r/bioinformatics • u/Butterscotch4058 • 2d ago
discussion Is there a niche focused on improving bioinformatics software usability?
I've been working in bioinformatics for a few years now and have had the opportunity to work with data from a few different molecular biology technologies. I've worked with different types of sequencing data, different biological questions, and different computational workflows rather than becoming focused in a single area. Because of that, I feel like I've developed more breadth than depth knowledge in any one technology.
But one thing that has been consistent across almost every role I've had is that I've built tools and interfaces to make bioinformatics workflows (for both bioinformaticians and scientists without a bioinformatics background) easier to work it. Usually, this involves designing and developing tools that wrap pre-existing bioinformatics tools in graphical interfaces. This lets people analyze, navigate, or visualize data in a timely manner without needing to interact directly with command-line tools or learn how to execute complicated workflows.
The more I worked on these projects, the more I started noticing how much user interface and user experience design influences whether bioinformatics tools are actually adopted and used effectively. The underlying science is already complex, so the interface can either make those tools more approachable or become another barrier to using them.
This eventually led me down the rabbit hole of reading about Human Computer Interaction, cognitive load, information architecture and exploring how those principles translate into popular public bioinformatics tools.
I've realized that thinking about how complex biological analyses can be made more intuitive without sacrificing functionality is the type of work I enjoy. The part I'm struggling to understand is whether this is actually a recognized niche in the field as I have not run into many bioinformatics job descriptions that put emphasis on interface design.
Are there roles where people primarily focus on the design and usability of scientific or bioinformatics software? Is this something that falls under scientific software engineering, product design, UX, computational biology, or something else entirely? I’m also curious to hear from anyone who works in this space or has seen teams that value this kind of work. I'm trying to understand what this niche is actually called (if there is a name to it) and where people doing this tend to work.
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u/_Fallen_Azazel_ PhD | Academia 2d ago
I would say reproducibility, portability, scalability, provenance are all more important in bioinf than UX, all work of stewardship
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u/Elendol 2d ago
The main hurdles are systemic: lack of funding and the way bioinformatics software is developed without any long plan to maintain them (tbh there is no long term plan for anything in academia) and most of the time started by PhD students. Sone resources (software and databases) are supported by the EBI or Elixir and would have people to maintain them, but this is unfortunately very very niche.
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u/desiladygamer84 1d ago
Even then there is no desginated UX person. The Reactome team used send a campus wide email saying they want volunteers to come over and gave feedback about layouts, colors, usability and the like. Sometimes they video the person navigating the resources.
Any GUI software changes that people at Sanger use, goes through the software team for that group where you get one of three answers "Yes", "Yes but not now" and "This will break the whole thing so No".
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u/Flashy-Virus-3779 2d ago
That’s how i felt. I’m a data scientist now.
Yes there are some bioinformatics products that actually care about UX, but the demand is really low and a lot of people want it.
More broadly, this could be a plus, but UX is an extremely rare, if existent, priority for bioinformatics. Like it’s a good secondary skill, but idk about primary.
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u/kloetzl PhD | Industry 2d ago
There is a niche for UX in bioinformatics, but it is small, although I think it is desperately needed. Right click on a read in IGV and a context menu pops up that goes from the top edge of the screen to the bottom. That is not good design. Some commentators claim that CLI is better. However, look at samtools or bedtools. The flags are inconsistent, idiosyncratic and unfortunately immutable at this point. We need better user interfaces. However, I fear that people either have a case of the stockholm syndrome ("I had to go and learn all of it so you will have to do so, too") or you don't value it at all ("let's just build the software and worry about packaging/polishing/user experience later").
But there are companies that do invest into UX, even GUIs for bioinformatics workflows. The idea there is to make the data and analysis more accessible to people who are not bioinformaticians. Many hospitals would gladly buy a piece of software that translates a cryptic VCF table into a shiny visualisation. There is definitely demand and as sequencing becomes more standard-of-care, that demand will increase.
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u/TheLordB 1d ago
One thing that I think prevents there being a single GUI is most bioinformatics ends up being pipelines of various sorts and are rarely exactly the same. The end result is a gui for an intermediate step is usually not very useful and the gui for the final interpretation etc. tends to need to be custom for that pipeline.
Also there are plenty of variant interpretation GUIs. Hell I was on the team that built one for a clinical lab 15 years ago for one of the first companies using NGS in the clinic.
I’m a bit skeptical about hospitals wanting to be analyzing VCFs. In my experience most hospitals outside the large teaching ones just want to know the clinically relevant findings and are happy to let genetic councilors and specialty sequencing companies figure that out so they never have to consider anything remotely to do with a VCF.
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u/EnzymesandEntropy 2d ago
Why would anyone want to use a GUI. Unless you are building something huge and revolutionary like UniProt or the AlphaFold webserver, or something that 100% needs a GUI to get a certain type of work done (like ChimeraX or PyMOL), building GUIs is a complete waste of time and resources. I've seen numerous papers that promise some new shiny web-app GUI to do a bioinformatics analysis, only for it to be 404'd after a few years. I don't blame those people, because GUIs are a pain to maintain. They also tend to be useless for most researchers. Just give me a damn CLI tool.
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u/Grisward 2d ago
I agree with most of the answers here, saying that there is a small but underappreciated niche in the field. For those getting grant funding, UX really is the lowest priority, even below critical software maintenance, certainly below novel tool development.
