Sustaining the development of research-focused software

Recently I was asked by someone at a funding organization about the term "hardening software"; I wrote a blog post asking others what they thought, and this got a number of great comments (as well as spurring Dan Katz to write a blog post of his own). I'd already written an initial response to my friend at the funder (which I'll publish separately), but the comments I got from the blogosphere made me think more broadly about how researchers mentally model software development.

I see two pretty divergent ways of thinking about software development in my research community. The first I would call "consumer product", and the second, "community project". (I'm excluding infrastructure and workflow projects from this discussion, because they don't provide domain specific research functionality.)

In "consumer product" software, a company or research group builds some software and releases it for the wider world to use, often through a publication or a preprint. The goal of the developers is to allow other people to use the software. They may be quite passionate about this, providing good documentation and test data sets along with help forums. However, there will generally be little to no developer documentation available: the goal is to recruit users, not developers.

In "community project" software, a company or research group builds some software, and (as above) releases it to the wider world to use. Here, the producers usually want to let people use the software directly, but there is an additional emphasis on the software being something malleable - something that others can work on and with, and mold or adapt themselves to fit their needs or the needs of a broader community.

With both kinds of projects, the software can be more or less mature, and can be targeted at novice or expert users, and can have a broad or a narrow technical vision, etc etc. The key question is whether the software is the product, or the software project is the product.

It's not hard to find consumer product-type software in the bioinformatics world. Most assemblers and mappers are essentially opaque blobs of software that users interact with via the command line, and bugs, issues, and feature requests are communicated to a core set of developers, who then deal (or not) with them.

It's quite a bit harder to find full community projects in bioinformatics; while I'm sure I'll think of many the moment I hit "post", I don't have a shining exemplar in mind, although velvet and samtools come close. This lack may be due to a lack of developers, but is perhaps also because of the way academic funding works. I'll talk more about this below.

Sustainability and software needs - why do we care, and what do we want?

Software is fast becoming a sine qua non in research, and researchers and funding agencies have been trying with increasing urgency to figure out how to support sustainable software development. There's a whole NSF program devoted to sustainable research software, and I think it's fair to say that one of the main subsurface goals of the BD2K program is to tackle the question of software (PSA: data isn't much use without software). The USDA and bio bits of DOE are also running smack into the problem that the research programs they fund are utterly dependent on software, yet investments in software are often secondary and rarely yield software that is usable past the end of the grant. It turns out that software development for research is a rather intransigent beast.

Fundamentally, stable research software is a way of accelerating research. I believe there to be a lot of interest in & need for the domain-specific software set - software that is more specific than (say) Linux, Python and R, or RStudio and IPython/Project Jupyter, or the various major R and Python packages for data analysis. These have large user bases and are generically quite useful, so while supporting them is still a challenge, their support options are more varied than domain software. Recently, the Moore, Sloan, and Helmsley Foundations have stepped up here with focused investments. But what about software closer to the domain?

It's been very hard to meet the tremendous need for sustained development of domain-specific software - for example, in bioinformatics, I understand that very few mappers or assemblers or parsing libraries are actively supported by funding agencies for more than one round. When they are, it's almost always for new methods development, not for supporting and sustaining the software; these goals are somewhat at odds, to say the least. (See The three porridge bowls of sustainable scientific software development for more on this conundrum.) The software that is supported directly usually is a "best of breed" software package that wins because it's first-to-market, and/or because of existing user bases, and/or because it's useful for biomedically-relevant missions; moreover, it's often produced by a few groups at well-known institutions. While these tools are often quite good in and of themselves, I don't think this approach serves tool and algorithm diversity. We need an ecosystem of tools, not just one tool in each domain that is "owned" by one or two actors.

So, to rephrase the question more specifically: how can we build and sustain an ecosystem of research-focused software to support and accelerate inquiry with flexible domain-specific computational tools?

The lesson we can take from the open source world is that, in the absence of a business model, only "community project" software is sustainable in the long term.

When I write that, it seems almost tautological - of course if a project doesn't have a business model, the project won't be sustainable without a larger community! But there is essentially no business model behind most research software. (The most common approach seems to be assume that anything important will continue to be funded - a dangerous assumption in these days of 10% funding lines; the next most common approach is to build software to be at the core of a research program, and then get funding for the surrounding research program. Both of these approaches have obvious failure modes.) And so I think that we should be focusing on community project software.

In support of this thesis, I would point out that all of the more general packages I mentioned above (Linux, Python, R, RStudio, IPython/Project Jupyter, and things like scikit-learn) are full open source community projects, with a robust contribution process, a wide body of regular and part-time developers, and open and ongoing conversations about future directions. All of these packages have demonstrated long-term sustainability. I can't robustly conclude that this is a causal relationship, but I would strongly bet that it is.

Shoving software out into the community is no guarantee, but it's easier now than it used to be.

Lest people think that slapping a contributor process on software is enough to make it "community supported", let me just say that I know it's much more complicated than that. In addition to all the skills you had to have to write the software in the first place (the technical and algorithmic skills, the scientific background, and at least some software engineering knowledge) you also need to engage with the community online, solicit feedback and improvements, manage contributions and bug reports, and otherwise be responsive.

The transition to a successful community project seems challenging to me. From tracking this in the open source world (mostly in retrospect), you need some combination of luck, skill, and robust community-facing efforts. In the scientific world, I'm not sure how to guide funding towards projects where this transition is likely to be successful. My first thought would be to go with the NSF structure of SSE/SSI - fund new projects to get them started off, then provide transition grants to see if they can engage with a larger community, and then fund them as part of the community. One problem I see is that the time scale is so long - it's 5-10 years to take a project from nothing to something - and maintaining funding across that period is fraught with challenges.

