%0 Journal Article %J PLoS One %D 2019 %T Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model. %A Klann, Jeffrey G %A Joss, Matthew A H %A Embree, Kevin %A Murphy, Shawn N %X

BACKGROUND: The All Of Us Research Program (AOU) is building a nationwide cohort of one million patients' EHR and genomic data. Data interoperability is paramount to the program's success. AOU is standardizing its EHR data around the Observational Medical Outcomes Partnership (OMOP) data model. OMOP is one of several standard data models presently used in national-scale initiatives. Each model is unique enough to make interoperability difficult. The i2b2 data warehousing and analytics platform is used at over 200 sites worldwide, which uses a flexible ontology-driven approach for data storage. We previously demonstrated this ontology system can drive data reconfiguration, to transform data into new formats without site-specific programming. We previously implemented this on our 12-site Accessible Research Commons for Health (ARCH) network to transform i2b2 into the Patient Centered Outcomes Research Network model.

METHODS AND RESULTS: Here, we leverage our investment in i2b2 high-performance transformations to support the AOU OMOP data pipeline. Because the ARCH ontology has gained widespread national interest (through the Accrual to Clinical Trials network, other PCORnet networks, and the Nebraska Lexicon), we leveraged sites' existing investments into this standard ontology. We developed an i2b2-to-OMOP transformation, driven by the ARCH-OMOP ontology and the OMOP concept mapping dictionary. We demonstrated and validated our approach in the AOU New England HPO (NEHPO). First, we transformed into OMOP a fake patient dataset in i2b2 and verified through AOU tools that the data was structurally compliant with OMOP. We then transformed a subset of data in the Partners Healthcare data warehouse into OMOP. We developed a checklist of assessments to ensure the transformed data had self-integrity (e.g., the distributions have an expected shape and required fields are populated), using OMOP's visual Achilles data quality tool. This i2b2-to-OMOP transformation is being used to send NEHPO production data to AOU. It is open-source and ready for use by other research projects.

%B PLoS One %V 14 %P e0212463 %8 2019 %G eng %N 2 %R 10.1371/journal.pone.0212463 %0 Journal Article %J Eur J Ophthalmol %D 2019 %T Eye injuries in children - incidence and outcomes: An observational study at a dedicated children's eye casualty. %A Jolly, Rohit %A Arjunan, Mousindha %A Theodorou, Maria %A Dahlmann-Noor, Annegret H %K Adolescent %K Child %K Child, Preschool %K Emergency Service, Hospital %K Eye Injuries %K Female %K Humans %K Incidence %K Infant %K Male %K Prognosis %K Quality of Life %K Retrospective Studies %K Treatment Outcome %K Vision Disorders %K Visual Acuity %X

PURPOSE: Trauma is an important cause of visual loss in children and may affect their quality of life. Prevention and legislation can reduce the incidence of trauma, and appropriate and timely treatment can improve prognosis. We aimed to describe incidence of eye injuries in children and the adherence to national and local management guidelines.

METHODS: Retrospective service evaluation at a tertiary hospital (Moorfields Eye Hospital, London, UK) which operates a dedicated children's eye casualty. The electronic patient administration system and electronic patient record system (Openeyes) were used to identify children who presented with eye injuries between January 2015 and December 2015.

RESULTS: Of 2397 first-time attendances to our children's casualty, 508 were for injuries (estimated incidence 21.1%, 95% confidence interval: 19.5%-22.7%). Mean age at presentation was 7.51 (standard deviation: 7.97) years; boys were more commonly affected than girls (69%). The most common injury was corneal abrasion, followed by blunt and chemical injury; severe injuries such as penetrating trauma were rare. Injuries were sustained mostly during play or sports. Two children sustained permanent loss of vision in the affected eye.

CONCLUSION: Our findings are comparable to other published reports. Adherence to management guidelines is high, but documentation of advice given to families can be improved. Regular training of staff and collaboration with organisations outside the hospital can increase awareness of eye injuries in children.

%B Eur J Ophthalmol %V 29 %P 499-503 %8 2019 Sep %G eng %N 5 %R 10.1177/1120672118803512 %0 Journal Article %J Bioinformatics %D 2019 %T PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title. %A Glicksberg, Benjamin S %A Oskotsky, Boris %A Thangaraj, Phyllis M %A Giangreco, Nicholas %A Badgeley, Marcus A %A Johnson, Kipp W %A Datta, Debajyoti %A Rudrapatna, Vivek %A Rappoport, Nadav %A Shervey, Mark M %A Miotto, Riccardo %A Goldstein, Theodore C %A Rutenberg, Eugenia %A Frazier, Remi %A Lee, Nelson %A Israni, Sharat %A Larsen, Rick %A Percha, Bethany %A Li, Li %A Dudley, Joel T %A Tatonetti, Nicholas P %A Butte, Atul J %X

MOTIVATION: Electronic Health Records (EHR) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.

RESULTS: We present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership Common Data Model (CDM) format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open-source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.

AVAILABILITY: PatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

%B Bioinformatics %8 2019 Jun 19 %G eng %R 10.1093/bioinformatics/btz409 %0 Journal Article %J JMIR Med Educ %D 2018 %T Development and Evaluation of a New Security and Privacy Track in a Health Informatics Graduate Program: Multidisciplinary Collaboration in Education. %A Zhou, Leming %A Parmanto, Bambang %A Joshi, James %X

BACKGROUND: The widespread application of technologies such as electronic health record systems, mobile health apps, and telemedicine platforms, has made it easy for health care providers to collect relevant data and deliver health care regimens. While efficacious, these new technologies also pose serious security and privacy challenges.

OBJECTIVE: The training program described here aims at preparing well-informed health information security and privacy professionals with enhanced course materials and various approaches.

METHODS: A new educational track has been built within a health informatics graduate program. Several existing graduate courses have been enhanced with new security and privacy modules. New labs and seminars have been created, and students are being encouraged to participate in research projects and obtain real-world experience from industry partners. Students in this track receive both theoretical education and hands-on practice. Evaluations have been performed on this new track by conducting multiple surveys on a sample of students.

RESULTS: We have succeeded in creating a new security track and developing a pertinent curriculum. The newly created security materials have been implemented in multiple courses. Our evaluation indicated that students (N=72) believed that receiving security and privacy training was important for health professionals, the provided security contents were interesting, and having the enhanced security and privacy training in this program was beneficial for their future career.

CONCLUSIONS: The security and privacy education for health information professionals in this new security track has been significantly enhanced.

%B JMIR Med Educ %V 4 %P e19 %8 2018 Dec 21 %G eng %N 2 %R 10.2196/mededu.9081 %0 Journal Article %J Sci Rep %D 2018 %T Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach. %A Vandaele, Rémy %A Aceto, Jessica %A Muller, Marc %A Péronnet, Frédérique %A Debat, Vincent %A Wang, Ching-Wei %A Huang, Cheng-Ta %A Jodogne, Sébastien %A Martinive, Philippe %A Geurts, Pierre %A Marée, Raphaël %K Algorithms %K Animals %K Body Weights and Measures %K Drosophila %K Humans %K Image Processing, Computer-Assisted %K Software %K Zebrafish %X

The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research.

