- 
+
+
-Software installation for data analysis is complex and involves multiple dependencies.
+
Software installation for data analysis is complex and involves multiple dependencies.
- 
+
+
-HPC architectures vary between institutions and accessibility is a lottery.
+
HPC architectures vary between institutions and accessibility is a lottery.
- 
+
+
-Metagenomic analyses involve large datasets and take a long time to run.
+
Metagenomic analyses involve large datasets and take a long time to run.
- 
+
@@ -170,15 +170,15 @@
+
-Big data ’omics analyses using HPC are not core skills for researchers and have a steep learning curve.
+
Big data ’omics analyses using HPC are not core skills for researchers and have a steep learning curve.
- 
+
+
-We use cloud-based containerised instances with pre-installed software which are scalable and easy to access.
+
We use cloud-based containerised instances with pre-installed software which are scalable and easy to access.
- 
+
+
-We deliver high quality training with a low barrier to participation - absolutely zero previous experience needed!
+
We deliver high quality training with a low barrier to participation - absolutely zero previous experience needed!
- 
+
+
-We offer training in both self-study and workshop formats, with a mix of online and in-person teaching
+
We offer training in both self-study and workshop formats, with a mix of online and in-person teaching
- 
+
+
-We are building a community of practice: a community of bioinformaticians who can support one another.
+
We are building a community of practice: a community of bioinformaticians who can support one another.
- 
+
-
+
+
-We are following open science principles and making our resources FAIR (findable, accessible, interoperable, reusable).
+
We are following open science principles and making our resources FAIR (findable, accessible, interoperable, reusable).
diff --git a/docs/search.json b/docs/search.json
index f5fb3d7..b29be47 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -95,21 +95,14 @@
"href": "upcoming/Core R/index.html",
"title": "Core R",
"section": "",
- "text": "Info about Core R Hello"
+ "text": "Info about Core R\nThis online two-hour workshop is an introduction to R for complete beginners. It teaches you how to find your way round RStudio, use the basic data types and structures in R and how to organise your work with scripts and projects. It also teaches you how to import data, summarise it and create and format a graph. The workshop assumes no prior experience of coding.\n\nLearning outcomes\nBy the end of the course you will be able to;\n\nfind your way around RStudio\nuse the basic data types and structures in R\norganise your work with scripts and projects\nimport data, summarise it and create and format a graph\nThe workshop assumes no prior experience of coding.\n\n\n\nRegistration\nRegistration for this course is now closed.\nThere are 30 places available for this online course. Priority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.\nApplication deadline: 12pm Monday 5th June. Applicants will be notified by Tuesday 6th June if they have been allocated a place. Scholarships and funding for headsets and monitors will be available. Scholarships and additional support\nWe recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of workshop to those participants who attend the session.\nWe offer Scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. To apply for a scholarship please complete the relevant questions in the registration form before the deadline. Submissions after this date will not be considered. All applicants will be notified of the results 2-3 days after the submission deadline."
