Add 2 new blog posts

also rename blog folders with publication date

blogs.qmd

@@ -4,7 +4,7 @@ listing:
   contents: blogs
   type: grid
   sort: "date desc"
-  categories: false
+  categories: true
 page-layout: full
 title-block-banner: true
 ---

blogs/05-22-22/index.qmd

@@ -0,0 +1,41 @@
+---
+title: "Genomics Self-Study now LIVE! 🧬"
+date: 05-22-22
+author: Evelyn Greeves
+image: stock_dna.jpg
+categories:
+  - Genomics
+  - Announcements
+---
+
+**We are pleased to announce that the registration for Genomics self-study is now live!** 
+
+Here at Cloud-SPAN we recognise that all learners are individuals with specific needs and different levels of ability. This is why we have developed a Genomics 'self-study' option, where you can create your own schedule and learn at your own pace. These modules teach data management and analytical skills for genomic research. 
+
+Here's how to get involved:
+
+### Step 1 - [Register!](https://forms.gle/pgiBx3EbRdB9j6XX9)📝
+
+The educational materials are available free of charge, however we ask that you complete the registration form so we are able to send you updates and useful information. 
+
+### Step 2 - [Create your own instance](https://cloud-span.github.io/create-aws-instance-0-overview/)⛅
+
+Start with the 'Create your own instance' module, where you receive a step by step guide to creating your own Amazon Web Services instance. You will go on to use this instance to complete the subsequent Prenomics and Genomics modules.  
+
+### Step 3 - [Prenomics](https://cloud-span.github.io/prenomics00-intro/) 💻
+
+If you are new to the realm of navigating file systems and using the command line we recommend that you complete the Prenomics module. We have designed this module to allow more time for those with less experience to cover some foundation concepts. If you aren't sure how to gauge your skills take the [self-assessment quiz](https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why) to help you decide. 
+
+### **Step 4 - [Genomics](https://cloud-span.github.io/00genomics/)🧬**
+
+ The Genomics module allows you to move on to the more fun stuff as you develop your skills in managing data. You will tackle tasks such as assessing read quality, trimming and filtering, and variant calling. 
+
+### Step 5 - Community 🤸‍♂️
+
+After completing the modules we hope that you will be able to attend one of our regular [code retreats](https://cloud-span.york.ac.uk/community#h.ma5203jptwz0), where our course instructors will be on-hand to help solve any issues you encounter while applying your new skills to your own datasets. We also strongly encourage you to take advantage of our welcoming Cloud-SPAN community, so don't be afraid to lean on your peers for help or discussions on our [forum](https://cloudspan.peerboard.com/). 
+
+### Need support?
+
+*Join the Cloud-SPAN Slack workspace (you will receive a link upon registering), post on the [forum](https://cloudspan.peerboard.com/) or follow us on [social media](https://twitter.com/SpanCloud). All three are good options for you to continue on your mission to master the art of genomics!*
+
+*View the [website](https://cloud-span.york.ac.uk/home) for further information or drop us an email at cloud-span-project\@york.ac.uk if you have any questions.*

