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<br>



<p>
Since the emergence of the SARS-COV2 pandemic, many have become familiar with
the use of <b>virus genome data</b> to track the spread and evolution of pathogenic viruses
- e.g. via tools such as <a target="_blank" href="https://nextstrain.org/ncov/gisaid/global""><b>NextStrain</b></a>.
However, it is less widely appreciated that the same kinds of data sets and comparative genomic approaches
can also be used to explore the structural and functional basis of virus adaptations.
</p>

<p>
The
<a target="_blank" href="https://github.com/giffordlabcvr/gluetools"><b>GLUE software framework</b></a>
provides an extensible platform for implementing computational genomic
analysis of viruses in an <b>efficient, standardised and reproducible</b> way.
<b>GLUE projects</b> can not only incorporate all of the data items typically used in
comparative genomic analysis
(e.g. sequences, alignments, genome feature annotations) but can also represent the complex
semantic links between these data items via a <b>relational database</b>.
This 'poises' sequences and associated data for application in computational
analysis, minimising the requirement for labour-intensive pre-processing of datasets.
</p>

<p>
GLUE projects are equally suited for carrying out exploratory work
(e.g. using virus genome data to investigate structural and functional properties of viruses)
as they are for implementing operational procedures (e.g. producing
<a target="_blank" href="http://hcv-glue.cvr.gla.ac.uk/exampleReports/resistanceGeno1.html?hcvGlueVersion=0.1.68""><b>standardised reports</b></a>
in a public or animal health setting).
</p>

<p>
Hosting of GLUE projects in an online version control system (e.g. <b>GitHub</b>) provides
a mechanism for their stable, collaborative development, as shown below.
</p>

<p><img src="./website/assets/images/github-hosting.jpg" alt="GitHub illustration" /></p>





<br>
<h3>
<a id="WhatGlueProject" class="anchor" href="#glueProject" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>What is a GLUE project?</strong>
</h3>
<hr>


<p>
<a target="_blank" href="http://glue-tools.cvr.gla.ac.uk/"><b>GLUE</b></a> is an open, integrated
software toolkit that provides functionality for storage and interpretation of
sequence data.
</p>

<p>
<b>GLUE</b> supports the development of <b>“projects”</b> containing the data items
required for comparative genomic analysis
(e.g. sequences, multiple sequence alignments, genome feature annotations,
and other sequence-associated data).
</p>



<br>
<p><img src="./website/assets/images/glue-framework.png" alt="GLUE web" /></p>
<br>



<p>
Projects are loaded into the <b>GLUE "engine"</b>, creating a relational database
that represents the semantic relationships between data items.
This provides a robust foundation for the implementation of <b>systematic
comparative analyses</b> and the development of <b>sequence-based resources</b>.
</p>


<p>
Projects are loaded into the <b>GLUE "engine"</b>, creating a <b>relational database</b>
that represents the semantic relationships between data items.
This provides a robust foundation for the implementation of <b>systematic
comparative analyses</b> and the development of <b>sequence-based resources</b>.
The database schema can be extended to accommodate the idiosyncrasies of different projects.
GLUE provides a scripting layer (based on JavaScript) for developing custom analysis tools.
</p>


<p>

<ul>

<li>
<a target="_blank" href="http://cov-glue.cvr.gla.ac.uk/"><b>COV-GLUE</b></a>:
A GLUE resource for tracking genetic variation in SARS-COV2.
CoV-GLUE contains a database of amino acid replacements, insertions and
deletions which have been observed in GISAID hCoV-19 sequences sampled from the pandemic
</li>
<br>

<li>
<a target="_blank" href="http://rabv-glue.cvr.gla.ac.uk/"><b>RABV-GLUE</b></a>:
Tailored toward epidemiological tracking of rabies virus (RABV).
Includes a database of RABV sequences and metadata from NCBI, updated daily and arranged into major and minor clades, and
an analysis tool providing genotyping, analysis and visualisation of submitted FASTA sequences.
</li>
<br>

<li>
<a target="_blank" href="http://hcv-glue.cvr.gla.ac.uk/"><b>HCV-GLUE</b></a>:
This GLUE resource aims to support analysis of drug resistance and vaccine
escape in hepatitis C virus (HCV).
A database of HCV sequences and metadata from NCBI, updated daily and arranged
into clades (genotypes, subtypes). As well as pre-built multiple-sequence
alignments of NCBI sequences, it includes an analysis tool providing genotyping,
drug resistance analysis and visualisation of submitted FASTA sequences.
</li>

</ul>


</p>







<br>
<h3>
<a id="WhyGlueProject" class="anchor" href="#glueProject" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>What does building the Hepadnavirus-GLUE project offer?</strong>
</h3>
<hr>



<p>

Hepadnavirus-GLUE offers a number of advantages for performing comparative sequence
analysis of hepadnaviruses:

