From c5db30858a36c11825de00c9d923ff711e85539d Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Wed, 18 Sep 2024 09:10:11 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- blogs.html | 54 ++-- impact.html | 665 ++++++++++++++++++++++++++++++++++++++++++ listings.json | 8 +- search.json | 245 ++++++++-------- sitemap.xml | 124 ++++---- upcoming_courses.html | 12 +- 7 files changed, 893 insertions(+), 217 deletions(-) create mode 100644 impact.html diff --git a/.nojekyll b/.nojekyll index 4e41cd5..3ab54be 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -231fa54e \ No newline at end of file +bced5672 \ No newline at end of file diff --git a/blogs.html b/blogs.html index e11cb38..29325c8 100644 --- a/blogs.html +++ b/blogs.html @@ -266,7 +266,7 @@
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A graphic showing the Cloud-SPAN logo.

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A graphic showing the Cloud-SPAN logo.

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A graphic showing a photo and the comment of one our participants to a previous code retreat

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A graphic plot showing the feedback results for the Prenomics course

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A graphic NortherBUG meeting.

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A graphic showing the Cloud-SPAN logo.

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A dumbbell plot with themes Command Line, Genomics and Project Organisation each having two dumbbells, one representing Genomics without Prenomics and one representing Genomics with Prenomics. The graph indicates the rating given before the course was taken and the score after, with a line joining the two. For all themes the score increases, usually by two or so points. The increase is greater for the 'with prenomics' dumbbells.

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Emma Rand's student, Chloe Brook, presenting her work at a Northern BUG meeting.

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A graphics showing four icons labelled Hardware, Time, Skills and Software, with a note Challenges in Environmental Omics and the Cloud-SPAN logo.

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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)

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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.

diff --git a/impact.html b/impact.html new file mode 100644 index 0000000..37cf516 --- /dev/null +++ b/impact.html @@ -0,0 +1,665 @@ + + + + + + + + + +Impact – Cloud-SPAN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Impact

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Our Impact: Cloud-SPAN February 2021 - June 2024

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Since the launch of the Cloud-SPAN project in February 2021, the team has worked hard to develop and deliver accessible training resources that enable interdisciplinary researchers to generate and analyse big data using cloud- based high performance computing.

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View the impact report.

