@article {1301, title = {Use of cost-effective technologies for a routine clinical pathology laboratory}, journal = {Lab on a Chip}, year = {2021}, month = {2021}, pages = { - }, abstract = {Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last years. 3D printing and Arduino approaches can provide up to 94\% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of Point-of-Care-Tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.}, isbn = {1473-0197}, url = {http://dx.doi.org/10.1039/D1LC00658D}, author = {Vazquez, Mercedes and Anfossi, L. and Ben-Yoav, Hader and Di{\'e}guez, Lorena and Karopka, Thomas and Della Ventura, Bartolomeo and Abalde-Cela, Sara and Minopoli, Antonio and Di Nardo, Fabio and Kumar Shukla, Vikas and Teixeira, Alexandra and Tvarijonaviciute, Asta and Franco, Lorena} } @article {1220, title = {CODE STROKE ALERT-Concept and Development of a Novel Open-Source Platform to Streamline Acute Stroke Management.}, journal = {Front Neurol}, volume = {10}, year = {2019}, month = {2019}, pages = {725}, abstract = {

Effective, time-critical intervention in acute stroke is crucial to mitigate mortality rate and morbidity, but delivery of reperfusion treatments is often hampered by pre-, in-, or inter-hospital system level delays. Disjointed, repetitive, and inefficient communication is a consistent contributor to avoidable treatment delay. In the era of rapid reperfusion therapy for ischemic stroke, there is a need for a communication system to synchronize the flow of clinical information across the entire stroke journey. A multi-disciplinary development team designed an electronic communications platform, integrated between web browsers and a mobile application, to link all relevant members of the stroke treatment pathway. The platform uses tiered notifications, geotagging, incorporates multiple clinical score calculators, and is compliant with security regulations. The system safely saves relevant information for audit and research. Code Stroke Alert is a platform that can be accessed by emergency medical services (EMS) and hospital staff, coordinating the flow of information during acute stroke care, reducing duplication, and error in clinical information handover. Electronic data logs provide an auditable trail of relevant quality improvement metrics, facilitating quality improvement, and research. Code Stroke Alert will be freely available to health networks globally. The open-source nature of the software offers valuable potential for future development of plug-ins and add-ons, based on individual institutional needs. Prospective, multi-site implementation, and measurement of clinical impact are underway.

}, issn = {1664-2295}, doi = {10.3389/fneur.2019.00725}, author = {Seah, Huey Ming and Burney, Moe and Phan, Michael and Shell, Daniel and Wu, Jamin and Zhou, Kevin and Brooks, Owen and Coulton, Bronwyn and Maingard, Julian and Tang, Jennifer and Yazdabadi, Gohar and Tahayori, Bahman and Barras, Christen and Kok, Hong Kuan and Chandra, Ronil and Thijs, Vincent and Brooks, Duncan Mark and Asadi, Hamed} } @article {1286, title = {Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations.}, journal = {Proteomics Clin Appl}, volume = {13}, year = {2019}, month = {2019 01}, pages = {e1800057}, abstract = {

PURPOSE: Digital histology is being increasingly used in research and clinical applications. In parallel, new tissue imaging methods (e.g., imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis.

EXPERIMENTAL DESIGN: The open science paradigm is followed to develop new features in the web-based Cytomine software to support next-generation digital pathology bridged to molecular investigations.

RESULTS: New open-source developments allow to explore whole-slide classical histology with Matrix Assisted Laser Desorption Ionisation (MALDI) imaging and to support preprocessing for biomarker discovery using laser microdissection-based microproteomics.

CONCLUSIONS AND CLINICAL RELEVANCE: The updated version of Cytomine is the first open and web-based tool to enable sharing data from classical histology, molecular imaging, and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology.

}, keywords = {Intersectoral Collaboration, Multimodal Imaging, Pathology, Proteomics, Software, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization}, issn = {1862-8354}, doi = {10.1002/prca.201800057}, author = {Rubens, Ulysse and Hoyoux, Renaud and Vanosmael, Laurent and Ouras, Mehdy and Tasset, Maxime and Hamilton, Christopher and Longuesp{\'e}e, R{\'e}mi and Mar{\'e}e, Rapha{\"e}l} } @article {1281, title = {Eye injuries in children - incidence and outcomes: An observational study at a dedicated children{\textquoteright}s eye casualty.}, journal = {Eur J Ophthalmol}, volume = {29}, year = {2019}, month = {2019 Sep}, pages = {499-503}, abstract = {

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{\textquoteright}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{\textquoteright}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.