},
{
"objectID": "upcoming/NERC Metagenomics/index.html",
"href": "upcoming/NERC Metagenomics/index.html",
"title": "NERC Metagenomics",
"section": "",
- "text": "Info about NERC Metagenomics\nMetagenomics explores all the genetic material in an environmental sample. It can be used to characterise the taxonomic characteristics of microbial communities.\nThis online module will be delivered over a three-week period from Monday 6th to Friday 24th November 2023.\nMetagenomics analyses involve a lot of data and can take hours to days to complete! But don’t worry! The format of the workshop takes account of this. For longer analyses there will be scheduled online zoom sessions to cover concepts and get started followed by offline time for the analysis run and for you to complete some exercises. These will be supported by online drop-ins and a Slack channel for trouble-shooting.\n\nTarget audience\nUK based Environmental Science researchers at any career stage or anyone with an interest in Metagenomics. We assume no prior experience of the command line or high performance computing. Due to our funding, we prioritise places to researchers within the NERC remit.\nCheck out testimonials from previous attendees!\n\n“This course was fantastic in both helping me to understand the concepts behind metagenomic polishing/assembly processes and in actually learning how to do it ourselves. I have learnt a lot that I can confidently go and apply to my own research.”\n\n\n“Really recommend this course! The content was great, covering command line fundamentals and the whole metagenomics workflow in a way that was really easy to understand. The team were super engaged and helpful throughout!”\n\n\n“Really pleased with how the course was ran. The instructors were clear and patient, and the online course materials were thorough. I really enjoyed the taxonomic analysis as it brought everything we learned together. This course is super applicable for when I collect and analyse my data further into my PhD project. :)”\n\n\n\nRegistration\nThere are 30 places available for this online workshop, please register using the online form. Priority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.\nApplication deadline: 12pm Wednesday 18th October. Applicants will be notified by Monday 23rd October if they have been allocated a place. Scholarships and funding for headsets and monitors will be available.\n\n\nProgramme\nWe start by teaching the essential tools used in High Performance computing such as file systems and the command-line to connect to and use cloud computing for file navigation and script writing. We then introduce metagenomics and building a metagenomic assembly. In the second week, you will learn how to improve your assembly by ‘polishing’, separate your assembled metagenome into individual genomes (MAGS) and conduct taxonomic assignment and analysis. But if you can’t get something to work, we have a Slack channel and a weekly drop-in to help.\nWin £25 in Amazon vouchers for showing commitment to your learning!\nAt Cloud-SPAN we know it’s difficult to find time to train so we’ve come up with a little incentive for learners signed up for the online course. For the Metagenomics course there will be a prize draw and two people will win a £25 Amazon voucher! All you have to do to enter the prize draw is go through the exercises - we will use your command history to verify your efforts. It doesn’t matter if you make mistakes or can’t get something to work, it is your commitment that matters!\nHappy learning!\nWeek 1\n\n\n\n\n\n\n\n\nMonday 6 November\n14:00 - 16:00\nCommand-line programming: file systems, files and directories\n\n\nTuesday 7 November\n14:00 - 16:00\nCommand-line programming: using the command line\n\n\nThursday 9 November\n10:00 - 13:30\nAn introduction to metagenomics, quality control and assembly.\n\n\n\n\nOffline time for assembly to complete.\n\n\n\nWeek 2\n\n\n\n\n\n\n\n\nMonday 13 November\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\nWednesday 15 November\n10:00 - 11:30\nPolishing your metagenome assembly.\n\n\n\n\nOffline time for the polishing to complete\n\n\nFriday 17 November\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\n\nWeek 3\n\n\n\n\n\n\n\n\nTuesday 21 November\n10:00 - 11:30\nBinning a metagenome assembly into individual genomes (MAGS)\n\n\n\n\nOffline time for the binning to complete\n\n\nTuesday 21 November\n10:00 - 11:00\nOnline troubleshooting drop-in session (optional)\n\n\nFriday 24 November\n13:00 - 16:00\nTaxonomic Assignment and Analysis\n\n\n\nIf you are unable to attend an online session, recordings will be distributed. You will have access to your instance until Friday 1 December (one week after the course is completed) to give you time to consolidate your learning. Usage of the instances will be monitored; instances which are inactive will be closed down as a daily charge is incurred.\nWe recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.\n\n\nPre-requisites\nYou will need familiarity with biological concepts, including the concept of microbiome. We assume no prior experience of the command line or high performance computing. Windows users will need to install GitBash.\nYou don’t need to worry about installing metagenomics software or putting the data on your own computer! You will have access to an Amazon Web Services instance with all the data and software and will only need to log in to it.\n\n\nLearning outcomes\nFollowing completion of this course, learners will be able to:\n\nexplain the hierarchical structure of a file system and describe the files and file structure used in the course\nexplain what is meant by a working directory, a path and a relative path and write down paths that they will need for the course\nstart a Terminal (Mac) or Git Bash Terminal (Windows)\nnavigate a file system using the command line\nlog in to and exit their AWS instance (the cloud)\nuse common commands such as ls, pwd and cd, on the command line\nknow the difference between genomics and metagenomics\ndescribe the steps in a metagenomic workflow\nperform quality control on reads and assemble them into a metagenome\nperform polishing to improve an assembly\nuse binning to separate the metagenome into different species or MAGs (Metagenome-Assembled Genomes)\nuse Kraken 2 to assign taxonomy to reads and contigs and phyloseq in R to analyse taxonomic diversity\n\n\n\nScholarships and additional support\nWe recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. Please complete the relevant section in the application form before 12pm on Wednesday 18th October."
