Association for Academic Surgery (AAS)

Inspiring and Developing Young Academic Surgeons

Open Source in Academic Surgery

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“Open source” has become nothing less than a revolutionary intellectual movement, arising from the software development community. All software is provided as traditional “binary” programs that run on computers, mobile devices and on web sites, but open source software also distributes the source code that makes the programs work. Other programmers are then free to examine, improve, expand or combine that source code to make new programs (or just make old programs better). In short, open source leverages the skill and insight of interested communities to make software better, faster, more capable and more secure.

The output from open source computer programming impacts our daily lives in ways that are difficult to quantify, yet nonetheless profound. The web browser you are using to read this post, the web server that’s hosting this site, the operating system that runs on your mobile phone, and dozens of other devices or services with which you will interact today run either wholly or partly open source software. According to one recent survey, 63% of large companies had active open source projects supporting their internal business functions.1 Microsoft – long held in low esteem in the open source community for its preference for “closed source” development – has come to embrace the open source movement, integrating open source technologies into its core products and even purchasing the leading source code host. That subsidiary (GitHub) currently serves 31 million users and hosts 96 million code repositories2 containing source code for education, games, databases artificial intelligence, web hosting, and thousands more incomprehensibly abstruse projects. The open source ethos has become pervasive, catalyzing innovation in fields from computer processor design3 to seismology4 to agriculture.5

One could understandably ask, “why would so many people give away valuable intellectual property for use by anyone that asks?” The answer to that question is that writing mobile apps or Android video drivers or road traffic analytics entails a lot of drudgery. Writing programs from scratch forces programmers to “reinvent a wheel” that hundreds or thousands of programmers have already coded and debugged over hours to weeks; and then another wheel, and then another. Rather than replicate effort spanning hundreds or thousands of lines of code, programmers that judiciously use open source can save time and frustration by leveraging the vast collective efforts preserved in repositories like GitHub. The time that they save can in turn be spent contributing new code or improving old code that lives on in the cloud, ready to be repurposed. The process is a virtuous circle, albeit an occasionally messy one.

There is much to admire in this approach. When you think of your early academic career or your first weeks in the lab, how much of your time was consumed finding your bearings or trying to extract useful information from your colleagues? How many dark alleys did you wander down before someone pointed you in the right direction? How many days or weeks did you spend reinventing the wheel? If there was ready-made “source code” to jumpstart your career as a surgeon investigator, how much tedium could have been avoided?

The temptation is to consign early academic inertia to the success or failure of faculty mentorship, but mentors are constrained to their areas of expertise. Within that domain, they provide a wealth of actionable guidance, but their ability to support truly novel investigations will be constrained. Academic surgery is a far-flung enterprise with only so many experts to go around. The traditional model of the annual society Congress and the peer-reviewed journal article remain the best solution to disseminate results, but this model is too sclerotic to deliver the timely practical knowledge that keeps research trundling along. While invaluable, the nuts and bolts are insufficiently glamorous to merit presentation from the podium or publication in JSR. Yet practical advice is often precisely what junior investigators need so desperately to avoid spinning their wheels, exhausting their grants and giving up on worthy but ambitious undertakings.

Open source acolytes in the world of software development often devote substantial effort toward community projects not supported by their employers, projects which will never be commercialized. They do so for altruistic purposes often enough, but many do so because the scale of the contributions confers status within their industry. Our profession would do well to emulate this mindset, to publish and promulgate best practices that can clear away the clutter and drudgery that so often plague the early-stage academic surgeon. Such investments in our scientific community are already being made in the areas of surgical simulation6 and modeling the benefits of bariatric surgery.7

What does open source academic medicine look like? Consider the AAS Surgical Investigators’ Course (SIC) as a model. Organized annually at the Academic Surgical Congress and supported by seasoned academicians, the SIC is a testament to the transformative power of collaboration and innovation supporting new faculty. AAS can extend this model beyond its present focus on grant preparation and into a practical collection of Surgical Research Toolboxes (SRTs). Each SRT would be prepared by content experts and feature “Materials and Methods” targeting health services research, quality improvement, clinical trials, collaboration with industry, biostatistics, and emerging technologies like computer vision, neural networks, natural language processing. Rather than reinventing the wheel to get one’s research off the ground, new investigators would build on firm foundations and (in a similar virtuous circle) contribute to, refine and extend the SRTs, which would be freely available to anyone.

