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@@ -3,6 +3,10 @@
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diff --git a/search.json b/search.json
index 21ec41d..f2e01fe 100644
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"text": "How to Get Involved\nIf you like the sound of all this, why not sign up for one of our free self-study courses today? Our full catalogue of courses is listed on our website.\n\nUpcoming Courses\nPrenomics ➡ 6-7 December 2023 (online workshop or complete via self-study)\nGenomics ➡ 15-24 January 2024 (online workshop or complete via self-study)\n\n\n\n."
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"section": "",
- "text": "Join the University of York’s Bioinformatics Meeting on ‘Career pathways into bioinformatics’.\nHosted by Sarah Forrester, we have a jam packed hour and a half.\nEvelyn Greeves from the Cloud-SPAN team will be leading a short session on “Introduction to FAIR and metadata” with an opportunity for you to ask any questions that you may have. \nFollowing this, have you pondered what direction to take your career or how to use your data skills in future projects? We have 3 speakers who explain how data analysis has been incorporated into their work. \n🔸 Emma Rand highlights the different paths into academia and using big data skills. \n🔸 James Chong explains how learning bioinformatics was the only way to get past the bottleneck of being able to analyse data he was generating.\n🔸 Sarah Forrester explores how bioinformatics opens doors to moving between different research niches. \nWe will then have a discussion with all speakers for the remainder of the session, which will include signposting resources. \nSession slides will be available following the event. \nEvent details: Wednesday, 6th July, 15:00-16:30 in room B/T/019 University of York. \nContact us on cloud-span-project@york.ac.uk to be added to the Bioinformatics regular mailing list!\n\n\n\n."
+ "text": "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:\n\nFirst thing’s first... positive feedback!\nWe had some amazing feedback from our first run-through! We asked our participants to rate their level of comfort with a number of topics before and after completing the course.\nAs you can see in the graph below, on average our participants felt that their level of comfort had improved after taking the course for all topics. This is great news!\nIn 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.\n\n\n\nThe BIG Problem: Time flies\nThe biggest problem we ran into was time. We just didn’t have enough of it...\n...and that means we need to seriously rethink how we structure the content of our course. You can see from the graph above that the topics people felt they had improved their confidence the least in were those relating to genomics - assessing read quality, trimming and filtering, and variant calling.\nThat’s because before we could teach those topics, we had to make sure people felt really comfortable using the command line and organising their files. Unfortunately, as we got more and more behind schedule, this meant the genomics topics got less and less time allocated to them.\nThis is a problem, because the title of the course was Foundational Genomics. If participants are finishing our course feeling like they are not comfortable with variant calling (which is what a score of 3 means) then we need to make some changes. Plus, the genomics bit is meant to be the fun bit!\nThe written feedback we had from participants after the course, while mostly positive, generally reflected this sentiment too.\n\n\nThe BIG Solution: Course structure\nIn light of this feedback, we’ve decided to split our 4 x half-day Foundational Genomics course into two shorter courses: one 2 x half-day “Prenomics” course and one 4 x half-day “Genomics” course.\nThe Prenomics course will be aimed at complete beginners and will be a gentle introduction to file directories, working paths and basic command line commands. By giving ourselves two half-days to cover this content we should be able to ensure all participants are fully on board before we move onto anything more complex.\nThis course will also be optional for those who already have some basic experience using the command line. We plan to screen potential attendees using a self-test to help them determine whether they would benefit from attending the Prenomics course, or skipping straight to Genomics.\nThe Genomics course will follow directly on from Prenomics, using many of the same commands and building on them further. We should have much more time to cover essential topics such as read quality and variant calling which were rushed last time, allowing us to offer a much better educational experience.\n\n\nSome smaller problems which this change also solves...\n\nWe plan to run the Genomics course over two weeks, with 2 x half days per week. This, combined with a hopefully much less stressful volume of content to cover, will decrease pressure on our instructors and helpers, most of whom have multiple other work and teaching commitments.\nSome of our participants felt the course went far too slowly; others felt it went too fast. By screening for those who have the least experience working in the command line, we should be able to both provide more support to those who need it and stop more experienced participants from getting bored.\n\n\n\nOther updates in the pipeline\nThese two new courses, Prenomics and Genomics, will make up the ‘Foundational’ element of our content. We still have plans to developed ‘Advanced’ modules on topics such as automation and setting up cloud instances. We asked our participants to let us know what they’d like to see, and we’ll be taking these suggestions into account as we go.\nWe also have plans to run some (hopefully) in-person ‘hack days’ for alumni of our Foundational courses, where we can help participants apply the skills learned in the course to their own problems, and assist in troubleshooting any problems. We hope this will help develop our community of practice further by providing opportunities for networking and building relationships.\nAnd that’s it. Thanks for reading this far - we hope it explains some of our rationale for why the course is structured the way it is. We’re really proud of our achievements with our first ever course, and we’re looking forward to trying some new stuff out next time.\nTill next time! 👋"
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- "text": "We are excited to announce that our next Code Retreat will take place on Monday 9th January 2023 at the University of York. It provides a chance for course alumni to come together and work on their own data problems with the support of Cloud-SPAN instructors.\n\nWhat happens at a Code Retreat?\nAt previous retreats some people took the opportunity to revisit course materials and ask questions about the topics they didn't understand. There are plenty of helpers on hand to answer questions and test understanding.\nYou could also apply the workflows and analyses taught in the Genomics course to your own datasets. Helpers are also on hand to discuss topics such as:\n\nhow to organise bioinformatics projects;\nwhich tools are most effective;\nhow to approach a problem;\nwhat analysis is best for a certain type of data;\n\nas well as many others. \nSome participants already know what help they will need and have specific questions to address during the day. Those with a less clear understanding of their problem could benefit from talking through their data and getting guidance from our experienced instructors. You could even try out new software tools.\n\n\nWhat do previous participants have to say?\n“I had a great time at the Cloud-Span retreat. I went from Lancaster just for it, and it was worth it. I got support in analysing the data I had in hand. That was really satisfying applying what we preciously learned (using our data this time). Having the Cloud-Span Team around to support us was essential. It's been great learning with them, and I would 100% recommend them!”\n\n\n\n.\n\n\n\n\nJoin us for our next event!\nOur next Code Retreat for Cloud-SPAN Alumni will take on 10:30-15:30, Monday 9th January 2023 at the University of York. Feel free to stay for the whole event or drop in when you are free. Lunch will be provided and we offer support to cover travel expenses.\nSign up using the registration form\n\n\nTraining courses\nIf you are interested in attending our free training courses please visit our website for further information."