}, keywords = {Adolescent, Child, Child, Preschool, Emergency Service, Hospital, Eye Injuries, Female, Humans, Incidence, Infant, Male, Prognosis, Quality of Life, Retrospective Studies, Treatment Outcome, Vision Disorders, Visual Acuity}, issn = {1724-6016}, doi = {10.1177/1120672118803512}, author = {Jolly, Rohit and Arjunan, Mousindha and Theodorou, Maria and Dahlmann-Noor, Annegret H} } @article {1266, title = {From paper maps to digital maps: enhancing routine immunisation microplanning in Northern Nigeria.}, journal = {BMJ Glob Health}, volume = {4}, year = {2019}, month = {2019}, pages = {e001606}, abstract = {

Geographical information systems (GIS) can be effective decision-support tools. In this paper, we detail a GIS approach implemented by the Bauchi and Sokoto state primary healthcare development agencies in Nigeria to generate and convert routine immunisation (RI) paper maps to digital maps for microplanning. The process involved three stages: primary and secondary data collection and reconciliation, geospatial data processing and analysis, and production and validation of maps. The data collection and reconciliation stage identified a number of challenges with secondary data sources, including the need to standardise and reconcile health facility and settlement names. The study team was unable to apply population estimates generated from the Global Polio Eradication Initiative to RI planning because operational boundaries for polio activities are defined differently from RI activities. Application of open-source GIS software enabled the combination of multiple datasets and analysis of geospatial data to calculate catchment areas for primary health centres (PHCs) and assign vaccination strategies to communities. The activity resulted in the development of PHC catchment area digital maps, and captured next steps and lessons learnt for RI microplanning in the two states. While the digital maps provided input into the microplanning process, more work is needed to build capacity, standardise processes and ensure the quality of data used to generate the maps. RI service providers and communities must be engaged in the process to validate, understand the data, the contextual factors that influence decisions about which vaccination strategies RI microplans include and how resources are allocated.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2019-001606}, author = {Dougherty, Leanne and Abdulkarim, Masduq and Mikailu, Fiyidi and Tijani, Usman and Owolabi, Kazeem and Gilroy, Kate and Naiya, Ahmed and Abdullahi, Adamu and Bodinga, Hadiza and Olayinka, Folake and Moise, Imelda} } @article {1228, title = {PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.}, journal = {Bioinformatics}, year = {2019}, month = {2019 Jun 19}, abstract = {

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.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btz409}, author = {Glicksberg, Benjamin S and Oskotsky, Boris and Thangaraj, Phyllis M and Giangreco, Nicholas and Badgeley, Marcus A and Johnson, Kipp W and Datta, Debajyoti and Rudrapatna, Vivek and Rappoport, Nadav and Shervey, Mark M and Miotto, Riccardo and Goldstein, Theodore C and Rutenberg, Eugenia and Frazier, Remi and Lee, Nelson and Israni, Sharat and Larsen, Rick and Percha, Bethany and Li, Li and Dudley, Joel T and Tatonetti, Nicholas P and Butte, Atul J} } @article {1216, title = {Transforming Two Decades of ePR Data to OMOP CDM for Clinical Research.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {233-237}, abstract = {

This paper presents the extract-transform-and-load (ETL) process from the Electronic Patient Records (ePR) at the Heart Institute (InCor) to the OMOP Common Data Model (CDM) format. We describe the initial database characterization, relational source mappings, selection filters, data transformations and patient de-identification using the open-source OHDSI tools and SQL scripts. We evaluate the resulting InCor-CDM database by recreating the same patient cohort from a previous reference study (over the original data source) and comparing the cohorts{\textquoteright} descriptive statistics and inclusion reports. The results exhibit that up to 91\% of the reference patients were retrieved by our method from the ePR through InCor-CDM, with AUC=0.938. The results indicate that the method that we employed was able to produce a new database that was both consistent with the original data and in accordance to the OMOP CDM standard.

}, issn = {1879-8365}, doi = {10.3233/SHTI190218}, author = {Lima, Daniel M and Rodrigues-Jr, Jose F and Traina, Agma J M and Pires, Fabio A and Gutierrez, Marco A} } @article {1268, title = {Census-independent population mapping in northern Nigeria.}, journal = {Remote Sens Environ}, volume = {204}, year = {2018}, month = {2018 Jan}, pages = {786-798}, abstract = {

Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areas within the states of Kano and Kaduna in northern Nigeria. Using supervised texture-based classifiers with very high resolution satellite imagery, we produce a binary map of human settlement at 8-meter resolution across the two states and then a more refined classification consisting of 7 residential types and 1 non-residential type. Using the residential types and a model linking them to the population density observations, we produce population estimates across the two states in a gridded raster format, at approximately 90-meter resolution. We also demonstrate a simulation framework for capturing uncertainty and presenting estimates as prediction intervals for any region of interest of any size and composition within the study region. Used in concert with previously published demographic estimates, our population estimates allowed for predictions of the population under 5 in ten administrative wards that fit strongly with reference data collected during polio vaccination campaigns.

}, issn = {0034-4257}, doi = {10.1016/j.rse.2017.09.024}, author = {Weber, Eric M and Seaman, Vincent Y and Stewart, Robert N and Bird, Tomas J and Tatem, Andrew J and McKee, Jacob J and Bhaduri, Budhendra L and Moehl, Jessica J and Reith, Andrew E} } @article {1236, title = {Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone.}, journal = {J Med Internet Res}, volume = {19}, year = {2017}, month = {2017 08 21}, pages = {e294}, abstract = {

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.