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+ + + + + + \ No newline at end of file diff --git a/listings.json b/listings.json index 557f2a9..63eea12 100644 --- a/listings.json +++ b/listings.json @@ -31,10 +31,6 @@ "/blogs/genomics_reflection_dec21/index.html" ] }, - { - "listing": "/self_study_courses.html", - "items": [] - }, { "listing": "/upcoming_courses.html", "items": [ @@ -46,6 +42,10 @@ "/upcoming/Code Retreat/index.html" ] }, + { + "listing": "/self_study_courses.html", + "items": [] + }, { "listing": "/index.html", "items": [] diff --git a/search.json b/search.json index 7172c78..a93d44e 100644 --- a/search.json +++ b/search.json @@ -238,88 +238,109 @@ "text": "Why use AWS instances?\n\n\n\nAnnouncements\n\n\nOpen science\n\n\nResources\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2024-03-05\n\n\n\n\n\n\n\n\n\n\n\n\nJoin the team!\n\n\n\nAnnouncements\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-11-21\n\n\n\n\n\n\n\n\n\n\n\n\nAdditional funding to expand training courses\n\n\n\nAnnouncements\n\n\n\n\n\n\n\nEmma Rand\n\n\n2023-11-21\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics and Genomics\n\n\n\nPrenomics\n\n\nOpen science\n\n\nGenomics\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-11-15\n\n\n\n\n\n\n\n\n\n\n\n\nNEW online workshop - Introduction to R\n\n\n\nAnnouncements\n\n\nR\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-05-09\n\n\n\n\n\n\n\n\n\n\n\n\nCongratulations to James Chong and the team!\n\n\n\nAnnouncements\n\n\nEnvironmental omics\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-04-26\n\n\n\n\n\n\n\n\n\n\n\n\nNorthernBUG Meeting\n\n\n\nAnnouncements\n\n\nExternal opportunities\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-04-19\n\n\n\n\n\n\n\n\n\n\n\n\nCloud-SPAN Code Retreat\n\n\n\nAnnouncements\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2023-04-19\n\n\n\n\n\n\n\n\n\n\n\n\nIn depth: course feedback\n\n\n\nPrenomics\n\n\nGenomics\n\n\nMetagenomics\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2023-02-02\n\n\n\n\n\n\n\n\n\n\n\n\nCloud-SPAN Code Retreat\n\n\n\nAnnouncements\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-12-16\n\n\n\n\n\n\n\n\n\n\n\n\n💸Scholarships to attend the Northern Bioinformatics User Group meeting 13th Jan\n\n\n\nAnnouncements\n\n\nOpen science\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-12-16\n\n\n\n\n\n\n\n\n\n\n\n\nHow do we support our learners?\n\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-11-07\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics: Lowering barriers to participation\n\n\n\nBehind-the-scenes\n\n\nPrenomics\n\n\nGenomics\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-10-18\n\n\n\n\n\n\n\n\n\n\n\n\n📢 Online workshop on FAIR data hosted by the UK Reproducibility Network\n\n\n\nAnnouncements\n\n\nExternal opportunities\n\n\nOpen science\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-10-11\n\n\n\n\n\n\n\n\n\n\n\n\nScholarships, funding and so much more!\n\n\n\nBehind-the-scenes\n\n\nAnnouncements\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-10-11\n\n\n\n\n\n\n\n\n\n\n\n\nCloud-SPAN awarded NERC funding to expand training courses\n\n\n\nAnnouncements\n\n\nMetagenomics\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-09-05\n\n\n\n\n\n\n\n\n\n\n\n\nOur Solutions to Challenges in Environmental ’Omics\n\n\n\nEnvironmental omics\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-08-31\n\n\n\n\n\n\n\n\n\n\n\n\n💸Scholarships to attend the Northern Bioinformatics User Group meeting 9th September\n\n\n\nAnnouncements\n\n\nExternal opportunities\n\n\n\n\n\n\n\nEmma Rand\n\n\n2022-07-18\n\n\n\n\n\n\n\n\n\n\n\n\nChallenges in Environmental ’Omics\n\n\n\nEnvironmental omics\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-07-13\n\n\n\n\n\n\n\n\n\n\n\n\nMaking the Prenomics summary poster\n\n\n\nPrenomics\n\n\nBehind-the-scenes\n\n\nResources\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-07-06\n\n\n\n\n\n\n\n\n\n\n\n\nFAIR at Cloud-SPAN\n\n\n\nOpen science\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-06-29\n\n\n\n\n\n\n\n\n\n\n\n\nBioinformatics Meeting on ‘Career pathways into bioinformatics’\n\n\n\nAnnouncements\n\n\nExternal opportunities\n\n\n\n\n\n\n\nSarah Dowsland\n\n\n2022-06-22\n\n\n\n\n\n\n\n\n\n\n\n\nCloud-SPAN April Code Retreat\n\n\n\nAnnouncements\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-06-14\n\n\n\n\n\n\n\n\n\n\n\n\nMore online computational training for life scientists!\n\n\n\nAnnouncements\n\n\nExternal opportunities\n\n\n\n\n\n\n\nEmma Rand\n\n\n2022-06-08\n\n\n\n\n\n\n\n\n\n\n\n\nWhat is FAIR data?\n\n\n\nOpen science\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-05-31\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGenomics Self-Study now LIVE! 🧬\n\n\n\nGenomics\n\n\nAnnouncements\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2022-05-22\n\n\n\n\n\n\n\n\n\n\n\n\nCourse Update\n\n\n\nGenomics\n\n\nBehind-the-scenes\n\n\n\n\n\n\n\nEvelyn Greeves\n\n\n2021-12-14\n\n\n\n\n\n\n\n\nNo matching items" }, { - "objectID": "self_study/Automated Management of Amazon Web Services (AWS) instances/index.html", - "href": "self_study/Automated Management of Amazon Web Services (AWS) instances/index.html", + "objectID": "self_study/Create Your Own AWS Instance/index.html", + "href": "self_study/Create Your Own AWS Instance/index.html", + "title": "Create Your Own AWS Instance", + "section": "", + "text": "Info about Create Your Own AWS Instance" + }, + { + "objectID": "self_study/Automated Management of AWS instances/index.html", + "href": "self_study/Automated Management of AWS instances/index.html", "title": "Automated Management of AWS Instances", "section": "", "text": "Info about AWS" }, { - "objectID": "self_study/Metagenomics for Microbiologists/index.html", - "href": "self_study/Metagenomics for Microbiologists/index.html", - "title": "Metagenomics for Microbiologists", + "objectID": "self_study/Prenomics/index.html", + "href": "self_study/Prenomics/index.html", + "title": "Prenomics", "section": "", - "text": "Info about Metagenomics for Microbiologists" + "text": "Info about Prenomics" }, { - "objectID": "self_study/Genomics/index.html", - "href": "self_study/Genomics/index.html", - "title": "Genomics", + "objectID": "upcoming_courses.html", + "href": "upcoming_courses.html", + "title": "Upcoming Courses", "section": "", - "text": "Info about Genomics" + "text": "The Cloud-SPAN project was scheduled to run until June 2024, therefore we do not have any courses available at the moment. New dates and courses will be released when we have secured additional funding.