blogs/05-31-22/index.qmd

@@ -0,0 +1,49 @@
+---
+title: "What is FAIR data?"
+date: 05-31-22
+author: Evelyn Greeves
+categories:
+  - Open science
+---
+
+At Cloud-SPAN we care deeply about making science as open as possible. A lot of this comes down to project management and data organisation - which we teach as part of our Genomics course. Today we want to introduce you to the FAIR data principles, which are a framework for thinking about how to ensure the scientific community gets the most out of the data we produce. In this case, this means making it easier for people to find and reuse our hard-earned data!
+
+The FAIR framework aims to encourage data reuse by both humans and computers by improving the findability, accessibility, interoperability and reusability of data and other resources. So what are the steps involved in FAIR-ifying data?
+
+<img src="FAIR acronym graphic with attr.png" alt="A graphic showing the 4 FAIR Principles: Findable (illustrated with a magnifying glass), Accessible (illustrated with an open lock), Interoperable (illustrated with interlocking gears) and Reusable (illustrated with a green recycling symbol)" width="600">
+
+### F is for Findable
+
+Before data can be reused, we need to make sure it can be found. One way to do this is by tagging it with **metadata** (information about the data), such as what type of data it is, who collected it, the conditions used, and so on. This allows it to be indexed in a **searchable registry** so more people will see it. Metadata is important for both helping people find your data and for understanding the context they were generated in.
+
+Another key way to make sure data is findable is by assigning it a **persistent identifier**. This is a long-lasting digital reference which ensures a resource can always be found, no matter where it\'s stored. **DOIs** (digital object identifiers) are one type of persistent identifier that you have probably heard of before - they can be applied to things like journal articles, data sets and other publications.
+
+### A is for Accessible
+
+Once we\'ve made sure people can find our data, we need to make sure they can access it if they have permission. This means making it retrievable using some kind of **standardised protocol**, without any need for specialised or proprietary tools. We also need to tell people how they can get access, so we should include this as one of our metadata fields.
+
+A common misconception is that all FAIR data is \'open\' or \'free\'. Heavily protected or private data can still be FAIR as long as it is clear under which conditions the data is accessible.
+
+### I is for Interoperable
+
+So now we\'ve made it possible for someone to find and access our data. How can we make sure they can actually use it? There are two aspects to interoperability. The first is using **standardised and open formats** so that data can be exchanged and used across multiple different applications and systems. This means avoiding proprietary formats and conforming with **field-specific standards** about what format data should come in.
+
+The second relates to how computers understand our data in comparison with other data. This is possible using a **\'controlled vocabulary\'** or **\'ontology\'** which ensures that everyone is using the same words for the same thing. Again, we should try and conform with field-specific standards around ontologies.
+
+### R is for Reusable
+
+This final principle emphasises the idea that by following the previous three principles- findable, accessible, interoperable- we should be aiming to make our data as reusable as possible. This means using accurate and richly described metadata that gives a full overview of our experimental process and data analysis workflow.
+
+We should also make it clear what rights the discoverer has when reusing our data. This is achieved by applying a **licence**, and clearly specifying this in the metadata. For example, a **Creative Commons Attribution 4.0 International** licence (or CC-BY for short) lets anyone reuse, remix and adapt material as long as credit is given to the original creator. 
+
+### **Summary**
+
+The FAIR framework guides us through ensuring that our data is easy to find, easy to understand and easy to reuse. This ensures that our data is used to the fullest extent possible.
+
+The FAIR principles apply to digital objects beyond just data. At Cloud-SPAN we are working hard to make sure our learning resources are as FAIR as possible. Find out what we\'re doing to achieve this by [visiting our handbook](https://cloud-span.github.io/CloudSPAN-handbook/fair-principles.html#what-is-fair-data), or look out for our next blog post!
+
+**Further reading:**
+
+-   [The 10 FAIR Principles](https://www.go-fair.org/fair-principles/)
+
+-   [Paper in Nature: The FAIR Guiding Principles for scientific data management and stewardship](https://www.nature.com/articles/sdata201618)

blogs/Course Update/index.qmd → blogs/12-14-21/index.qmd

@@ -1,7 +1,10 @@
 ---
 title: "Course Update"
-date: 14-12-21
+date: 12-14-21
 author: Evelyn Greeves
+categories:
+ - Genomics
+ - Behind-the-scenes
 ---
 
 Well, it's been a couple of weeks since we ran our first course and we've certainly learned a lot from it! Most of the problems we stumbled into were minor teething issues, but we're also going to be making some fairly major changes based on what we learned. Here's a bit of an update:
@@ -14,7 +17,7 @@ As you can see in the graph below, on average our participants felt that their l
 
 In particular, participants ended the course feeling really comfortable with using the command line to navigate file directories, create and modify files and search for keywords.
 
-<img src="dumbbell plot g_11_21.png" alt="A dumbbell plot with each topic covered in the course on its own line. The graph indicates the rating given before the course was taken and the score after, with a line joining the two. For all topics the score increases, usually by two or so points." width="800" height="auto">
+<img src="dumbbell plot g_11_21.png" alt="A dumbbell plot with each topic covered in the course on its own line. The graph indicates the rating given before the course was taken and the score after, with a line joining the two. For all topics the score increases, usually by two or so points." width="800" height="auto"/>
 
 ### The BIG Problem: Time flies
 

docs/blogs.html

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@@ -143,7 +143,7 @@
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@@ -160,9 +160,11 @@ <h1 class="title">Blogs</h1>
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+<p class="card-img-top"><img src="blogs\05-31-22\FAIR acronym graphic with attr.png" alt="A graphic showing the 4 FAIR Principles: Findable (illustrated with a magnifying glass), Accessible (illustrated with an open lock), Interoperable (illustrated with interlocking gears) and Reusable (illustrated with a green recycling symbol)" style="height: 150px;"  class="thumbnail-image card-img"/></p>
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-Well, it’s been a couple of weeks since we ran our first course and we’ve certainly learned a lot from it!…
+At Cloud-SPAN we care deeply about making science as open as possible. A lot of this comes down to project management and data organisation - which we teach as part of our…
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 Evelyn Greeves
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+Genomics Self-Study now LIVE! 🧬
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+<strong>We are pleased to announce that the registration for Genomics self-study is now live!</strong>&nbsp;
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+Evelyn Greeves
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+Evelyn Greeves
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