- },
- {
- "objectID": "upcoming/NERC Metagenomics/index.html#target-audience",
- "href": "upcoming/NERC Metagenomics/index.html#target-audience",
- "title": "NERC Metagenomics",
- "section": "Target audience",
- "text": "Target audience\nUK based Environmental Science researchers at any career stage or anyone with an interest in Metagenomics. We assume no prior experience of the command line or high performance computing. Due to our funding, we prioritise places to researchers within the NERC remit.\nCheck out testimonials from previous attendees!\n\n“This course was fantastic in both helping me to understand the concepts behind metagenomic polishing/assembly processes and in actually learning how to do it ourselves. I have learnt a lot that I can confidently go and apply to my own research.”\n\n\n“Really recommend this course! The content was great, covering command line fundamentals and the whole metagenomics workflow in a way that was really easy to understand. The team were super engaged and helpful throughout!”\n\n\n“Really pleased with how the course was ran. The instructors were clear and patient, and the online course materials were thorough. I really enjoyed the taxonomic analysis as it brought everything we learned together. This course is super applicable for when I collect and analyse my data further into my PhD project. :)”"
+ "text": "Metagenomics explores all the genetic material in an environmental sample. It can be used to characterise the taxonomic characteristics of microbial communities.\nThis online module will be delivered over a three-week period from Monday 6th to Friday 24th November 2023.\nMetagenomics analyses involve a lot of data and can take hours to days to complete! But don’t worry! The format of the workshop takes account of this. For longer analyses there will be scheduled online zoom sessions to cover concepts and get started followed by offline time for the analysis run and for you to complete some exercises. These will be supported by online drop-ins and a Slack channel for trouble-shooting.\n\nTarget audience\nUK based Environmental Science researchers at any career stage or anyone with an interest in Metagenomics. We assume no prior experience of the command line or high performance computing. Due to our funding, we prioritise places to researchers within the NERC remit.\nCheck out testimonials from previous attendees!\n\n“This course was fantastic in both helping me to understand the concepts behind metagenomic polishing/assembly processes and in actually learning how to do it ourselves. I have learnt a lot that I can confidently go and apply to my own research.”\n\n\n“Really recommend this course! The content was great, covering command line fundamentals and the whole metagenomics workflow in a way that was really easy to understand. The team were super engaged and helpful throughout!”\n\n\n“Really pleased with how the course was ran. The instructors were clear and patient, and the online course materials were thorough. I really enjoyed the taxonomic analysis as it brought everything we learned together. This course is super applicable for when I collect and analyse my data further into my PhD project. :)”\n\n\n\nRegistration\nThere are 30 places available for this online workshop, please register using the online form. Priority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.\nApplication deadline: 12pm Wednesday 18th October. Applicants will be notified by Monday 23rd October if they have been allocated a place. Scholarships and funding for headsets and monitors will be available.\n\n\nProgramme\nWe start by teaching the essential tools used in High Performance computing such as file systems and the command-line to connect to and use cloud computing for file navigation and script writing. We then introduce metagenomics and building a metagenomic assembly. In the second week, you will learn how to improve your assembly by ‘polishing’, separate your assembled metagenome into individual genomes (MAGS) and conduct taxonomic assignment and analysis. But if you can’t get something to work, we have a Slack channel and a weekly drop-in to help.