SPARC Data and Resource Center Aims to Accelerate Research with Open Science
Interview by Hayleigh Culliton
As part of an initiative with the inaugural American Physiological Society Summit, I spoke with Sue Tappan, PhD, a member of the Stimulating Peripheral Activity to Relieve Conditions Data and Resource Center (SPARC DRC). During this interview Sue and I spoke at length about the importance of open science and the SPARC DRC, discussing their current initiatives and goals, as well as future directions for the program.
“I want to underscore that the SPARC Data and Resource Center is committed to assisting anybody who wants to learn more about fair and open data processes. While the SPARC Portal is specific to neuromodulation and the periphery (inclusive of the brainstem and spinal cord), any researcher who wants to understand how to structure their data so that it can be easily shared with others, can use the same principles that we apply. It may be a little intimidating to get started, but we’re happy to help.”
Introduce yourself and describe SPARC to someone who doesn’t know you.
My name is Sue Tappan, and I am a member of the SPARC Data and Resource Center. The SPARC Data and Resource Center is funded by the National Institutes of Health to create a destination for peripheral and autonomic nervous system datasets for the purpose of encouraging and accelerating discovery in the neuromodulation of organ function.
Tell us a bit about the platform technology.
The platform is designed to not only bring together datasets generated across a diverse number of organs and modalities, but also includes integrated viewers, a connected cloud-based simulation platform, and on-line maps coupled to a knowledge base that includes connectivity information obtained from Portal data, published sources, and scientific experts to facilitate this experience. The standards also harmonize the data available so that anyone who would like to discover experimental data about a particular organ system can have a similar experience. The goal is to permit others to understand the data, understand its purpose, and see if it suits their needs for their own reuse potential.
How many active users do you have on the platform?
There are different aspects of what you might consider an active user because the Portal offers a lot of different ways to interact with and use the housed data. The SPARC Portal currently has about 6,000 users. Anybody can contribute data, and that data and all the resources that we create with the SPARC Data and Resource Center or otherwise contributed by the SPARC program are free to use and free to access by any interested researcher in the cloud. This year approximately 200 datasets have been downloaded so far, and the protocols have been a very popular aspect of our resource with over 39,000 views. Downloading data can incur a fee imposed by AWS, depending on data size, but it works out to about 14 cents a gigabyte. We expect the numbers of users to continue to grow as we welcome additional investigators who are interested in contributing their own data.
Is there a vetting process to the contributor or to the data itself?
The data is intended to be raw and without interpretation, without any “quality” vetting process per se. However, there is an extensive curation process to ensure that the file formats are open, the metadata is complete and explanatory, and the Portal is designed to present the information in an easily understandable way for anyone who comes to explore the data.
Explore all current available maps, models, ongoing projects, and datasets available from the SPARC Data and Resource Center.
How is this technology going to enable faster discovery and a more collaborative future for the scientific community?
What a great question. That really speaks to something that we’re really passionate about because the SPARC Initiative and the Common Fund Program from the National Institutes of Health are really focused on fair and open science. ‘Fair’ in our context, stands for findable, accessible, interoperable, and reusable. ‘FAIR data’ will accelerate science because you can utilize this data to augment experiments that you are either in the process of conducting, or one area that I think is really exciting is, virtual hypothesis testing. So you can see data sets that have similar components to a question that you might want to explore and then actually use some simulation capability to assess whether or not your experimental design either has enough power or can be tweaked to determine how best to initiate your own experiment.
It’s obvious what the motivation would be for someone to consume the data that’s available, but what are the motivations for scientists to contribute to the repository?
There are many concrete benefits for scientists contributing their research to the SPARC repository. Beyond the ability to publish explorable supplemental images, analyses, and models along with your papers, one receives credit for usage of generated data and models by other researchers. Additionally, computational models become reproducible and sustainably conserved, and it enables collaborative model building without requiring extensive coding expertise. Contributing to the SPARC repository is a great way to keep all your experimental data in context and together in the way that you actually do science. Our goal is to not only meet the requirements of the NIH data mandate, but to be an effective resource. Right now, you may think of cardiac experimentation as very specific to the heart. Yet the heart is innervated by the vagus nerve, which also innervates the stomach, bladder, and colon. By bringing together the extensive research being done within the peripheral and autonomic nervous systems, regardless of modality or target organ, will allow us to see the similarities and find the gaps for the next experiment.
“It’s really exciting and everybody can contribute; it’s meant to be open. We are a global consortium, and not for profit. This is really a resource for scientists – by scientists.”
You’ve mentioned the NIH a couple of times. Can you talk to us a little bit about the relationship that you have there?
Yes, so the National Institutes of Health had developed this Common Fund program called the SPARC Initiative; it stands for Stimulating Peripheral Activity to Relieve Conditions. The idea behind the SPARC program is that there are opportunities to influence and modulate organ function with bioelectronic medicine. Stimulation devices function similar to the way a pacemaker can augment or modify the contractility of the heart, and could potentially exist for other organs as well. Stomach and bladder are two common and successful modes of intersection between neuromodulatory devices and improved outcomes, and yet we don’t quite understand how using stimulation devices are actually changing organ function. We want to be able to develop better devices that are selectively placed and tuned so that we don’t have inappropriate off-target effects. The SPARC program consists of two arms: there’s the individual researchers who are doing the experiments in the given organ systems to understand the anatomy and physiology of the organs, and the relationship to the autonomic nervous system. The SPARC Data and Resource Center creates the SPARC Portal, along with additional resources to make that data open, understandable, and provide mechanisms to further integrate that knowledge and data. We bring it all in together to create maps, models, and computational simulations.
