bioinformatics.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0001-8320-660X">orcid.org/0000-0001-8320-660X</a></p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/felix.jpg"/>
<div class="p_bio">
<h4>Felix Shaw</h4>
<p class="p_position">Earlham Institute</p>
Felix is a Research Software Engineer working on the COPO platform; a tool for creating,
depositing and searching for bundles of research objects. His PhD is in Computer Science studying
facial
animation, computer graphics, signal processing and machine learning. His current interests are in
the fields of data science, open source and how to apply machine learning techniques in these areas
to improve the tools available to researchers.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0001-9649-5906">orcid.org/0000-0001-9649-5906</a></p>
</div>
</div>
</div>
<div class="row">
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/Susanna.jpg"/>
<div class="p_bio">
<h4>Susanna Sansone</h4>
<p class="p_position">Oxford e-Research Centre</p>
Susanna is Associate Director at the University of Oxford e-Research Centre. Her interests are in
the areas of knowledge and information management, and interoperability of
applications. Since 2000, her projects have focused on improving the collection, curation and
representation of multi-dimensional life, environmental and biomedical sciences data, to support
data reproducibility and the evolution of scholarly publishing.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0001-5306-5690">orcid.org/0000-0001-5306-5690</a></p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/david.png"/>
<div class="p_bio">
<h4>David Johnson</h4>
<p class="p_position">Oxford e-Research Centre</p>
David Johnson is a Senior Research Associate / Research Software Engineer in the Oxford e-Research
Centre. His work concerns the development of data infrastructure to support data-intensive research
in the life, natural, and biomedical sciences. In the COPO project, David is part of the ISA Team
developing the underlying 'omics standards framework that COPO uses.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0002-2323-6847">orcid.org/0000-0002-2323-6847</a></p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/Alejandra.jpg"/>
<div class="p_bio">
<h4>Alejandra Gonzalez Beltran</h4>
<p class="p_position">Oxford e-Research Centre</p>
Alejandra is a Research Lecturer at the University of Oxford e-Research Centre, where she focuses on
developing methodologies and software tools for data science, including
knowledge management and data analysis. She mainly deals with heterogeneous biological and
biomedical data, within the context of the ISA infrastructure. She brings these skills along with a
wealth of software engineering experience to the COPO project.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0003-3499-8262">orcid.org/0000-0003-3499-8262</a></p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/Philippe.jpg"/>
<div class="p_bio">
<h4>Philippe Rocca-Serra</h4>
<p class="p_position">Oxford e-Research Centre</p>
Phillipe has been an active member of several standardisation efforts aimed at promoting the vision
for open data and open science. As part of several EU projects in toxicogenomics and nutrigenomics,
he coordinated the development of the ISA project, which now continues at the University of Oxford
e-Research Centre. As part of the COPO project he provides technical expertise with regards to
metadata collection and experimental design.
<p class="p_orcid"><img src="assets/img/orcid.png"><a
href="http://orcid.org/0000-0001-9853-5668">orcid.org/0000-0001-9853-5668</a></p>
</div>
</div>
</div>
<div class="row">
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/katherine.png"/>
<div class="p_bio">
<h4>Katherine Denby</h4>
<p class="p_position">University of York</p>
Katherine is a Professor in the Department of Biology at the University of York. She uses experimental and computational/mathematical tools to elucidate gene regulatory networks underlying plant responses to the environment and re-engineer these networks to enhance stress tolerance, particularly disease resistance. She has expertise in large scale data analysis and integration, and interest in making such data easily discoverable and accessible for others.
<p class="p_orcid"><img src="assets/img/orcid.png"><a href="http://orcid.org/0000-0002-7857-6814">orcid.org/0000-0002-7857-6814</a></p>
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/paul.png"/>
<div class="p_bio">
<h4>Paul Kersey</h4>
<p class="p_position">EMBL EBI</p>
Paul works at EMBL-EBI where he has been in charge Ensembl covering non-vertebrate species,
including human pathogens, disease vectors, crop plants,
and model species.
The role of EMBL-EBI in COPO is to support data from through COPO to the public archives, and to
disseminate integrated data sets prepared through the COPO infrastructure through Ensembl Plants and
other public resources.
</div>
</div>
<div class="col-md-3 col-md-3 col-sm-3 person">
<img src="assets/img/ruth.jpg"/>
<div class="p_bio">
<h4>Ruth Bastow</h4>
<p class="p_position">Global Plant Council</p>
Ruth manages the day-to-day operations of the Global Plant Council which is a coalition of 28 learned plant, crop and agricultural science societies across the globe and represents ~55,000 researchers. Ruth has a proven track record in national and international project management for a number of different research projects and networks. In additional to her current administrative, policy, and advocacy work in the plant sciences she also has a background in plant science data standards, ontologies, and data sharing.
</div>
</div>
</div>
</div>
</section>
<!-- Contact Section -->
<section class="color-light " id="contact-sec">
<div class="container">
<div class="row text-center">
<div class="col-md-8 col-md-offset-2 ">
<h2>Contact Us</h2>
<h4>
<strong>
If you have queries, support issues or would like to contribute to COPO, we would love to hear
from you.
</strong>
</h4>
</div>
</div>
<div class="row">
<div class="col-md-6 contact-cls">
<h3>Physical Locations</h3>
<div>
<h4><i class="fa fa-home"></i>  Earlham Institute <span class="small">Norwich Research Park, Norwich, NR4 7UH</span>
</h4>
<h4><i class="fa fa-home"></i>  Oxford e-Research Centre <span class="small">7 Keble Road, Oxford, OX1 3QG</span>
</h4>
<h4><i class="fa fa-home"></i>  EMBL/EBI <span class="small">Wellcome Genome Campus, Hinxton, CB10 1SD</span>
</h4>
<h4><i class="fa fa-home"></i>  University of Warwick <span
class="small">Coventry, CV4 7AL</span></h4>
</div>
</div>
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<form id="email_form">
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<div class="col-md-6 col-sm-6">
<div class="form-group">
<input type="text" class="form-control" required="required" placeholder="Name">
</div>
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<div class="form-group">
<input type="text" class="form-control" required="required" placeholder="Email address">
</div>
</div>
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<div class="col-md-12 col-sm-12">
<div class="form-group">
<textarea name="message" id="message" required="required" class="form-control" rows="3"
placeholder="Message"></textarea>
</div>
<div class="form-group">
<button id="email_submit" type="submit" class="btn btn-default">Submit Request</button>
</div>
</div>
</div>
</form>
<br/>
<div id="social-icon">
</div>
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</div>
</div>
</section>
<!--End Contact Section -->
<div class="for-full-back " id="footer">
<span class="pull-left"><a href="https://www.jetbrains.com/pycharm/"><img style="margin-top: -10px" height="40px" src="assets/img/icon_PyCharm.png">  COPO is written using PyCharm. Its awesome!</a></span>
<a href="https://github.com/collaborative-open-plant-omics">https://github.com/collaborative-open-plant-omics</a>
</div>
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