Cytoscape Automation: empowering workflow-based network analysis

Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.

On the impact of service-oriented patterns on software evolvability: a controlled experiment and metric-based analysis

BACKGROUND

Design patterns are supposed to improve various quality attributes of software systems. However, there is controversial quantitative evidence of this impact. Especially for younger paradigms such as service- and Microservice-based systems, there is a lack of empirical studies.

OBJECTIVE

In this study, we focused on the effect of four service-based patterns-namely Process Abstraction, Service Façade, Decomposed Capability, and Event-Driven Messaging-on the evolvability of a system from the viewpoint of inexperienced developers.

METHOD

We conducted a controlled experiment with Bachelor students (N = 69). Two functionally equivalent versions of a service-based web shop-one with patterns (treatment group), one without (control group)-had to be changed and extended in three tasks. We measured evolvability by the effectiveness and efficiency of the participants in these tasks. Additionally, we compared both system versions with nine structural maintainability metrics for size, granularity, complexity, cohesion, and coupling.

RESULTS

Both experiment groups were able to complete a similar number of tasks within the allowed 90 min. Median effectiveness was 1/3. Mean efficiency was 12% higher in the treatment group, but this difference was not statistically significant. Only for the third task, we found statistical support for accepting the alternative hypothesis that the pattern version led to higher efficiency. In the metric analysis, the pattern version had worse measurements for size and granularity while simultaneously having slightly better values for coupling metrics. Complexity and cohesion were not impacted.

INTERPRETATION

For the experiment, our analysis suggests that the difference in efficiency is stronger with more experienced participants and increased from task to task. With respect to the metrics, the patterns introduce additional volume in the system, but also seem to decrease coupling in some areas.

CONCLUSIONS

Overall, there was no clear evidence for a decisive positive effect of using service-based patterns, neither for the student experiment nor for the metric analysis. This effect might only be visible in an experiment setting with higher initial effort to understand the system or with more experienced developers.

Design and Development of a Sharable Clinical Decision Support System Based on a Semantic Web Service Framework

Clinical decision support (CDS) systems provide clinicians and other health care stakeholders with patient-specific assessments or recommendations to aid in the clinical decision-making process. Despite their demonstrated potential for improving health care quality, the widespread availability of CDS systems has been limited mainly by the difficulty and cost of sharing CDS knowledge among heterogeneous healthcare information systems. The purpose of this study was to design and develop a sharable clinical decision support (S-CDS) system that meets this challenge. The fundamental knowledge base consists of independent and reusable knowledge modules (KMs) to meet core CDS needs, wherein each KM is semantically well defined based on the standard information model, terminologies, and representation formalisms. A semantic web service framework was developed to identify, access, and leverage these KMs across diverse CDS applications and care settings. The S-CDS system has been validated in two distinct client CDS applications. Model-level evaluation results confirmed coherent knowledge representation. Application-level evaluation results reached an overall accuracy of 98.66 % and a completeness of 96.98 %. The evaluation results demonstrated the technical feasibility and application prospect of our approach. Compared with other CDS engineering efforts, our approach facilitates system development and implementation and improves system maintainability, scalability and efficiency, which contribute to the widespread adoption of effective CDS within the healthcare domain.

Lessons learned from implementing service-oriented clinical decision support at four sites: A qualitative study

OBJECTIVE

To identify challenges, lessons learned and best practices for service-oriented clinical decision support, based on the results of the Clinical Decision Support Consortium, a multi-site study which developed, implemented and evaluated clinical decision support services in a diverse range of electronic health records.

METHODS

Ethnographic investigation using the rapid assessment process, a procedure for agile qualitative data collection and analysis, including clinical observation, system demonstrations and analysis and 91 interviews.

RESULTS

We identified challenges and lessons learned in eight dimensions: (1) hardware and software computing infrastructure, (2) clinical content, (3) human-computer interface, (4) people, (5) workflow and communication, (6) internal organizational policies, procedures, environment and culture, (7) external rules, regulations, and pressures and (8) system measurement and monitoring. Key challenges included performance issues (particularly related to data retrieval), differences in terminologies used across sites, workflow variability and the need for a legal framework.

DISCUSSION

Based on the challenges and lessons learned, we identified eight best practices for developers and implementers of service-oriented clinical decision support: (1) optimize performance, or make asynchronous calls, (2) be liberal in what you accept (particularly for terminology), (3) foster clinical transparency, (4) develop a legal framework, (5) support a flexible front-end, (6) dedicate human resources, (7) support peer-to-peer communication, (8) improve standards.

CONCLUSION

The Clinical Decision Support Consortium successfully developed a clinical decision support service and implemented it in four different electronic health records and four diverse clinical sites; however, the process was arduous. The lessons identified by the Consortium may be useful for other developers and implementers of clinical decision support services.

Requirements for data integration platforms in biomedical research networks: a reference model

Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure, we developed a reference model for the requirements. The reference model consists of five reference goals and 15 reference requirements. Using the Unified Modeling Language, the goals and requirements are set into relation to each other. In addition, all goals and requirements are described textually in tables. This reference model can be used by research networks as a basis for a resource efficient acquisition of their project specific requirements. Furthermore, a concrete instance of the reference model is described for a research network on liver cancer. The reference model is transferred into a requirements model of the specific network. Based on this concrete requirements model, a service-oriented information technology architecture is derived and also described in this paper.