Skip to content

Commit

Permalink
Built site for gh-pages
Browse files Browse the repository at this point in the history
  • Loading branch information
Quarto GHA Workflow Runner committed Jul 19, 2024
1 parent 461aecf commit fd66cb5
Show file tree
Hide file tree
Showing 6 changed files with 104 additions and 190 deletions.
2 changes: 1 addition & 1 deletion .nojekyll
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
e0e5fa7b
a583d650
94 changes: 18 additions & 76 deletions about.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -192,8 +192,8 @@ <h1 class="title">About</h1>
</header>


<p>Cloud-SPAN trains researchers, and the research software engineers that support them, to run specialised analyses on cloud-based high-performance computing (HPC) infrastructure.</p>
<p>We host live training workshops and have also created educational training materials on topics such as using the command line, genomic analysis and whole metagenome sequencing (WMS) workflows. All of the training materials and live workshops are offered <strong>free of charge</strong>.</p>
<p>Cloud-SPAN is a collaboration between the <a href="https://www.york.ac.uk/">University of York</a> and <a href="https://www.software.ac.uk/">The Software Sustainability Institute</a> funded by the <a href="https://www.ukri.org/news/initiatives-boost-health-and-bioscience-skills-and-industry/">UKRI Innovation Scholars award</a>. Project Reference: <a href="https://gtr.ukri.org/projects?ref=MR%2FV038680%2F1">MR/V038680/1</a>.</p>
<p>We host live training workshops and have also created educational training materials on topics such as using the command line, genomic analysis and whole metagenome sequencing (WMS) workflows. Our goal is to train researchers, and the research software engineers that support them, to run specialised analyses on cloud-based high-performance computing (HPC) infrastructure. All of the training materials and live workshops are offered <strong>free of charge</strong>.</p>
<section id="our-approach" class="level1">
<h1>Our approach</h1>
<ul>
Expand All @@ -208,77 +208,9 @@ <h1>Our approach</h1>
<section id="our-learning-resources" class="level1">
<h1>Our learning resources</h1>
<p><strong>Core skills</strong></p>
<p>Core R and Prenomics were created to introduce the fundamentals of the command line and to help learners gain confidence in their programming skills.</p>
<p><a href="(https://cloud-span.github.io/core-r/02_intro_to_r_and_working_with_data.html#1)">Core R</a> and <a href="https://cloud-span.github.io/prenomics00-intro/">Prenomics</a> were created to introduce the fundamentals of the command line and to help learners gain confidence in their programming skills.</p>
<p><strong>Specialised skills</strong></p>
<p>Learners who were already confident with their command line abilities were encouraged to complete Genomics and Metagenomics. An <a href="https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why">online assessment</a> was developed for learners to self assess their level of knowledge and help them to gauge which course would be most appropriate for them. These modules enhancing specialised skills provide researchers with the advanced knowledge and skills required to generate and analyse ’omics data using Cloud HPC resources.</p>
</section>
<section id="core-skills" class="level1">
<h1>Core Skills</h1>
<section id="prenomics" class="level3">
<h3 class="anchored" data-anchor-id="prenomics">Prenomics</h3>
<p><a href="https://cloud-span.github.io/prenomics00-intro/">Prenomics</a> is an interactive online course on understanding file systems and using the command line which takes place over 2 half days (roughly six hours of content). We developed this course after finding that people taking the Genomics course vary in their experiencing of navigating file systems and the command line (shell).</p>
<p>Topics covered include:</p>
<ul>
<li>file directory structure</li>
<li>logging onto a cloud instance</li>
<li>basic shell commands</li>
<li>using the shell to manipulate and search files</li>
</ul>
<p>NO prior experience is necessary.</p>
</section>
<section id="core-r" class="level2">
<h2 class="anchored" data-anchor-id="core-r">Core R</h2>
<p>This <a href="https://cloud-span.github.io/core-r/02_intro_to_r_and_working_with_data.html#1">short 2 hour course</a> provides a whistle-stop tour of the R programming language and RStudio environment for total beginners. You will learn how to navigate RStudio, use the manual, import data and summarise/visualise it with a plot.</p>
<section id="genomics" class="level3">
<h3 class="anchored" data-anchor-id="genomics">Genomics</h3>
<p><a href="https://cloud-span.github.io/00genomics/">Genomics</a> is a practical, tutor-led course taking place over 4 half days or 2 full days (roughly twelve hours of content). It teaches data management and analytical skills using cloud resources for genomic research.</p>
<p>Topics covered include:</p>
<ul>
<li>project management for cloud genomics</li>
<li>writing shell scripts</li>
<li>assessing read quality</li>
<li>trimming/filtering reads</li>
<li>finding sequence variants.</li>
</ul>
<p>A basic knowledge of the shell is required, which can be obtained by attending/self-studying the Prenomics course.</p>
</section>
</section>
</section>
<section id="specialised-skills" class="level1">
<h1>Specialised Skills</h1>
<section id="metagenomics" class="level2">
<h2 class="anchored" data-anchor-id="metagenomics">Metagenomics</h2>