+ "text": "Save the date - registration opening soon!\nJoin us for this free online two-hour workshop which provides an introduction to R for complete beginners. By 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\n\nThe workshop assumes no prior experience of coding. We allow plenty of time for questions and we provide a high level of support for each learner. The workshop will be delivered by Emma Rand, an excellent instructor with a passion for teaching.\n\n\nEvent details\n💻 Core R Workshop\n🗓️ Tuesday 20th June 2023\n🕑 2-4 pm\n📍 Online\n\n\nPlaces available\nThere are 30 places available for this online course.\nPriority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply.\nApplication deadline: Friday 9th June. Applicants will be notified by Tuesday 13th June if they have been allocated a place.\n\n\nRegistration fee\nThis workshop is funded by the Natural Environment Research Council (NERC) and therefore it is free to attend for candidates based in the UK.\n\n\nHow to register\nRegistration will open shortly; an online registration form will be available on the Cloud-SPAN website. If you so wish, you can also register your interest in the workshop and we will contact you when registration opens.\n\n\nKeep in touch!\nLinkedIn\nTwitter\nCloud-SPAN website\n\n\n\n."
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- "text": "Here’s what we’re doing at Cloud-SPAN to address the challenges we discussed previously.\nJust to recap, here are our four main challenges:\nAt Cloud-SPAN we have two main weapons in our arsenal against these challenges: cloud computing and training. Let’s look at each of those in detail."
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- "text": "Cloud HPC\nWe use commercially-available cloud computing resources to address the challenges of hardware, software and time.\nHere’s how it works: we teach our courses inside a containerised instance, which is a virtual environment containing pre-loaded software and files. The instance runs on hardware borrowed from a commercial provider (in our case, Amazon Web Services). All our learners have to do is log into the cloud instance we provide, and they will have access to all of the software and data used in the course. The instances all start out identical, so the file structure always looks the same, and they run on enough borrowed resources to make analysis relatively quick and easy.\nUsing this kind of pre-loaded instance benefits our learners by removing complications around different HPC setups and the installation of software onto a cluster. It also makes it easier for us to teach - we know that everyone is starting with the same setup, so we can offer our courses to anyone regardless of institution. It allows us to model best practices for directory structure and project organisation, and save time when troubleshooting issues.\nAnother major advantage of running analyses on cloud resources is that we don’t have to wait in a queue for resources to be available, as we’ve already loaned out the resources we need. This can save a lot of time for large analyses, and is especially useful for teaching.\nAfter completing one of our courses, learners can go away and apply their new skills to their own data by setting up their own cloud instance, which is identical to the one used in the course. It contains all the same software and basic file structures, so provides a familiar environment for further learning and analysis. Using these kinds of services outside of the course does incur a cost, but we also support learners in applying for research credits."
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- "text": "Training\nOur other main solution is providing high quality, free-of-charge training courses with a low barrier to entry and no assumptions of prior knowledge. These courses allow us to address challenges around skills and the skills gap.\nAll of our courses are underpinned by a core ‘Prenomics’ module, which provides a supportive and carefully paced introduction to navigating directories and using the UNIX command line. Accessing the cloud HPC services described above is impossible without these skills. Using our purpose-built environment we guide new learners through the basics with a strong focus on contextualising new skills within the field of environmental ’omics.\nWe also provide core modules in using the programming language R, again with a focus on analysis and visualisation of ’omics data, and on creating cloud instances.\nOur specialised courses follow on from Prenomics and cover topics such as genomics, metagenomics, automating analyses and designing statistically useful experiments. Again, we keep the barrier to participation low by contextualising learning and keeping new ideas to the bare minimum - no frills!"
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- "text": "Summary\nIn summary, the Cloud-SPAN project combines high-quality training with cloud computing expertise to address four major challenges in the field of environmental ’omics. Using our unique containerised instances we can provide adequate resources for efficient analysis with software pre-installed, saving time and effort. Our courses are designed to equip learners with the skills they need to perform analyses on these cloud instances and beyond, with the overall aim to lessen the load of learning on the backs of researchers and help them improve analysis times and efficiency.\nOur containerised instances solve the challenges of:\n\nHardware, by providing a harmonised HPC platform across institutions and potentially increasing the compute resources available to individuals.\nSoftware, by providing pre-installed software which removes the time-consuming step of software installation.\nTime, by speeding up analyses and eradicating the need to queue to access HPC.\n\nOur training approach solves the challenge of:\n\nSkills, by ensuring a low barrier to participation and equipping researchers with vital skills.\n\nFind out for yourself how our solutions to these challenges could benefit you. Read more about the courses we offer or take a look at our introductory ‘Prenomics’ course materials or specialised Genomics course to see how our training can equip you better\n\n\n\n."
+ "text": "Here at Cloud-SPAN HQ our official tagline is that we are here to upskill researchers and enable them to perform complex analyses on cloud-based platforms. Which we are achieving through the provision of training courses and online modules. However, as a member of the team who works behind the scenes as project manager, I feel that we are offering much more than that."
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- "text": "The Cloud-SPAN team has been awarded a grant to expand our training to the Natural Environment Research Council (NERC) remit under the Advanced training for early-career environmental scientists call. We will be developing an accessible online course “Getting started with High Performance Computing: FAIR training for environmental scientists” using the same cloud-based infrastructure used in our other courses. We will supply AWS services to up to 60 participants undertaking the course either in tutor-led workshops or by self-study.\nThose needing funds for childcare or accessibility to enable their participation in the training will be able apply for a Scholarship and up to 30 participants will receive headsets and second monitors facilitate online engagement. The course will be running in April 2023 - please let your ecology colleagues know to look out for the course!\n\nKey info\n🔷 Metagenomics with High Performance Computing ▶ 11-21 April (Online workshop)\n🔷 Scholarship deadline 13 March\n🔷 Register for the online workshop\n🔷 Register for the self-study mode\n\n\n\n."
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+ "section": "Welcoming learning environment",
+ "text": "Welcoming learning environment\nUp until now we have delivered courses online and held code retreats in person. The course materials and delivery are excellent thanks to our talented instructors. I find the real added value here is that the learning environment is very welcoming, encouraging and inclusive. A lot of our participants are complete beginners or new to this world of big data, command line and cloud computing. And learning such new skills could be very daunting for some. At our courses there aren’t any big egos, there’s just someone there to work through questions and find solutions to your problems."
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- "text": "We’ve finished our analysis of the feedback from our courses held at the end of last year: Prenomics, Genomics and Metagenomics. We’re pleased to see that on average participants saw an improvement across all of the learning outcomes for all of our courses - if they didn't we'd be doing something wrong!"
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+ "text": "Community\nWe can see that through the provision of these events it has created valuable networks between the learners. We know that on an everyday basis they may be the only one in their lab or team working on this type of work and they lack contact with a colleague where they can chat through ideas or get some advice. We offer a Slack channel, weekly online help sessions and code retreats to help support learners. We are also pleased to be working closely with SSI, NorthernBUG, EBnet and University of York Bioinformatics Group which also enables learners a wider access to learning resources and opportunity to network."
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- "text": "Prenomics\nOverall the biggest improvements were seen in our Prenomics course, which is what we might expect. Most participants started with little to no knowledge of most of the topics discussed, and we saw their confidence soar over the two day course. Prenomics is designed to give participants a gentle introduction to the command line and provide a confidence boost for those who might feel intimidated, so we're really happy to see that this seems to be working.\nIn particular participants saw a big leap in their confidence using the command line with a mean score increase of almost 3.5 points. On average learners finished the course feeling somewhere between \"comfortable most of the time\" (5) and \"confident\" (6), which is excellent news.\n\n\n\n."
