Rachel Berkson
Education Manager at Wellcome Connecting Science, UK. Background in cancer genetics then education. Particularly interested in inclusive education.
Location UK
Activity
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In step 3.13, you will find a text entry box where you can submit the report for your assignment. You don't need to paste it into the comment section. Unfortunately FutureLearn accepts only plain text submissions, but if you include URLs, your reviewer should be able to copy and paste them to open the web viewer.
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Rachel Berkson replied to Jessica Ody
Great answer. We hadn't anticipated that URLs might be too long for the discussion section altogether! If you run into this problem again you can try a link shortener such as tinyurl.com
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Great! The last Activity at the end of week 3 will show you how to do this on a technical level. Completing week 3 should also give you a clearer idea of what sort of analysis you can do once you have installed BTK on your own computer.
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Rachel Berkson replied to Asime Oba
Hi Asime. I can see you've applied some filters based on GC content and coverage, but you still have mutiple sequences in your plot. You might want to choose a region of the plot that only has one circle away from the rest of the plot, so that you can easily filter down to only one sequence.
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Hi Taiwo. You may want to change the view from squares to circles - the squares view is the default when an assembly has a very large number of small contigs. You'll learn more about this is in week 2. For now, go to the Settings menu, and select the circle icon from the Shape menu. See if that gives you a plot that might be easier to understand.
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Rachel Berkson replied to yan tong
Hi there, I hope you're enjoying the course. Please avoid copying comments from other learners. That makes it hard for the Educators to understand what ideas are yours and what support you need.
Just to let you know, you don't need to comment on every step. If you just click the "Mark as complete" button when you've done the step, that's all you need to...
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Hi Alexandre, you did well at finding an organism and generating the BTK plot for your sparrow. Just be careful about reporting GC content - it's on a scale from 0 to 1, so when you read 0.4 off the X axis, that means 40% GC, not 0.4%. The percentage of GC in the genome will always be somewhere around 50%, you wouldn't expect to see a genome with 200X as many...
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Good analysis! There could potentially be two different proteobacteria in the assembly but it's more likely that one very small contig has been assigned incorrectly. In week 2 you'll learn more about how to drill down into more detail and examine the evidence for how many different species are really present.
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Rachel Berkson replied to Legana Fingerhut
No-hit means that Blast was not able to find a definitive match to a known organism. The colour assigned to no-hit here is quite similar to the light blue representing Ascomycota, so it's hard to see, but these contigs (which happen to be quite small) are present in the plot. Later in the course you'll learn about how to use filters to examine no-hit blobs...
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Rachel Berkson replied to Rachel Gray
This is a great question, @RachelGray . In week 2 you'll hear more about how to deal with assemblies where some of the information is missing.
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Thanks for this report, Keeley. It seems that some learners didn't fully understand the assignment task, which points to problems with how the course is constructed. I'm sorry that you had a disappointing experience with peer review, but I hope you found it informative to work on your own course design.
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Rachel Berkson replied to M G
I'm really glad to hear that you got some useful and encouraging feedback as well as the disheartening response that didn't match the effort you put in. It definitely is useful for us as educators to hear that the peer review task was only partially successful. We'll be reflecting on how to improve the instructions for submitting and marking the assignments...
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Rachel Berkson replied to M G
Thanks for reporting on your experience, M G. This peer review task was fairly complex, and it's a useful learning point to realize that not everybody understood how to complete the assignment. Thanks for persevering and giving what feedback you could, even if one of your assignments didn't have a clear structure.
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Rachel Berkson replied to Susan C
@SusanC @KeeleyMcCabe I understand your concerns. Although the course is officially three weeks in duration, the educator team are still around and we do try to catch up with comments that have come in a bit later. The course will remain open for 6 weeks after the official end date, so you will still have plenty of time to review the material and work on your...
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Rachel Berkson replied to Lovely Gama
Thanks for reporting that you were unable to see the video. I'm sorry that you had that experience; the best suggestion I have is that you can read the transcript linked below the video and in the Downloads area. That way you can read what this week's instructors have to say even if you can't hear them.
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That's great, Bahar. Much clearer articulation of the aims and goals of the course. I look forward to seeing how this develops as you work through this week and next.
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Rachel Berkson replied to Rachel Berkson
@SusanC I find H5P really easy to use - they have a lot of pre-built templates that you can just slot your content into, but also flexible as you can tweak the code as much as you need to. Personally, I have only used the site as part of FutureLearn courses ie purely online, not in a face-to-face classroom.
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Can you say a bit more? What aspect of Public Health Genomics? Can you think about your goals and objectives and why this training is needed?
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This is a great idea, Mara! Effective design is important in informal training too. A short lab meeting activity introducing the Pseudomonas genome database sounds like it will be really valuable both for you and your colleagues.
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Rachel Berkson replied to Nicole Dames
Your learning outcomes are coming together and give me an idea of the level and content of your course, which is a great start. The one about the Unix command-line could do with more specifics; what sort of data? What sort of analysis? Using the command-line is a fairly complex skillset in itself, so perhaps you could give an idea of the level of competence...
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Rachel Berkson replied to Ramez Tannous
This set of LOs gives me a pretty clear idea what will be in your course. I think perhaps the first one would benefit from some refinement: how will you know whether students understand these key concepts? Will they be able to explain them? Use them in calculations? Use them to describe or predict the behaviour of a structure?
