Front Line Genomics recently launched its ‘Single Cell and Spatial Buyer’s Guide’ to support anyone looking at performing a single cell or spatialomics project. As part of this, they spoke to one of our Scientific Business Analysts, Dara McCreary, about getting the most out of your single-cell and spatial data (and how the Sapio ELN and LIMS can help with this).

Dara’s interview provides invaluable advice for anyone trying to deal with the overwhelming volume of data that single cell and spatial experiments can generate. Read the full interview with Dara below, and download the buyer’s guide here.

Q: How does the Sapio Platform help single-cell and spatial scientists?

A: First of all, the fact the Sapio Platform allows you to have everything in one place, which makes a huge amount of difference. If you’ve ever worked in a lab, you’ll know that you often have important data spread across multiple spreadsheets and you regularly waste your time looking for things. Having everything in one place enables you to work more efficiently, more collaboratively, and increases transparency across teams. The platform also has loads of inbuilt tools for different modules; for example, we’ve got a flow cytometry module and a histopathology module. There’s a range of different options in the Sapio Platform. You don’t have to do an experiment, get the information from an instrument, pop it on a USB and possibly lose your data. The Sapio Platform can be integrated with nearly any lab instrument so you don’t lose your data. It’s about working smarter; it’s about being more efficient.

For example, I’m working with customers who are doing in vivo studies at the moment. If they have a mouse in one hand and their tablet in the other, they can use our platform to record measurements digitally there and then. Some customers do experiments in the lab, write everything down on paper, and then at the end of the day they go into the office and type everything up. Now, they can just bring their laptop with them. We also integrate directly with many different instruments, so you can get rid of that USB stick! We also have new tools for the platform, like Sapio Jarvis and ELaiN. Jarvis is our science-aware scientific data integration platform. With Jarvis, you can consolidate all of your scientific data in one place, and then search, visualize and analyze it in a way that works for a scientist.

It could be archived data from years ago, disparate lab informatics platforms, or data from an instrument in another lab. And because Jarvis is science-aware, you can use Jarvis to look at the data, create graphs, and understand what’s going on. For example, you might have two different labs using two different ELNs. You could be doing genetics in one area and proteomics in another, and you want to analyze those results together. Rather than having to go to two different locations to access the data, it’s all in one place with Jarvis. The other tool is ELaiN, our AI lab assistant for scientists. ELaiN allows you to ask natural language questions to your ELN or LIMS and get an instant answer. For example, you can ask ELaiN to create an experiment based on the criteria you give it, and ELaiN will build that experiment template for you. Or you can ask it how much of a particular reagent you’ve got in stock, or even get it to write a Python script for you. The aim of ELaiN is to reduce the time scientists are spending on manual or repetitive tasks so they can focus on the science itself.

Ultimately, the Sapio Platform is helping scientists to be more efficient, so that they don’t have to constantly move between different tools and platforms. In my previous role, I worked in one hospital, and I had a colleague who worked in a different hospital, and we were working on the same patient data. For us to work together, we would have to ring each other up or send each other emails, which became very time-consuming. Whereas if we’d both been on the Sapio Platform, we’d be able to look at the live data coming in and both be aware at the same time of how a particular clinical experiment was going. On top of that, the clinical doctors that I’m working with can see a patient’s progress in real-time. I used to get phone calls at 2:00 am saying, ‘Where’s my sample? Have you got results?’. If they were using Sapio, they’d be able to just log on and see the progress of the experiment and know when they’ll have their results.

Q: What is Sapio ELaiN?

A: ELaiN is integrated into the Sapio Platform. ELaiN is an AI-powered scientific assistant, built using large language models (LLM), that can answer questions you’ve got about your data in the Sapio platform. In other words, it’s a virtual assistant that you can ask basically anything about the platform, using natural language prompts. And that means that you can also use voice to interact with ELaiN. For example, imagine you’re in a clean room and you have a microphone and mask on – you don’t really want to be touching things. Instead, what you can do is talk to ELaiN and say, ‘Hey, I’ve got 96 samples, make me a plate layout with 96 samples of X, Y, and Z’. And there it is. It’s really going to make things more efficient and it’s a really useful tool in the scientist’s arsenal. I think it is going to put us to the forefront of lab informatics.

We’re also training ELaiN on new things all the time. You can ask it about writing a Python script. You could also ask it if you have a reagent in-house; it will go look and give you an answer. If you don’t have it, it will give you a link to where you can buy it. If you wanted a chart made, you can say, ‘Hey, ELaiN, can I get the results from X, Y, and Z’, and out pops a chart. But that’s only the start – there’s lots more planned for ELaiN and it is only going to get better.

Q: What types of data can the Sapio Platform handle?

A: We’re constantly adding to our list of modules available in the Sapio Platform. If there’s a need, the development team can work to create modules for that need. I’m sure they’re working on things that I don’t even know about at the moment; these modules are always evolving, based on customer needs and requirements. One thing I really do like is our flow cytometry module, which we think rivals FlowJo. This means that you don’t have to have a USB with a FlowJo license on it to do your experiment. You just need to integrate the Sapio Platform with that instrument and all that data is then stored on the Sapio Platform. This means you don’t have to open FlowJo, get the results and extract them; we have it already inbuilt. From the beginning of the experiment, once you get those sample requests in, you can track them, and you can do placements and assay design – it’s as simple as drag and drop.