One piece of good news is that it's become a lot easier to manage the technical infrastructure. GitHub or BitBucket can host your code, make it easy for people to work off the latest version, and provide tools to manage patch contributions and code review; ReadTheDocs and github and other sites can host your documentation; Travis-CI and other continuous integration platforms can run your tests, there are lots of places to host mailing lists, Twitter and blogs can help you gather your community 'round, and teleconferencing can help you coordinate developers.

The bad news is that the new skills that are required are community building and social interaction skills - something that many faculty are unprepared for, and probably won't have time for, and so they need to outsource them (just like most software engineering, or experimental work). This leads to a problem: community projects are bigger.

Community software projects are bigger, and therefore harder to fund

From the funding perspective, another problem is that community software projects are just... bigger, and hence more expensive. You need to pay attention not just to the research aspect of things, but also the community and the software quality. This probably means that you need at least two full time efforts for even a small project - a community liaison/release manager/testing manager, and technical lead to drive the project's software engineering forward. (This is in addition to whatever science you're doing, too ;).

From the applying-to-funder perspective, this makes life a bit of a nightmare. You have to successfully navigate continued software development, the building out of a community, and scientific progress, and then justify this all in an "ask" to a funding body, with a pretty low chance of making it. Add in the fact that very few programs will fund software development directly, and the difficulty rises.

I don't think anyone in industry is going to be surprised by the notion that you have to deliver value (here, "innovation") while building robust software. The contrast here is really that researchers often toss "grad ware" out the door as if it's good, robust, usable software, and we often have no funding plan beyond "publish it and then apply for a bunch of grants." This isn't sustainable, we shouldn't view it as sustainable, and the only surprise is that anyone ever thought it was sustainable. But the corollary may be that we need to figure out how to engage with a larger community, and support them, around developing individual research software packages, rather than trying to productize each and everyone one.

But if that engagement costs more, it's going to be difficult for funding agencies to support.

Focusing on community software projects solves a lot of problems

When people are asking for grant support to continue developing sofar, it's frequently difficult to figure out if the software is actually useful. But if there's a broad, robust community associated with it, it's probably useful. (I don't really know how to measure the size and quality of the community, note.)

We probably need fewer community projects overall. Maybe grad students could extend existing software, instead of writing a whole new package; I gather this is what happens in the VTK world.

Community projects will inevitably have less tolerance for crap software, at least on average. (I haven't thought through this thoroughly, but (a) no one wants to join your software project if they can't get it to run, and (b) your project will die if every release has more new bugs in it than were fixed.) So the poor quality, lousy adherence to community standards, and miserable packaging that afflicts many current bioinformatics projects would probably just go away in a model where only community-backed projects were given continued funding.

Community projects also have a built-in succession mechanism - when a principle investigator loses interest in a particular project, or retires, or lapses in funding, there is a decent chance that other PIs will be able to pick up the project and move forward with it.

Communities also channel software development in specific ways that are more democratic. If the project leads aren't responsible for implementing everything but have to rely on the community to implement and support features, then they are less likely to add useless features.

A more fundamental point is that I often think that we don't really know how to set our goals in research software development. Something that open source approaches excel at is channeling the needs of its users into functioning software. Explicitly acknowledging the community's role in deciding the future of a software project means that the project is committed to meeting the needs of its users, which I think probably fits with many goals of funders.

What does this all mean?

In sum, I think one way - perhaps the best way - to sustainably develop research software is to build a community around its development

One way for funders to do this might be to provide support for software making the transition from a small project to a community project.

While funding might still be needed to maintain the core of the project (I think a full-time developer and a full-time community liaison are minimal requirements) this funding would be leveraged better by supporting a full-on community of developers, rather than just supporting a small team product

A corollary might be that software grants should be reviewed equally on their community engagement plan, not just on their innovation in methods.

Formalizing the notion that some research software isn't meant for further use is probably good. In particular, a community-based approach can provide some guidance for research software that IS meant for further use (see Please destroy this software after publication. kthxbye. for my thoughts on the rest of research software -- the "No success without quality" section of Gael Varoquaux's post is an excellent follow-up ;).

One interesting direction (suggested by Tracy Teal) is to think about ways that granting programs could separate funding for the community/maintenance parts of a project from the research parts. For example, communities could be awarded grants to hire community developers or liaisons who are somewhat self-directed. Alternatively, institutes like the Software Sustainability Institute could provide personnel through a granting program.

More generally, project structure starts to matter a lot more once you explicitly have the community involved. In retrospect, a lot of my internal tension around future directions in khmer comes from a divergence in perspective between what the community needs and what the research needs; having separate funding and decision making could have helped here.

Some problems with this perspective

I do worry a lot that we don't have the robust community of developers in biology to support the necessary software development. If all you have is users, who in the community develops the software??

Open source is hardly a panacea, and open source processes aren't bulletproof. Lots of open source software is really bad. I do think that the ones that attract a community are likely to be less bad, though ;).

Balancing innovation and stability is super hard. We need to think a lot harder about this. Matthew Turk pointed out that process may overtake innovation as projects become more stable; is this good, or bad? How can this be managed with a small community?

Open source isn't exactly noted for a diversity of perspectives (or participation). Academia has its problems here, too.

Community coalescence may be more strongly related to star power and social media savviness than technical excellence.

Scientists (at least in biology) don't get rewarded for community involvement and community development. On the flip side, maybe getting grants explicitly for doing that would provide a mechanism of reward.

Researchers still need to figure out how to do good software engineering, which is hard. Community projects can help here, too, by providing standards and guidelines and on-boarding documentation.

A concluding sentence or two

This might all be obvious to everyone already. If so, apologies :)


Thanks to Tracy Teal, Matthew Turk, and Ethan White for their helpful comments on a draft of this blog post!

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