<p><a href="https://cloud-span.github.io/nerc-metagenomics-v2q/">Metagenomics</a> teaches data analysis for metagenomics projects. It runs asynchronously with a mixture of taught sessions, offline self-study and drop-in sessions.</p>
<p>Topics covered include:</p>
<ul>
<li>an introduction to metagenomics and what it can be used for</li>
<li>performing quality control on long and short reads</li>
<li>improving your assembly with polishing</li>
<li>binning into species/metagenome-assembled genomes (MAGs)</li>
<li>taxonomic assignment and functional annotation</li>
</ul>
<p>No prior knowledge of the shell is required as this course includes two sessions of <a href="#prenomics">Prenomics</a> material.</p>
</section>
<section id="Statistically-Useful-Experimental-Design" class="level2">
<h2 class="anchored" data-anchor-id="Statistically-Useful-Experimental-Design">Statistically Useful Experimental Design</h2>
<p>The workshop was developed to help researchers to:</p>
<ul>
<li>understand the issues underpinning good experimental design</li>
<li>to ensure that reproducible techniques are used to produce data.</li>
</ul>
</section>
<section id="create-aws" class="level2">
<h2 class="anchored" data-anchor-id="create-aws">Create Your Own AWS Instance</h2>
<p>This course shows you how to <a href="https://cloud-span.github.io/create-aws-instance-0-overview/">create and manage an Amazon Web Service instance</a> like the ones used in all our courses, in order to:</p>
<ul>
<li>study course materials further</li>
<li>perform more complex analyses on your own data.</li>
</ul>
</section>
<section id="cloud-admin" class="level2">
<h2 class="anchored" data-anchor-id="cloud-admin">Automated Management of AWS Instances</h2>
<p><a href="https://cloud-span.github.io/cloud-admin-guide-v2q/">Automated Management of AWS Instances</a> is aimed at experienced command line users who have an interest in deploying and managing cloud resources for training purposes.</p>
<p>No prior knowledge of AWS concepts or tools is needed but learners should have significant experience with the Unix terminal and programming with Bash.</p>
<p>Learners who were already confident with their command line abilities were encouraged to complete <a href="https://cloud-span.github.io/00genomics/">Genomics</a> and <a href="https://cloud-span.github.io/nerc-metagenomics-v2q/">Metagenomics</a>. An <a href="https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why">online assessment</a> was developed for learners to self assess their level of knowledge and help them to gauge which course would be most appropriate for them. These modules enhancing specialised skills provide researchers with the advanced knowledge and skills required to generate and analyse ’omics data using Cloud HPC resources. In addtion there is also materials for <a href="https://cloud-span.github.io/cloud-admin-guide-v2q/">Automated Management of AWS Instances</a> which is aimed at experienced command line users who have an interest in deploying and managing cloud resources for training purposes. Statistically Useful Experimental Design {#Statistically-Useful-Experimental-Design} was developed to help researchers to understand the issues underpinning good experimental design and also ensure that reproducible techniques are used to produce data.</p>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
Expand All @@ -293,12 +225,22 @@ <h2 class="anchored" data-anchor-id="cloud-admin">Automated Management of AWS In
</div>
</div>
</section>
</section>
<section id="community" class="level1">
<h1>Community</h1>
<p>We have established a welcoming online community to support learners, including self-paced learners, in the application of training materials to their own research data. Slack Code Retreats Handbook X and LinkedIn Links to Doctoral Training Partnerships</p>
<section id="our-community" class="level1">
<h1>Our Community</h1>
<p>The Cloud-SPAN team are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. We hope to develop a community of practice around our materials. We have a <a href="https://cloud-span.github.io/CloudSPAN-handbook/">Handbook</a> that gives:</p>
<p>⭐ An introduction to the Cloud-SPAN project</p>
<p>🤝 Our Code of Conduct</p>
<p>🎓 More information on our Courses</p>
<p>👪 An open invitation to the Cloud-SPAN Community</p>
<p>📌 Information about the FAIR Principles</p>
<section id="licences" class="level2">
<h2 class="anchored" data-anchor-id="licences">Licences</h2>
<p>This instructional material is made available for reuse and remixing under the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution license</a>.</p>
<p>The Cloud-SPAN Genomics course consists of materials derived from Data Carpentry’s <a href="https://datacarpentry.org/genomics-workshop/">Genomics Workshop</a>. This material is not endorsed by <a href="https://datacarpentry.org">Data Carpentry</a> or <a href="https://carpentries.org/">the Carpentries</a> in general.</p>
<p>Cloud-SPAN is a collaboration between the <a href="https://www.york.ac.uk/">University of York</a> and <a href="https://www.software.ac.uk/">The Software Sustainability Institute</a> funded by the <a href="https://www.ukri.org/news/initiatives-boost-health-and-bioscience-skills-and-industry/">UKRI Innovation Scholars award</a>. Project Reference: <a href="https://gtr.ukri.org/projects?ref=MR%2FV038680%2F1">MR/V038680/1</a>.</p>


</section>
</section>

</main> <!-- /main -->
Expand Down
Loading

0 comments on commit fd66cb5

Please sign in to comment.