I want to put in a bid with the South-West Creative Technology Network to fund for continued work on ReSeq. The theme is “data” so we need to put genetics data, or some other data, front and centre. If we can tie this in with COVID-19 (public education about the RNA of viruses?) then even better.
If anyone can think of any data-scientists, geneticists or bioinformatics people, ideally based in the South-West of England, that would be interested in a project like this, please ask them to get in touch with me. Any ideas or other input from anyone in the group is very much appreciated. The deadline is September 7th. This is the call:
Hi Kasper, I dunno how to shoehorn it into something that would meet the criteria. The best I can think of is some sort of outreach aimed at bringing microscopy into the school setting. This could be in the form of man-in-a-van doing school visits and running classes or you could get a covid tie-in by running a “virtual lab” where students operate the microscope (or indeed, other gadgets) remotely via a web interface to conduct experiments in conjunction with a helper in the physical lab. That would enable funding for a front end - which is essentially what we need if we’re using Kunal’s back-end. For that use-case you’d probably want a local science teacher or similar on board to see what activities would be most useful from their perspective. A less structured offering might just be web-based access to the hi-seq for development work or web-based access to that and other microscopes (like openflexure or flypi or something) with pre-loaded samples of different sorts. I’m not sure if this is sufficiently data-centric though. I didn’t look but are there examples of previous successful applications?
Looks like everyone is too busy for a call. Should you and I have a quick chat soon @jmarkham? We can then catch up and I can explain how we connect all of this to data, outreach and creative tech for this application. Just pick the next closest time that works for you and send me an email.
https://fo.am/studios/kernow/ based in penryn not sure if they are in the catchment(high chance they are, but welsh), but are data scientists and transdisciplinal (if thats even a word)
cheers
B
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FoAM Kernow is a non-profit organisation founded and run by Dave Griffiths and Dr. Amber Griffiths, and we are one of seven collaborative FoAM studios dotted around Europe.
Most of our time is spent on projects to better understand the ecosystems we are part of, encourage more sustainable behaviours, design bespoke appropriate technology (things that can be understood, fixed, repurposed, sometimes off-grid or even elephant-proof), reduce inequalities, and enable people to develop creative and confident relationships with science and technology.
In practical terms, you’ll find us designing workshops, building hardware and electronics, writing software, creating exhibitions and unusual opportunities, giving a voice to our communities, publishing our work, teaching at all levels, advocating for political change, and giving people a leg-up wherever we possibly can.
We see transdisciplinarity (working outside established boundaries) as the only viable approach to tackling the most pressing problems, and routinely embed co-design and citizen science as essential approaches for encouraging and including broader perspectives. Once you start with a problem and work your way out, disciplines become a bit nonsensical.
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Thanks DrBrian, will see if I can have a chat with them at least.
We just had the catch up call with @jmarkham, @gaudi@bengtsjolen and me. Here’s a question that would be useful to get ideas for:
If we were to run some remote workshops using the HiSeqs. What kinds of things would be good to look at, take some images of and maybe extract “data” from. What could people learn from it?
Apologies for the slow reply Kaspar. With minimal or no modification you have (i) a fluorescent microscope/slide scanner and (ii) some extra chemistry stuff including a system for reliably mounting and plumbing a flow cell.
Used as a fluorescence microscope it can view stuff like is shown here:
I notice that the pre-prepared slides are very expensive but I link to them because this scope should be able to capture similar images. While doing your own staining is possible it’s probably not something you wanna do in your average maker-space for safety reasons. That leaves you with looking at samples which are naturally fluorescent or getting cast-offs from a friendly lab who does a lot of fluorescent microscopy. First, naturally occurring. Most living things auto-fluoresce but at low levels and they don’t provide much contrast. Notable exceptions are fluorescent jelly fish and model organisms that have had fluorescent genes akin to the fluorescing jelly fish gene inserted. I know you can get zebrafish and axolotls that glow and I would expect there’s yeast too, although I haven’t looked. Both of those would look great (until you fried the cells and they died). As for cast-offs, any developmental biology lab that looks at embryogenesis using model organisms such as c. elegans, drosophila and xenopis would be a good bet. I’m sure there will be willing labs. The the issue will be safety which I think is addressable.
Regarding (ii) from above - the chemistry and stage is what differentiates the hi-seq from a standard fluorescent microscope. There’s a couple of ways this could go. The stage is temperature controlled and you can perfuse liquid through the flow cell in a precise way. That means that one could do live cell imaging on the stage and make movies of things growing or reacting to changes in conditions (such as fluorescent zebrafish embryo https://www.youtube.com/watch?v=wJNRIDWjX-o, fluorescent yeast, or regenerating bits of fluorescent axlotl etc). Such activities would not require use of hazardous reagents. The other area that the chemistry and stage is useful for is molecular biology. This is what Kunal is doing and best describes what I was up to. It also includes sequencing DNA (ie. the intended use). For me, this is the main reason to keep the machine whole (as opposed to pulling out a “portable” microscope as Urs has done). I would describe it as a development platform for microfluidics/molecular biology. It can do in high throughput, in situ ligation, amplification, editing and quantification of DNA/RNA.
As I recall, your grant requires some sort of path to commercialisation. If you sell it as a tool for education/outreach then I guess your customers/partners are schools. If you sell it as a development platform for microfluidics then your customers/partners are research institutes and bio-hacking groups who want to DIY various kinds of assays for research and diagnostic purposes.
they are up to 5mm