%B Sci Rep %V 8 %P 538 %8 2018 01 11 %G eng %N 1 %R 10.1038/s41598-017-18993-5 %0 Journal Article %J Computers in Biology and Medicine %D 2018 %T The mobile sleep lab app: {An} open-source framework for mobile sleep assessment based on consumer-grade wearable devices %A Burgdorf, Andreas %A Güthe, Inga %A Jovanović, Marko %A Kutafina, Ekaterina %A Kohlschein, Christian %A Bitsch, Jó Ágila %A Jonas, Stephan M. %K Mobile sleep laboratory %K Sleep screening %K Smartphone %K Telemedicine %K Wearable technology %X BACKGROUND: Sleep disorders have a prevalence of up to 50% and are commonly diagnosed using polysomnography. However, polysomnography requires trained staff and specific equipment in a laboratory setting, which are expensive and limited resources are available. Mobile and wearable devices such as fitness wristbands can perform limited sleep monitoring but are not evaluated well. Here, the development and evaluation of a mobile application to record and synchronize data from consumer-grade sensors suitable for sleep monitoring is presented and evaluated for data collection capability in a clinical trial. METHODS: Wearable and ambient consumer-grade sensors were selected to mimic the functionalities of clinical sleep laboratories. Then, a modular application was developed for recording, processing and visualizing the sensor data. A validation was performed in three phases: (1) sensor functionalities were evaluated, (2) self-experiments were performed in full-night experiments, and (3) the application was tested for usability in a clinical trial on primary snoring. RESULTS: The evaluation of the sensors indicated their suitability for assessing basic sleep characteristics. Additionally, the application successfully recorded full-night sleep. The collected data was of sufficient quality to detect and measure body movements, cardiac activity, snoring and brightness. The ongoing clinical trial phase showed the successful deployment of the application by medical professionals. CONCLUSION: The proposed software demonstrated a strong potential for medical usage. With low costs, it can be proposed for screening, long-term monitoring or in resource-austere environments. However, further validations are needed, in particular the comparison to a clinical sleep laboratory. %B Computers in Biology and Medicine %V 103 %P 8–16 %G eng %R 10.1016/j.compbiomed.2018.09.025 %0 Journal Article %J J Digit Imaging %D 2018 %T The Orthanc Ecosystem for Medical Imaging. %A Jodogne, Sébastien %K Diagnostic Imaging %K Humans %K Radiology Information Systems %X

This paper reviews the components of Orthanc, a free and open-source, highly versatile ecosystem for medical imaging. At the core of the Orthanc ecosystem, the Orthanc server is a lightweight vendor neutral archive that provides PACS managers with a powerful environment to automate and optimize the imaging flows that are very specific to each hospital. The Orthanc server can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise-ready databases. It is shown how software developers and research engineers can easily develop external software or Web portals dealing with medical images, with minimal knowledge of the DICOM standard, thanks to the advanced programming interface of the Orthanc server. The paper concludes by introducing the Stone of Orthanc, an innovative toolkit for the cross-platform rendering of medical images.

%B J Digit Imaging %V 31 %P 341-352 %8 2018 06 %G eng %N 3 %R 10.1007/s10278-018-0082-y %0 Journal Article %J J Med Internet Res %D 2017 %T Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone. %A Oza, Shefali %A Jazayeri, Darius %A Teich, Jonathan M %A Ball, Ellen %A Nankubuge, Patricia Alexandra %A Rwebembera, Job %A Wing, Kevin %A Sesay, Alieu Amara %A Kanter, Andrew S %A Ramos, Glauber D %A Walton, David %A Cummings, Rachael %A Checchi, Francesco %A Fraser, Hamish S %K electronic health records %K Epidemics %K Hemorrhagic Fever, Ebola %K Humans %K Infection Control %K Sierra Leone %K Telemedicine %X

BACKGROUND: Stringent infection control requirements at Ebola treatment centers (ETCs), which are specialized facilities for isolating and treating Ebola patients, create substantial challenges for recording and reviewing patient information. During the 2014-2016 West African Ebola epidemic, paper-based data collection systems at ETCs compromised the quality, quantity, and confidentiality of patient data. Electronic health record (EHR) systems have the potential to address such problems, with benefits for patient care, surveillance, and research. However, no suitable software was available for deployment when large-scale ETCs opened as the epidemic escalated in 2014.

OBJECTIVE: We present our work on rapidly developing and deploying OpenMRS-Ebola, an EHR system for the Kerry Town ETC in Sierra Leone. We describe our experience, lessons learned, and recommendations for future health emergencies.

METHODS: We used the OpenMRS platform and Agile software development approaches to build OpenMRS-Ebola. Key features of our work included daily communications between the development team and ground-based operations team, iterative processes, and phased development and implementation. We made design decisions based on the restrictions of the ETC environment and regular user feedback. To evaluate the system, we conducted predeployment user questionnaires and compared the EHR records with duplicate paper records.

RESULTS: We successfully built OpenMRS-Ebola, a modular stand-alone EHR system with a tablet-based application for infectious patient wards and a desktop-based application for noninfectious areas. OpenMRS-Ebola supports patient tracking (registration, bed allocation, and discharge); recording of vital signs and symptoms; medication and intravenous fluid ordering and monitoring; laboratory results; clinician notes; and data export. It displays relevant patient information to clinicians in infectious and noninfectious zones. We implemented phase 1 (patient tracking; drug ordering and monitoring) after 2.5 months of full-time development. OpenMRS-Ebola was used for 112 patient registrations, 569 prescription orders, and 971 medication administration recordings. We were unable to fully implement phases 2 and 3 as the ETC closed because of a decrease in new Ebola cases. The phase 1 evaluation suggested that OpenMRS-Ebola worked well in the context of the rollout, and the user feedback was positive.

CONCLUSIONS: To our knowledge, OpenMRS-Ebola is the most comprehensive adaptable clinical EHR built for a low-resource setting health emergency. It is designed to address the main challenges of data collection in highly infectious environments that require robust infection prevention and control measures and it is interoperable with other electronic health systems. Although we built and deployed OpenMRS-Ebola more rapidly than typical software, our work highlights the challenges of having to develop an appropriate system during an emergency rather than being able to rapidly adapt an existing one. Lessons learned from this and previous emergencies should be used to ensure that a set of well-designed, easy-to-use, pretested health software is ready for quick deployment in future.

%B J Med Internet Res %V 19 %P e294 %8 2017 08 21 %G eng %N 8 %R 10.2196/jmir.7881 %0 Journal Article %J Sci Rep %D 2017 %T QuPath: Open source software for digital pathology image analysis. %A Bankhead, Peter %A Loughrey, Maurice B %A Fernández, José A %A Dombrowski, Yvonne %A McArt, Darragh G %A Dunne, Philip D %A McQuaid, Stephen %A Gray, Ronan T %A Murray, Liam J %A Coleman, Helen G %A James, Jacqueline A %A Salto-Tellez, Manuel %A Hamilton, Peter W %K Algorithms %K Biomarkers, Tumor %K Colonic Neoplasms %K Humans %K Image Interpretation, Computer-Assisted %K Kaplan-Meier Estimate %K Programmed Cell Death 1 Ligand 2 Protein %K User-Computer Interface %X

QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath's flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

%B Sci Rep %V 7 %P 16878 %8 2017 12 04 %G eng %N 1 %R 10.1038/s41598-017-17204-5 %0 Journal Article %J Biol Open %D 2016 %T 3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software. %A Jackson, Brandon E %A Evangelista, Dennis J %A Ray, Dylan D %A Hedrick, Tyson L %X

Ecological, behavioral, and biomechanical studies often need to quantify animal movement and behavior in three dimensions. In laboratory studies, a major tool to accomplish these measurements is the use of multiple, calibrated high-speed cameras. Until very recently, the complexity, weight, and cost of such cameras have made their deployment in field situations risky; furthermore, such cameras are not affordable to many researchers. Here we show how inexpensive, consumer-grade cameras can accomplish these measurements both within the laboratory and in the field. Combined with our methods and open source software, the availability of inexpensive, portable and rugged cameras will open up new areas of biological study by providing precise 3D tracking and quantification of animal and human movement to researchers in a wide variety of field and laboratory contexts.