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+ "section": "Equality and diversity",
+ "text": "Equality and diversity\nWhen organising courses and online sessions we strive to accommodate individuals’ specific needs to ensure that all learners have the same equal access and opportunities to our learning resources. We recognise that unfortunately it is still the case that women, members of the LGBTQ community, people with disabilities and those from ethnic-minorities or socially-disadvantaged groups are consistently underrepresented in research and HPC. To try and combat this, we offer Equality and Diversity Scholarships to help those from underrepresented groups to support costs related to completing the training courses such as travel, childcare etc."
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- "text": "Genomics\nWe also saw big improvements in confidence in Genomics. We also saw great improvement in Genomics topics - approximately equal across all themes. Most participants started the course with a middling level of confidence using the command line, likely as a result of taking part in Prenomics beforehand. The average increase in score was between 2 and 2.5 points depending on the topic, with the average score after taking the course hovering around 5 - \"fairly comfortable most of the time\".\n\n\n\n."
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+ "text": "Funding\nWe understand that financial hardship and lack of available funding is a key player in preventing people accessing and attending training activities, a problem which has been exacerbated by the recent increases in cost of living. Therefore we have recently introduced Hardship Scholarships which are available to anyone who requires financial assistance to attend Cloud-SPAN courses and events. Scholarships can be used to cover travel, childcare or general costs associated with completing the training."
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- "text": "Metagenomics\nThe Metagenomics course feedback was of particular interest as it was the first time we had run the course, so we were keen to see how people got on. Overall, participants finished the course with an average understanding score between 4 (\"Fairly comfortable in some aspects\") and 5 (\"Comfortable most of the time\") for all of the topics. Most learners started the course with a higher initial understanding for core knowledge such as command line and sequencing, so the scope for improvement was more limited than in, for example, the Prenomics course. Overall we're pleased with the increase in understanding but are looking at how we can make things even clearer during the course, to boost confidence even further.\n\n\n\n."
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+ "section": "How to apply for funding",
+ "text": "How to apply for funding\nCheck your eligibility on the scholarships page on our website. To apply for funding please complete the course registration form and include the relevant information in the scholarship section. All applications received before the Scholarship deadline will be reviewed by the Scholarship Panel."
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- "text": "Upcoming courses\nWe will be running our Metagenomics course again from Tuesday 11 April until Friday 21 April 2023. This course is aimed at environmental scientists looking to use high performance computing for metagenomics analysis, but would be suitable for anyone with an interest in metagenomics. ➡️ Register here! ⬅️\nWe will also be running a workshop on Statistically Useful Experimental Design on Friday 14 April 2023. This course will be held in-person at University of York campus and is primarily discussion-based. ➡️ Register here! ⬅️"
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+ "text": "Upcoming scholarship deadlines\n🔷 Scholarship deadline 13 March Metagenomics with High Performance Computing 11-21 April (Online workshop)\n🔷 Scholarship deadline 31 March Statistically useful experimental design 14 April 2023 (University of York)\nAny questions get in touch cloud-span-project@york.ac.uk or follow us @SpanCloud\n\n\n\n."
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- "text": "Hardware\nThe size and nature of ‘omics data means it is often necessary to employ high performance computing (HPC) resources for analysis. This presents an inherent challenge as use of such resources requires a specific skill set that not all researchers will have (see ‘skills’ below for more details).\nA secondary challenge relating to hardware is the rapidly changing HPC landscape. Between institutions HPC architectures can vary wildly. Although the basic skills needed to access them remain the same, the setup and execution of jobs may look quite different. Even within institutions, HPC setups mature and are replaced regularly as new technologies develop and the demand for resources grows. For example, the Biology department at the University of York has had access to three different setups (c2d2, YARCC and Viking) in the last nine years, with a new iteration (Viking2) currently in the works. This frequent turnover requires users to continually adjust and adapt their workflows to the new system.\n\n\nSoftware\nThere are several issues surrounding the software involved in analysis of environmental omics datasets. Firstly, software tends to have a steep learning curve, requiring a substantial time investment for researchers. This investment will not necessarily always pay off, if the end result is not what is required. \nSecondly, even if a piece of software does do what is needed, it is not guaranteed that it will be usable on the HPC architecture available. Installation of software is not always straightforward, if it is allowed in the first place. The rapid turnover and replacement of HPC architectures only serves to compound this problem, and the heterogeneity of HPC setups between institutions makes it difficult to find bespoke instructions for software installation.\nThe final, broader issue is around access to learning resources and tutorials. Some popular, non-field-specific tools such as R or Python have countless online tutorials and instructions dedicated to their use, aimed at all different levels of understanding. Others, especially more niche software programs, have very few resources. Those that do exist may be out of date, or assume a level of knowledge beyond that of most novices (for example, many documentation pages are entirely inaccessible to a newcomer). As new software emerges and supersedes previously popular programs, the lack of help available only worsens.\n\n\nSkills\nAs previously mentioned, environmental omics analysis has a steep learning curve. A major challenge for many new researchers is grappling with previously unencountered skills such as using the UNIX command line, navigating file systems, writing shell scripts, grappling with dependencies and specifying resources for HPC. This is all before any specific pieces of software are involved, each of which will require its own set of skills and understanding.\nThese skills are required on top of the experimental design and data collection skills needed to generate datasets in the first place. Often those collecting data are the ones best placed to know how to interrogate it, as all experiments are different and bespoke analysis is crucial. This requires researchers to learn and juggle a large collection of skills, not all of which are immediately relevant to their chosen area of study.\n\n\nTime\nFinally, there are time investments involved in all of the above challenges. There is the ‘brain time’ involved in learning new skills, problem-solving and working with new software. Then, once an analysis is ready to run, it will take time to run. HPC resources are usually shared across many users, with jobs being added to a queue to run when resources are available - analyses requiring large amounts of compute may be queued for days or weeks waiting for the required resources to come available. In addition, some analyses take a long time to run given the size of the datasets involved and the complexity of the analysis.\nOnce analysis is completed time must be invested in interpreting and visualising the results. If parameters need to be adjusted following this, then the whole process must begin again. This makes optimisation of analysis difficult and time-consuming to the point that it may not even happen at all.\nAt Cloud-SPAN our goal is to help you overcome these challenges. Read more about the courses we offer or take a look at our introductory ’Prenomics’ course materials or specialised Genomics course to see how our training can equip you better!\n\n\n\n."
+ "text": "We are currently recruiting for a Research Training Lead to join us on a 6 month contract, with the opportunity to work remotely or on campus at the University of York.\nYou will be responsible for the development and (mainly online) delivery of teaching covering the skills required to generate and analyse omics data using Cloud HPC resources. View our current set of courses. The role could be carried out by two part-time appointments.\n\nAre you a data enthusiast who loves to share their expertise?\nWant to improve the UK’s capacity to address global challenges such as environmental protection, bio-remediation and resource recovery?\n\nWe really welcome and encourage applications from people without the listed desirable attributes but who love learning new skills. Empathy for learners and a willingness and demonstrated ability to learn new skills are more important than extensive experience!\nFurther details can be found on the University of York’s Website.\n\n\n\n."