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGenomics\n\n\nLearn data management and analytical skills for genomics research\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nInstructor Training: How to manage AWS Instances\n\n\nLearn how to configure, create, manage, and delete, one or multiple instances\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics\n\n\nLearn the basics of command-line programming.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMetagenomics\n\n\nLearn more about metagenomics, a way to explore all the genetic material in an environmental sample.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCore R\n\n\nLearn about R and RStudio in this introductory course.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCode Retreat\n\n\nJoin us for a code retreat to apply your new skills to your own data and network with other genomics researchers.\n\n\n\n\n\n\n\n\n\n\n\n\nNo matching items" }, { - "objectID": "self_study_courses.html", - "href": "self_study_courses.html", - "title": "Self-study Courses", + "objectID": "upcoming/Code Retreat/index.html", + "href": "upcoming/Code Retreat/index.html", + "title": "Code Retreat", "section": "", - "text": "Start learning for free with our free online modules covering different subjects! You can work through the online materials at your own pace.\n\n\n\n\n\n\n\n\n\n\nCreate Your Own AWS Instance\n\n\nLearn how to set up an Amazon Web Services instance.\n\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics\n\n\nLearn how to use the command line to navigate a file system and carry out simple tasks.\n\n\n\n\n\n\n\n\n\n\n\n\n\nGenomics\n\n\nLearn about data management and analytical skills for genomic research.\n\n\n\n\n\n\n\n\n\n\n\n\n\nMetagenomics\n\n\nLearn more about metagenomics, a way to explore all the genetic material in an environmental sample.\n\n\n\n\n\n\n\n\n\n\n\n\n\nCore R\n\n\nLearn about R and RStudio in this introductory course.\n\n\n\n\n\n\n\n\n\n\n\n\n\nAutomated Management of AWS Instances\n\n\nLearn how to configure, create, manage, and delete, one or multiple instances\n\n\n\n\n\n\n\nNo matching items" + "text": "Dates for our next Code Retreat will be confimred shortly.\nOur instructors will be on hand to help you problem-solve the issues that arise as you work. Lunch will be provided and funding is available to support travel to the Code Retreat." }, { - "objectID": "upcoming/Core R/index.html", - "href": "upcoming/Core R/index.html", - "title": "Core R", + "objectID": "upcoming/Code Retreat/index.html#what-could-you-achieve", + "href": "upcoming/Code Retreat/index.html#what-could-you-achieve", + "title": "Code Retreat", + "section": "What could you achieve?", + "text": "What could you achieve?\n\nWorking with your peers and with help from our instructors, you could:\nRevise our Metagenomics course\nGet help organising and documenting your own analysis\nApply tools taught in Metagenomics to your own data\nGet help with Creating your own Amazon Web Services instance for Genomics\nNetwork with other genomics researchers" + }, + { + "objectID": "upcoming/Code Retreat/index.html#pre-requisites", + "href": "upcoming/Code Retreat/index.html#pre-requisites", + "title": "Code Retreat", + "section": "Pre-requisites", + "text": "Pre-requisites\n\nAttendees should have completed the a Cloud-SPAN course\nAttendees will need to bring their own laptop to this event" + }, + { + "objectID": "upcoming/Code Retreat/index.html#scholarships", + "href": "upcoming/Code Retreat/index.html#scholarships", + "title": "Code Retreat", + "section": "Scholarships", + "text": "Scholarships\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our code retreats.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\n\nYou will need to reclaim these expenses by completing a form and submitting receipts after participation in the retreat.\nTo request a scholarship please indicate this in the registration form at least one week before the event is scheduled to take place." + }, + { + "objectID": "upcoming/NERC Metagenomics/index.html", + "href": "upcoming/NERC Metagenomics/index.html", + "title": "Metagenomics", "section": "", - "text": "Registration is now closed.\n\n\n\n\n\n\nThis online two-hour workshop 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.\nThe next workshop will take place from 2-4pm on Thursday 25th April 2024.\n\nTarget Audience\nThis workshop is an introduction to R for complete beginners.\nCheck out testimonials from previous attendees!\n\n“I would definitely recommend this course to any beginner in R. An insightful and comprehensive foundation to coding.”\n\n\n“I had some background knowledge in R, but needed to refresh my memory for my PhD data analysis. I expected a dull and slow course, but instead was pleasantly surprised when the course was easy to follow, snappy and very informative! I left the workshop feeling confident using R going forward - I definitely recommend this course for anyone who needs to use R!”\n\n\n“This course was a very good introduction to the basic workings of R and RStudio. After completing this course I now feel comfortable with basic scripting, reading/summarising data and creating/exporting plots. Two hours very well spent!”\n\n\n\nRegistration\n\n\n\n\n\n\nNote\n\n\n\nRegistration is now closed.\n\n\nThere are 30 places available for this online course. Priority will be given to researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.\nApplication deadline: 12pm Monday 15th April. Applicants will be notified by Wednesday 17th April if they have been allocated a place.