%B Biol Open %8 2016 Jul 21 %G eng %R 10.1242/bio.018713 %0 Journal Article %J Stud Health Technol Inform %D 2016 %T Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes. %A Jurcău, Daniel-Alexandru %A Stoicu-Tivadar, Vasile %X

This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

%B Stud Health Technol Inform %V 226 %P 127-30 %8 2016 %G eng %0 Journal Article %J BMJ Glob Health %D 2016 %T Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals. %A Tuti, Timothy %A Bitok, Michael %A Malla, Lucas %A Paton, Chris %A Muinga, Naomi %A Gathara, David %A Gachau, Susan %A Mbevi, George %A Nyachiro, Wycliffe %A Ogero, Morris %A Julius, Thomas %A Irimu, Grace %A English, Mike %X

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya. We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals' paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network. In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians' initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning. We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.

%B BMJ Glob Health %V 1 %P e000028 %8 2016 May 24 %G eng %N 1 %R 10.1136/bmjgh-2016-000028 %0 Journal Article %J Med Image Anal %D 2016 %T Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience. %A Kapur, Tina %A Pieper, Steve %A Fedorov, Andriy %A Fillion-Robin, J-C %A Halle, Michael %A O'Donnell, Lauren %A Lasso, Andras %A Ungi, Tamas %A Pinter, Csaba %A Finet, Julien %A Pujol, Sonia %A Jagadeesan, Jayender %A Tokuda, Junichi %A Norton, Isaiah %A Estepar, Raul San Jose %A Gering, David %A Aerts, Hugo J W L %A Jakab, Marianna %A Hata, Nobuhiko %A Ibanez, Luiz %A Blezek, Daniel %A Miller, Jim %A Aylward, Stephen %A Grimson, W Eric L %A Fichtinger, Gabor %A Wells, William M %A Lorensen, William E %A Schroeder, Will %A Kikinis, Ron %X

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

%B Med Image Anal %8 2016 Jul 7 %G eng %R 10.1016/j.media.2016.06.035 %0 Journal Article %J Journal of Biomolecular Screening %D 2016 %T Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform} %A Moutsatsos, Ioannis K. %A Hossain, Imtiaz %A Agarinis, Claudia %A Harbinski, Fred %A Abraham, Yann %A Dobler, Luc %A Zhang, Xian %A Wilson, Christopher J. %A Jenkins, Jeremy L. %A Holway, Nicholas %A Tallarico, John %A Parker, Christian N. %K CellProfiler %K continuous integration %K high-content screening %K high-performance computing %X High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. %B Journal of Biomolecular Screening %G eng %R 10.1177/1087057116679993 %0 Journal Article %J PLoS Pathog %D 2016 %T Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. %A Van Voorhis, Wesley C %A Adams, John H %A Adelfio, Roberto %A Ahyong, Vida %A Akabas, Myles H %A Alano, Pietro %A Alday, Aintzane %A Alemán Resto, Yesmalie %A Alsibaee, Aishah %A Alzualde, Ainhoa %A Andrews, Katherine T %A Avery, Simon V %A Avery, Vicky M %A Ayong, Lawrence %A Baker, Mark %A Baker, Stephen %A Ben Mamoun, Choukri %A Bhatia, Sangeeta %A Bickle, Quentin %A Bounaadja, Lotfi %A Bowling, Tana %A Bosch, Jürgen %A Boucher, Lauren E %A Boyom, Fabrice F %A Brea, Jose %A Brennan, Marian %A Burton, Audrey %A Caffrey, Conor R %A Camarda, Grazia %A Carrasquilla, Manuela %A Carter, Dee %A Belen Cassera, Maria %A Chih-Chien Cheng, Ken %A Chindaudomsate, Worathad %A Chubb, Anthony %A Colon, Beatrice L %A Colón-López, Daisy D %A Corbett, Yolanda %A Crowther, Gregory J %A Cowan, Noemi %A D'Alessandro, Sarah %A Le Dang, Na %A Delves, Michael %A DeRisi, Joseph L %A Du, Alan Y %A Duffy, Sandra %A Abd El-Salam El-Sayed, Shimaa %A Ferdig, Michael T %A Fernández Robledo, José A %A Fidock, David A %A Florent, Isabelle %A Fokou, Patrick V T %A Galstian, Ani %A Gamo, Francisco Javier %A Gokool, Suzanne %A Gold, Ben %A Golub, Todd %A Goldgof, Gregory M %A Guha, Rajarshi %A Guiguemde, W Armand %A Gural, Nil %A Guy, R Kiplin %A Hansen, Michael A E %A Hanson, Kirsten K %A Hemphill, Andrew %A Hooft van Huijsduijnen, Rob %A Horii, Takaaki %A Horrocks, Paul %A Hughes, Tyler B %A Huston, Christopher %A Igarashi, Ikuo %A Ingram-Sieber, Katrin %A Itoe, Maurice A %A Jadhav, Ajit %A Naranuntarat Jensen, Amornrat %A Jensen, Laran T %A Jiang, Rays H Y %A Kaiser, Annette %A Keiser, Jennifer %A Ketas, Thomas %A Kicka, Sebastien %A Kim, Sunyoung %A Kirk, Kiaran %A Kumar, Vidya P %A Kyle, Dennis E %A Lafuente, Maria Jose %A Landfear, Scott %A Lee, Nathan %A Lee, Sukjun %A Lehane, Adele M %A Li, Fengwu %A Little, David %A Liu, Liqiong %A Llinás, Manuel %A Loza, Maria I %A Lubar, Aristea %A Lucantoni, Leonardo %A Lucet, Isabelle %A Maes, Louis %A Mancama, Dalu %A Mansour, Nuha R %A March, Sandra %A McGowan, Sheena %A Medina Vera, Iset %A Meister, Stephan %A Mercer, Luke %A Mestres, Jordi %A Mfopa, Alvine N %A Misra, Raj N %A Moon, Seunghyun %A Moore, John P %A Morais Rodrigues da Costa, Francielly %A Müller, Joachim %A Muriana, Arantza %A Nakazawa Hewitt, Stephen %A Nare, Bakela %A Nathan, Carl %A Narraidoo, Nathalie %A Nawaratna, Sujeevi %A Ojo, Kayode K %A Ortiz, Diana %A Panic, Gordana %A Papadatos, George %A Parapini, Silvia %A Patra, Kailash %A Pham, Ngoc %A Prats, Sarah %A Plouffe, David M %A Poulsen, Sally-Ann %A Pradhan, Anupam %A Quevedo, Celia %A Quinn, Ronald J %A Rice, Christopher A %A Abdo Rizk, Mohamed %A Ruecker, Andrea %A St Onge, Robert %A Salgado Ferreira, Rafaela %A Samra, Jasmeet %A Robinett, Natalie G %A Schlecht, Ulrich %A Schmitt, Marjorie %A Silva Villela, Filipe %A Silvestrini, Francesco %A Sinden, Robert %A Smith, Dennis A %A Soldati, Thierry %A Spitzmüller, Andreas %A Stamm, Serge Maximilian %A Sullivan, David J %A Sullivan, William %A Suresh, Sundari %A Suzuki, Brian M %A Suzuki, Yo %A Swamidass, S Joshua %A Taramelli, Donatella %A Tchokouaha, Lauve R Y %A Theron, Anjo %A Thomas, David %A Tonissen, Kathryn F %A Townson, Simon %A Tripathi, Abhai K %A Trofimov, Valentin %A Udenze, Kenneth O %A Ullah, Imran %A Vallieres, Cindy %A Vigil, Edgar %A Vinetz, Joseph M %A Voong Vinh, Phat %A Vu, Hoan %A Watanabe, Nao-Aki %A Weatherby, Kate %A White, Pamela M %A Wilks, Andrew F %A Winzeler, Elizabeth A %A Wojcik, Edward %A Wree, Melanie %A Wu, Wesley %A Yokoyama, Naoaki %A Zollo, Paul H A %A Abla, Nada %A Blasco, Benjamin %A Burrows, Jeremy %A Laleu, Benoît %A Leroy, Didier %A Spangenberg, Thomas %A Wells, Timothy %A Willis, Paul A %X

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

%B PLoS Pathog %V 12 %P e1005763 %8 2016 Jul %G eng %N 7 %R 10.1371/journal.ppat.1005763 %0 Journal Article %J Int J Med Inform %D 2016 %T Open-source LIMS in Vietnam: The path toward sustainability and host country ownership. %A Landgraf, Kenneth M %A Kakkar, Reshma %A Meigs, Michelle %A Jankauskas, Paul T %A Phan, Thi Thu Huong %A Nguyen, Viet Nga %A Nguyen, Duy Thai %A Duong, Thanh Tung %A Nguyen, Thi Hoa %A Bond, Kyle B %X

OBJECTIVE: The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs.