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- "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": "We are currently recruiting for a Research Training Lead to join us on a 6 month contract, with the opportunity to work remotely or on campus at the University of York.\nYou will be responsible for the development and (mainly online) delivery of teaching covering the skills required to generate and analyse omics data using Cloud HPC resources. View our current set of courses. The role could be carried out by two part-time appointments.\n\nAre you a data enthusiast who loves to share their expertise?\nWant to improve the UK’s capacity to address global challenges such as environmental protection, bio-remediation and resource recovery?\n\nWe really welcome and encourage applications from people without the listed desirable attributes but who love learning new skills. Empathy for learners and a willingness and demonstrated ability to learn new skills are more important than extensive experience!\nFurther details can be found on the University of York’s Website.\n\n\n\n."
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- "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."
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+ "text": "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!\nThe 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?\n\n\nF is for Findable\nBefore 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.\nAnother 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.\n\n\nA is for Accessible\nOnce 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.\nA 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.\n\n\nI is for Interoperable\nSo 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.\nThe 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.\n\n\nR is for Reusable\nThis 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.\nWe 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. \n\n\nSummary\nThe 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.\nThe 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, or look out for our next blog post!\nFurther reading:\n\nThe 10 FAIR Principles\nPaper in Nature: The FAIR Guiding Principles for scientific data management and stewardship"
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- "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."
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+ "text": "Just to let you know regarding an event happening on Wednesday 19th October which might be of interest: the UK Reproducibility Network are running an online workshop on FAIR data in the life sciences which should be really informative and useful. You’ll learn about what FAIR data is, why it’s important and where you can go for further training on this issue. Plus, our very own Cloud-SPAN’s Evelyn Greeves will be talking about Cloud-SPAN and how we’ve made our courses FAIR!\nIf you’re:\n👩🔬👩🏿🔬👨🏽🔬 someone who produces and analyses data\n📊 a bioinformatician\n👩🏻💻👨🏾💻 a research software engineer\n🔢 a statistician\n \nthen this workshop is for you. You can read more about the workshop here and register to attend here. We hope to see some of you there!\nUpcoming Cloud-SPAN Courses \nPrenomics: 22-23 November 2022 (online workshop or complete via self-study)\nGenomics: 6-7 December 2022 (in-person workshop or complete via self-study)\nGenomics self-study: registration now open - start at anytime\n\n\n\n."
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- "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)."
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+ "text": "The Cloud-SPAN team would like to let you know about more opportunities for online training! Ed-DaSH from the University of Edinburgh, is a Data Science training programme for Health and Biosciences funded under the same scheme as Cloud-SPAN (UKRI innovation scholars award). Like Cloud-SPAN, Ed-DaSH is partnered with the The Software Sustainability Institute and you will find similarities in our approach to teaching computational topics to life scientists. Their upcoming workshops are:\n\n13:00-17:00 14-17 June – FAIR in (Biological) Practice\n10:00-13:00 5-8 July – Introduction to Statistics with R(this is a course written by Cloud-SPAN’s Emma Rand and Univerity of York Biology PhD student Ezra Herman)\n09:30-13:00 26-29 July – High dimensional statistics with R\n13:00-16:00 23-26 August – Machine learning\n\n You can register via the University of Edinburgh ePay system - the courses are free but have a refundable deposit. Contact them at ed-dash@ed.ac.uk or on Twitter @EdDaSH_Training, with any questions.\n\n\n\n."
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- "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."
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+ "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."
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+ "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."
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- "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": "Register using the [online form]\nGenomics teaches data management and analysis for genomics research including:\nDates for the next Genomics workshop will be finalised shortly."
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- "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"
+ "text": "Target audience\n\nLearners who have completed the Prenomics Course\nPhD Students & Researchers\nThis course would be appropriate for learners with experience using the command line, who are expecting to generate a dataset in the future or those who already have a dataset and would like guidance on how to analyse it."
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- "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."
+ "text": "Registration\nThere are 30 places available for this online workshop, please register using the [online form]. This course is free of charge."
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- "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\nKnowledge: learners should have completed the Prenomics course or be able to successfully complete the self-assessment quiz. Learners are also expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Software: view the required software set-up."
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- "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\n\n\n\n\n\n\n\n\nMonday\n10:00 - 13:00\nSession 1 - Project management for cloud genomics\n\n\n\n\n• Learn how to structure your data and metadata • Plan for an NGS project • Learn about the benefits of cloud computing\n\n\nWednesday\n10:00 - 12:30\nSession 2 - Data preparation and organisation\n\n\n\n\n• Learn how to automate commonly used workflows • Organise your file system for a new project • Use command-line tools for quality control.\n\n\nMonday\n10:00 - 13:00\nSession 3 - Assessing read quality; trimming and filtering reads.\n\n\n\n\n• Trimming and filtering • Learn how to filter out poor quality data • Assessing read quality\n\n\nWednesday\n11:00 - 14:00\nSession 4 - Finding sequence variants\n\n\n\n\n• Understand the steps involved in variant calling • Describe the types of data formats encountered during variant calling • Use command line tools to perform variant calling • Instructors will give a demonstration on how to use the Integrative Genomics Viewer (IGV), an interactive tool for the visual exploration of genomic data."
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+ "text": "Learning outcomes\nFollowing completion of this course, learners will be able to\n\nstructure their data and metadata and plan for an NGS project\norganise and document genomics data and bioinformatics workflows\nunderstand what information is needed by a sequencing facility\ngain practice navigating file systems, creating, copying, moving, and removing files and directories\nuse command-line tools to assess read quality and perform quality control\nalign reads to a reference genome, and identify and visualise sequence variants\nwork with Amazon AWS cloud computing and transfer data between a local computer and cloud resources"
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+ "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"
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+ "text": "Pre-requisites\n\nAttendees should have completed the a Cloud-SPAN course\nAttendees will need to bring their own laptop to this event"
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+ "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."
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- "text": "Register using the [online form]\nGenomics teaches data management and analysis for genomics research including:\nDates for the next Genomics workshop will be finalised shortly."
+ "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:"
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- "text": "Target audience\n\nLearners who have completed the Prenomics Course\nPhD Students & Researchers\nThis course would be appropriate for learners with experience using the command line, who are expecting to generate a dataset in the future or those who already have a dataset and would like guidance on how to analyse it."
+ "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"
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- "text": "Registration\nThere are 30 places available for this online workshop, please register using the [online form]. This course is free of charge."
+ "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."
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- "text": "Pre-requisites\nKnowledge: learners should have completed the Prenomics course or be able to successfully complete the self-assessment quiz. Learners are also expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Software: view the required software set-up."
+ "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."
