Journal:Custom software development for use in a clinical laboratory

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Full article title Custom software development for use in a clinical laboratory
Journal Journal of Pathology Informatics
Author(s) Sinard, John H.; Gershkovich, Peter
Author affiliation(s) Yale University School of Medicine
Primary contact Email: Available with log-in
Year published 2012
Volume and issue 3
Page(s) 44
DOI 10.4103/2153-3539.104906
ISSN 2153-3539
Distribution license Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
Download (PDF)


In-house software development for use in a clinical laboratory is a controversial issue. Many of the objections raised are based on outdated software development practices, an exaggeration of the risks involved, and an underestimation of the benefits that can be realized. Buy versus build analyses typically do not consider total costs of ownership, and unfortunately decisions are often made by people who are not directly affected by the workflow obstacles or benefits that result from those decisions. We have been developing custom software for clinical use for over a decade, and this article presents our perspective on this practice. A complete analysis of the decision to develop or purchase must ultimately examine how the end result will mesh with the departmental workflow, and custom-developed solutions typically can have the greater positive impact on efficiency and productivity, substantially altering the decision balance sheet. Involving the end-users in preparation of the functional specifications is crucial to the success of the process. A large development team is not needed, and even a single programmer can develop significant solutions. Many of the risks associated with custom development can be mitigated by a well-structured development process, use of open-source tools, and embracing an agile development philosophy. In-house solutions have the significant advantage of being adaptable to changing departmental needs, contributing to efficient and higher quality patient care.

Keywords: Buy versus build, clinical use, custom software, in-house development, open source


Facing unmet needs

Computer software is an integral part of the day-to-day operation of any clinical laboratory. The major nidus for this activity is the laboratory information system (LIS), typically a suite of integrated modules purchased from a single vendor and designed specifically for the operation of the laboratory. LISs have matured substantially over the past few decades, providing greater operational efficiency and improving patient safety.

Yet, even the most advanced LISs do not fully meet the needs of every laboratory. Although some labs may be able to function adequately on their LIS, larger labs and labs providing specialty services typically can identify information management needs which are not met by their LIS. This is because LIS vendors build their software to meet the needs common to the majority of the labs in their current or intended client base rather than to meet the needs of a particular lab, and every lab has some unique needs due to their size, subtleties of their local environment, people, and the clinical focus of their clients. Thus, a needed functionality is lacking, either because it does not exist at all in the LIS, or because it exists in a way that does not mesh well with the workflow in the lab.

When the LIS functionality falls short of an identified need, labs have a choice: (1) make do with what they have, perhaps adjusting their workflow to accommodate; (2) contract with the LIS vendor to add the needed functionality to their LIS, or to modify it to meet their workflow needs; (3) purchase third-party software which meets the need, (4) develop their own custom software in-house, or (5) purchase a new LIS. Purchasing a new LIS is a huge undertaking and outside of the scope of this discussion. In fact, most labs choose to go with option 1. There can be many ways to accomplish a task in the lab, and labs can adapt to what their LIS is able to do. If the need is great and funds can be identified, option 2 may be chosen. Having your LIS vendor develop integrated customizations assures compatibility with the rest of the LIS, but this can be an expensive and time-consuming process. Nonetheless, LIS vendors rely on at least some clients choosing this option because this funds enhancements to their product. When laboratory science or the regulatory environment creates a general need, the client with the lowest threshold, greatest need, and available capital funds the development of the solution with their vendor. This client has the advantage of dictating how the workflow for the new feature will be designed. After delivery and testing (and payment), the vendor typically incorporates the new feature into a subsequent version of the LIS software, either as a free enhancement or available for an additional charge.

Third-party solutions can be a good option, and certainly should be investigated. If your lab has an unmet need, others probably have a similar need. There are a number of smaller companies that are more nimble than the major LIS vendors and that can respond more quickly to a need and provide a solution. The less specific the need is to pathology (e.g., transcription, image acquisition), the more likely it is that there will be multiple solutions from which to choose. If the solution can operate independent of the LIS, there are no integration concerns. If it needs to be integrated, the company may be able to handle it themselves, unless modifications are needed to the LIS system, in which case the third-party company will then likely have to enter into some sort of agreement with the LIS vendor. There are many examples of successful third-party solutions, the most common of which is "middleware" in the clinical laboratories, which manages communication between analytical instruments and the LIS.

However, if the need is novel or specific for your environment, third-party products that adequately meet that need are often simply not available. In this situation, in-house custom software development may be the best solution.