<ol>

<li> <strong>Reproducibility</strong>.
For many reasons, bioinformatics analyses are notoriously difficult to reproduce.
The GLUE framework supports the implementation of fully reproducible
comparative genomics through the introduction of data standards and the use
of a relational database to capture the semantic links between data items.
</li>
<br>

<li> <strong>Reusable data objects and analysis logic</strong>.
For many - if not most - comparative genomic analyses, data preparation is nine
tenths of the battle. The GLUE framework has been designed to ensure that
work spent preparing high-value data items such as multiple sequence alignments
need only be performed once. Hosting of GLUE projects in an online version control
system such as GitHub allows for collaborative management of important data items
and community testing of hypotheses.
</li>
<br>


<li> <strong>Validation</strong>.
Building GLUE projects entails mapping the semantic links between data items
(e.g. sequences, tabular data, multiple sequence alignments).
This process provides an opportunity
for cross-validation, and thereby enforces a high level of data integrity.
</li>
<br>

<li> <strong>Standardisation of the genomic co-ordinate space</strong>. GLUE
projects allow all sequences to utilise the coordinate space of a chosen
reference sequence. Contingencies associated with insertions and deletions
(indels) are handled in a systematic way.
</li>
<br>

<li> <strong>Predefined, fully annotated reference sequences</strong>:
This project includes fully-annotated reference sequences for major lineages
within the <i>Hepadnaviridae</i> family.
</li>
<br>

<li> <strong>Alignment trees</strong>:
GLUE allows linking of alignments constructed at distinct taxonomic levels
via an
"<a target="_blank" href="./website/html/alignmenttree.html"><b>alignment tree</b></a>"
data structure. In the alignment tree, each alignment
is constrained to a standard reference sequence, thus all multiple sequence
alignments are linked to one another via a standardised coordinate system.
</li>

</ol>

</p>

<br>



<br>

<p>


<b>There are a wide variety of ways in which the Hepadnavirus-GLUE resource can be used</b>:

<ul>

<li> To perform comparative genomic studies across the family <i>Hepadnaviridae</i>,
e.g. as part of an investigation of hepadnavirus diversity.
</li>

<br>

<li> To facilitate in-depth comparative investigations of any virus species or group
within the family <i>Hepadnaviridae</i>.
</li>

<br>

<b>NOTE: For those specifically interested in <b>hepatitis B virus (HBV)</b>, we suggest to investigate
our separate
<a target="_blank" href="https://github.com/giffordlabcvr/HBV-GLUE">HBV-GLUE</a> resource.</b>

<br>
<br>

<li> As a source of systematically organised information about
<a href="./website/html/paleoviruses.html"><b>endogenous viral elements (EVEs) derived from hepadnaviruses</b></a>.
</li>

</ul>

</p>



<br>
<h3>
<a id="installGlueProject" class="anchor" href="#glueProject" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Installing Hepadnaviridae-GLUE</strong>
</h3>
<hr>



<p>

On computers with <a href="http://glue-tools.cvr.gla.ac.uk/#/installation">GLUE installed</a>,
the <b>Hepadnavirus-GLUE</b> project can be instantiated by navigating to the project folder,
initiating GLUE, and issuing the following command in the GLUE shell:

<pre>
<code>Mode path: /
GLUE> run file buildCoreProject.glue</code></pre>

</p>

This will build the Hepadnavirus-GLUE core project by executing the commands in
<a href="https://github.com/giffordlabcvr/Hepadnaviridae-GLUE/blob/master/buildHepadnaviridaeCoreProject.glue"><b>this file</b></a>.

</p>


<p>
The <i>Hepadnavirus-GLUE</i> project can be further extended to incorporate
EVE sequences by executing the commands in
<a href="https://github.com/giffordlabcvr/Hepadnaviridae-GLUE/blob/master/buildHepadnaviridaePaleoProject.glue"><b>this file</b></a>,
as follows.

<pre>
<code>Mode path: /
GLUE> run file buildPaleoProject.glue</code></pre>

</p>

<p>
The <b>paleovirus</b> extension of incorporates a set of endogenous
viral elements (EVEs) recovered from the genomes of metazoan species. Building
the paleovirus extension allows automated alignment and phylogeny reconstruction
for individual eHBV lineages in the project, based on the classifications in
<a target="blank" href="https://github.com/giffordlabcvr/Hepadnaviridae-GLUE/blob/master/tabular/eve/"><b>these files</b></a>.
Individual eHBV sequences have been classified into sets considered likely to
have arisen from the same germline colonisation event. Loci have been named using
a systematic approach (see
<a href="./website/paleoviruses.html"><b>here</b></a> for details).

</p>

<h3>
<a id="license" class="anchor" href="#license" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>License</strong>
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