\n\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\nScholarships and additional support\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 12pm on Monday 15th April. Submissions after this date will not be considered. All applicants will be notified of the results 2-3 days after the submission deadline." + "text": "Register for this course using the [online form]\n\n\n\n\n\n\nRegistration for this course is now closed and new dates will be finalised shortly.\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.\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.\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\n\n\n\n\n\n\nRegister for this course using the [online form]\n\n\n\n\n\n\nRegistration for this course is now closed and new dates will be finalised shortly.\nThere are 30 places available and this workshop is free of charge.\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. During the sessions a soil microbiome example is used however all principles are relevant to any metagenomic analysis. 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.\nHappy learning!\nWeek 1\n\n\n\n\n\n\n\n\nTuesday\n9:30 - 11:30\nCommand-line programming: file systems, files and directories\n\n\nWednesday\n9:30 - 11:30\nCommand-line programming: using the command line\n\n\nFriday\n9:30 - 13:00\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\n13:00 - 14:00\nOnline troubleshooting drop-in session (optional)\n\n\nWednesday\n13:00 - 14:30\nPolishing your metagenome assembly.\n\n\n\n\nOffline time for the polishing to complete\n\n\nFriday\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\n\nWeek 3\n\n\n\n\n\n\n\n\nTuesday\n9:30 - 11:00\nBinning a metagenome assembly into individual genomes (MAGS)\n\n\n\n\nOffline time for the binning to complete\n\n\nThursday\n9:30 - 10:30\nOnline troubleshooting drop-in session (optional)\n\n\nFriday\n9:30 - 12:30\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 one week after the final taught session 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.\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 offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\nsecond monitors and headsets.\n\nTo request a scholarship please indicate this in the registration form by the deadline. Submissions after this date will not be considered. We will contact you 2-3 days after the deadline to confirm whether you have been awarded a scholarship." }, { - "objectID": "upcoming/Prenomics/index.html", - "href": "upcoming/Prenomics/index.html", - "title": "Prenomics", + "objectID": "upcoming/How to manage AWS Instances/index.html", + "href": "upcoming/How to manage AWS Instances/index.html", + "title": "Instructor Training: How to manage AWS Instances", "section": "", - "text": "Registration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.\nDates for the next Prenomics workshop will be finalised shortly.\nPrenomics teaches the basics of command-line programming, including:" + "text": "Do you train non-experts to do analyses on high performance computing?\nWould you like to learn how to efficiently manage fully configured Amazon Web Services (AWS) instances (Linux virtual machines) to deliver workshops to diverse participants?\nWould you like to learn how to configure and manage your own Amazon Machine Image (AMI) templates (from which instances are created) with specific data and software analysis tools?\nWe have created instructor training for anyone interested in deploying and managing cloud resources. This workshop will enable you to facilitate training at your own institution or workplace utilising the Cloud-SPAN learning materials. This module teaches how to manage Amazon Web Services (AWS) instances — each instance being a Linux virtual machine. Using Bash Shell scripts, it is shown how to configure, create, stop, start, and delete, one or multiple instances with a single invocation of a script.\nCloud-SPAN instructors are available to deliver this 3 hour training session at your institution at no cost to you. They can teach you and your team the method they have used for over 2 years to efficiently manage AWS instances and AMIs for many workshops. For the training session participants only need the Terminal/Shell and ssh programs on their laptops." }, { - "objectID": "upcoming/Prenomics/index.html#target-audience", - "href": "upcoming/Prenomics/index.html#target-audience", - "title": "Prenomics", - "section": "Target audience", - "text": "Target audience\n\nLearners who are intending to do bioinformatics but do not have any prior experience.\nPhD Students & Researchers\nLearners who wish to complete the Genomics Course\n\nCheck out testimonials from previous attendees!\n\n“The prenomics module run by Cloud-SPAN is the best course for people interested in bioinformatics and recognises people with no experience. It was my first time using a command line to navigate the computer file system. It was worth the time. You guys are amazing with what you do. The patience, time, and demonstration of knowledge were all important in delivering the lectures. Thank you so much for this opportunity. As a first-year PhD student, this experience will be instrumental during my bioinformatics analysis and subsequently in the future. I am hoping to join the next course on genomics.” Doctoral student | University of Nottingham\n\n\n“I really enjoyed the Prenomics course. I was initially worried going into it as I was a complete beginner but the leaders were amazing at explaining everything which made for a comfortable environment to ask any questions. I will definitely be recommending this course to others!” Early Career Researcher | Deep Branch\n\n\n“I was scared of bash or using the Terminal previously. But, after attending Prenomics, I manage to conquer the fear:) Thanks to the team! Early Career Researcher | University of Leeds" + "objectID": "upcoming/How to manage AWS Instances/index.html#how-to-schedule-a-training-workshop", + "href": "upcoming/How to manage AWS Instances/index.html#how-to-schedule-a-training-workshop", + "title": "Instructor Training: How to manage AWS Instances", + "section": "How to schedule a training workshop?", + "text": "How to schedule a training workshop?