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- "text": "Programme\n\n\n\n\n\n\n\n\nMonday\n10:00 - 13:00\nSession 1 - Project management for cloud genomics\n\n\n\n\n• Learn how to structure your data and metadata • Plan for an NGS project • Learn about the benefits of cloud computing\n\n\nWednesday\n10:00 - 12:30\nSession 2 - Data preparation and organisation\n\n\n\n\n• Learn how to automate commonly used workflows • Organise your file system for a new project • Use command-line tools for quality control.\n\n\nMonday\n10:00 - 13:00\nSession 3 - Assessing read quality; trimming and filtering reads.\n\n\n\n\n• Trimming and filtering • Learn how to filter out poor quality data • Assessing read quality\n\n\nWednesday\n11:00 - 14:00\nSession 4 - Finding sequence variants\n\n\n\n\n• Understand the steps involved in variant calling • Describe the types of data formats encountered during variant calling • Use command line tools to perform variant calling • Instructors will give a demonstration on how to use the Integrative Genomics Viewer (IGV), an interactive tool for the visual exploration of genomic data."
+ "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"
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+ "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"
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+ "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."
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- "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": "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."
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- "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."
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+ "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."
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- "text": "The Cloud-SPAN team would like to let you know about more opportunities for online training! Ed-DaSH from the University of Edinburgh, is a Data Science training programme for Health and Biosciences funded under the same scheme as Cloud-SPAN (UKRI innovation scholars award). Like Cloud-SPAN, Ed-DaSH is partnered with the The Software Sustainability Institute and you will find similarities in our approach to teaching computational topics to life scientists. Their upcoming workshops are:\n\n13:00-17:00 14-17 June – FAIR in (Biological) Practice\n10:00-13:00 5-8 July – Introduction to Statistics with R(this is a course written by Cloud-SPAN’s Emma Rand and Univerity of York Biology PhD student Ezra Herman)\n09:30-13:00 26-29 July – High dimensional statistics with R\n13:00-16:00 23-26 August – Machine learning\n\n You can register via the University of Edinburgh ePay system - the courses are free but have a refundable deposit. Contact them at ed-dash@ed.ac.uk or on Twitter @EdDaSH_Training, with any questions.\n\n\n\n."
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+ "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."
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- "text": "Just to let you know regarding an event happening on Wednesday 19th October which might be of interest: the UK Reproducibility Network are running an online workshop on FAIR data in the life sciences which should be really informative and useful. You’ll learn about what FAIR data is, why it’s important and where you can go for further training on this issue. Plus, our very own Cloud-SPAN’s Evelyn Greeves will be talking about Cloud-SPAN and how we’ve made our courses FAIR!\nIf you’re:\n👩🔬👩🏿🔬👨🏽🔬 someone who produces and analyses data\n📊 a bioinformatician\n👩🏻💻👨🏾💻 a research software engineer\n🔢 a statistician\n \nthen this workshop is for you. You can read more about the workshop here and register to attend here. We hope to see some of you there!\nUpcoming Cloud-SPAN Courses \nPrenomics: 22-23 November 2022 (online workshop or complete via self-study)\nGenomics: 6-7 December 2022 (in-person workshop or complete via self-study)\nGenomics self-study: registration now open - start at anytime\n\n\n\n."
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+ "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)."
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- "text": "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!\nThe 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?\n\n\nF is for Findable\nBefore 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.\nAnother 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.\n\n\nA is for Accessible\nOnce 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.\nA 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.\n\n\nI is for Interoperable\nSo 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.\nThe 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.\n\n\nR is for Reusable\nThis 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.\nWe 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. \n\n\nSummary\nThe 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.\nThe 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, or look out for our next blog post!\nFurther reading:\n\nThe 10 FAIR Principles\nPaper in Nature: The FAIR Guiding Principles for scientific data management and stewardship"
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+ "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."
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- "text": "We are currently recruiting for a Research Training Lead to join us on a 6 month contract, with the opportunity to work remotely or on campus at the University of York.\nYou will be responsible for the development and (mainly online) delivery of teaching covering the skills required to generate and analyse omics data using Cloud HPC resources. View our current set of courses. The role could be carried out by two part-time appointments.\n\nAre you a data enthusiast who loves to share their expertise?\nWant to improve the UK’s capacity to address global challenges such as environmental protection, bio-remediation and resource recovery?\n\nWe really welcome and encourage applications from people without the listed desirable attributes but who love learning new skills. Empathy for learners and a willingness and demonstrated ability to learn new skills are more important than extensive experience!\nFurther details can be found on the University of York’s Website.\n\n\n\n."
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+ "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."
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- "text": "We are currently recruiting for a Research Training Lead to join us on a 6 month contract, with the opportunity to work remotely or on campus at the University of York.\nYou will be responsible for the development and (mainly online) delivery of teaching covering the skills required to generate and analyse omics data using Cloud HPC resources. View our current set of courses. The role could be carried out by two part-time appointments.\n\nAre you a data enthusiast who loves to share their expertise?\nWant to improve the UK’s capacity to address global challenges such as environmental protection, bio-remediation and resource recovery?\n\nWe really welcome and encourage applications from people without the listed desirable attributes but who love learning new skills. Empathy for learners and a willingness and demonstrated ability to learn new skills are more important than extensive experience!\nFurther details can be found on the University of York’s Website.\n\n\n\n."
+ "text": "Hardware\nThe size and nature of ‘omics data means it is often necessary to employ high performance computing (HPC) resources for analysis. This presents an inherent challenge as use of such resources requires a specific skill set that not all researchers will have (see ‘skills’ below for more details).\nA secondary challenge relating to hardware is the rapidly changing HPC landscape. Between institutions HPC architectures can vary wildly. Although the basic skills needed to access them remain the same, the setup and execution of jobs may look quite different. Even within institutions, HPC setups mature and are replaced regularly as new technologies develop and the demand for resources grows. For example, the Biology department at the University of York has had access to three different setups (c2d2, YARCC and Viking) in the last nine years, with a new iteration (Viking2) currently in the works. This frequent turnover requires users to continually adjust and adapt their workflows to the new system.\n\n\nSoftware\nThere are several issues surrounding the software involved in analysis of environmental omics datasets. Firstly, software tends to have a steep learning curve, requiring a substantial time investment for researchers. This investment will not necessarily always pay off, if the end result is not what is required. \nSecondly, even if a piece of software does do what is needed, it is not guaranteed that it will be usable on the HPC architecture available. Installation of software is not always straightforward, if it is allowed in the first place. The rapid turnover and replacement of HPC architectures only serves to compound this problem, and the heterogeneity of HPC setups between institutions makes it difficult to find bespoke instructions for software installation.\nThe final, broader issue is around access to learning resources and tutorials. Some popular, non-field-specific tools such as R or Python have countless online tutorials and instructions dedicated to their use, aimed at all different levels of understanding. Others, especially more niche software programs, have very few resources. Those that do exist may be out of date, or assume a level of knowledge beyond that of most novices (for example, many documentation pages are entirely inaccessible to a newcomer). As new software emerges and supersedes previously popular programs, the lack of help available only worsens.\n\n\nSkills\nAs previously mentioned, environmental omics analysis has a steep learning curve. A major challenge for many new researchers is grappling with previously unencountered skills such as using the UNIX command line, navigating file systems, writing shell scripts, grappling with dependencies and specifying resources for HPC. This is all before any specific pieces of software are involved, each of which will require its own set of skills and understanding.\nThese skills are required on top of the experimental design and data collection skills needed to generate datasets in the first place. Often those collecting data are the ones best placed to know how to interrogate it, as all experiments are different and bespoke analysis is crucial. This requires researchers to learn and juggle a large collection of skills, not all of which are immediately relevant to their chosen area of study.\n\n\nTime\nFinally, there are time investments involved in all of the above challenges. There is the ‘brain time’ involved in learning new skills, problem-solving and working with new software. Then, once an analysis is ready to run, it will take time to run. HPC resources are usually shared across many users, with jobs being added to a queue to run when resources are available - analyses requiring large amounts of compute may be queued for days or weeks waiting for the required resources to come available. In addition, some analyses take a long time to run given the size of the datasets involved and the complexity of the analysis.\nOnce analysis is completed time must be invested in interpreting and visualising the results. If parameters need to be adjusted following this, then the whole process must begin again. This makes optimisation of analysis difficult and time-consuming to the point that it may not even happen at all.\nAt Cloud-SPAN our goal is to help you overcome these challenges. Read more about the courses we offer or take a look at our introductory ’Prenomics’ course materials or specialised Genomics course to see how our training can equip you better!\n\n\n\n."