The model I propose may seem unorthodox, but its design and embrace of open, non-discriminatory standards is the engine that built the Internet8,9 and the web.10 AAS can serve as a technical and cultural platform to make this model a reality. We can and we must do much more to extend the impact and reach of this organization and open source holds tremendous promise to achieve our greatest aspiration: a genuine legacy to those who will follow us.

 

References:

  1. TODO Group. GitHub – todogroup/survey: Open Source Programs Survey. https://github.com/todogroup/survey. Published 2018. Accessed August 14, 2019.
  2. GitHub. The State of the Octoverse. 2018. https://octoverse.github.com/. Accessed August 14, 2019.
  3. OpenRISC Community. Architecture – OpenRISC. https://openrisc.io/architecture. Published 2019. Accessed August 14, 2019.
  4. dGB Earth Sciences. Free Software – OpendTect. https://www.dgbes.com/index.php/software/free. Published 2018. Accessed August 14, 2019.
  5. farmOS project. farmOS.org. https://farmos.org/. Published 2019. Accessed August 14, 2019.
  6. Gavrilovic B, Fahy AS, Carrillo B, Nasr A, Gerstle JT, Azzie G. Development of an Open-Source Laparoscopic Simulator Capable of Motion and Force Assessment: High Tech at Low Cost. J Laparoendosc Adv Surg Tech A. 2018;28(10):1253-1260. doi:10.1089/lap.2018.0126
  7. Johnston SS, Morton JM, Kalsekar I, Ammann EM, Hsiao C-W, Reps J. Using Machine Learning Applied to Real-World Healthcare Data for Predictive Analytics: An Applied Example in Bariatric Surgery. Value Heal. 2019;22(5):580-586. doi:10.1016/j.jval.2019.01.011
  8. International Telecommunication Union. About ITU. https://www.itu.int/en/about/Pages/default.aspx. Published 2019. Accessed August 19, 2019.
  9. Internet Engineering Task Force. Rrquest for Comments. https://www.ietf.org/standards/rfcs/. Published 2019. Accessed August 19, 2019.
  10. World Wide Web Consortium. About W3C. 2019. https://www.w3.org/Consortium/. Accessed August 19, 2019.
Dominic Papandria MD

Dominic Papandria MD

Dr. Papandria received his MD degree from the University of North Carolina School of Medicine, where he also completed his internship in general surgery. He completed the PGY-2 year of his general surgery residency at Johns Hopkins, after which he completed a pediatric surgery clinical and research fellowship at that institution. He resumed his residency training in General Surgery at St. Vincent Hospital in Indianapolis, and then pursued fellowship training in surgical critical care at the Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, and in minimally invasive surgery at Nationwide Children's Hospital in Columbus, OH. During the latter fellowship, he served as a faculty member for Nationwide Children's minimally invasive surgical skills laboratory at several national and international pediatric surgery meetings. He was also appointed clinical assistant professor at Ohio State University College of Medicine. Board certified in general surgery and surgical critical care, Dr. Papandria is currently faculty in the Division of General and Gastrointestinal Surgery at Emory University Hospital Midtown in Atlanta, GA.
Dominic Papandria MD
Dominic Papandria MD

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About Dominic Papandria MD

Dr. Papandria received his MD degree from the University of North Carolina School of Medicine, where he also completed his internship in general surgery. He completed the PGY-2 year of his general surgery residency at Johns Hopkins, after which he completed a pediatric surgery clinical and research fellowship at that institution. He resumed his residency training in General Surgery at St. Vincent Hospital in Indianapolis, and then pursued fellowship training in surgical critical care at the Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, and in minimally invasive surgery at Nationwide Children’s Hospital in Columbus, OH. During the latter fellowship, he served as a faculty member for Nationwide Children’s minimally invasive surgical skills laboratory at several national and international pediatric surgery meetings. He was also appointed clinical assistant professor at Ohio State University College of Medicine. Board certified in general surgery and surgical critical care, Dr. Papandria is currently faculty in the Division of General and Gastrointestinal Surgery at Emory University Hospital Midtown in Atlanta, GA.