\nTo schedule a workshop between March and May 2024, please contact us on cloud-span-project@york.ac.uk This training opportunity is free of charge." }, { - "objectID": "upcoming/Prenomics/index.html#registration", - "href": "upcoming/Prenomics/index.html#registration", - "title": "Prenomics", - "section": "Registration", - "text": "Registration\nRegistration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.\nThere are 30 places available for this online workshop. This course is free of charge." + "objectID": "upcoming/How to manage AWS Instances/index.html#target-audience", + "href": "upcoming/How to manage AWS Instances/index.html#target-audience", + "title": "Instructor Training: How to manage AWS Instances", + "section": "Target audience", + "text": "Target audience\nThe target audience of the course is anyone in charge of, or interested in, deploying and managing cloud resources. While the module is focused on AWS, and particularly Elastic Compute Cloud (EC2) instances, the scripts can be adapted for use with other cloud providers and other types of cloud services." }, { - "objectID": "upcoming/Prenomics/index.html#pre-requisites", - "href": "upcoming/Prenomics/index.html#pre-requisites", - "title": "Prenomics", + "objectID": "upcoming/How to manage AWS Instances/index.html#pre-requisites", + "href": "upcoming/How to manage AWS Instances/index.html#pre-requisites", + "title": "Instructor Training: How to manage AWS Instances", "section": "Pre-requisites", - "text": "Pre-requisites\nKnowledge: To ensure that you would benefit from participating in this course please complete the short self-assessment quiz self-assessment quiz. This course assumes no prior experience with the tools covered in the workshop however learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population.\nSoftware: view the required software set-up." + "text": "Pre-requisites\nThe workshop assumes no prior experience with the AWS concepts and tools covered but you will need experience of the Linux Terminal (Shell/Command Line Interface)." }, { - "objectID": "upcoming/Prenomics/index.html#programme", - "href": "upcoming/Prenomics/index.html#programme", - "title": "Prenomics", + "objectID": "upcoming/How to manage AWS Instances/index.html#programme", + "href": "upcoming/How to manage AWS Instances/index.html#programme", + "title": "Instructor Training: How to manage AWS Instances", "section": "Programme", - "text": "Programme\n\n\n\n\n\n\n\n\nDay 1\n10:00 - 12:30\nSession 1 - Project management for cloud genomics\n\n\n\n\n• Intro to local and remote files, hierarchical structure of files and folders • Intro to the files which will be used in the Genomics course • Logging onto the Cloud • Introducing the Shell.\n\n\nDay 2\n10:00 - 12:30\nSession 2 - Using the command line\n\n\n\n\n• Navigating Files and Directories • Working with Files and Directories • Redirection" + "text": "Programme\nThe workshop is based on the final 3 lessons from the self-study course Automated Management of AWS Instances topics covered include; Instance Management Tasks Using the Scripts, AMIs Management and The Scripts Design.\n\nTopic 1 Setting up the work environment - Learn how to set up your working environment, your AWS account and your shell terminal configuration, to be able to run the scripts.\nTopic 2 Managing AWS instances - Learn some best practices to deploy and manage AWS instances for a course, for testing software configurations, for creating new AMIs.\nTopic 3 Managing AMIs, Scripts - Learn the blurry bits of the scripts, how to control changes to the scripts with GitHub, the Cloud-SPAN AMIs, when and how to create and control AMI versions, updating an AMI Linux and software tools, and more." }, { - "objectID": "upcoming/Prenomics/index.html#learning-outcomes", - "href": "upcoming/Prenomics/index.html#learning-outcomes", - "title": "Prenomics", + "objectID": "upcoming/How to manage AWS Instances/index.html#learning-outcomes", + "href": "upcoming/How to manage AWS Instances/index.html#learning-outcomes", + "title": "Instructor Training: How to manage AWS Instances", "section": "Learning outcomes", - "text": "Learning outcomes\nFollowing completion of this course, learners will be able to\n\nexplain the hierarchical structure of a file system\nunderstand the structure of the file system on their own machine\nfind, create, move and delete folders and files on their machine\nexplain what is meant by a working directory, a path and a relative path\nwrite down paths that they will need for the Prenomics and Genomics courses\ndescribe the files and file structure used in Prenomics and Genomics courses\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" - }, - { - "objectID": "upcoming/Prenomics/index.html#scholarships", - "href": "upcoming/Prenomics/index.html#scholarships", - "title": "Prenomics", - "section": "Scholarships", - "text": "Scholarships\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\nsecond monitors and headsets.\n\nTo request a scholarship please indicate this in the registration form, before the given deadline. Submissions after this date will not be considered. We will contact you within a week after the deadline to confirm whether you have been awarded a scholarship." + "text": "Learning outcomes\nFollowing completion of this course, learners will be able to\n\nconfigure and run the scripts to create and manage instances for workshops, manage late registrations and cancellations, and troubleshooting\ncreate, manage and configure AMI templates (from which instances are created) with their own data and software analysis tools\nunderstand how the scripts work so they can customise them." }, { "objectID": "upcoming/Genomics/index.html", @@ -371,109 +392,95 @@ "text": "Scholarships\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\nsecond monitors and headsets.\n\nYou will need to reclaim these expenses by completing a form and submitting receipts after participation in the course.