A year-old editorial regarding computational infrastructure sustainability

Note: A year ago, I wrote this in response to an editorial request. Ultimately they weren't interested in publishing it, and I got distracted and this languished on my hard disk. So when I remembered it recently, I decided to just push it out to my blog, where I should have put it in the first place. --titus

All things come to an end eventually, including funding for computational services. What is a field to do?

As biology steadily becomes more and more data intensive, the need for community-wide analysis software, databases, data curation, and Internet services grows. While writing software and gathering data are both expensive, the cost of maintaining software and curating data sets over time can dwarf the upfront costs; in the software industry, for example, software maintenance and support costs can be 10-or 100-fold the initial investment to develop the software. Despite this, there is often little sustained academic funding for software maintenance, data curation, and Internet service support; in part, this may be because the maintenance costs for existing data and software could easily consume all of the available funding! Yet this lack of infrastructure is increasingly problematic, as data set sizes and curation needs grow, and tools to interpret and integrate data sets become ever more critical to forward progress in biology. How can we develop and maintain robust infrastructure services while enabling creative development of new resources and software?

The volume, velocity, and variety of data in biology is stunning, and would challenge even the handling capacity of more established data-intensive fields with larger computational investments. For example, by analogy with astronomy, Golden et al. (2012) propose bringing processing pipelines closer to the data generating instrument (in this case, the sequencing machine). While this approach can certainly help address the volume and velocity of sequencing data, it fails to address the variety -- there are dozens of types of sequencing output, with perhaps hundreds of different processing pipelines, the choice of which depends critically on the biological system being analyzed and the questions being asked of the data. Some subfields of biology may well be able to standardize -- for example, variation analysis for the human genome is increasingly using only a few processing pipelines -- but for environmental sequencing, the types of systems and the metadata being gathered are extremely diverse and nowhere near standardization. We must recognize that our knowledge of the natural biological world is so shallow, and the data gathering needs so great, that the field is very immature compared to other data-intensive sciences like particle physics and astronomy.

How can we build sustained computational analysis and data storage services, in the face of increasingly large and diverse biological data sets, with fast-moving analysis needs? This question has been brought into sharp relief in recent years, with the lapses in funding of TAIR, Tranche, and CAMERA.

While substantial investments have been made in a variety of genomic and transcriptomic analysis services, only a few projects have achieved sustained funding independent of large host institutes. Chief among these are the biomedically relevant projects, which include Wormbase, Flybase, and SGD, all of which have been funded for well over a decade by the NIH. Many others, including iPlant Collaborative and KBase, are in a ramp-up phase and are still exploring options for long-term support. With rare exceptions, it is safe to say that no large cyberinfrastructure effort has successfully weaned itself from continued large-scale support from a granting agency - and some have failed to find this continued funding, and have no clear future.

The challenges for sustainability of cyberinfrastructure are significant. The necessary mix of data storage, research software development, database curation, and service hosting requires substantial and diverse computational expertise, large compute resources, and extensive community involvement to ensure relevance. Even individually, these can be hard to find, and yet projects often try to combine all four of these: to a large extent they buy their own hardware, manage it with their own infrastructure software, develop their own research analysis software, store their data, and curate their databases. Hybrid models exist -- for example, iPlant Collaborative works with a number of external computational biologists to develop and integrate tools -- but these efforts are often centrally managed and continue to require substantial funding for this integration.

Another challenge is that of maintaining innovation in algorithm and software development while continuing to provide robust services. Many innovative computational tools have emerged from small labs and become more broadly useful, but it can be hard for small labs to engage with large, centralized infrastructure projects. Moreover, even in these models, the larger efforts can only engage deeply with a few collaborators; these choices privilege some tools over others, and may not be based on technical merit or community need. This may also arise from the tension between engineering and research needs: large projects prize engineering stability, while research innovation is inherently unstable.

There is the hope of a more sustainable path, rooted in two approaches -- one old, and one new. The old and proven approach is that of open source. The open source community has existed for almost half a century now, and has proven to be remarkably capable: open source languages such as R and Python are widely used in data analysis and modeling, and the Linux operating system dominates scientific computing. Moreover, the open source workflow closely tracks the ideal of a scientific community, with a strong community ethic, widespread collaboration, and high levels of reproducibility and good computational practice (Perez and Millman, 2014). The new approach is cloud computing, where the advent of ubiquitous virtualization technology has made it possible for entire companies to dynamically allocate disk and compute infrastructure as needed with no upfront hardware cost. Open source approaches provide an avenue for long-term research software sustainability, while cloud computing allows cyberinfrastructure projects to avoid upfront investment in hardware and lets them grow with their needs.

Interestingly, two notable exceptions to the cyberinfrastructure sustainability dilemma exploit both open source practices and cloud computing. The Galaxy Project develops and maintains an open source Web-based workflow interface that can be deployed on any virtual machine, and in recent years has expanded to include cloud-enabled services that lets users manage larger clusters of computers for more compute-intensive tasks. Importantly, users pay for their own compute usage in the cloud: tasks that consume more compute resources will cost more. Since Galaxy is also locally deployable, heavy users can eschew the cost of the cloud by installing it on existing local compute resources. And, finally, large providers such as iPlant Collaborative can host Galaxy instances for their user communities. Likewise, the Synapse project is an open source project developed by Sage Bionetworks that hosts data and provenance information for cooperative biomedical analysis projects. While less broadly used than Galaxy, Synapse is -- from an infrastructure perspective -- infinitely expandable: the Sage Bionetworks developers rely entirely on the Amazon cloud to host their infrastructure, and scale up their computing hardware as their computing needs increase.

A general approach using open source and cloud computing approaches could separate data set storage from provision of services, active database curation, and software development. One example could look like this: first, long-term community-wide cyberinfrastructure efforts would focus on static data storage and management, with an emphasis on building and extending metadata standards and metadata catalogs. These efforts would place data in centralized cloud storage, accessible to everyone. There, separately funded data services would actively index and serve the data to address the questions and software stacks of specific fields. In tandem, separately funded new data curation and research software development efforts would work to refine and extend capabilities.

If we follow this path, substantial upfront investment in tool development and data curation will still be needed -- there's no such thing as a free lunch. However, when the project sunsets or funding lapses, with the open source/open data route there will still be usable products at the end. And, if it all rests on cloud computing infrastructure, communities can scale their infrastructure up or down with their needs and only pay for what they use.

Funders can help push their projects in this direction by requiring open data and open source licenses, encouraging or even requiring multiple deployments of the core infrastructure on different cloud platforms, and ultimately by only funding projects that build in sustainability from the beginning. Ultimately, funders must request, and reviewers require, an end-of-life plan for all infrastructure development efforts, and this end-of-life plan should be "baked in" to the project from the very beginning.

In the end, providing robust services while developing research software and storing and curating data is both challenging and expensive, and this is not likely to change with a top-down funding or management paradigm. We need new processes and approaches that enable bottom-up participation by small and large research groups; open approaches and cloud computing infrastructure can be a solution.

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