Our experience

At our institution, the pathology department provides anatomic pathology services only (laboratory medicine is a separate department). We have our own Pathology Informatics Unit that provides both operational services (i.e., information technology services) and software development. We also have three other full-time faculty members with academic informatics programs, but they are not involved in the software development for clinical use. Our clinical development team has developed a variety of clinical applications that are used every day in our anatomic pathology practice. Some of these solutions are integrated into and/or interact with our LIS, and some are standalone solutions. Our development team consists of three people. One is a pathologist, who also has other significant clinical and administrative needs and thus spends only about 20% of his time on software development. His primary role is in specification development and in programming the department's LIS to interact with the custom software (we have a unique arrangement without LIS vendor which allows us to introduce our own customizations into the commercial software, which was nicely designed to allow for this process). Another developer handles the user interface creation (according to the provided specifications) and also handles deployment, user training, and initial support of the custom applications. The third developer spends approximately two-thirds of his time on development, predominantly the business logic of the standalone components of the application, with the other third spent on management of the operational informatics unit in the department. Thus, in total, this represents about 1.6 FTEs (full-time equivalents) of true development resources. Our LIS is Cerner CoPathPlus. Our standalone components are developed in Java, predominantly as web applications.

Over the past several years, solutions we have developed and deployed include: Digital image file management[1], scanned document file management[2], dictation/transcription management[3], an outreach support system for orders and report delivery, an outreach client interface system, a repetitive task scheduling engine[4], frozen section management and diagnosis communication to operating rooms[5], histology asset tracking[6][7], trainee diagnosis tracking and evaluation[8], and numerous databases to support trainee interviewing and recruitment, graduate trainee tracking, computer hardware tracking, research histology, and graphics services billing. This article is based on our collective experience with this development and deployment process.


  1. Sinard, J.H.; Mattie, M.E. (2005). "Overcoming the limitations of integrated clinical digital imaging solutions". Archives of Pathology & Laboratory Medicine 129 (9): 1118-26. doi:10.1043/1543-2165(2005)129[1118:OTLOIC]2.0.CO;2. PMID 16119983. 
  2. Sinard, J.H.; Gershkovich, P. (2009). "Semiautomated Archiving of Scanned Requisition Documents in Anatomic Pathology - Advancing Practice, Instruction, and Innovation Through Informatics (APIII 2008) Conference". Archives of Pathology & Laboratory Medicine 133 (7): 1148-1165. doi:10.1043/1543-2165-133.7.1148. 
  3. Sinard, J.H.; Gershkovich, P. (2010). "Integrating Digital Dictation and the Anatomic Pathology Laboratory Information System - Advancing Practice, Instruction, and Innovation Through Informatics (APIII 2009) Conference". Archives of Pathology & Laboratory Medicine 134 (6): 936-948. doi:10.1043/1543-2165-134.6.936. 
  4. Sinard, J.H.; Gershkovich, P. (2009). "Use of a Repetitive Task Scheduling Engine for Workflow Automation and Rare Event Detection in a Clinical Environment - Advancing Practice, Instruction, and Innovation Through Informatics (APIII 2008) Conference". Archives of Pathology & Laboratory Medicine 133 (7): 1148-1165. doi:10.1043/1543-2165-133.7.1148. 
  5. Gershkovich, P.; Mutnick, N.; Sinard, J.H. (September 2010). "FSLink-Frozen Section Management Software with Real-Time Communication with the OR". Association for Pathology Informatics, 2010 Annual Meeting, Boston, MA. Association for Pathology Informatics. 
  6. Sinard, J.H.; Mutnick, N.; Gershkovich, P. (September 2010). "Histology Asset Tracking: Hidden Practices and Their Consequences". Association for Pathology Informatics, 2010 Annual Meeting, Boston, MA. Association for Pathology Informatics. 
  7. Sinard, J.H.; Mutnick, N.; Gershkovich, P. (September 2010). "Histology Asset Tracking Dashboard: Real-Time Monitoring and Dynamic Work Lists". Association for Pathology Informatics, 2010 Annual Meeting, Boston, MA. Association for Pathology Informatics. 
  8. Sinard, J.H.; Mutnick, N.; Gershkovich, P. (2011). "Facilitating Feedback and Education on the Hot Seat Rotation - Abstracts: Pathology Informatics 2011 Meeting". Journal of Pathology Informatics 2: 43. PMC PMC3238568. 


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.