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June 5, 2018

Visualising biologics discovery: dealing with complex data

UK-based Dotmatics has announced a new version of its data visualisation tool, Vortex for Bioinformatics, bringing visualisation and informatics tools into the hands of ordinary lab scientists. Abi Millar finds out how the tool can be used.

By Abi Millar

The last few years have seen a huge push in biologics drug discovery, with over 200 approved drugs on the market and hundreds of new products in the pipeline. While the successes have been huge (biologics accounted for six of the top eight drugs by revenue in 2016), the failures have been plentiful and the drug development process can be singularly challenging.

One of the key issues for biologists is the sheer volume of data they’re dealing with. If you’re developing a small molecule drug, it’s relatively easy to understand its chemical composition – the compound, after all, has most likely been created in a lab. Biologics, however, are large and complex molecules with an intricate structure.

Typically, each compound requires genetic sequencing at various stages of the development process, with a view to ensuring it is stable and hasn’t undergone harmful mutations.

Demand for specialists

“In biologics drug discovery the main currency is sequencing, whether that’s a sequence for DNA or RNA or a protein or peptide sequence,” says Andrew LeBeau, senior manager of biologics marketing at Dotmatics. “Those sequences are how we biologists understand these molecules – when they’ve mutated, and how the changes we make can affect their activity. So drug discovery is essentially a process of refining the sequence, which leads to the structure, which leads to the function of the biologics.”

With so much data being generated, managing and analysing that data is often beyond the scope of a lab scientist. This has led to a high demand for specialist bioinformaticians.

“Bioinformatics tools have tended to be the remit of the bioinformaticians and computational biologists,” says LeBeau. “A lab scientist might get some data from their experiments, get to a certain point in analysing it and then find they don’t have the tools or the skills to go to the next stage. So they have to bring their work to a halt and ask a bioinformatician to continue the analysis for them.”

The scientist then must wait hours or even days for results, interrupting the flow of research.

“We think that’s a really inefficient way to do science in general, and certainly in the drug discovery industry, where every minute counts,” says LeBeau.

Speedy sequencing

Dotmatics, a scientific informatics company, recently updated one of its tools with a view to redressing this problem. Vortex for Bioinformatics, a data visualisation tool, has been around since 2016 and is currently used by a wide range of biologists. The latest release brings data management within the purview of ordinary lab scientists.

“All scientists in my view need tools for analysing and interpreting data, and part of that is visualising data in graphs and charts and tables,” says LeBeau. “One of our big focuses with Vortex is to make it a self-service tool – it can be used by scientists who just need half an hour of good analysis, so they can make a decision and move on.”

Following the latest enhancements, Vortex can quickly process large data volumes. As LeBeau explains, time is money in the drug discovery industry, and it’s crucial to do your analysis as fast as possible.

“We have improved the visualisation and computation performance, so now you can load millions of sequences into Vortex and scroll through it easily, managing what‘s on the screen at any given time,” he says. “You can do very large sequence alignment and sequence clustering in the time it takes to make a cup of coffee.”

Several new features have been added too. These include manual sequencing editing capabilities; improvements in the sequence annotation capabilities; sequence search capabilities; and various functions specific to antibody research, such as tools to identify and number the complementarity-determining regions (CDRs).

Rather than treating biologics as a single class of drug, the tool intrinsically understands different biological data types and strives to meet the challenges of different research areas.

“There’s been a tendency in the industry to lump all biologics together, but really biologics is lots of different types of drug discovery – if you’re working with antibodies it’s different to working with small peptides or vaccines,” says LeBeau. “So the tools we provide have to be more specific for each of them, and I think this version of Vortex is a major step along the way.”

Making sense of the data

Of course, if complex bioinformatics is now accessible to the average lab scientist, we might wonder what happens to the bioinformaticians. LeBeau says that rather than rendering them obsolete, Vortex actually frees them up to focus on more creative endeavours.

“Humans will never be taken out of the cycle, not in my lifetime anyway,” he says. “What we’re trying to do is provide the tools and capabilities so each type of user can do what they’re best at – the lab biologist uses self-service tools to get their results, and the bioinformaticians can develop new algorithms rather than performing routine analysis.”

He points out that, while biologists are now producing reams of data, we’re currently much better at generating the data than we are in extracting knowledge from it.

“There’s still a huge amount of work to do in terms of understanding how biology works and how we can generate computational algorithms to understand the data,” he says. “We want to free up bioinformaticians to attack that huge volume of data and make sense out of it.”

Since Vortex has scripting capabilities, the bioinformaticians can code new algorithms into the tool and make those available to regular biologists.

“Biologists don’t need to understand the details of that algorithm – they just need to know how to do the analysis, and what buttons to push to get results,” says LeBeau.

Future evolutions

Over the next few years, LeBeau thinks there will be a greater need than ever for tools of this kind. While chemistry software is already a relatively mature market, biology software has typically relied on open sourcing and is only now beginning to catch up.

“With the demands of high volumes of data, the need for commercial grade software in biology has really evolved,” he says. “Companies are moving towards more consistent systems, so we’ll need to focus not just on individual tools but on the ways they integrate with software from commercial vendors.”

He adds that biologics drug discovery is changing rapidly, meaning Vortex for Bioinformatics will need to evolve with the times. As a result, Dotmatics will continue its existing strategy – engaging heavily with customers, and supplementing its own developmental roadmaps by asking users what they need from the tool.

“Every week we hear about a new type of biologic, and CRISPR is a huge potential therapeutic,” says LeBeau. “So Vortex is something we’re very happy with now, but we’ve got a lot more to do to support different types of biologics drug discovery. We need to stay aligned with what our customers are doing every day.”

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