Journal:MaPSeq, a service-oriented architecture for genomics research within an academic biomedical research institution
|Full article title||MaPSeq, a service-oriented architecture for genomics research within an academic biomedical research institution|
|Author(s)||Reilly, J.; Ahalt, S.; McGee, J.; Owen, P.; Schmitt, C.; Wilhelmsen, K.|
|Author affiliation(s)||University of North Carolina at Chapel Hill|
|Primary contact||Phone: +1 919-445-9619 (Wilhelmsen)|
|Volume and issue||2 (3)|
|Distribution license||Creative Commons Attribution 4.0 International|
|Download||[hhttp://www.mdpi.com/2227-9709/2/3/20/pdf http://www.mdpi.com/2227-9709/2/3/20/pdf] (PDF)|
Genomics research presents technical, computational, and analytical challenges that are well recognized. Less recognized are the complex sociological, psychological, cultural, and political challenges that arise when genomics research takes place within a large, decentralized academic institution. In this paper, we describe a Service-Oriented Architecture (SOA) — MaPSeq — that was conceptualized and designed to meet the diverse and evolving computational workflow needs of genomics researchers at our large, hospital-affiliated, academic research institution. We present the institutional challenges that motivated the design of MaPSeq before describing the architecture and functionality of MaPSeq. We then discuss SOA solutions and conclude that approaches such as MaPSeq enable efficient and effective computational workflow execution for genomics research and for any type of academic biomedical research that requires complex, computationally-intense workflows.
Keywords: service-oriented architecture; genomics; massively parallel sequencing; computational workflow; academic biomedical research; decentralized organization; distributed decision-making
Genomics research presents well-recognized technical, computational, and analytical challenges. For example, while the technology for massively parallel genomic sequencing has progressed to the point where large amounts of data can be generated at a rapid pace and for a reasonable cost, the analytical burden presented by this massive amount of data can quickly overwhelm the genomic analyst. Indeed, the analysis and interpretation of genetic findings is generally considered the rate-limiting step in the translation of genomic sequencing data into clinical practice and patient care.
Less recognized challenges to research in genomics and any biomedical field are the sociological, psychological, cultural, and political barriers, many of which arise from the organizational structure within which the research takes place. Indeed, research organizations tend to fall somewhere on a continuum between completely centralized and completely decentralized. Each of these extremes has advantages and disadvantages. Centralized organizations traditionally function within a simple organizational design, with singular decision-making, top-level operational control, a consolidated budget, strong/clear communication channels, uniform culture and politics, and a high degree of efficiency, but at the expense of flexibility. Decentralized organizations, in contrast, generally operate within a complex organizational design, with distributed decision-making, local operational control, regionalized budgets, numerous weak or broken communication channels, inconsistent (and sometimes conflicting) culture and politics, and a high degree of flexibility, but at the expense of efficiency. The conceptualization, design, development, and implementation of information technology (IT) solutions for research in genomics and any biomedical field must therefore involve careful consideration of not only the needs of the user base, but also the organizational structure within which the research takes place.
Herein, we present a Service-Oriented Architecture (SOA) application — termed MaPSeq — that was conceptualized and designed to address the organizational challenges of computation-intensive biomedical research within a decentralized academic institution. In this article, we first describe the challenges that contributed to the conceptualization and design of MaPSeq. We then provide an overview of the technical architecture and capabilities of MaPSeq. Finally, we provide a discussion of service-oriented solutions such as MaPSeq.
Challenges driving the conceptualization and SOA design of MaPSeq
The design of MaPSeq was motivated by challenges that arose during the implementation of a genomic sequencing project titled “North Carolina Clinical Genomic Evaluation by NextGen Exome Sequencing” (NCGENES). This project, which is funded by the National Human Genome Resource Institute, aims to conduct whole exome sequencing of 500 patient samples drawn from multiple disease categories. NCGENES is a complex project, with both research and clinical arms. Soon after the project was initiated, the research and clinical teams realized that there were numerous barriers and roadblocks that needed to be overcome in order to achieve the analytical goals of the project. (See Table 1 for overview.)
Academic institutions face the challenge of balancing the needs of large, funded, research projects that typically support the development of an informatics infrastructure with the needs of smaller, often unfunded, research projects that cannot afford significant development costs. Furthermore, few research projects are sufficiently funded to support future development needs. Our institution faced these challenges when trying to balance the needs of the NCGENES investigative team with those of other investigative teams and anticipate future needs. The scale, general applicability, and complexity of massively parallel sequencing favored the development of an SOA approach to support both current and future needs related to genomic and non-genomic computationally-intense serial workflows.
As is typical for an academic institution, our genomics infrastructure developed in an ad hoc manner, with multiple investigative teams working independently across the university campus. The result was a burgeoning, uncoordinated cluster of distributed compute resources. Compounding this challenge were the numerous network idiosyncrasies that prevented administrators within one network from accessing compute resources within a different network; thus, access privileges to campus compute resources were determined locally and required on-site (rather than remote) access.
Decision-making at large academic institutions tends to be decentralized, with numerous decision makers enforcing different (and often conflicting) policies and procedures. This organizational structure inevitably leads to political and cultural conflicts and resistance to change, particularly when “external” IT teams attempt to change the processes in place among “central” investigative teams. Political and cultural resistance to the NCGENES project was encountered early on as the investigative team identified many barriers to the automation of human user-controlled workflow processes. While the existing human user-run workflows met the needs of small genomic sequencing projects and user groups, these workflows were inefficient for the computationally-demanding, whole-exome sequencing needs of NCGENES. Moreover, the use of a human contact as the point of access to an existing workflow created a roadblock to the execution of NCGENES, reduced the efficiency of genomic analysis, and threatened the security of sensitive patient data.
Numerous Workflow Management Systems and workflow pipelines for genomic analysis exist, including COSMOS, Ergatis, i2b2, LONI, NG6, NGSANE, Orione, RUbioSeq, SeqInCloud, STATegra EMS, TREVA, and Pegasus.
Our team evaluated each of these systems for their ability to overcome the challenges described above. We found that existing solutions could address some, but not all, of the roadblocks and barriers that were hindering progress on the NCGENES project and that a new solution was needed. While all of the existing workflow systems and pipelines have proven to be effective, each has limitations . MaPSeq is not unique in this regard, but it is responsive to the key features of a decentralized research organization. Specifically, as an SOA, MaPSeq allows for integration with multiple clients and distributed systems, whether local, open source, or commercial, and provides tailored, reusable, automated service solutions that address the varying and evolving needs and preferences of decentralized decision-makers. MaPSeq is scalable and can support both small- and large-scale projects and thus is responsive to the computational needs of all investigators. MaPSeq is efficient and allows for seamless, opportunistic use of distributed compute resources. Finally, the service-oriented, automated approach requires little coordination or communication among individual user groups and thus avoids local nuances in politics and culture.
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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.