METHODS: This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices.

RESULTS: LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam.

CONCLUSION: Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing.

%B Int J Med Inform %V 93 %P 92-102 %8 2016 Sep %G eng %R 10.1016/j.ijmedinf.2016.06.010 %0 Journal Article %J Behav Res Methods %D 2016 %T TACIT: An open-source text analysis, crawling, and interpretation tool. %A Dehghani, Morteza %A Johnson, Kate M %A Garten, Justin %A Boghrati, Reihane %A Hoover, Joe %A Balasubramanian, Vijayan %A Singh, Anurag %A Shankar, Yuvarani %A Pulickal, Linda %A Rajkumar, Aswin %A Parmar, Niki Jitendra %X

As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

%B Behav Res Methods %8 2016 Mar 4 %G eng %R 10.3758/s13428-016-0722-4 %0 Journal Article %J J Prosthet Dent %D 2015 %T Anterior loop of the inferior alveolar nerve: Averages and prevalence based on CT scans. %A Juan, Del Valle Lovato %A Grageda, Edgar %A Crespo, Salvador Gómez %X

STATEMENT OF PROBLEM: The treatment of edentulous patients by using a complete implant-supported fixed prosthetic with distal extension has been widely studied; success is mainly dependent upon the placement of the distal implants. The location of the inferior alveolar nerve determines implant placement, but the length, prevalence, and symmetry between the left and right side of the anterior loop of the alveolar nerve are unknown.

PURPOSE: The purpose of this clinical study was to measure the anterior loop of the inferior alveolar nerve, which determines the placement of distal implants, in a group of 55 Mexican participants. The study expected to ascertain the average length, prevalence, and symmetry between left and right side and any sex differences. To differentiate the inferior alveolar nerve path, a new technique was applied using Hounsfield unit (HU) thresholds. The null hypothesis was that no significant differences would be found between the left and right sides or between men and women for the anterior loop of the inferior alveolar nerve.

MATERIAL AND METHODS: Fifty-five computed tomography (CT) scans were made (Somatom Sensation 16; Siemens Healthcare) and were visualized with InVesalius software. Anterior loop measurements were made on 3-dimensional surfaces. To determine statistical differences between the left and right side and between the sexes, the t test was used. The interclass correlation coefficient test was also applied to verify the reliability of the measurements.

RESULTS: Ninety percent of participants showed the anterior loop of the inferior alveolar nerve. The length of the anterior loop ranged between 0 and 6.68 mm, with a mean of 2.19 mm. No significant differences were found between the left and right sides or between men and women.

CONCLUSIONS: The mean length for the anterior loop in the sample was 2.19 mm. As the anterior loop length shows a high degree of variability, these findings suggest that a CT scan for each patient is recommended in order to visualize a safety zone before placing implants close to the mental foramen.

%B J Prosthet Dent %8 2015 Oct 9 %G eng %R 10.1016/j.prosdent.2015.06.025 %0 Journal Article %J Journal of biomedical informatics %D 2015 %T caTissue Suite to OpenSpecimen: developing an extensible, open source, web-based biobanking management system %A McIntosh, Leslie D %A Sharma, Mukesh K %A Mulvihill, David %A Gupta, Snehil %A Juehne, Anthony %A George, Bijoy %A Khot, Suhas B %A Kaushal, Atul %A Watson, Mark A %A Nagarajan, Rakesh %X The National Cancer Institute (NCI) Cancer Biomedical Informatics Grid(®) (caBIG(®)) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions. %B Journal of biomedical informatics %V 57 %P 456 - 464 %8 2015/10/ %@ 1532-04641532-0480 %G eng %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772150/ %! J Biomed Inform %R 10.1016/j.jbi.2015.08.020 %0 Journal Article %J Stud Health Technol Inform %D 2015 %T Design and development of an EMR for Ebola Treatment Centers in Sierra Leone using OpenMRS. %A Jazayeri, Darius %A Oza, Shefali %A Ramos, Glauber %A Fraser, Hamish %A Teich, Jonathan M %A Kanter, Andrew S %A Ball, Ellen %X

Ebola treatment presents unique challenges for medical records because strict infection control requirements rule out most conventional record-keeping systems. We used the OpenMRS platform to rapidly develop an EMR system for the recently opened Kerry Town, Sierra Leone Ebola Treatment Centre. This system addresses the need for recording patient data and communicating it between the infectious and non-infectious zones, and is specifically designed for maximum usability by staff wearing cumbersome protective equipment. This platform is interoperable with other key eHealth systems in the country, and is extensible to other sites and diseases.

%B Stud Health Technol Inform %V 216 %P 916 %8 2015 %G eng %0 Journal Article %J Cad Saude Publica %D 2015 %T Going open source: some lessons learned from the development of OpenRecLink. %A Camargo Jr, Kenneth Rochel de %A Coeli, Claudia Medina %K Databases, Factual %K Medical Record Linkage %K Software %K Software Design %X

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.

%B Cad Saude Publica %V 31 %P 257-63 %8 2015 Feb %G eng %N 2 %0 Journal Article %J J Am Med Inform Assoc %D 2015 %T OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data. %A Kass-Hout, Taha A %A Xu, Zhiheng %A Mohebbi, Matthew %A Nelsen, Hans %A Baker, Adam %A Levine, Jonathan %A Johanson, Elaine %A Bright, Roselie A %X

OBJECTIVE: The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs).

MATERIALS AND METHODS: Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges.

RESULTS: Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event.

CONCLUSION: With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

%B J Am Med Inform Assoc %8 2015 Dec 7 %G eng %R 10.1093/jamia/ocv153 %0 Journal Article %J J Am Med Inform Assoc %D 2015 %T Virtualization of Open-Source Secure Web Services to Support Data Exchange in a Pediatric Critical Care Research Network. %A Frey, Lewis J %A Sward, Katherine A %A Newth, Christopher Jl %A Khemani, Robinder G %A Cryer, Martin E %A Thelen, Julie L %A Enriquez, Rene %A Shaoyu, Su %A Pollack, Murray M %A Harrison, Rick E %A Meert, Kathleen L %A Berg, Robert A %A Wessel, David L %A Shanley, Thomas P %A Dalton, Heidi %A Carcillo, Joseph %A Jenkins, Tammara L %A Dean, J Michael %X

OBJECTIVES: To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality.

MATERIAL AND METHODS: Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers.

RESULTS: Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation.

CONCLUSIONS: Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes.