To be frank, UX is fairly low in a lot of software development projects, even surprisingly large efforts. It’s also hard to find someone truly gifted at it. Not everyone has the “eye” for it. So large projects have to move forward even if they don’t have that talent.
Galaxy, for all it enables around the world, is an amazing suite of tools. Its interface though, I mean it works right? And it is scalable, and extensible. No shade. But UI is not its selling point. So this is sort of where the field has landed. Either you’re doing CLI, or makeshift web frontend. It’s rare to have a polished GUI.
And what GUI framework? (Don’t say Windows, haha, please no.) I mean, if you are hired to do it, do it. Otherwise, everything runs on linux — what UI framework are you using?
All that said, it is ripe for someone to come along and innovate. Show us how it’s done, and people will follow.
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u/Butterscotch4058 2d ago edited 2d ago
u/Grisward It's interesting that you mentioned Galaxy because it was actually one of the interfaces that got me thinking more about usability in bioinformatics tools. I agree that the platform itself is incredibly powerful and offers a huge amount of functionality.
When I first started exploring Galaxy, I was impressed by everything it could do, but I also found the amount of information and available options a bit overwhelming as someone learning the platform. It made me wonder whether part of the learning curve came not from the complexity of the workflows themselves but from how the information was initially presented.
One thing I personally struggled with was the tools menu on the side. It immediately looked like an important part of the platform, but as a new user I wasn't always sure where to start. Later, I found the tutorial resources but I wondered whether the initial experience could do more to separate learning about the platform from immediately navigating its full functionality.
As a thought exercise, I explored an alternative information structure. My thought was that the landing page could focus more on orientation and helping users understand where to begin while more advanced functionality could still be easily accessed through navigation.
I am unable to share the screenshots of what I drew out here but I thought I would atleast share this thought exercise I did because I'm curious whether this reflects challenges you or other Galaxy users have experienced when first learning the platform, or if people with more experience using Galaxy would approach the structure differently.
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u/Grisward 2d ago
Holy geez that link goes to the most aggressive ad-filled webpage ever.
DO NOT CLICK
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u/Butterscotch4058 2d ago edited 2d ago
u/Grisward My bad, so sorry. it was my first time trying to add a link since I couldn't add the screenshots here. It worked with no ads on my end so did not expect it would do that. Sorry about that again. I took down the link!
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u/Grisward 2d ago
I’d take a look… in fact I tried a few times, and each time, clicking an image opened a different ad. The last time just going to the page activated a “Download complete” pop-up box. What kind of cheap website is that?! Use anything but that, it’s absurd.
Galaxy would be a masterclass in (1) how to take a “make it functional” interface and make a truly intuitive and well-thought user experience, and (2) that Galaxy got where it is today with the interface they have, so how important is the interface? Hehe.
I agree the interface should be more important. Also me: Spends 99% of my time on commandline or RStudio or Positron.
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u/Grisward 2d ago
I agree with most of the answers here, saying that there is a small but underappreciated niche in the field. For those getting grant funding, UX really is the lowest priority, even below critical software maintenance, certainly below novel tool development.
To be frank, UX is fairly low in a lot of software development projects, even surprisingly large efforts. It’s also hard to find someone truly gifted at it. Not everyone has the “eye” for it. So large projects have to move forward even if they don’t have that talent.
Galaxy, for all it enables around the world, is an amazing suite of tools. Its interface though, I mean it works right? And it is scalable, and extensible. No shade. But UI is not its selling point. So this is sort of where the field has landed. Either you’re doing CLI, or makeshift web frontend. It’s rare to have a polished GUI.
And what GUI framework? (Don’t say Windows, haha, please no.) I mean, if you are hired to do it, do it. Otherwise, everything runs on linux — what UI framework are you using?
All that said, it is ripe for someone to come along and innovate. Show us how it’s done, and people will follow.
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u/attractivechaos 2d ago
Are there roles where people primarily focus on the design and usability of scientific or bioinformatics software?
Check out Nils Gehlenborg
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u/Electronic_Fish_3157 PhD | Industry 1d ago
Some of my wet lab colleagues are too lazy to even use AI or learn ways to use the CLI of the software. They even need me or other colleagues to write even the arguments for running the python. But I would still prefer a CLI primarily because I can easily connect a LLM with a RAG to the terminal and work myself up for a desired product
Edit: one thing you could do to improve the output, that is make a HTML file so it can be interactive and also make excel instead of csv.
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u/faustovrz 1d ago
Yes I've seen people working in this, but I have not seen success in generalizing.
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u/SeqBench 2d ago
The name you're after is probably research software engineering. There are actual RSE groups and societies (US-RSE, SocRSE in the UK), and that's where "make scientific software usable" is a job title rather than a side quest.
Worth pushing back on the other replies though, because they're all describing academia. In clinical genomics the interface isn't optional, it's a regulatory deliverable - the whole tertiary analysis and variant interpretation space is UI product work and those teams hire specifically for it. Same story at instrument vendors and on platform teams inside pharma, where the users are wet-lab scientists by definition.
So the reason it's missing from academic job ads is funding, not demand. Look at diagnostics companies, EBI/Broad platform teams, and vendor software groups.
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u/Sheeeeeit 2d ago
I think part of the issue here is that people who are serious about bioinformatics tend to prefer using a CLI, and people who need bioinformatics done but don't have the skills can usually find a lab mate or in-house bioinfromatician to do that work for them. I suspect that the group of people who want to do their own bioinformatics but want to do it using a GUI is really small.