A Systematic Review of Open Source Clinical Software on GitHub for Improving Software Reuse in Smart Healthcare

Shen, Zhengru; Spruit, Marco

doi:10.3390/app9010150

Cited by 12 publications

(7 citation statements)

References 19 publications

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“…Push for “Code Reuse”. Both open access publishing and open source software repositories present important models which can support the growth, replication, consistency, and inclusivity across clinical research [ 108 , 109 ]. We found that 44% of the studies identified in this review were open access, which is well above the 28% average [ 108 ].…”

Section: Discussionmentioning

confidence: 99%

Wearable Inertial Sensors for Gait Analysis in Adults with Osteoarthritis—A Scoping Review

Kobsar

Masood

Khan

et al. 2020

Sensors

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Our objective was to conduct a scoping review which summarizes the growing body of literature using wearable inertial sensors for gait analysis in lower limb osteoarthritis. We searched six databases using predetermined search terms which highlighted the broad areas of inertial sensors, gait, and osteoarthritis. Two authors independently conducted title and abstract reviews, followed by two authors independently completing full-text screenings. Study quality was also assessed by two independent raters and data were extracted by one reviewer in areas such as study design, osteoarthritis sample, protocols, and inertial sensor outcomes. A total of 72 articles were included, which studied the gait of 2159 adults with osteoarthritis (OA) using inertial sensors. The most common location of OA studied was the knee (n = 46), followed by the hip (n = 22), and the ankle (n = 7). The back (n = 41) and the shank (n = 40) were the most common placements for inertial sensors. The three most prevalent biomechanical outcomes studied were: mean spatiotemporal parameters (n = 45), segment or joint angles (n = 33), and linear acceleration magnitudes (n = 22). Our findings demonstrate exceptional growth in this field in the last 5 years. Nevertheless, there remains a need for more longitudinal study designs, patient-specific models, free-living assessments, and a push for “Code Reuse” to maximize the unique capabilities of these devices and ultimately improve how we diagnose and treat this debilitating disease.

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Section: Discussionmentioning

confidence: 99%

Wearable Inertial Sensors for Gait Analysis in Adults with Osteoarthritis—A Scoping Review

Kobsar

Masood

Khan

et al. 2020

Sensors

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“…Likewise, we found that no studies provided any open software to accompany their articles. Open-source software repositories (i.e., GitHub) can support cost-effective replication, advancement, and growth of software for clinical research [ 107 ]. Although limited, such examples are already present in the field of wearable technology [ 108 , 109 ].…”

Section: Discussionmentioning

confidence: 99%

Applications of Wearable Technology in a Real-Life Setting in People with Knee Osteoarthritis: A Systematic Scoping Review

Cudejko

Button

Willott

et al. 2021

JCM

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With the growing number of people affected by osteoarthritis, wearable technology may enable the provision of care outside a traditional clinical setting and thus transform how healthcare is delivered for this patient group. Here, we mapped the available empirical evidence on the utilization of wearable technology in a real-world setting in people with knee osteoarthritis. From an analysis of 68 studies, we found that the use of accelerometers for physical activity assessment is the most prevalent mode of use of wearable technology in this population. We identify low technical complexity and cost, ability to connect with a healthcare professional, and consistency in the analysis of the data as the most critical facilitators for the feasibility of using wearable technology in a real-world setting. To fully realize the clinical potential of wearable technology for people with knee osteoarthritis, this review highlights the need for more research employing wearables for information sharing and treatment, increased inter-study consistency through standardization and improved reporting, and increased representation of vulnerable populations.

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“…Some papers review the state of the open source implementations for a given topic. For example, Shen et al surveyed open source implementations of clinical software available in GitHub [67]. Both Dozmorov and Russel et al [60,22] use GitHub to survey open source implementations of bioinformatics software.…”

Section: Related Workmentioning

confidence: 99%

A systematic review of Python packages for time series analysis

Siebert¹,

Groß²,

Schroth³

2021

Preprint

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This paper presents a systematic review of Python packages focused on time series analysis. The objective is first to provide an overview of the different time series analysis tasks and preprocessing methods implemented, but also to give an overview of the development characteristics of the packages (e.g., dependencies, community size, etc.). This review is based on a search of literature databases as well as GitHub repositories. After the filtering process, 40 packages were analyzed. We classified the packages according to the analysis tasks implemented, the methods related to data preparation, and the means to evaluate the results produced (methods and access to evaluation data). We also reviewed the licenses, the packages community size, and the dependencies used. Among other things, our results show that forecasting is by far the most implemented task, that half of the packages provide access to real datasets or allow generating synthetic data, and that many packages depend on a few libraries (the most used ones being numpy, scipy and pandas). One of the lessons learned from this review is that the process of finding a given implementation is not inherently simple, and we hope that this review can help practitioners and researchers navigate the space of Python packages dedicated to time series analysis.

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A Systematic Review of Open Source Clinical Software on GitHub for Improving Software Reuse in Smart Healthcare

Cited by 12 publications

References 19 publications

Wearable Inertial Sensors for Gait Analysis in Adults with Osteoarthritis—A Scoping Review

Wearable Inertial Sensors for Gait Analysis in Adults with Osteoarthritis—A Scoping Review

Applications of Wearable Technology in a Real-Life Setting in People with Knee Osteoarthritis: A Systematic Scoping Review

A systematic review of Python packages for time series analysis

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