Breaking Down Data Barriers – A Smart Data Foundry…
New research data sources and how those are used for the public good.
Why did you start using protocols.io?
There is quite a bit of background to this. I work in a core facility, which means I help other people with their research. Often what happens is that researchers give us a sample, and we take it through a pipeline. To researchers, this can often be a bit of a “black box” – they don’t really know what we have done, they just assume we have done everything right.
I started getting more interested in open research and attended some of the Edinburgh Open Research Initiative talks on Microsoft Teams. The group is very welcoming, and got me thinking, for example, how open research is not just applicable to academics, but can be implemented by technicians as well. One talk in particular highlighted a “buffet approach” to open research – where you do the bits that are important to you, and leave the rest. I got a lot of confidence from this, and decided to try and use more open research practices to showcase what we do as technicians. I attended the Open Research Conference last year and started using protocols.io and OSF. I just found out that I had an abstract accepted for the Edinburgh Open Research Conference for this coming year.
Picture of Alan Maclean, Research Technician using the MP FastPrep-24 to extract DNA from stool samples.
Congratulations! Can you tell us more about your protocols.io project?
I was doing a project with ECAT fellow Morven Allan, who is a colorectal cancer surgeon and ECAT Clinical Lecturer. She wanted to understand more about microbiomes, and took biopsies from various colons and corresponding stool samples. My team was tasked with extracting the microbiome DNA from both the colon sample and stool sample, and enriching it to increase its visibility.
Working with the stool sample microbiome was easy, we have an SOP for that. However, sequencing the gut lining microbiome was more difficult, we had not done that before and the gut tissue has lots of human background material, so it is harder to isolate the microbiome. We read various papers and decided on a method, which also required new bits of kit. We documented the workflow carefully – this was initially for the benefit of my team, but I was also keen to publish it more widely so that Morven and other researchers can see it and reference it. This is where protocols.io came in.
What was your experience like using protocols.io?
The University has a subscription, so I used EASE to login which was straightforward. I watched videos on the protocols.io webpage and the University website to help me get started. I assumed we could just upload an SOP, but it was a bit more manual and clunky than that. I ended up breaking the protocol into two separate ones. I got a lot out of the manual upload, although I know there are other ways to do it more quickly and probably there also some shortcuts that I missed.
Once the protocol is uploaded it is great: you can press play and it takes you right through it. I have currently only uploaded the protocol on how we extracted the microbiome DNA from the gut tissue. I am now in the process of uploading the protocol on how we enriched the gut microbiome DNA to make it more visible.
View training videos View protocol 1 View protocol 2Where do you see the benefits of using protocols.io?
One of the best things about protocols.io is that it gives you a DOI. This means that Morven and other researchers can easily see and reference the protocol. It allows technicians to get some credit and bring the workflow together. Because of the permanent identifier, the protocol is much less likely to get lost. Without a DOI, this can happen quite easily, for instance when technicians move on to a new role. I was also surprised that protocols.io linked to my Pure profile automatically, so it becomes visible to others that way.
View Pure
Finally, any tips for new users?
There is a bit of a learning curve; at first it may seem difficult to get stuff on there, especially if it is not properly linked yet. What I would say is that it is worth keeping at it. It is really good once everything is finished and finalised. I think it is particularly useful for other core facilities.