%B J Am Med Inform Assoc %8 2015 Mar 21 %G eng %R 10.1093/jamia/ocv009 %0 Journal Article %J BMC Genomics %D 2014 %T High dimensional biological data retrieval optimization with NoSQL technology. %A Wang, Shicai %A Pandis, Ioannis %A Wu, Chao %A He, Sijin %A Johnson, David %A Emam, Ibrahim %A Guitton, Florian %A Guo, Yike %K Database Management Systems %K Databases, Genetic %K High-Throughput Nucleotide Sequencing %K Humans %K Information Storage and Retrieval %K Medical Informatics %K Multiple Myeloma %K Oligonucleotide Array Sequence Analysis %K Transcriptome %X

BACKGROUND: High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data.

RESULTS: In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB.

CONCLUSIONS: The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data.

%B BMC Genomics %V 15 Suppl 8 %P S3 %8 2014 %G eng %R 10.1186/1471-2164-15-S8-S3 %0 Journal Article %J J Digit Imaging %D 2014 %T Simplifying electronic data capture in clinical trials: workflow embedded image and biosignal file integration and analysis via web services. %A Haak, Daniel %A Samsel, Christian %A Gehlen, Johan %A Jonas, Stephan %A Deserno, Thomas M %K Algorithms %K Automatic Data Processing %K Clinical Trials as Topic %K Database Management Systems %K Humans %K Image Processing, Computer-Assisted %K Information Storage and Retrieval %K Internet %K Medical Records Systems, Computerized %K Systems Integration %K Workflow %X

To improve data quality and save cost, clinical trials are nowadays performed using electronic data capture systems (EDCS) providing electronic case report forms (eCRF) instead of paper-based CRFs. However, such EDCS are insufficiently integrated into the medical workflow and lack in interfacing with other study-related systems. In addition, most EDCS are unable to handle image and biosignal data, although electrocardiography (EGC, as example for one-dimensional (1D) data), ultrasound (2D data), or magnetic resonance imaging (3D data) have been established as surrogate endpoints in clinical trials. In this paper, an integrated workflow based on OpenClinica, one of the world's largest EDCS, is presented. Our approach consists of three components for (i) sharing of study metadata, (ii) integration of large volume data into eCRFs, and (iii) automatic image and biosignal analysis. In all components, metadata is transferred between systems using web services and JavaScript, and binary large objects (BLOBs) are sent via the secure file transfer protocol and hypertext transfer protocol. We applied the close-looped workflow in a multicenter study, where long term (7 days/24 h) Holter ECG monitoring is acquired on subjects with diabetes. Study metadata is automatically transferred into OpenClinica, the 4 GB BLOBs are seamlessly integrated into the eCRF, automatically processed, and the results of signal analysis are written back into the eCRF immediately.

%B J Digit Imaging %V 27 %P 571-80 %8 2014 Oct %G eng %N 5 %R 10.1007/s10278-014-9694-z %0 Journal Article %J Stud Health Technol Inform %D 2013 %T E-health systems for management of MDR-TB in resource-poor environments: a decade of experience and recommendations for future work. %A Fraser, Hamish S F %A Habib, Ali %A Goodrich, Mark %A Thomas, David %A Blaya, Joaquin A %A Fils-Aime, Joseph Reginald %A Jazayeri, Darius %A Seaton, Michael %A Khan, Aamir J %A Choi, Sharon S %A Kerrison, Foster %A Falzon, Dennis %A Becerra, Mercedes C %K Developing Countries %K electronic health records %K Electronic Prescribing %K Extensively Drug-Resistant Tuberculosis %K Haiti %K Health Information Management %K Humans %K Medication Systems, Hospital %K Pakistan %K Remote Consultation %X

INTRODUCTION: Multi-drug resistant TB (MDR-TB) is a complex infectious disease that is a growing threat to global health. It requires lengthy treatment with multiple drugs and specialized laboratory testing. To effectively scale up treatment to thousands of patients requires good information systems to support clinical care, reporting, drug forecasting, supply chain management and monitoring.

METHODS: Over the last decade we have developed the PIH-EMR electronic medical record system, and subsequently OpenMRS-TB, to support the treatment of MDR-TB in Peru, Haiti, Pakistan, and other resource-poor environments.

RESULTS: We describe here the experience with implementing these systems and evaluating many aspects of their performance, and review other systems for MDR-TB management.

CONCLUSIONS: We recommend a new approach to information systems to address the barriers to scale up MDR-TB treatment, particularly access to the appropriate drugs and lab data. We propose moving away from fragmented, vertical systems to focus on common platforms, addressing all stages of TB care, support for open data standards and interoperability, care for a wide range of diseases including HIV, integration with mHealth applications, and ability to function in resource-poor environments.

%B Stud Health Technol Inform %V 192 %P 627-31 %8 2013 %G eng %0 Journal Article %J J Med Internet Res %D 2013 %T What do electronic health record vendors reveal about their products: an analysis of vendor websites. %A Yeung, Natalie K %A Jadad, Alejandro R %A Shachak, Aviv %K Commerce %K electronic health records %K Humans %K Internet %K Marketing of Health Services %K Ontario %K Telemedicine %X

BACKGROUND: Purchasing electronic health records (EHRs) typically follows a process in which potential adopters actively seek information, compare alternatives, and form attitudes towards the product. A potential source of information on EHRs that can be used in the process is vendor websites. It is unclear how much product information is presented on EHR vendor websites or the extent of its value during EHR purchasing decisions.

OBJECTIVE: To explore what features of EHR systems are presented by vendors in Ontario, Canada, on their websites, and the persuasive means they use to market such systems; to compare the online information available about primary care EHR systems with that about hospital EHR systems, and with data compiled by OntarioMD, a regional certifying agency.

METHODS: A list of EHR systems available in Ontario was created. The contents of vendor websites were analyzed. A template for data collection and organization was developed and used to collect and organize information on the vendor, website content, and EHR features. First, we mapped information on system features to categories based on a framework from the Institute of Medicine (IOM). Second, we used a grounded theory-like approach to explore information for building consumer confidence in the vendor and product, and the various persuasive strategies employed on vendor websites. All data were first coded by one researcher. A peer reviewer independently analyzed a randomly chosen subset of the websites (10 of 21; 48%) and provided feedback towards a unified coding scheme. All data were then re-coded and categorized into themes. Finally, we compared information from vendor websites and data gathered by OntarioMD.

RESULTS: Vendors provided little specific product information on their websites. Only two of five acute care EHR websites (40%) and nine of 16 websites for primary care systems (56%) featured seven or all eight of the IOM components. Several vendor websites included system interface demonstrations: screenshots (six websites), public videos or slideshows (four websites), or for registered viewers only (three websites). Persuasive means used by vendors included testimonials on 14/21 (67%) websites, and directional language. Except for one free system, trial EHR versions were not available. OntarioMD provided more comprehensive information about primary care systems than the vendors' websites. Of 14 points of comparison, only the inclusion of templates and bilingual interfaces were fully represented in both data sources. For all other categories, the vendor websites were less complete than the OntarioMD site.

CONCLUSIONS: EHR vendor websites employ various persuasive means, but lack product-specific information and do not provide options for trying systems on a limited basis. This may impede the ability of potential adopters to form perceptions and compare various offerings. Both vendors and clients could benefit from greater transparency and more specific product information on the Web.

TRIAL REGISTRATION: N/A.

