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1. IntrAnat Electrodes: A Free Database and Visualization Software for Intracranial Electroencephalographic Data Processed for Case and Group Studies (PubMed)

IntrAnat Electrodes: A Free Database and Visualization Software for Intracranial Electroencephalographic Data Processed for Case and Group Studies In some cases of pharmaco-resistant and focal epilepsies, intracranial recordings performed epidurally (electrocorticography, ECoG) and/or in depth (stereoelectroencephalography, SEEG) can be required to locate the seizure onset zone and the eloquent cortex before surgical resection. In SEEG, each electrode contact records brain's electrical activity

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2018 Frontiers in neuroinformatics

2. An open source algorithm to detect natural gas leaks from mobile methane survey data. (PubMed)

An open source algorithm to detect natural gas leaks from mobile methane survey data. The data collected by mobile methane (CH4) sensors can be used to find natural gas (NG) leaks in urban distribution systems. Extracting actionable insights from the large volumes of data collected by these sensors requires several data processing steps. While these survey platforms are commercially available, the associated data processing software largely constitute a black box due to their proprietary nature

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2019 PLoS ONE

3. Open-source automated chemical vapor deposition system for the production of two- dimensional nanomaterials. (PubMed)

Open-source automated chemical vapor deposition system for the production of two- dimensional nanomaterials. The study of two- dimensional (2D) materials is a rapidly growing area within nanomaterials research. However, the high equipment costs, which include the processing systems necessary for creating these materials, can be a barrier to entry for some researchers interested in studying these novel materials. Such process systems include those used for chemical vapor deposition, a preferred (...) method for making these materials. To address this challenge, this article presents the first open-source design for an automated chemical vapor deposition system that can be built for less than a third of the cost for a comparable commercial system. The materials and directions for the system are divided by subsystems, which allows the system to be easily built, customized and upgraded, depending upon the needs of the user. We include the details for the specific hardware that will be needed

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2019 PLoS ONE

4. Rift Valley fever: An open-source transmission dynamics simulation model. (PubMed)

Rift Valley fever: An open-source transmission dynamics simulation model. Rift Valley fever (RVF) is one of the major viral zoonoses in Africa, affecting humans and several domestic animal species. The epidemics in eastern Africa occur in a 5-15 year cycle coinciding with abnormally high rainfall generally associated to the warm phase of the El Niño event. However, recently, evidence has been gathered of inter-epidemic transmission. An open-source, easily applicable, accessible and modifiable (...) simulation was put on both the dynamics and composition of vector populations in three ecological zones, in order to elucidate the respective roles played by different vector species: the model output did indicate the necessity of Culex involvement and also indicated that vertical transmission in Ædes mcintoshi may be underestimated. This model, being built with open-source software and with an easy-to-use interface, can be adapted by researchers and control program managers to their specific needs

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2019 PLoS ONE

5. Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software (PubMed)

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration (...) -driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse).Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together

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2018 JMIR medical informatics

6. Implementing an Open Source Electronic Health Record System in Kenyan Health Care Facilities: Case Study (PubMed)

Implementing an Open Source Electronic Health Record System in Kenyan Health Care Facilities: Case Study The Kenyan government, working with international partners and local organizations, has developed an eHealth strategy, specified standards, and guidelines for electronic health record adoption in public hospitals and implemented two major health information technology projects: District Health Information Software Version 2, for collating national health care indicators and a rollout (...) Software Version 2 system.We aimed to present a descriptive case study of the implementation of an open source electronic health record system in public health care facilities in Kenya.We conducted a landscape review of existing literature concerning eHealth policies and electronic health record development in Kenya. Following initial discussions with the Ministry of Health, the World Health Organization, and implementing partners, we conducted a series of visits to implementing sites to conduct

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2018 JMIR medical informatics

7. RaCaT: An open source and easy to use radiomics calculator tool. (PubMed)

RaCaT: An open source and easy to use radiomics calculator tool. The widely known field 'Radiomics' aims to provide an extensive image based phenotyping of e.g. tumors using a wide variety of feature values extracted from medical images. Therefore, it is of utmost importance that feature values calculated by different institutes follow the same feature definitions. For this purpose, the imaging biomarker standardization initiative (IBSI) provides detailed mathematical feature descriptions

