@article {1213, title = {Governance and Sustainability of an Open Source Electronic Health Record: An Interpretive Case Study of OpenDolphin in Japan.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {739-743}, abstract = {

Electronic Health Records (EHRs) are at the heart of reforms aiming for improving the efficiency and quality of citizens healthcare services. Although there is still some skepticism, open source (OS) EHR is a growing phenomenon in health informatics. Given the widespread adoption of OS software (OSS) in several domains, including operating systems, and enterprise systems, the repeated shortfalls faced by healthcare organizations with dominant proprietary EHRs create an opportunity for other alternatives, such as OSS to demonstrate their abilities in addressing these well-documented problems, including inflexibility, high costs, and low interoperability. However, scholars have expressed extensive concerns about the sustainability of OS EHR. Recognizing that OSS project sustainability relies on their governance arrangements, this case study reports on the evolution of the governance and sustainability of a Japanese OS EHR project and provides rich insights to other open source EHR initiative stakeholders, including physicians, developers, researchers, and policymakers.

}, issn = {1879-8365}, doi = {10.3233/SHTI190321}, author = {Poba-Nzaou, Placide and Kume, Naoto and Kobayashi, Shinji} } @article {1145, title = {A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.}, journal = {Methods Inf Med}, volume = {54}, year = {2015}, month = {2015}, pages = {455-60}, abstract = {

OBJECTIVE: Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied the process when harmonizing data from three sites for the Lung Cancer Phenotype Database within the German Center for Lung Research.

METHODS: We developed a spreadsheet-based solution as tool to support the harmonization process for lung cancer data and a data integration procedure based on Talend Open Studio.

RESULTS: The harmonization process consists of eight steps describing a systematic approach for defining and reviewing source data elements and standardizing common data elements. The steps for defining common data elements and harmonizing them with local data definitions are repeated until consensus is reached. Application of this process for building the phenotype database led to a common basic data set on lung cancer with 285 structured parameters. The Lung Cancer Phenotype Database was realized as an i2b2 research data warehouse.

CONCLUSION: Data harmonization is a challenging task requiring informatics skills as well as domain knowledge. Our approach facilitates data harmonization by providing guidance through a uniform process that can be applied in a wide range of projects.

}, issn = {0026-1270}, doi = {10.3414/ME14-02-0030}, author = {Firnkorn, D and Ganzinger, M and Muley, T and Thomas, M and Knaup, P} } @article {981, title = {Going open source: some lessons learned from the development of OpenRecLink.}, journal = {Cad Saude Publica}, volume = {31}, year = {2015}, month = {2015 Feb}, pages = {257-63}, abstract = {

Record linkage is the process of identifying and merging records across different databases belonging to the same entity. The health sector is one of the pioneering areas of record linkage techniques applications. In 1998 we began the development of a software package, called RecLink that implemented probabilistic record linkage techniques. In this article we report the development of a new, open-source version of that program, now named OpenRecLink. The aim of this article is to present the main characteristics of the new version and some of the lessons learned during its development. The new version is a total rewrite of the program, based on three goals: (1) to migrate to a free and open source software (FOSS) platform; (2) to implement a multiplatform version; (3) to implement the support for internationalization. We describe the tools that we adopted, the process of development and some of the problems encountered.

}, keywords = {Databases, Factual, Medical Record Linkage, Software, Software Design}, issn = {1678-4464}, author = {Camargo Jr, Kenneth Rochel de and Coeli, Claudia Medina} } @article {865, title = {GBM volumetry using the 3D Slicer medical image computing platform.}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {1364}, abstract = {

Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer - a free platform for biomedical research - provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61\% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 {\textpm} 5.23\% and a Hausdorff Distance of 2.32 {\textpm} 5.23 mm.

}, issn = {2045-2322}, doi = {10.1038/srep01364}, author = {Egger, Jan and Kapur, Tina and Fedorov, Andriy and Pieper, Steve and Miller, James V and Veeraraghavan, Harini and Freisleben, Bernd and Golby, Alexandra J and Nimsky, Christopher and Kikinis, Ron} } @inbook {springerlink:10.1007/978-3-642-01932-6_45, title = {GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes}, booktitle = {Functional Imaging and Modeling of the Heart}, series = {Lecture Notes in Computer Science}, volume = {5528}, year = {2009}, note = {10.1007/978-3-642-01932-6_45}, pages = {417-426}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computational models, which is extensible through the development of application-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and commercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart.}, url = {http://dx.doi.org/10.1007/978-3-642-01932-6_45}, author = {Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and Bijnens, Bart and Frangi, Alejandro}, editor = {Ayache, Nicholas and Delingette, Herv{\'e} and Sermesant, Maxime} } @article {907, title = {A glass slipper? For cash-strapped organizations with EMR dreams, open-source software may be a perfect fit.}, journal = {Healthcare informatics : the business magazine for information and communication systems}, volume = {26}, year = {2009}, pages = {32{\textendash}36}, abstract = {Open-source EMR software is a potential, and relatively economical, option for hospital organizations that can{\textquoteright}t afford proprietary commercial EMR software, or whose leaders want a non-commercial option. While access to VistA{\textquoteright}s source code is free, any hospital organization seeking to implement commercialized VistA will need assistance from one of the vendors supporting that software. Implementing open-source is a bit closer to self-development than to implementing proprietary, commercial EMR software. CCHIT recently announced it will introduce new channels for certification of open-source EMR software, addressing the concerns of those in healthcare who want to pursue the open-source option while also applying for funding under ARRA-HITECH.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958156637\&partnerID=40\&md5=8657014eaf815ec3c47c548544084909}, author = {Hagland, M} } @article {19198666, title = {Generating Stimuli for Neuroscience Using PsychoPy.}, journal = {Frontiers in neuroinformatics}, volume = {2}, year = {2008}, month = {2008}, pages = {10}, abstract = {PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.). The structure of scripts is simple and intuitive. As a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. PsychoPy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. This paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.}, author = {Peirce, Jonathan W} }