\nTo request a scholarship please indicate this in the registration form, before the given deadline. Submissions after this date will not be considered. We will contact you one week after the deadline to confirm whether you have been awarded a scholarship." }, { - "objectID": "upcoming/How to manage AWS Instances/index.html", - "href": "upcoming/How to manage AWS Instances/index.html", - "title": "Instructor Training: How to manage AWS Instances", + "objectID": "upcoming/Prenomics/index.html", + "href": "upcoming/Prenomics/index.html", + "title": "Prenomics", "section": "", - "text": "Do you train non-experts to do analyses on high performance computing?\nWould you like to learn how to efficiently manage fully configured Amazon Web Services (AWS) instances (Linux virtual machines) to deliver workshops to diverse participants?\nWould you like to learn how to configure and manage your own Amazon Machine Image (AMI) templates (from which instances are created) with specific data and software analysis tools?\nWe have created instructor training for anyone interested in deploying and managing cloud resources. This workshop will enable you to facilitate training at your own institution or workplace utilising the Cloud-SPAN learning materials. This module teaches how to manage Amazon Web Services (AWS) instances — each instance being a Linux virtual machine. Using Bash Shell scripts, it is shown how to configure, create, stop, start, and delete, one or multiple instances with a single invocation of a script.\nCloud-SPAN instructors are available to deliver this 3 hour training session at your institution at no cost to you. They can teach you and your team the method they have used for over 2 years to efficiently manage AWS instances and AMIs for many workshops. For the training session participants only need the Terminal/Shell and ssh programs on their laptops." + "text": "Registration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.\nDates for the next Prenomics workshop will be finalised shortly.\nPrenomics teaches the basics of command-line programming, including:" }, { - "objectID": "upcoming/How to manage AWS Instances/index.html#how-to-schedule-a-training-workshop", - "href": "upcoming/How to manage AWS Instances/index.html#how-to-schedule-a-training-workshop", - "title": "Instructor Training: How to manage AWS Instances", - "section": "How to schedule a training workshop?", - "text": "How to schedule a training workshop?\nTo schedule a workshop between March and May 2024, please contact us on cloud-span-project@york.ac.uk This training opportunity is free of charge." + "objectID": "upcoming/Prenomics/index.html#target-audience", + "href": "upcoming/Prenomics/index.html#target-audience", + "title": "Prenomics", + "section": "Target audience", + "text": "Target audience\n\nLearners who are intending to do bioinformatics but do not have any prior experience.\nPhD Students & Researchers\nLearners who wish to complete the Genomics Course\n\nCheck out testimonials from previous attendees!\n\n“The prenomics module run by Cloud-SPAN is the best course for people interested in bioinformatics and recognises people with no experience. It was my first time using a command line to navigate the computer file system. It was worth the time. You guys are amazing with what you do. The patience, time, and demonstration of knowledge were all important in delivering the lectures. Thank you so much for this opportunity. As a first-year PhD student, this experience will be instrumental during my bioinformatics analysis and subsequently in the future. I am hoping to join the next course on genomics.” Doctoral student | University of Nottingham\n\n\n“I really enjoyed the Prenomics course. I was initially worried going into it as I was a complete beginner but the leaders were amazing at explaining everything which made for a comfortable environment to ask any questions. I will definitely be recommending this course to others!” Early Career Researcher | Deep Branch\n\n\n“I was scared of bash or using the Terminal previously. But, after attending Prenomics, I manage to conquer the fear:) Thanks to the team! Early Career Researcher | University of Leeds" }, { - "objectID": "upcoming/How to manage AWS Instances/index.html#target-audience", - "href": "upcoming/How to manage AWS Instances/index.html#target-audience", - "title": "Instructor Training: How to manage AWS Instances", - "section": "Target audience", - "text": "Target audience\nThe target audience of the course is anyone in charge of, or interested in, deploying and managing cloud resources. While the module is focused on AWS, and particularly Elastic Compute Cloud (EC2) instances, the scripts can be adapted for use with other cloud providers and other types of cloud services." + "objectID": "upcoming/Prenomics/index.html#registration", + "href": "upcoming/Prenomics/index.html#registration", + "title": "Prenomics", + "section": "Registration", + "text": "Registration\nRegistration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.\nThere are 30 places available for this online workshop. This course is free of charge." }, { - "objectID": "upcoming/How to manage AWS Instances/index.html#pre-requisites", - "href": "upcoming/How to manage AWS Instances/index.html#pre-requisites", - "title": "Instructor Training: How to manage AWS Instances", + "objectID": "upcoming/Prenomics/index.html#pre-requisites", + "href": "upcoming/Prenomics/index.html#pre-requisites", + "title": "Prenomics", "section": "Pre-requisites", - "text": "Pre-requisites\nThe workshop assumes no prior experience with the AWS concepts and tools covered but you will need experience of the Linux Terminal (Shell/Command Line Interface)." + "text": "Pre-requisites\nKnowledge: To ensure that you would benefit from participating in this course please complete the short self-assessment quiz self-assessment quiz. This course assumes no prior experience with the tools covered in the workshop however learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population.\nSoftware: view the required software set-up." }, { - "objectID": "upcoming/How to manage AWS Instances/index.html#programme", - "href": "upcoming/How to manage AWS Instances/index.html#programme", - "title": "Instructor Training: How to manage AWS Instances", + "objectID": "upcoming/Prenomics/index.html#programme", + "href": "upcoming/Prenomics/index.html#programme", + "title": "Prenomics", "section": "Programme", - "text": "Programme\nThe workshop is based on the final 3 lessons from the self-study course Automated Management of AWS Instances topics covered include; Instance Management Tasks Using the Scripts, AMIs Management and The Scripts Design.