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- "text": "Here at Cloud-SPAN HQ our official tagline is that we are here to upskill researchers and enable them to perform complex analyses on cloud-based platforms. Which we are achieving through the provision of training courses and online modules. However, as a member of the team who works behind the scenes as project manager, I feel that we are offering much more than that."
+ "text": "We’ve finished our analysis of the feedback from our courses held at the end of last year: Prenomics, Genomics and Metagenomics. We’re pleased to see that on average participants saw an improvement across all of the learning outcomes for all of our courses - if they didn't we'd be doing something wrong!"
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- "text": "Welcoming learning environment\nUp until now we have delivered courses online and held code retreats in person. The course materials and delivery are excellent thanks to our talented instructors. I find the real added value here is that the learning environment is very welcoming, encouraging and inclusive. A lot of our participants are complete beginners or new to this world of big data, command line and cloud computing. And learning such new skills could be very daunting for some. At our courses there aren’t any big egos, there’s just someone there to work through questions and find solutions to your problems."
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+ "text": "Prenomics\nOverall the biggest improvements were seen in our Prenomics course, which is what we might expect. Most participants started with little to no knowledge of most of the topics discussed, and we saw their confidence soar over the two day course. Prenomics is designed to give participants a gentle introduction to the command line and provide a confidence boost for those who might feel intimidated, so we're really happy to see that this seems to be working.\nIn particular participants saw a big leap in their confidence using the command line with a mean score increase of almost 3.5 points. On average learners finished the course feeling somewhere between \"comfortable most of the time\" (5) and \"confident\" (6), which is excellent news.\n\n\n\n."
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- "text": "Community\nWe can see that through the provision of these events it has created valuable networks between the learners. We know that on an everyday basis they may be the only one in their lab or team working on this type of work and they lack contact with a colleague where they can chat through ideas or get some advice. We offer a Slack channel, weekly online help sessions and code retreats to help support learners. We are also pleased to be working closely with SSI, NorthernBUG, EBnet and University of York Bioinformatics Group which also enables learners a wider access to learning resources and opportunity to network."
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+ "text": "Genomics\nWe also saw big improvements in confidence in Genomics. We also saw great improvement in Genomics topics - approximately equal across all themes. Most participants started the course with a middling level of confidence using the command line, likely as a result of taking part in Prenomics beforehand. The average increase in score was between 2 and 2.5 points depending on the topic, with the average score after taking the course hovering around 5 - \"fairly comfortable most of the time\".\n\n\n\n."
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- "text": "Equality and diversity\nWhen organising courses and online sessions we strive to accommodate individuals’ specific needs to ensure that all learners have the same equal access and opportunities to our learning resources. We recognise that unfortunately it is still the case that women, members of the LGBTQ community, people with disabilities and those from ethnic-minorities or socially-disadvantaged groups are consistently underrepresented in research and HPC. To try and combat this, we offer Equality and Diversity Scholarships to help those from underrepresented groups to support costs related to completing the training courses such as travel, childcare etc."
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+ "text": "Metagenomics\nThe Metagenomics course feedback was of particular interest as it was the first time we had run the course, so we were keen to see how people got on. Overall, participants finished the course with an average understanding score between 4 (\"Fairly comfortable in some aspects\") and 5 (\"Comfortable most of the time\") for all of the topics. Most learners started the course with a higher initial understanding for core knowledge such as command line and sequencing, so the scope for improvement was more limited than in, for example, the Prenomics course. Overall we're pleased with the increase in understanding but are looking at how we can make things even clearer during the course, to boost confidence even further.\n\n\n\n."
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- "text": "Funding\nWe understand that financial hardship and lack of available funding is a key player in preventing people accessing and attending training activities, a problem which has been exacerbated by the recent increases in cost of living. Therefore we have recently introduced Hardship Scholarships which are available to anyone who requires financial assistance to attend Cloud-SPAN courses and events. Scholarships can be used to cover travel, childcare or general costs associated with completing the training."
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+ "text": "Upcoming courses\nWe will be running our Metagenomics course again from Tuesday 11 April until Friday 21 April 2023. This course is aimed at environmental scientists looking to use high performance computing for metagenomics analysis, but would be suitable for anyone with an interest in metagenomics. ➡️ Register here! ⬅️\nWe will also be running a workshop on Statistically Useful Experimental Design on Friday 14 April 2023. This course will be held in-person at University of York campus and is primarily discussion-based. ➡️ Register here! ⬅️"
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- "text": "How to apply for funding\nCheck your eligibility on the scholarships page on our website. To apply for funding please complete the course registration form and include the relevant information in the scholarship section. All applications received before the Scholarship deadline will be reviewed by the Scholarship Panel."
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+ "text": "The Cloud-SPAN team has been awarded a grant to expand our training to the Natural Environment Research Council (NERC) remit under the Advanced training for early-career environmental scientists call. We will be developing an accessible online course “Getting started with High Performance Computing: FAIR training for environmental scientists” using the same cloud-based infrastructure used in our other courses. We will supply AWS services to up to 60 participants undertaking the course either in tutor-led workshops or by self-study.\nThose needing funds for childcare or accessibility to enable their participation in the training will be able apply for a Scholarship and up to 30 participants will receive headsets and second monitors facilitate online engagement. The course will be running in April 2023 - please let your ecology colleagues know to look out for the course!\n\nKey info\n🔷 Metagenomics with High Performance Computing ▶ 11-21 April (Online workshop)\n🔷 Scholarship deadline 13 March\n🔷 Register for the online workshop\n🔷 Register for the self-study mode\n\n\n\n."