We have a histopathology module as well. You can track all your samples and see where the sample has gone throughout its history. It’s like a pedigree or a tree of life, you can see your sample in the middle and you can see that it’s gone to flow cytometry, histopathology, or NGS. So, if a sample hasn’t gone somewhere, or if there’s an issue, you can look at the history and say, ‘Okay, it’s gone here, and we’re waiting on the results for that.’ And then you can bring all this information back and it’s all in one place. In a regular lab, you’ve got Excel sheets for tracking, you’ve got FlowJo, the histopathology lab, your ELN, and whatever way you’re tracking your histopathology. That’s all in one place if you’re using the Sapio Platform.

There are other useful aspects to the modules too. They are high throughput – we have customers with vast amounts of samples, and we can track all of them within the platform. Also, when it comes to producing results, if you’re using R, we have that integrated into the platform itself. Anything you’re doing in R we can do within the platform, there’s really no need to go and process your results elsewhere. The process can be modularized too. The data can be sent off to the next person whose expertise is flow cytometry, and they’ll go do that work. The results can then be sent back, and the bioinformatics guy can then work on it. It’s very collaborative. These modules are constantly evolving. We work with the scientists themselves, if there’s something that they see isn’t right, or isn’t working correctly, we can tweak it.

Q: Can the Sapio Platform integrate with specific single cell and spatial software packages?

A: Yeah, there are ways of bringing it in. I’m not a technical person, so that’s usually where I leave it up to a Solution Architect! We very much integrate with instruments; we integrate with other platforms. We do Python binding; we work with Java as well. So, there are ways around it. This is the great thing with this team, when you’re working with Solution Architects, they use their experience and give you the best options. They’ll handhold you if you need it, and if you don’t need it, they’ll just give you the documentation. But they’re always on hand to help. It is a real team and customer-focused effort.

Q: Can the Sapio Platform easily integrate new single-cell and spatial instruments?

A: The Sapio Platform already integrates with over 200 machines, and we’re adding new ones all the time; if there’s a way in, we will find it. For example, we have a customer who’s working with the new 10x Genomics Chromium workflow. We hadn’t worked with that before. When we spoke with one of our Solution Architects about it, they said, ‘That’s fine. We can make that work’. As part of this, it was important to the customer that they could switch between doing the experiment manually or automate it, depending on the number of samples they need to run that day. So, we have both types of templates set up for the client. – If they don’t have high throughput they can do it manually, or, by switching a button, they can take an automated approach and put it on the Chromium. And you can even use ELaiN to help with integrations. At our recent SapioCon event, we demonstrated the ‘give me the Python script for…’ prompt and ELaiN was able to generate a script to speed up integrations with instruments. The integration is only going to get quicker and better. If you ask if there’s any instrument we can integrate with, the answer will be yes. It just takes a bit of time. But I think it’s going to get quicker as we continue to build on our advanced AI capabilities within the company.

Q: How does the Sapio Platform provide real-time analysis and visualization of scientific data?

A: For example, if I’m using a sequencer, we can track what’s happening on that sequencer. You can have real-time monitoring within the platform. So, if you’re at home and you want to know how your sequencing run is going, that information is there. As a lab manager, you may want to see how efficient a certain worker or a certain workflow is, and the platform allows you to track that visually. You can see it’s taken ‘X’ length of time for whole genome sequencing, and you can delve into it and say, ‘Okay, this section is taking a little bit longer, we have to think about how to fix that.’

Q: Why do people switch to Sapio LIMS and Sapio ELN?

Dara McCreary: My main reason – and this is me personally – is that it’s collaborative. Everything you’re working on is stored in the Sapio Platform, so it is much easier for teams to work together on a project. If I need something I can find it easily, rather than having it spread across all these Excel files, across different computers, across USBs. Everything is in one place, and it’s searchable. And it gives transparency across the team – a lab manager can see what everybody else is doing and all scientists can work collaboratively.

With this in mind, my favorite feature in the app is the ‘@’ button. You can ‘@’ someone, and they can see exactly what you’re working on so you can work together. You could be at a conference in Singapore, and I could be working in the lab here, and we could work on a document or experiment together at the same time. An example would be if I was working on a rare genetic disease, and I found a variant. I would need to find out if anybody else had seen it. If I’m working at an organization with a number of different labs and they’re all using Sapio, I can search, ‘Is there any patient with X?’, or ‘Has anybody else found X?’. I can take a look at their data to see if the profiles match and whether I discovered something of interest. We want to help identify those rare events, or interesting findings to make a real impact on patients’ lives. Sapio’s platform enables you to search and find those insights inside your own data in a fast and effective manner.

Download the Front Line Genomics Spatial and Single Cell Buyer’s Guide here. And if you’d like to see the Sapio Platform in action and learn how it can support your single cell and spatialomics experiments, speak to our team.