\nWin £25 in Amazon vouchers for showing commitment to your learning!\nAt Cloud-SPAN we know it’s difficult to find time to train so we’ve come up with a little incentive for learners signed up for the online course. For the Metagenomics course there will be a prize draw and two people will win a £25 Amazon voucher! All you have to do to enter the prize draw is go through the exercises - we will use your command history to verify your efforts. It doesn’t matter if you make mistakes or can’t get something to work, it is your commitment that matters!\nHappy learning!\nWeek 1\n\n\n\n\n\n\n\n\nMonday 6 November\n14:00 - 16:00\nCommand-line programming: file systems, files and directories\n\n\nTuesday 7 November\n14:00 - 16:00\nCommand-line programming: using the command line\n\n\nThursday 9 November\n10:00 - 13:30\nAn introduction to metagenomics, quality control and assembly.\n\n\n\n\nOffline time for assembly to complete.\n\n\n\nWeek 2\n\n\n\n\n\n\n\n\nMonday 13 November\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\nWednesday 15 November\n10:00 - 11:30\nPolishing your metagenome assembly.\n\n\n\n\nOffline time for the polishing to complete\n\n\nFriday 17 November\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\n\nWeek 3\n\n\n\n\n\n\n\n\nTuesday 21 November\n10:00 - 11:30\nBinning a metagenome assembly into individual genomes (MAGS)\n\n\n\n\nOffline time for the binning to complete\n\n\nTuesday 21 November\n10:00 - 11:00\nOnline troubleshooting drop-in session (optional)\n\n\nFriday 24 November\n13:00 - 16:00\nTaxonomic Assignment and Analysis\n\n\n\nIf you are unable to attend an online session, recordings will be distributed. You will have access to your instance until Friday 1 December (one week after the course is completed) to give you time to consolidate your learning. Usage of the instances will be monitored; instances which are inactive will be closed down as a daily charge is incurred.\nWe recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.\n\n\nPre-requisites\nYou will need familiarity with biological concepts, including the concept of microbiome. We assume no prior experience of the command line or high performance computing. Windows users will need to install GitBash.\nYou don’t need to worry about installing metagenomics software or putting the data on your own computer! You will have access to an Amazon Web Services instance with all the data and software and will only need to log in to it.\n\n\nLearning outcomes\nFollowing completion of this course, learners will be able to:\n\nexplain the hierarchical structure of a file system and describe the files and file structure used in the course\nexplain what is meant by a working directory, a path and a relative path and write down paths that they will need for the course\nstart a Terminal (Mac) or Git Bash Terminal (Windows)\nnavigate a file system using the command line\nlog in to and exit their AWS instance (the cloud)\nuse common commands such as ls, pwd and cd, on the command line\nknow the difference between genomics and metagenomics\ndescribe the steps in a metagenomic workflow\nperform quality control on reads and assemble them into a metagenome\nperform polishing to improve an assembly\nuse binning to separate the metagenome into different species or MAGs (Metagenome-Assembled Genomes)\nuse Kraken 2 to assign taxonomy to reads and contigs and phyloseq in R to analyse taxonomic diversity\n\n\n\nScholarships and additional support\nWe recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of course to those participants who regularly attended the online sessions.\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. Please complete the relevant section in the application form before 12pm on Wednesday 18th October."