\n\nTopic 1 Setting up the work environment - Learn how to set up your working environment, your AWS account and your shell terminal configuration, to be able to run the scripts.\nTopic 2 Managing AWS instances - Learn some best practices to deploy and manage AWS instances for a course, for testing software configurations, for creating new AMIs.\nTopic 3 Managing AMIs, Scripts - Learn the blurry bits of the scripts, how to control changes to the scripts with GitHub, the Cloud-SPAN AMIs, when and how to create and control AMI versions, updating an AMI Linux and software tools, and more." + "text": "Programme\n\n\n\n\n\n\n\n\nDay 1\n10:00 - 12:30\nSession 1 - Project management for cloud genomics\n\n\n\n\n• Intro to local and remote files, hierarchical structure of files and folders • Intro to the files which will be used in the Genomics course • Logging onto the Cloud • Introducing the Shell.\n\n\nDay 2\n10:00 - 12:30\nSession 2 - Using the command line\n\n\n\n\n• Navigating Files and Directories • Working with Files and Directories • Redirection" }, { - "objectID": "upcoming/How to manage AWS Instances/index.html#learning-outcomes", - "href": "upcoming/How to manage AWS Instances/index.html#learning-outcomes", - "title": "Instructor Training: How to manage AWS Instances", + "objectID": "upcoming/Prenomics/index.html#learning-outcomes", + "href": "upcoming/Prenomics/index.html#learning-outcomes", + "title": "Prenomics", "section": "Learning outcomes", - "text": "Learning outcomes\nFollowing completion of this course, learners will be able to\n\nconfigure and run the scripts to create and manage instances for workshops, manage late registrations and cancellations, and troubleshooting\ncreate, manage and configure AMI templates (from which instances are created) with their own data and software analysis tools\nunderstand how the scripts work so they can customise them." + "text": "Learning outcomes\nFollowing completion of this course, learners will be able to\n\nexplain the hierarchical structure of a file system\nunderstand the structure of the file system on their own machine\nfind, create, move and delete folders and files on their machine\nexplain what is meant by a working directory, a path and a relative path\nwrite down paths that they will need for the Prenomics and Genomics courses\ndescribe the files and file structure used in Prenomics and Genomics courses\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" }, { - "objectID": "upcoming/NERC Metagenomics/index.html", - "href": "upcoming/NERC Metagenomics/index.html", - "title": "Metagenomics", - "section": "", - "text": "Register for this course using the [online form]\n\n\n\n\n\n\nRegistration for this course is now closed and new dates will be finalised shortly.\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.\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.\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\n\n\n\n\n\n\nRegister for this course using the [online form]\n\n\n\n\n\n\nRegistration for this course is now closed and new dates will be finalised shortly.\nThere are 30 places available and this workshop is free of charge.\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. During the sessions a soil microbiome example is used however all principles are relevant to any metagenomic analysis. 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.\nHappy learning!\nWeek 1\n\n\n\n\n\n\n\n\nTuesday\n9:30 - 11:30\nCommand-line programming: file systems, files and directories\n\n\nWednesday\n9:30 - 11:30\nCommand-line programming: using the command line\n\n\nFriday\n9:30 - 13:00\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\n13:00 - 14:00\nOnline troubleshooting drop-in session (optional)\n\n\nWednesday\n13:00 - 14:30\nPolishing your metagenome assembly.\n\n\n\n\nOffline time for the polishing to complete\n\n\nFriday\n14:00 - 15:00\nOnline troubleshooting drop-in session (optional)\n\n\n\nWeek 3\n\n\n\n\n\n\n\n\nTuesday\n9:30 - 11:00\nBinning a metagenome assembly into individual genomes (MAGS)\n\n\n\n\nOffline time for the binning to complete\n\n\nThursday\n9:30 - 10:30\nOnline troubleshooting drop-in session (optional)\n\n\nFriday\n9:30 - 12:30\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 one week after the final taught session 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.\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 offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\nsecond monitors and headsets.\n\nTo request a scholarship please indicate this in the registration form by the deadline. Submissions after this date will not be considered. We will contact you 2-3 days after the deadline to confirm whether you have been awarded a scholarship." + "objectID": "upcoming/Prenomics/index.html#scholarships", + "href": "upcoming/Prenomics/index.html#scholarships", + "title": "Prenomics", + "section": "Scholarships", + "text": "Scholarships\nWe offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.\nThe scholarship scheme can cover approximately £150 per application, for costs such as:\n\nchildcare\naccessibility needs\nother costs that might otherwise prevent participation\nsecond monitors and headsets.\n\nTo request a scholarship please indicate this in the registration form, before the given deadline. Submissions after this date will not be considered. We will contact you within a week after the deadline to confirm whether you have been awarded a scholarship." }, { - "objectID": "upcoming/Code Retreat/index.html", - "href": "upcoming/Code Retreat/index.html", - "title": "Code Retreat", + "objectID": "upcoming/Core R/index.html", + "href": "upcoming/Core R/index.html", + "title": "Core R", "section": "", - "text": "Dates for our next Code Retreat will be confimred shortly.