Journal:The growing need for microservices in bioinformatics
| Full article title | The growing need for microservices in bioinformatics |
|---|---|
| Journal | Journal of Pathology Informatics |
| Author(s) | Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G.J. |
| Author affiliation(s) | University of Michigan |
| Primary contact | Email: Available w/ login |
| Year published | 2016 |
| Volume and issue | 7 |
| Page(s) | 45 |
| DOI | 10.4103/2153-3539.194835 |
| ISSN | 2153-3539 |
| Distribution license | Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported |
| Website | http://www.jpathinformatics.org |
| Download | http://www.jpathinformatics.org/temp/JPatholInform7145-5650543_154145.pdf (PDF) |
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Abstract
Objective: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems.
In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development.
Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements.
Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics
Conclusions: Use of the microservices framework is an effective methodology for the fabrication and implementation of reliable and innovative software, made possible in a highly collaborative setting.
Keywords: Bioinformatics, crowd sourcing, defect analysis, failure mode analysis, information technology, microservices, pathology, reliability engineering, software engineering
Introduction
The modern software ecosystem is rapidly changing. The emergence of cloud computing has spurred developers to compartmentalize applications into small, easily maintainable functional units that can be replicated on demand. This application segmentation is commonly referred to as microservices (or microservice architecture). The enabling technology for microservices was first introduced into the UNIX kernel as early as 1979[1], but this field has only recently experienced an exponential growth in popularity. Many industry leaders, dependent on their information technology (IT) infrastructure, have embraced this model, including Amazon, Capital One Financial Corp., Google, and PayPal Holdings Inc.[2], among many others.
Discussion
Microservice architecture has taken hold in application design for a number of reasons [Figure 1], but ultimately, the fundamental driver has been the opportunity for significant increase in productivity. Gains are achieved by dividing larger, more complex applications into small, manageable projects that encapsulate common functionality. Each microservice represents a "black-box" with a well-defined application programming interface (API) bundled with its own integral resources, thus eliminating external dependencies. This encapsulation simplifies the division of labor for teams of software developers and reduces the inherent overhead of multiple developers working on the same sections of code. The narrow scope of functionality of a single microservice allows for thorough testing and optimization of each component in isolation, leading to higher reliability and performance of the overall parent application. The encapsulated nature of the microservice methodology inherently allows for future reuse of existing modules with minimal effort. A portfolio of proven, production-use microservices can be valuable for accelerating the development of subsequent projects.
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Source of support
None
Conflicts of interest
None
References
- ↑ Topjian, J. (13 November 2013). "Contain your enthusiasm - Part One: A history of operating system containers". Tech Radar Blog. Cybera. http://www.cybera.ca/news-and-events/tech-radar/contain-your-enthusiasm-part-one-a-history-of-operating-system-containers/. Retrieved 05 January 2016.
- ↑ 2.0 2.1 Miller, M. (5 October 2015). "Innovate or Die: The Rise of Microservices". The Wall Street Journal. Dow Jones & Company, Inc. http://blogs.wsj.com/cio/2015/10/05/innovate-or-die-the-rise-of-microservices/. Retrieved 05 January 2016.
- ↑ "GE Uses Docker to Enable Self-Service for their Developers". Docker, Inc. 2016. https://www.docker.com/customers/ge-uses-docker-enable-self-service-their-developers. Retrieved 29 August 2016.
- ↑ "Flexible, Portable, Secure". Hewlett Packard Enterprise Development LP. 2016. https://www.docker.com/customers/ge-uses-docker-enable-self-service-their-developers. Retrieved 28 August 2016.
- ↑ Ho, A. (11 November 2015). "Microservices at Amazon". Developer Blog. Apigee, Inc. https://apigee.com/about/blog/developer/microservices-amazon. Retrieved 28 August 2016.
- ↑ Piesche, S. (23 March 2015). "Microservices at Constant Contact". Tech Blog. Constant Contact, Inc. https://apigee.com/about/blog/developer/microservices-amazon. Retrieved 28 August 2016.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.