%B J Med Internet Res %V 15 %P e36 %8 2013 Feb 19 %G eng %N 2 %R 10.2196/jmir.2312 %0 Journal Article %J Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology %D 2012 %T Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software. %A Kim, Gihyeon %A Jung, Ho-Joong %A Lee, Han-Jun %A Lee, Jae-Sung %A Koo, Seungbum %A Chang, Seung-Hwan %X There is a growing interest in three-dimensional computed tomography (3D-CT) as a research tool for the study of bone, joint anatomy, and kinematics. However, when CT data are processed and handled manually using image processing programs to yield 3D image and coordinate value, systematic and random errors should be validated. We evaluated the accuracy and reliability of length measurement on CT with OsiriX software. 3D-CT scans were made of 14 frozen pig knees with five transosseous holes in the metaphyseal portion of femur. The lengths between tunnel orifices were measured using Mitutoyo Digimatic digital calipers to establish the gold standard, and with the OsiriX program in 3D multi-planar reformatting mode for comparison. All measurements were recorded by a principal (replicate 1, trial 1) and a secondary observer (replicate 2, trial 1) and were repeated once by each observer (trial 2). The mean differences between OsiriX and real measurements were less than 0.1 mm in both replicates, and maximum differences were less than 0.3 mm. There were no significant differences between the replicates and real measurements (p = 0.544 and 0.622 for replicates 1 and 2, respectively). The intraclass correlation coefficients (ICC) were very high between trials and between replicates (ICC = 0.998 and 0.999, respectively). For kinematic analysis of the knees, length measurements on 3D-CT using OsiriX program can be used as alternatives to real measurements with less than 0.3-mm accuracy and very high reliability. %B Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology %8 2012 Jan 20 %G ENG %1 http://www.ncbi.nlm.nih.gov/pubmed/22270788?dopt=Abstract %R 10.1007/s10278-012-9458-6 %0 Journal Article %J Journal of the American Medical Informatics Association %D 2012 %T The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis %A Kapur, T.a %A Pieper, S.b %A Whitaker, R.c %A Aylward, S.d %A Jakab, M.a %A Schroeder, W.d %A Kikinis, R.a %X The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis. %B Journal of the American Medical Informatics Association %V 19 %P 176–180 %G eng %U http://www.scopus.com/inward/record.url?eid=2-s2.0-84857161947&partnerID=40&md5=c7d7cbab9304114a219812cb7c5091ee %0 Journal Article %J J Am Med Inform Assoc %D 2012 %T The NIH National Center for Integrative Biomedical Informatics (NCIBI). %A Athey, Brian D %A Cavalcoli, James D %A Jagadish, H V %A Omenn, Gilbert S %A Mirel, Barbara %A Kretzler, Matthias %A Burant, Charles %A Isokpehi, Raphael D %A DeLisi, Charles %K Biomedical Research %K Databases as Topic %K Forecasting %K Goals %K Information Dissemination %K Integrative Medicine %K Medical Informatics %K National Institutes of Health (U.S.) %K United States %X

The National Center for Integrative and Biomedical Informatics (NCIBI) is one of the eight NCBCs. NCIBI supports information access and data analysis for biomedical researchers, enabling them to build computational and knowledge models of biological systems to address the Driving Biological Problems (DBPs). The NCIBI DBPs have included prostate cancer progression, organ-specific complications of type 1 and 2 diabetes, bipolar disorder, and metabolic analysis of obesity syndrome. Collaborating with these and other partners, NCIBI has developed a series of software tools for exploratory analysis, concept visualization, and literature searches, as well as core database and web services resources. Many of our training and outreach initiatives have been in collaboration with the Research Centers at Minority Institutions (RCMI), integrating NCIBI and RCMI faculty and students, culminating each year in an annual workshop. Our future directions include focusing on the TranSMART data sharing and analysis initiative.

%B J Am Med Inform Assoc %V 19 %P 166-70 %8 2012 Mar-Apr %G eng %N 2 %R 10.1136/amiajnl-2011-000552 %0 Journal Article %J Phys Med Biol %D 2012 %T STIR: software for tomographic image reconstruction release 2. %A Thielemans, Kris %A Tsoumpas, Charalampos %A Mustafovic, Sanida %A Beisel, Tobias %A Aguiar, Pablo %A Dikaios, Nikolaos %A Jacobson, Matthew W %K Algorithms %K Animals %K Computers %K Image Processing, Computer-Assisted %K Mice %K Software %K Tomography %X We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++ for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net. %B Phys Med Biol %V 57 %P 867-83 %8 2012 Feb 21 %G eng %N 4 %R 10.1088/0031-9155/57/4/867 %0 Journal Article %J Bioinformatics %D 2011 %T DDN: a caBIG® analytical tool for differential network analysis. %A Zhang, Bai %A Tian, Ye %A Jin, Lu %A Li, Huai %A Shih, Ie-Ming %A Madhavan, Subha %A Clarke, Robert %A Hoffman, Eric P %A Xuan, Jianhua %A Hilakivi-Clarke, Leena %A Wang, Yue %K Animals %K Computational Biology %K Epigenesis, Genetic %K Female %K Gene Regulatory Networks %K Mammary Glands, Animal %K Rats %K Software %K Systems Biology %X

UNLABELLED: Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG®'s In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.

AVAILABILITY: The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htm.

%B Bioinformatics %V 27 %P 1036-8 %8 2011 Apr 1 %G eng %N 7 %R 10.1093/bioinformatics/btr052 %0 Journal Article %J J Am Med Inform Assoc %D 2011 %T The Yale cTAKES extensions for document classification: architecture and application. %A Garla, Vijay %A Lo Re, Vincent %A Dorey-Stein, Zachariah %A Kidwai, Farah %A Scotch, Matthew %A Womack, Julie %A Justice, Amy %A Brandt, Cynthia %K Connecticut %K Data Mining %K Decision Support Systems, Clinical %K electronic health records %K Humans %K Liver Failure %K Natural Language Processing %K Pattern Recognition, Automated %K Radiology Information Systems %X

BACKGROUND: Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text; however, feature extraction and representation for document classification pose technical challenges.

METHODS: The authors developed extensions to the clinical Text Analysis and Knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation.

RESULTS AND DISCUSSION: The F(1)-Score of the system for the retrieval of abdominal radiology reports was 96%, and was 79%, 91%, and 95% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://code.google.com/p/ytex.

%B J Am Med Inform Assoc %V 18 %P 614-20 %8 2011 Sep-Oct %G eng %N 5 %R 10.1136/amiajnl-2011-000093 %0 Conference Proceedings %B AMIA 2010 Symposium %D 2010 %T Comprehensive Yet Scalable Health Information Systems for Low Resource Settings: A Collaborative Effort in Sierra Leone %A Braaa, Jørn %A Kanterb, Andrew S. %A Leshc, Neal %A Crichtond, Ryan %A Jolliffea, Bob %A Sæbøe, Johan %A Kossia, Edem %A Seebregts, Christopher J %X We address the problem of how to integrate health informa- tion systems in low-income African countries in which techni- cal infrastructure and human resources vary wildly within countries. We describe a set of tools to meet the needs of dif- ferent service areas including managing aggregate indicators, patient level record systems, and mobile tools for community outreach. We present the case of Sierra Leone and use this case to motivate and illustrate an architecture that allows us to provide services at each level of the health system (na- tional, regional, facility and community) and provide different configurations of the tools as appropriate for the individual area. Finally, we present a, collaborative implementation of this approach in Sierra Leone. %B AMIA 2010 Symposium %8 11/2010 %U http://proceedings.amia.org/127frh %0 Journal Article %J Stud Health Technol Inform %D 2010 %T Experience implementing a point-of-care electronic medical record system for primary care in Malawi. %A Waters, Evan %A Rafter, Jeff %A Douglas, Gerald P %A Bwanali, Mwatha %A Jazayeri, Darius %A Fraser, Hamish S F %K Database Management Systems %K electronic health records %K Equipment Design %K Information Storage and Retrieval %K Malawi %K Point-of-Care Systems %K Primary Health Care %K Software %X

Due to the fact that health care professionals in Malawi are often overstretched, the use and quality of health data can be compromised. The Malawi Health Management Information System (HMIS) has streamlined data collection and reporting and increased the use of data to improve care. Obstacles remain, including incomplete reporting and low staff morale. With the Baobab Health Trust and the Malawi Ministry of Health, Partners In Health piloted an innovative point-of-care data system for primary care that functions alongside OpenMRS, an open source medical record platform. The system has given access to a patient-level primary care dataset in real time. Initial results highlight some of the benefits of a point-of-care system such as improved data quality, emphasize the importance of sharing data with clinical practitioners, and shed light on how this approach could strengthen HMIS.