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Rachel Berkson made a comment
Interesting to see enthusiasm for hybrid design in the comments here. Hybrid really can be the best of both worlds, but be aware that it can be a lot of work to create training that can work in either format. If you need flexibility to be able to switch formats at short notice, or if you have a mixture of in-person and online learners in the same activity,...
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A workshop giving an introduction to the field could be a great design project. I'm interested to see what ideas you come up with as you progress through the course.
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Rachel Berkson replied to Aneth David
That's a great question, Aneth. I would say giving adults a say in the content and process is not the same as giving them completely free choice with no direction or guidance.
For example, the curriculum may specify that the students need to learn how to perform a sequence alignment with a particular tool, but you might give them a choice of exactly which...
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Rachel Berkson replied to Nicole Dames
I like Nicole's description that undergraduates are "between adulthood and childhood". There is no hard-and-fast rule about the exact boundary of who counts as an adult learner - it depends on the context, the culture, the structure and expectations of the course etc. Personally I have facilitated successful learning activities by applying andragogy...
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Rachel Berkson replied to Olugbenga Ajulo
What an amazing example of using reflection and evaluation to improve your teaching, and seeing a measurable impact.
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Rachel Berkson replied to Monica Abrudan
@HeatherGibling That's fine, Heather. The course will remain open for a further 6 weeks after this weekend. If you submit your assignment next week or later, you will be 'paired' with another learner who is also taking things a bit more slowly, so that hopefully you will get feedback and get an opportunity to review another learner's assignment.
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Please can you avoid copying and pasting comments from other learners on the course? You don't have to reply to every step - just clicking the 'Mark as complete' button will register that you have done the step so you can get the certificate at the end of the course. If you copy from others it's hard for fellow learners and Educators to know what is really...
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It's impressive that you were able to change the course on the fly to cover more basic research skills. This is a really good illustration of why it's important to find out as much as possible about your students' prior knowledge, and also to be flexible and responsive as the course progesses.
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That's a really good observation. We've had similar trouble with live online sessions, if trainees don't have reliable internet access there can be real problems. You came up with a good solution by following up afterwards to check progress and understanding even if trainees couldn't attend the contact sessions. But that does create a lot of extra work for the...
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It's certainly hard to argue that we need experts in detection and surveillance of viral infections! It will be interesting to see as the week goes on how you will approach training people in these skills. You're looking at producing experts, and you've outlined that your learners will need to know a lot of different areas; doing PCR to amplify viral genomes...
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Great start. I particularly like how you've divided up your theoretical knowledge from your practical skills. Having those categories clear in your mind should help with designing appropriate learning activities.
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Your description sounds good to me. At this stage we're only trying to decide the high-level objectives for the course, it's fine if your specific learning outcomes need a bit more refinement before you're ready to submit your final project.
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Creating an MSc module which can also be a stand-alone course can be a real challenge, and it's likely to prompt some really strong design decisions. I'm looking forward to hearing more about this as the next two weeks progress.
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Interesting concept, designing training for one person. Many of us have to train new colleagues but we may not put thought into the design as the training happens fairly informally. Starting from good design practice could be really beneficial here!
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It will be really useful to be thinking about improvements for a course you have already run for real. What do you think would make the biggest difference to your analysis module?
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That's great, Heather. We recently developed a similar course as a FutureLearn MOOC and there was huge demand for those topics. The course isn't currently open but you can have a look at the landing page with overview and learning outcomes: https://www.futurelearn.com/courses/linux-for-bioinformatics/1
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Rachel Berkson replied to Daniela Brites
This course uses the basic format of a MOOC (massive open online course), and the learning approach is referred to as 'conversational learning' with the emphasis on the discussion section. Another term I might apply would be 'semi-synchronous' - although you are not all online simultaneously, you are working through the material at roughly the same pace,...
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Rachel Berkson made a comment
To clear up some potential confusion: when we refer to 'evaulation' in this course we are talking about evaluation of the course or learning activity itself. We use the term 'assessment' to refer to measuring the performance of students. Of course, knowing how the students are doing and whether they achieve the Learning Outcomes might be one element of your...
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Rachel Berkson replied to xen Neu
The Bloom pyramid is by no means the only way of classifying different learning activities and outcomes, it's just very commonly used in education. The important thing is to make sure your learning plan is aligned: the learning activities and assessment should be relevant to the level of the intended outcomes.
As you point out, if you want learners to be...
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Rachel Berkson replied to Heather Gibling
That is a great point about the difficulty of adaptation to the learners' needs in an asynchronous course. The approach we are using here is for educators to monitor the course, and if we see that several learners are struggling with a particular topic or activity, we can "pin" a comment with further explanation or additional resources at the top of the...
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Rachel Berkson replied to Elton Vasconcelos
This is not necessarily true. A short course can be very suitable for learning to analyse or evaluate. Learners might already have a good grounding in the subject area and are looking to build their skills in a specific technique. They might for example look at some previous experimental results and apply statistical methods to that data to argue for or...
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This seems like a good approach, Faisal. In this short introductory course there isn't enough time to develop a whole MSc, but you should be able to apply your learning to the design of an individual module.
The educator team mainly specialize in professional training, and we have drawn most of our examples from that domain. We do have experience in Higher...
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When we refer to 'evaulation' in this course we are talking about evaluation of the course itself. We use the term 'assessment' to refer to measuring the performance of students. Of course, knowing how the students are doing and whether they achieve the Learning Outcomes might be one element of your evaluation, so you could use assessment data as one of your...
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This is a great framing, I love the idea of teaching students, that is people, rather than only teaching a subject. We'll be discussing a lot more about bringing in students' life knowledge as we go through the course.
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