},
{
"objectID": "upcoming_courses.html",
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index adacf5f..dc89f1a 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -2,70 +2,70 @@
https://cloud-span.github.io/cloud-span-quarto-site/about.html
- 2023-09-20T13:22:49.335Z
+ 2023-09-20T15:03:02.104Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs/05-22-22/index.html
- 2023-09-20T13:14:58.829Z
+ 2023-09-20T15:03:03.250Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs/05-31-22/index.html
- 2023-09-20T13:15:01.547Z
+ 2023-09-20T15:03:04.244Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs/12-14-21/index.html
- 2023-09-20T13:15:03.857Z
+ 2023-09-20T15:03:05.515Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs/blog post 4/index.html
- 2023-09-20T13:15:05.904Z
+ 2023-09-20T15:03:07.252Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs/blog post 5/index.html
- 2023-09-20T13:15:07.953Z
+ 2023-09-20T15:03:09.162Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs.html
- 2023-09-20T13:29:14.054Z
+ 2023-09-20T15:03:11.889Z
https://cloud-span.github.io/cloud-span-quarto-site/index.html
- 2023-09-20T13:32:42.258Z
+ 2023-09-20T15:03:14.048Z
https://cloud-span.github.io/cloud-span-quarto-site/self_study/Create Your Own AWS Instance/index.html
- 2023-09-20T13:23:06.658Z
+ 2023-09-20T15:03:15.714Z
https://cloud-span.github.io/cloud-span-quarto-site/self_study/Genomics/index.html
- 2023-09-20T13:15:17.159Z
+ 2023-09-20T15:03:17.165Z
https://cloud-span.github.io/cloud-span-quarto-site/self_study/Metagenomics for Microbiologists/index.html
- 2023-09-20T13:15:19.365Z
+ 2023-09-20T15:03:18.545Z
https://cloud-span.github.io/cloud-span-quarto-site/self_study/Prenomics/index.html
- 2023-09-20T13:15:21.291Z
+ 2023-09-20T15:03:20.160Z
https://cloud-span.github.io/cloud-span-quarto-site/self_study_courses.html
- 2023-09-20T13:23:00.650Z
+ 2023-09-20T15:03:22.023Z
https://cloud-span.github.io/cloud-span-quarto-site/upcoming/Code Retreat/index.html
- 2023-09-20T13:15:25.721Z
+ 2023-09-20T15:03:23.704Z
https://cloud-span.github.io/cloud-span-quarto-site/upcoming/Core R/index.html
- 2023-09-20T13:15:27.509Z
+ 2023-09-20T15:03:25.283Z
https://cloud-span.github.io/cloud-span-quarto-site/upcoming/NERC Metagenomics/index.html
- 2023-09-20T13:27:04.392Z
+ 2023-09-20T15:03:27.188Z
https://cloud-span.github.io/cloud-span-quarto-site/upcoming_courses.html
- 2023-09-20T13:28:59.967Z
+ 2023-09-20T15:03:28.925Z
diff --git a/docs/upcoming/Core R/index.html b/docs/upcoming/Core R/index.html
index 6469690..32b0186 100644
--- a/docs/upcoming/Core R/index.html
+++ b/docs/upcoming/Core R/index.html
@@ -141,9 +141,29 @@
+
+
+
Core R
-Info about Core R Hello
+Info about Core R
+This online two-hour workshop is an introduction to R for complete beginners. It teaches you how to find your way round RStudio, use the basic data types and structures in R and how to organise your work with scripts and projects. It also teaches you how to import data, summarise it and create and format a graph. The workshop assumes no prior experience of coding.
+Learning outcomes
+By the end of the course you will be able to;
+-
+
- find your way around RStudio +
- use the basic data types and structures in R +
- organise your work with scripts and projects +
- import data, summarise it and create and format a graph +
- The workshop assumes no prior experience of coding. +
Registration
+Registration for this course is now closed.
+There are 30 places available for this online course. Priority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.
+Application deadline: 12pm Monday 5th June. Applicants will be notified by Tuesday 6th June if they have been allocated a place. Scholarships and funding for headsets and monitors will be available. Scholarships and additional support
+We recommend workshop participants have a second monitor and a headset. Dual monitors allow you to engage with the trainers, view materials shared on screen and other participants on one monitor while doing the activities on another. To support you with your learning we have funding to provide you with a headset and a monitor if you require this. To request this additional funding please indicate this in the registration form. Funds for the monitors and headsets will be distributed at the end of workshop to those participants who attend the session.
+We offer Scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses. To apply for a scholarship please complete the relevant questions in the registration form before the deadline. Submissions after this date will not be considered. All applicants will be notified of the results 2-3 days after the submission deadline.
+