Being that the entire SPARC program is grant supported, is there an end date to your relationship with the NIH?
Correct. Common Fund programs have a life span of 10 years and we’re in the midst of year six. These common fund programs are designed to kickstart and inspire a transformative new field of research. And so, while the Common Fund itself has a limited funding window, it is expected that future efforts will be supported by additional grant funds from the individual researchers. In our case, the Data and Resource Center is committed to sustaining the resource after Common Fund funding ends and has taken steps by expanding SPARC’s funding base and continuing our own research that we are passionate about.
Click here to learn more about the National Institutes of Health Common Fund.
If you are interested in learning more about the SPARC program, Portal, or the Data and Resource Center, or if you need help getting involved, click to join one of their weekly virtual office hours sessions.
Tell us a bit about the mission and how SPARC seeks to serve the research community.
The SPARC program’s mission is to advance our understanding of the peripheral nervous system and its organ control systems, and our goal is to accelerate device development from basic research at the bench, to beyond the bedside, to wearable/implantable devices for successful tunable therapeutics. To achieve this goal, it requires collaboration from different research domains, including anatomy, physiology, device design, and computational simulation. The SPARC program stands out by bringing together these diverse experimental domains, to accelerate progress towards successful therapeutics.
Have you had any issues or pushback from the research community about sharing their data/open science?
That’s one thing that is a big conversation right now, right? Because in the United States, there is a big push from federal funding agencies and from the White House to share data openly. And both require that you share your data on an open repository.
“Times are changing: it’s not a question of if researchers will share data, but how.”
SPARC encourages and enables that in a way that allows the researchers to prepare and share their data at the time of publication or when it makes sense to them, and we work with them to make sure that the datasets can meet the standards for open access in a way that actually benefits them. All data sets on the SPARC portal include a DOI and the SPARC standards require inclusion of a protocol that describes how the data was generated; and those two things are actually really important for inspiring trust in the data that you see. If you know a particular research group, you’re likely to trust their data because you have an understanding about them. But when it’s just on an anonymous style repository or you have to request access each time from the individual, you don’t quite know what you’re going to get.
The same is true for people who are contributing data. Is it going to be used successfully? Am I going to get credit for it? We have thought hard about how to encourage more of a community around data so that it really is extending from your colleagues to people you don’t know so that they understand where you were coming from when you created your data, making it easy for them to give you credit when they use your data for their own purposes.
How does SPARC plan to drive usership and expand the database?
We had some great interactions here at the APS inaugural Summit where we found some researchers who are already exploring the data we have available on the SPARC Portal and using it for virtual experimentation and hypothesis testing, which is really extraordinary and exciting. They’re using it to test and develop their machine learning and AI applications.
One other area that we’re really quite excited about is the potential for these highly curated and well-explained modules on the portal to be used for teaching. Some of these simulations, for example, are a great way to teach physiology, and it’s being done now.
So in addition to the basic research and the cross-species investigation that the raw data sets and the integrated spatial mapping provide, there’s also using the computational modeling to assess and optimize device safety and efficacy, by combining modeling of the device physics with simulations of physiological responses. Some are also using datasets as part of the courses they teach, and of course there is virtual experimentation which I think is really cool. The SPARC Portal continues to grow as new research is included – right now, it is expanding beyond a bioelectronic focus to related areas such as pain.
How do you see this initiative evolving in the future?
The SPARC program initially focused on the autonomic nervous system, including parasympathetic and sympathetic innervation, as well as enteric system. However, it’s important to consider the sensory and motor innervation of the vagus nerve as well.
“One program goal is to build a connectivity map of the autonomic nervous system, not just in an anatomical sense, but also in a physiological sense. This functional map can be extended to include other organs such as the uterus, testes, liver, and skin, making them part of the purview of the SPARC Portal.”
As a community repository, SPARC is positioning itself as a home for all peripheral nervous system research as there is a current gap in infrastructure dedicated to this community.
Learn more about The SPARC Data and Resource Centre
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is supported by the NIH Common Fund to provide a scientific and technological foundation for future bioelectronic medicine devices and protocols. The goal of the SPARC program is to identify neural targets and accelerate the development of therapeutic devices that modulate electrical activity in the vagus and other nerves to help treat diseases and conditions, such as hypertension and gastrointestinal disorders, by precisely adjusting organ function.
About the Author
Hayleigh Culliton is an accomplished scientific marketer with a background in Biology and Nursing. She obtained her Bachelor’s degree from Trent University, where she developed a strong passion for science communication. With 6 years of experience in scientific marketing, she has helped companies in the life sciences industry develop and execute effective marketing strategies and #ShareScience.