%B Stud Health Technol Inform %V 160 %P 96-100 %8 2010 %G eng %N Pt 1 %0 Journal Article %J Breast cancer research : BCR %D 2010 %T ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67. %A Tuominen, Vilppu J %A Ruotoistenmaki, Sanna %A Viitanen, Arttu %A Jumppanen, Mervi %A Isola, Jorma %X ABSTRACT: INTRODUCTION: Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. METHODS: The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n=50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n=50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. RESULTS: The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r=0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n=123, P=0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. CONCLUSIONS: We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens. %B Breast cancer research : BCR %V 12 %P R56 %8 2010 Jul 27 %N 4 %1 http://www.ncbi.nlm.nih.gov/pubmed/20663194?dopt=Abstract %0 Journal Article %J Stud Health Technol Inform %D 2010 %T Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique. %A Manders, Eric-Jan %A José, Eurico %A Solis, Manuel %A Burlison, Janeen %A Nhampossa, José Leopoldo %A Moon, Troy %K Database Management Systems %K Delivery of Health Care %K electronic health records %K HIV Infections %K Information Storage and Retrieval %K Medical Record Linkage %K Mozambique %K Population Surveillance %K Rural Health Services %X

We have adopted the Open Medical Record System (OpenMRS) framework to implement an electronic patient monitoring system for an HIV care and treatment program in Mozambique. The program provides technical assistance to the Ministry of Health supporting the scale up of integrated HIV care and support services in health facilities in rural resource limited settings. The implementation is in use for adult and pediatric programs, with ongoing roll-out to cover all supported sites. We describe early experiences in adapting the system to the program needs, addressing infrastructure challenges, creating a regional support team, training data entry staff, migrating a legacy database, deployment, and current use. We find that OpenMRS offers excellent prospects for in-country development of health information systems, even in severely resource limited settings. However, it also requires considerable organizational infrastructure investment and technical capacity building to ensure continued local support.

%B Stud Health Technol Inform %V 160 %P 411-5 %8 2010 %G eng %N Pt 1 %0 Journal Article %J NeuroImage %D 2009 %T Bayesian analysis of neuroimaging data in FSL. %A Woolrich, Mark W %A Jbabdi, Saad %A Patenaude, Brian %A Chappell, Michael %A Makni, Salima %A Behrens, Timothy %A Beckmann, Christian %A Jenkinson, Mark %A Smith, Stephen M %K Bayes Theorem %K Brain %K Diffusion Magnetic Resonance Imaging %K Humans %K Image Interpretation, Computer-Assisted %K Software %X Typically in neuroimaging we are looking to extract some pertinent information from imperfect, noisy images of the brain. This might be the inference of percent changes in blood flow in perfusion FMRI data, segmentation of subcortical structures from structural MRI, or inference of the probability of an anatomical connection between an area of cortex and a subthalamic nucleus using diffusion MRI. In this article we will describe how Bayesian techniques have made a significant impact in tackling problems such as these, particularly in regards to the analysis tools in the FMRIB Software Library (FSL). We shall see how Bayes provides a framework within which we can attempt to infer on models of neuroimaging data, while allowing us to incorporate our prior belief about the brain and the neuroimaging equipment in the form of biophysically informed or regularising priors. It allows us to extract probabilistic information from the data, and to probabilistically combine information from multiple modalities. Bayes can also be used to not only compare and select between models of different complexity, but also to infer on data using committees of models. Finally, we mention some analysis scenarios where Bayesian methods are impractical, and briefly discuss some practical approaches that we have taken in these cases. %B NeuroImage %V 45 %P S173-86 %8 2009 Mar %G eng %N 1 Suppl %1 http://www.ncbi.nlm.nih.gov/pubmed/19059349?dopt=Abstract %0 Conference Paper %B Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009) %D 2009 %T MediGrid – Facilitating Semantic-Based processing of Biomedical Data and Knowledge %A Jan Vejvalka %A Petr Lesný %A Tomáš Holeček %A Kryštof Slabý %A Adéla Jarolímková %A Helena Bouzková %B Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009) %@ 978-989-8111-79-1 %G eng %R 10.5220/0001828500180021 %0 Journal Article %J Int J Med Inform %D 2009 %T Millennium Global Village-Net: bringing together Millennium Villages throughout sub-Saharan Africa. %A Kanter, Andrew S %A Negin, Joel %A Olayo, Bernard %A Bukachi, Frederick %A Johnson, Edward %A Sachs, Sonia Ehrlich %K Africa South of the Sahara %K Community Health Services %K Developing Countries %K Healthy People Programs %K Humans %K Poverty %X

The Millennium Villages Project (MVP), based at The Earth Institute at Columbia University, is a bottom-up, community led approach to show how villages in developing countries can get out of the poverty trap that afflicts more than a billion people worldwide. With well-targeted, practical inputs can help the community invest in a path leading to self-sustaining development. There are 80 Millennium Villages clustered in 10 countries throughout sub-Saharan Africa. MVP is an important development process for empowering communities to invest in a package of integrated interventions aiming to increase food production, improve access to safe water, health care, education and infrastructure. The process benefits from synergies of the integrated approach and relies on community leadership as empowered by proven technological inputs. MVP is committed to a science-based approach to assess and monitor the progress of the communities towards clear objectives; the Millennium Development Goals (MDGs) and to do so with mechanisms that are scalable and sustainable. This approach offers much more than simply collecting and analyzing data since the mechanism used for recording progress would provide a bridge over the divide which separates the haves and the have-nots (by facilitating the sharing of solutions from one community to another bidirectionally). By so doing, it allows people to enhance their own futures in a sustainable manner. Solutions found in one community are transferable to similar communities in other MVP villages. To achieve this goal, the MVP requires an information and communication system which can provide both necessary infrastructure for monitoring and evaluation, and tools for communicating among the villages, cities and countries. This system is called the Millennium Global Village-Net (MGV-Net). It takes advantage of the latest in open source software (OpenMRS), databases (MySQL), interface terminology, a centralized concept dictionary, and uses appropriate technology locally for data entry.