\nOur instructors will be on hand to help you problem-solve the issues that arise as you work. Lunch will be provided and funding is available to support travel to the Code Retreat." - }, - { - "objectID": "upcoming/Code Retreat/index.html#what-could-you-achieve", - "href": "upcoming/Code Retreat/index.html#what-could-you-achieve", - "title": "Code Retreat", - "section": "What could you achieve?", - "text": "What could you achieve?\n\nWorking with your peers and with help from our instructors, you could:\nRevise our Metagenomics course\nGet help organising and documenting your own analysis\nApply tools taught in Metagenomics to your own data\nGet help with Creating your own Amazon Web Services instance for Genomics\nNetwork with other genomics researchers" - }, - { - "objectID": "upcoming/Code Retreat/index.html#pre-requisites", - "href": "upcoming/Code Retreat/index.html#pre-requisites", - "title": "Code Retreat", - "section": "Pre-requisites", - "text": "Pre-requisites\n\nAttendees should have completed the a Cloud-SPAN course\nAttendees will need to bring their own laptop to this event" + "text": "Registration is now closed.\n\n\n\n\n\n\nThis online two-hour workshop 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.\nThe next workshop will take place from 2-4pm on Thursday 25th April 2024.\n\nTarget Audience\nThis workshop is an introduction to R for complete beginners.\nCheck out testimonials from previous attendees!\n\n“I would definitely recommend this course to any beginner in R. An insightful and comprehensive foundation to coding.”\n\n\n“I had some background knowledge in R, but needed to refresh my memory for my PhD data analysis. I expected a dull and slow course, but instead was pleasantly surprised when the course was easy to follow, snappy and very informative! I left the workshop feeling confident using R going forward - I definitely recommend this course for anyone who needs to use R!”\n\n\n“This course was a very good introduction to the basic workings of R and RStudio. After completing this course I now feel comfortable with basic scripting, reading/summarising data and creating/exporting plots. Two hours very well spent!”\n\n\n\nRegistration\n\n\n\n\n\n\nNote\n\n\n\nRegistration is now closed.\n\n\nThere are 30 places available for this online course. Priority will be given to researchers from underrepresented groups, although we encourage everyone to apply. This course is free of charge.\nApplication deadline: 12pm Monday 15th April. Applicants will be notified by Wednesday 17th April if they have been allocated a place.\n\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\nScholarships and additional support\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 12pm on Monday 15th April. Submissions after this date will not be considered. 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You can work through the online materials at your own pace.\n\n\n\n\n\n\n\n\n\n\nCreate Your Own AWS Instance\n\n\nLearn how to set up an Amazon Web Services instance.\n\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics\n\n\nLearn how to use the command line to navigate a file system and carry out simple tasks.\n\n\n\n\n\n\n\n\n\n\n\n\n\nGenomics\n\n\nLearn about data management and analytical skills for genomic research.\n\n\n\n\n\n\n\n\n\n\n\n\n\nMetagenomics\n\n\nLearn more about metagenomics, a way to explore all the genetic material in an environmental sample.\n\n\n\n\n\n\n\n\n\n\n\n\n\nCore R\n\n\nLearn about R and RStudio in this introductory course.\n\n\n\n\n\n\n\n\n\n\n\n\n\nAutomated Management of AWS Instances\n\n\nLearn how to configure, create, manage, and delete, one or multiple instances\n\n\n\n\n\n\n\nNo matching items" }, { - "objectID": "upcoming_courses.html", - "href": "upcoming_courses.html", - "title": "Upcoming Courses", + "objectID": "self_study/Genomics/index.html", + "href": "self_study/Genomics/index.html", + "title": "Genomics", "section": "", - "text": "The Cloud-SPAN project was scheduled to run until June 2024, therefore we do not have any courses available at the moment. New dates and courses will be released when we have secured additional funding.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGenomics\n\n\nLearn data management and analytical skills for genomics research\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nInstructor Training: How to manage AWS Instances\n\n\nLearn how to configure, create, manage, and delete, one or multiple instances\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nPrenomics\n\n\nLearn the basics of command-line programming.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMetagenomics\n\n\nLearn more about metagenomics, a way to explore all the genetic material in an environmental sample.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCore R\n\n\nLearn about R and RStudio in this introductory course.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCode Retreat\n\n\nJoin us for a code retreat to apply your new skills to your own data and network with other genomics researchers.\n\n\n\n\n\n\n\n\n\n\n\n\nNo matching items" + "text": "Info about Genomics" }, { - "objectID": "self_study/Prenomics/index.html", - 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"text": "Info about Create Your Own AWS Instance" + "text": "Our Impact: Cloud-SPAN February 2021 - June 2024\nSince the launch of the Cloud-SPAN project in February 2021, the team has worked hard to develop and deliver accessible training resources that enable interdisciplinary researchers to generate and analyse big data using cloud- based high performance computing.\nView the impact report." }, { "objectID": "DaSH.html", diff --git a/sitemap.xml b/sitemap.xml index 1509607..f0b18cd 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,190 +2,194 @@ https://cloud-span.github.io/cloud-span-quarto-site/contact-us.html - 2024-09-18T08:58:41.962Z + 2024-09-18T09:09:33.903Z https://cloud-span.github.io/cloud-span-quarto-site/blogs/northern_bug_dec22/index.html - 2024-09-18T08:58:41.918Z + 2024-09-18T09:09:33.863Z https://cloud-span.github.io/cloud-span-quarto-site/blogs/challenges_solutions_aug22/index.html - 2024-09-18T08:58:41.866Z + 2024-09-18T09:09:33.807Z https://cloud-span.github.io/cloud-span-quarto-site/blogs/AWS_Management/index.html - 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Upcoming Courses