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- "section": "Upcoming scholarship deadlines",
- "text": "Upcoming scholarship deadlines\n🔷 Scholarship deadline 13 March Metagenomics with High Performance Computing 11-21 April (Online workshop)\n🔷 Scholarship deadline 31 March Statistically useful experimental design 14 April 2023 (University of York)\nAny questions get in touch cloud-span-project@york.ac.uk or follow us @SpanCloud\n\n\n\n."
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+ "href": "blogs/challenges_solutions_aug22/index.html",
+ "title": "Our Solutions to Challenges in Environmental ’Omics",
+ "section": "",
+ "text": "Here’s what we’re doing at Cloud-SPAN to address the challenges we discussed previously.\nJust to recap, here are our four main challenges:\nAt Cloud-SPAN we have two main weapons in our arsenal against these challenges: cloud computing and training. Let’s look at each of those in detail."
},
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- "href": "blogs/R_intro_may23/index.html",
- "title": "NEW online workshop - Introduction to R",
+ "objectID": "blogs/challenges_solutions_aug22/index.html#cloud-hpc",
+ "href": "blogs/challenges_solutions_aug22/index.html#cloud-hpc",
+ "title": "Our Solutions to Challenges in Environmental ’Omics",
+ "section": "Cloud HPC",
+ "text": "Cloud HPC\nWe use commercially-available cloud computing resources to address the challenges of hardware, software and time.\nHere’s how it works: we teach our courses inside a containerised instance, which is a virtual environment containing pre-loaded software and files. The instance runs on hardware borrowed from a commercial provider (in our case, Amazon Web Services). All our learners have to do is log into the cloud instance we provide, and they will have access to all of the software and data used in the course. The instances all start out identical, so the file structure always looks the same, and they run on enough borrowed resources to make analysis relatively quick and easy.\nUsing this kind of pre-loaded instance benefits our learners by removing complications around different HPC setups and the installation of software onto a cluster. It also makes it easier for us to teach - we know that everyone is starting with the same setup, so we can offer our courses to anyone regardless of institution. It allows us to model best practices for directory structure and project organisation, and save time when troubleshooting issues.\nAnother major advantage of running analyses on cloud resources is that we don’t have to wait in a queue for resources to be available, as we’ve already loaned out the resources we need. This can save a lot of time for large analyses, and is especially useful for teaching.\nAfter completing one of our courses, learners can go away and apply their new skills to their own data by setting up their own cloud instance, which is identical to the one used in the course. It contains all the same software and basic file structures, so provides a familiar environment for further learning and analysis. Using these kinds of services outside of the course does incur a cost, but we also support learners in applying for research credits."
+ },
+ {
+ "objectID": "blogs/challenges_solutions_aug22/index.html#training",
+ "href": "blogs/challenges_solutions_aug22/index.html#training",
+ "title": "Our Solutions to Challenges in Environmental ’Omics",
+ "section": "Training",
+ "text": "Training\nOur other main solution is providing high quality, free-of-charge training courses with a low barrier to entry and no assumptions of prior knowledge. These courses allow us to address challenges around skills and the skills gap.\nAll of our courses are underpinned by a core ‘Prenomics’ module, which provides a supportive and carefully paced introduction to navigating directories and using the UNIX command line. Accessing the cloud HPC services described above is impossible without these skills. Using our purpose-built environment we guide new learners through the basics with a strong focus on contextualising new skills within the field of environmental ’omics.\nWe also provide core modules in using the programming language R, again with a focus on analysis and visualisation of ’omics data, and on creating cloud instances.\nOur specialised courses follow on from Prenomics and cover topics such as genomics, metagenomics, automating analyses and designing statistically useful experiments. Again, we keep the barrier to participation low by contextualising learning and keeping new ideas to the bare minimum - no frills!"
+ },
+ {
+ "objectID": "blogs/challenges_solutions_aug22/index.html#summary",
+ "href": "blogs/challenges_solutions_aug22/index.html#summary",
+ "title": "Our Solutions to Challenges in Environmental ’Omics",
+ "section": "Summary",
+ "text": "Summary\nIn summary, the Cloud-SPAN project combines high-quality training with cloud computing expertise to address four major challenges in the field of environmental ’omics. Using our unique containerised instances we can provide adequate resources for efficient analysis with software pre-installed, saving time and effort. Our courses are designed to equip learners with the skills they need to perform analyses on these cloud instances and beyond, with the overall aim to lessen the load of learning on the backs of researchers and help them improve analysis times and efficiency.\nOur containerised instances solve the challenges of:\n\nHardware, by providing a harmonised HPC platform across institutions and potentially increasing the compute resources available to individuals.\nSoftware, by providing pre-installed software which removes the time-consuming step of software installation.\nTime, by speeding up analyses and eradicating the need to queue to access HPC.\n\nOur training approach solves the challenge of:\n\nSkills, by ensuring a low barrier to participation and equipping researchers with vital skills.\n\nFind out for yourself how our solutions to these challenges could benefit you. Read more about the courses we offer or take a look at our introductory ‘Prenomics’ course materials or specialised Genomics course to see how our training can equip you better\n\n\n\n."
+ },
+ {
+ "objectID": "blogs/code_retreat_dec22/index.html",
+ "href": "blogs/code_retreat_dec22/index.html",
+ "title": "Cloud-SPAN Code Retreat",
"section": "",
- "text": "Save the date - registration opening soon!\nJoin us for this free online two-hour workshop which provides an introduction to R for complete beginners. By 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\n\nThe workshop assumes no prior experience of coding. We allow plenty of time for questions and we provide a high level of support for each learner. The workshop will be delivered by Emma Rand, an excellent instructor with a passion for teaching.\n\n\nEvent details\n💻 Core R Workshop\n🗓️ Tuesday 20th June 2023\n🕑 2-4 pm\n📍 Online\n\n\nPlaces available\nThere are 30 places available for this online course.\nPriority will be given to NERC funded students and researchers, as well as researchers from underrepresented groups, although we encourage everyone to apply.\nApplication deadline: Friday 9th June. Applicants will be notified by Tuesday 13th June if they have been allocated a place.\n\n\nRegistration fee\nThis workshop is funded by the Natural Environment Research Council (NERC) and therefore it is free to attend for candidates based in the UK.\n\n\nHow to register\nRegistration will open shortly; an online registration form will be available on the Cloud-SPAN website. If you so wish, you can also register your interest in the workshop and we will contact you when registration opens.\n\n\nKeep in touch!\nLinkedIn\nTwitter\nCloud-SPAN website\n\n\n\n."