%B Int J Med Inform %V 78 %P 802-7 %8 2009 Dec %G eng %N 12 %R 10.1016/j.ijmedinf.2009.08.002 %0 Journal Article %J International journal of medical informatics %D 2009 %T The OpenMRS Implementers Network. %A Seebregts, Christopher J %A Mamlin, Burke W %A Biondich, Paul G %A Fraser, Hamish S F %A Wolfe, Benjamin A %A Jazayeri, Darius %A Allen, Christian %A Miranda, Justin %A Baker, Elaine %A Musinguzi, Nicholas %A Kayiwa, Daniel %A Fourie, Carl %A Lesh, Neal %A Kanter, Andrew %A Yiannoutsos, Constantin T %A Bailey, Christopher %X OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers. %B International journal of medical informatics %V 78 %P 711-20 %8 2009 Nov %U http://www.healthware.org/openmrs/openmrs.pdf %N 11 %1 http://www.ncbi.nlm.nih.gov/pubmed/19157968?dopt=Abstract %0 Journal Article %J International journal of medical informatics %D 2009 %T The state and profile of open source software projects in health and medical informatics. %A Janamanchi, Balaji %A Katsamakas, Evangelos %A Raghupathi, Wullianallur %A Gao, Wei %X PURPOSE: Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. METHODOLOGY: A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. RESULTS: Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. CONCLUSION: We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care. %B International journal of medical informatics %V 78 %P 457-72 %8 2009 Jul %N 7 %1 http://www.ncbi.nlm.nih.gov/pubmed/19321384?dopt=Abstract %0 Journal Article %J Journal on Information Technology in Healthcare %D 2008 %T Making available Clinical Decision Support in Service-Oriented Architectures %A Jens H. Jahnke-Weber %A Morgan Price %A Glen McCallum %X Computer-based clinical decision support (CDS) has great potential for cost savings and for increasing patient safety and quality of care. The cost of owning and particularly maintaining CDS systems is significant. Therefore, it makes good economic sense to share a CDS service installation among a larger set of client systems. The emerging paradigm of serviceoriented architectures (SOAs) embraces the idea of sharing and interaction between loosely coupled, co-operative services. Canada has based its planned architecture for realizing the electronic medical record (EMR) on the SOA paradigm. While CDS components are currently not in the set of services to be constructed for Canada’s health information infrastructure, they seems to be growing interest in adding them in the future, after the more essential services have been implemented. In this paper, we discuss the status of clinical decision support systems today and some challenges of making them available in SOA-based infrastructures. We report on design choices and solutions we have selected during the construction of the EGADSS (Electronic Guideline and Decision Support System) component. Our design decisions are based on domainspecific challenges such as knowledge, data and workflow interoperability as well as on technical considerations about construction high quality services for SOA-based infrastructures. EGADSS has been released under open-source license and is freely available. %B Journal on Information Technology in Healthcare %V 6 %P 54 %U http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.5385&rep=rep1&type=pdf %N 1 %& 42 %0 Journal Article %J Source code for biology and medicine %D 2008 %T OSPACS: Ultrasound image management system. %A Stott, Will %A Ryan, Andy %A Jacobs, Ian J %A Menon, Usha %A Bessant, Conrad %A Jones, Christopher %X ABSTRACT: BACKGROUND: Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. RESULTS: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. CONCLUSION: This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system. %B Source code for biology and medicine %V 3 %P 11 %8 2008 %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442597/ %1 http://www.ncbi.nlm.nih.gov/pubmed/18570637?dopt=Abstract %0 Journal Article %J J Digit Imaging %D 2007 %T The image-guided surgery toolkit IGSTK: an open source C++ software toolkit. %A Enquobahrie, Andinet %A Cheng, Patrick %A Gary, Kevin %A Ibanez, Luis %A Gobbi, David %A Lindseth, Frank %A Yaniv, Ziv %A Aylward, Stephen %A Jomier, Julien %A Cleary, Kevin %K Computer Systems %K Data Display %K Database Management Systems %K Humans %K Information Dissemination %K Information Storage and Retrieval %K Safety %K Software %K Software Design %K Software Validation %K Surgery, Computer-Assisted %K Systems Integration %K User-Computer Interface %X This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences. %B J Digit Imaging %V 20 Suppl 1 %P 21-33 %8 2007 Nov %G eng %R 10.1007/s10278-007-9054-3 %0 Book Section %B 11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007 %D 2007 %T O3-RWS: a Java-based, IHE-compliant open-source radiology workstation %A Faustini, Giorgio %A Inchingolo, P. %E Magjarevic, Ratko %E Jarm, Tomaz %E Kramar, Peter %E Zupanic, Anze %X Within the Open Three Consortium (O3) an open source radiological reporting workstation, called O3- RWS, has been studied, developed and experimented in the routine of European and US hospitals. The O3 Consortium is an international open-source project constituted in 2005 by Higher Education in Clinical Engineering (HECE) of the University of Trieste; it deals with the multi-centric integration of hospitals, RHIOs and citizen (care at home and on the move, and ambient assisted living). O3-RWS has been studied and developed with the goal to give a solution for the needs of the physician, who wants to have an easy-to-use, light and complete solution for the radiology reporting and report creation. O3-RWS, a very versatile platform-independent radiology workstation, providing user authentication and being easy to use also for private users, is able to retrieve, visualize and manage medical images; in an universal version, it is going to be able to deal with vital signs like ECG, hemodynamical and pneumological data. %B 11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007 %S IFMBE Proceedings %I Springer Berlin Heidelberg %V 16 %P 727-731 %@ 978-3-540-73044-6 %U http://dx.doi.org/10.1007/978-3-540-73044-6_189 %0 Journal Article %J IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society %D 2007 %T OpenSourcePACS: an extensible infrastructure for medical image management. %A Bui, Alex A T %A Morioka, Craig %A Dionisio, John David N %A Johnson, David B %A Sinha, Usha %A Ardekani, Siamak %A Taira, Ricky K %A Aberle, Denise R %A El-Saden, Suzie %A Kangarloo, Hooshang %X The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities. %B IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society %V 11 %P 94-109 %8 2007 Jan %U http://escholarship.org/uc/item/186368fv %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/17249408?dopt=Abstract %0 Journal Article %J Behavior research methods %D 2007 %T PyEPL: a cross-platform experiment-programming library. %A Geller, Aaron S %A Schlefer, Ian K %A Sederberg, Per B %A Jacobs, Joshua %A Kahana, Michael J %X PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL. %B Behavior research methods %V 39 %P 950-8 %8 2007 Nov %N 4 %1 http://www.ncbi.nlm.nih.gov/pubmed/18183912?dopt=Abstract %0 Journal Article %J AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium %D 2006 %T Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration. %A Mamlin, Burke W %A Biondich, Paul G %A Wolfe, Ben A %A Fraser, Hamish %A Jazayeri, Darius %A Allen, Christian %A Miranda, Justin %A Tierney, William M %X Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions. %B AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium %P 529-33 %8 2006 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638 %1 http://www.ncbi.nlm.nih.gov/pubmed/17238397?dopt=Abstract %0 Journal Article %J AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium %D 2006 %T The OpenMRS system: collaborating toward an open source EMR for developing countries. %A Wolfe, Benjamin A %A Mamlin, Burke W %A Biondich, Paul G %A Fraser, Hamish S F %A Jazayeri, Darius %A Allen, Christian %A Miranda, Justin %A Tierney, William M %X OpenMRS is an open source infrastructure for the creation of medical record systems in developing countries. Produced and maintained collaboratively across multiple institutions, this framework consists of an open source data model, a set of core application functions, and a default implementation. The goal of this implementation is to provide the beginnings of an EMR that is suitable for all groups involved with healthcare in developing countries. %B AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium %P 1146 %8 2006 %1 http://www.ncbi.nlm.nih.gov/pubmed/17238765?dopt=Abstract %0 Journal Article %J Energy %D 2005 %T ParaView : An End-User Tool for Large Data Visualization %A Ahrens, James %A Geveci, Berk %A Law, Charles %E Hansen, C R %E Johnson, C DEditors %B Energy %V 836 %P 717–732 %G eng %U http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle:ParaView:+An+end-user+tool+for+large+data+visualization#0 %0 Journal Article %J NeuroImage %D 2004 %T Advances in functional and structural MR image analysis and implementation as FSL. %A Smith, Stephen M %A Jenkinson, Mark %A Woolrich, Mark W %A Beckmann, Christian F %A Behrens, Timothy E J %A Johansen-Berg, Heidi %A Bannister, Peter R %A De Luca, Marilena %A Drobnjak, Ivana %A Flitney, David E %A Niazy, Rami K %A Saunders, James %A Vickers, John %A Zhang, Yongyue %A De Stefano, Nicola %A Brady, J Michael %A Matthews, Paul M %K Bayes Theorem %K Brain %K Databases, Factual %K Humans %K Image Processing, Computer-Assisted %K Magnetic Resonance Imaging %K Models, Neurological %K Models, Statistical %K Software %X The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL). %B NeuroImage %V 23 Suppl 1 %P S208-19 %8 2004 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/15501092?dopt=Abstract