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2019 PLoS ONE

8. GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization. (PubMed)

GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization. Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination

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2019 PLoS ONE

9. Open-source food: Nutrition, toxicology, and availability of wild edible greens in the East Bay. (PubMed)

Open-source food: Nutrition, toxicology, and availability of wild edible greens in the East Bay. Foraged leafy greens are consumed around the globe, including in urban areas, and may play a larger role when food is scarce or expensive. It is thus important to assess the safety and nutritional value of wild greens foraged in urban environments.Field observations, soil tests, and nutritional and toxicology tests on plant tissue were conducted for three sites, each roughly 9 square blocks

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2019 PLoS ONE

10. Flavor-cyber-agriculture: Optimization of plant metabolites in an open-source control environment through surrogate modeling. (PubMed)

Flavor-cyber-agriculture: Optimization of plant metabolites in an open-source control environment through surrogate modeling. Food production in conventional agriculture faces numerous challenges such as reducing waste, meeting demand, maintaining flavor, and providing nutrition. Contained environments under artificial climate control, or cyber-agriculture, could in principle be used to meet many of these challenges. Through such environments, phenotypic expression of the plant-mass, edible (...) to affect production of flavor-active molecules in edible plants) were applied under different regimes to basil plants (Ocimum basilicum) growing inside a hydroponic farm with an open-source design; (2) flavor-active volatile molecules were measured in each plant using gas chromatography-mass spectrometry (GC-MS); and (3) symbolic regression was used to construct a surrogate model of this chemistry from the input environmental variables, and this model was used to discover new combinations

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2019 PLoS ONE

11. CLEESE: An open-source audio-transformation toolbox for data-driven experiments in speech and music cognition. (PubMed)

CLEESE: An open-source audio-transformation toolbox for data-driven experiments in speech and music cognition. Over the past few years, the field of visual social cognition and face processing has been dramatically impacted by a series of data-driven studies employing computer-graphics tools to synthesize arbitrary meaningful facial expressions. In the auditory modality, reverse correlation is traditionally used to characterize sensory processing at the level of spectral or spectro-temporal (...) stimulus properties, but not higher-level cognitive processing of e.g. words, sentences or music, by lack of tools able to manipulate the stimulus dimensions that are relevant for these processes. Here, we present an open-source audio-transformation toolbox, called CLEESE, able to systematically randomize the prosody/melody of existing speech and music recordings. CLEESE works by cutting recordings in small successive time segments (e.g. every successive 100 milliseconds in a spoken utterance

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2019 PLoS ONE

12. Quanfima: An open source Python package for automated fiber analysis of biomaterials. (PubMed)

Quanfima: An open source Python package for automated fiber analysis of biomaterials. Hybrid 3D scaffolds composed of different biomaterials with fibrous structure or enriched with different inclusions (i.e., nano- and microparticles) have already demonstrated their positive effect on cell integration and regeneration. The analysis of fibers in hybrid biomaterials, especially in a 3D space is often difficult due to their various diameters (from micro to nanoscale) and compositions. Though

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2019 PLoS ONE

13. Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review. (PubMed)

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review. Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health (...) records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas.The aim of this study was to conduct

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2017 JMIR medical informatics

14. The State of Open Source Electronic Health Record Projects: A Software Anthropology Study (PubMed)

The State of Open Source Electronic Health Record Projects: A Software Anthropology Study Electronic health records (EHR) are a key tool in managing and storing patients' information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers' motivations. However, few published studies have focused (...) on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects.This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers.This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014

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2017 JMIR medical informatics

15. Open-source mobile digital platform for clinical trial data collection in low-resource settings (PubMed)

Open-source mobile digital platform for clinical trial data collection in low-resource settings Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we (...) piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study.Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach.The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source