+ "text": "We are excited to announce that our next Code Retreat will take place on Monday 9th January 2023 at the University of York. It provides a chance for course alumni to come together and work on their own data problems with the support of Cloud-SPAN instructors.\n\nWhat happens at a Code Retreat?\nAt previous retreats some people took the opportunity to revisit course materials and ask questions about the topics they didn't understand. There are plenty of helpers on hand to answer questions and test understanding.\nYou could also apply the workflows and analyses taught in the Genomics course to your own datasets. Helpers are also on hand to discuss topics such as:\n\nhow to organise bioinformatics projects;\nwhich tools are most effective;\nhow to approach a problem;\nwhat analysis is best for a certain type of data;\n\nas well as many others. \nSome participants already know what help they will need and have specific questions to address during the day. Those with a less clear understanding of their problem could benefit from talking through their data and getting guidance from our experienced instructors. You could even try out new software tools.\n\n\nWhat do previous participants have to say?\n“I had a great time at the Cloud-Span retreat. I went from Lancaster just for it, and it was worth it. I got support in analysing the data I had in hand. That was really satisfying applying what we preciously learned (using our data this time). Having the Cloud-Span Team around to support us was essential. It's been great learning with them, and I would 100% recommend them!”\n\n\n\n.\n\n\n\n\nJoin us for our next event!\nOur next Code Retreat for Cloud-SPAN Alumni will take on 10:30-15:30, Monday 9th January 2023 at the University of York. Feel free to stay for the whole event or drop in when you are free. Lunch will be provided and we offer support to cover travel expenses.\nSign up using the registration form\n\n\nTraining courses\nIf you are interested in attending our free training courses please visit our website for further information."
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- "href": "blogs/genomics_reflection_dec21/index.html",
- "title": "Course Update",
+ "objectID": "blogs/bioinformatics_meeting_careers_jun22/index.html",
+ "href": "blogs/bioinformatics_meeting_careers_jun22/index.html",
+ "title": "Bioinformatics Meeting on ‘Career pathways into bioinformatics’",
"section": "",
- "text": "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:\n\nFirst thing’s first... positive feedback!\nWe had some amazing feedback from our first run-through! We asked our participants to rate their level of comfort with a number of topics before and after completing the course.\nAs you can see in the graph below, on average our participants felt that their level of comfort had improved after taking the course for all topics. This is great news!\nIn 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.\n\n\n\nThe BIG Problem: Time flies\nThe biggest problem we ran into was time. We just didn’t have enough of it...\n...and that means we need to seriously rethink how we structure the content of our course. You can see from the graph above that the topics people felt they had improved their confidence the least in were those relating to genomics - assessing read quality, trimming and filtering, and variant calling.\nThat’s because before we could teach those topics, we had to make sure people felt really comfortable using the command line and organising their files. Unfortunately, as we got more and more behind schedule, this meant the genomics topics got less and less time allocated to them.\nThis is a problem, because the title of the course was Foundational Genomics. If participants are finishing our course feeling like they are not comfortable with variant calling (which is what a score of 3 means) then we need to make some changes. Plus, the genomics bit is meant to be the fun bit!\nThe written feedback we had from participants after the course, while mostly positive, generally reflected this sentiment too.\n\n\nThe BIG Solution: Course structure\nIn light of this feedback, we’ve decided to split our 4 x half-day Foundational Genomics course into two shorter courses: one 2 x half-day “Prenomics” course and one 4 x half-day “Genomics” course.\nThe Prenomics course will be aimed at complete beginners and will be a gentle introduction to file directories, working paths and basic command line commands. By giving ourselves two half-days to cover this content we should be able to ensure all participants are fully on board before we move onto anything more complex.\nThis course will also be optional for those who already have some basic experience using the command line. We plan to screen potential attendees using a self-test to help them determine whether they would benefit from attending the Prenomics course, or skipping straight to Genomics.\nThe Genomics course will follow directly on from Prenomics, using many of the same commands and building on them further. We should have much more time to cover essential topics such as read quality and variant calling which were rushed last time, allowing us to offer a much better educational experience.\n\n\nSome smaller problems which this change also solves...\n\nWe plan to run the Genomics course over two weeks, with 2 x half days per week. This, combined with a hopefully much less stressful volume of content to cover, will decrease pressure on our instructors and helpers, most of whom have multiple other work and teaching commitments.\nSome of our participants felt the course went far too slowly; others felt it went too fast. By screening for those who have the least experience working in the command line, we should be able to both provide more support to those who need it and stop more experienced participants from getting bored.\n\n\n\nOther updates in the pipeline\nThese two new courses, Prenomics and Genomics, will make up the ‘Foundational’ element of our content. We still have plans to developed ‘Advanced’ modules on topics such as automation and setting up cloud instances. We asked our participants to let us know what they’d like to see, and we’ll be taking these suggestions into account as we go.\nWe also have plans to run some (hopefully) in-person ‘hack days’ for alumni of our Foundational courses, where we can help participants apply the skills learned in the course to their own problems, and assist in troubleshooting any problems. We hope this will help develop our community of practice further by providing opportunities for networking and building relationships.\nAnd that’s it. Thanks for reading this far - we hope it explains some of our rationale for why the course is structured the way it is. We’re really proud of our achievements with our first ever course, and we’re looking forward to trying some new stuff out next time.\nTill next time! 👋"
+ "text": "Join the University of York’s Bioinformatics Meeting on ‘Career pathways into bioinformatics’.\nHosted by Sarah Forrester, we have a jam packed hour and a half.\nEvelyn Greeves from the Cloud-SPAN team will be leading a short session on “Introduction to FAIR and metadata” with an opportunity for you to ask any questions that you may have. \nFollowing this, have you pondered what direction to take your career or how to use your data skills in future projects? We have 3 speakers who explain how data analysis has been incorporated into their work. \n🔸 Emma Rand highlights the different paths into academia and using big data skills. \n🔸 James Chong explains how learning bioinformatics was the only way to get past the bottleneck of being able to analyse data he was generating.\n🔸 Sarah Forrester explores how bioinformatics opens doors to moving between different research niches. \nWe will then have a discussion with all speakers for the remainder of the session, which will include signposting resources. \nSession slides will be available following the event. \nEvent details: Wednesday, 6th July, 15:00-16:30 in room B/T/019 University of York. \nContact us on cloud-span-project@york.ac.uk to be added to the Bioinformatics regular mailing list!\n\n\n\n."
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https://cloud-span.github.io/cloud-span-quarto-site/blogs/AWS_Paper/index.html
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- 2024-09-23T09:30:00.387Z
+ 2024-09-23T09:37:55.568Z
https://cloud-span.github.io/cloud-span-quarto-site/contact-us.html
- 2024-09-23T09:30:00.389Z
+ 2024-09-23T09:37:55.570Z
https://cloud-span.github.io/cloud-span-quarto-site/blogs.html
- 2024-09-23T09:30:00.289Z
+ 2024-09-23T09:37:55.473Z
https://cloud-span.github.io/cloud-span-quarto-site/impact.html
- 2024-09-23T09:30:00.469Z
+ 2024-09-23T09:37:55.646Z
diff --git a/upcoming_courses.html b/upcoming_courses.html
index 50d0788..f50d500 100644
--- a/upcoming_courses.html
+++ b/upcoming_courses.html
@@ -264,7 +264,7 @@
Upcoming Courses