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2017 BMJ innovations

16. Meet Thomas Baden, Channel Editor PLOS Open Source Toolkit

Meet Thomas Baden, Channel Editor PLOS Open Source Toolkit Meet Thomas Baden, Channel Editor PLOS Open Source Toolkit | PLOS Blogs Network PLOS Blogs Staff Blogs Blogs by Topic Biology & Life Sciences Earth & Environmental Sciences Multi-disciplinary Sciences Medicine & Health Research Analysis & Scientific Policy Diverse perspectives on science and medicine Staff Blogs Blogs by Topic Biology & Life Sciences Earth & Environmental Sciences Multi-disciplinary Sciences Medicine & Health Research (...) Analysis & Scientific Policy Post navigation in Uncategorized Meet Thomas Baden, one of the PLOS Editors, and find out how he came to be a proponent of open source tools and a researcher working at the intersection of vision and neuroscience. Can you tell me about yourself and your current research, and how you came to be interested in this field? We are interested in how single and small groups of neurons compute information. To address aspects of this rather broad question, we work on early

2018 PLOS Blogs Network

17. Open-source sensor for measuring oxygen partial pressures below 100 microbars. (PubMed)

Open-source sensor for measuring oxygen partial pressures below 100 microbars. The ability to measure partial pressures of oxygen below 100 microbars and nanomolar dissolved oxygen concentrations in in situ laboratory systems benefits many fields including microbiology, geobiology, oceanography, chemistry, and materials science. Here, we present an easily constructible open-source design for a networked luminescence lifetime measurement system for in situ measurements in arbitrary laboratory (...) . Designs are also provided for attaching the sensor to various commercially available containers used in laboratories. The design files are released under an open source license, which enables other laboratories to build, customize, and use these sensors.

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2018 PLoS ONE

18. The Open Source Toolkit – meet our new Channel Editors for Software

The Open Source Toolkit – meet our new Channel Editors for Software The Open Source Toolkit – meet our new Channel Editors for Software | PLOS Blogs Network PLOS Blogs Staff Blogs Blogs by Topic Biology & Life Sciences Earth & Environmental Sciences Multi-disciplinary Sciences Medicine & Health Research Analysis & Scientific Policy Diverse perspectives on science and medicine Staff Blogs Blogs by Topic Biology & Life Sciences Earth & Environmental Sciences Multi-disciplinary Sciences Medicine (...) & Health Research Analysis & Scientific Policy Post navigation in Uncategorized The Open Source Toolkit welcomes Nikoleta E. Glynatsi and Yo Yehudi as Channel Editors for Software. The Open Source Toolkit gathers articles, projects and resources describing hardware and software that can be applied in research, education and/or healthcare settings. Until now, the emphasis has been on hardware, so we are delighted to welcome Nikoleta E. Glynatsi and Yo Yehudi as new Channel Editors with expertise

2018 PLOS Blogs Network

19. Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers. (PubMed)

Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers. The cost of specialized scientific equipment can be high and with limited funding resources, researchers and students are often unable to access or purchase the ideal equipment for their projects. In the fields of materials science and mechanical engineering, fundamental equipment such as tensile testing devices can cost tens to hundreds of thousands of dollars. While (...) a research lab often has access to a large-scale testing machine suitable for conventional samples, loading devices for meso- and micro-scale samples for in-situ testing with the myriad of microscopy tools are often hard to source and cost prohibitive. Open-source software has allowed for great strides in the reduction of costs associated with software development and open-source hardware and additive manufacturing have the potential to similarly reduce the costs of scientific equipment and increase

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2018 PLoS ONE

20. Kranion, an open-source environment for planning transcranial focused ultrasound surgery: technical note. (PubMed)

Kranion, an open-source environment for planning transcranial focused ultrasound surgery: technical note. Transcranial focused ultrasound (FUS) ablation is an emerging incision-less treatment for neurological disorders. The factors affecting FUS treatment efficiency are not well understood. Kranion is open-source software that allows the user to simulate the planning stages of FUS treatment and to "replay" previous treatments for off-line analysis. This study aimed to investigate

2019 Journal of Neurosurgery

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