}, keywords = {electronic health records, Epidemics, Hemorrhagic Fever, Ebola, Humans, Infection Control, Sierra Leone, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.7881}, author = {Oza, Shefali and Jazayeri, Darius and Teich, Jonathan M and Ball, Ellen and Nankubuge, Patricia Alexandra and Rwebembera, Job and Wing, Kevin and Sesay, Alieu Amara and Kanter, Andrew S and Ramos, Glauber D and Walton, David and Cummings, Rachael and Checchi, Francesco and Fraser, Hamish S} } @article {1160, title = {Donor{\textquoteright}s support tool: {Enabling} informed secondary use of patient{\textquoteright}s biomaterial and personal data}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {282{\textendash}292}, abstract = {PURPOSE: Biomedical research is being catalyzed by the vast amount of data rapidly collected through the application of information technologies (IT). Despite IT advances, the methods for involving patients and citizens in biomedical research remain static, paper-based and organized around national boundaries and anachronistic legal frameworks. The purpose of this paper is to study the current practices for obtaining consent for biobanking and the legal requirements for reusing the available biomaterial and data in EU and finally to present a novel tool to this direction enabling the secondary use of data and biomaterial. METHOD: We review existing European legislation for secondary use of patient{\textquoteright}s biomaterial and data for research, identify types and scopes of consent, formal requirements for consent, and consider their implications for implementing electronic consent tools. To this direction, we proceed further to develop a modular tool, named Donor{\textquoteright}s Support Tool (DST), designed to connect researchers with participants, and to promote engagement, informed participation and individual decision making. RESULTS: To identify the advantages of our solution we compare our tool with six other relevant approaches. The results show that our tool scores higher than the other tools in functionality, security and intelligence whereas it is the only one free and open-source. In addition, the potential of our solution is shown by a proof of concept deployment in an existing clinical setting, where it was really appreciated, as streamlining the relevant workflow.}, keywords = {Biobank, Dynamic consent, Electronic consent, Secondary use of biomaterial and personal data}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.10.019}, author = {Kondylakis, Haridimos and Koumakis, Lefteris and H{\"a}nold, Stephanie and Nwankwo, Iheanyi and Forg{\'o}, Nikolaus and Marias, Kostas and Tsiknakis, Manolis and Graf, Norbert} } @article {1294, title = {How the introduction of a human resources information system helped the Democratic Republic of Congo to mobilise domestic resources for an improved health workforce.}, journal = {Health Policy Plan}, volume = {32}, year = {2017}, month = {2017 Nov 01}, pages = {iii25-iii31}, abstract = {

The Democratic Republic of Congo has flagged health workforce management and compensation as issues requiring attention, including the problem of ghost workers (individuals on payroll who do not exist and/or show up at work). Recognising the need for reliable health workforce information, the government has worked to implement iHRIS, an open source human resources information system that facilitates health workforce management. In Kasa{\"\i} Central and Kasa{\"\i} Provinces, health workers brought relevant documentation to data collection points, where trained teams interviewed them and entered contact information, identification, photo, current job, and employment and education history into iHRIS on laptops. After uploading the data, the Ministry of Public Health used the database of over 11 500 verified health worker records to analyse health worker characteristics, density, compensation, and payroll. Both provinces had less than one physician per 10 000 population and a higher urban versus rural health worker density. Most iHRIS-registered health workers (57\% in Kasa{\"\i} Central and 73\% in Kasa{\"\i}) reported receiving no regular government pay of any kind (salaries or risk allowances). Payroll analysis showed that 27\% of the health workers listed as salary recipients in the electronic payroll system were ghost workers, as were 42\% of risk allowance recipients. As a result, the Ministries of Public Health, Public Service, and Finance reallocated funds away from ghost workers to cover salaries (n = 781) and risk allowances (n = 2613) for thousands of health workers who were previously under- or uncompensated due to lack of funds. The reallocation prioritised previously under- or uncompensated mid-level health workers, with 49\% of those receiving salaries and 68\% of those receiving risk allowances representing cadres such as nurses, laboratory technicians, and midwifery cadres. Assembling accurate health worker records can help governments understand health workforce characteristics and use data to direct scarce domestic resources to where they are most needed.

}, keywords = {Democratic Republic of the Congo, Health Personnel, Health Workforce, Humans, Management Information Systems, Personnel Management, Remuneration}, issn = {1460-2237}, doi = {10.1093/heapol/czx113}, author = {Likofata Esanga, Jean-Robert and Viadro, Claire and McManus, Leah and Wesson, Jennifer and Matoko, Nicaise and Ngumbu, Epiphane and Gilroy, Kate E and Trudeau, Daren} } @article {1172, title = {Automated population of an i2b2 clinical data warehouse from an {openEHR}-based data repository}, journal = {Journal of Biomedical Informatics}, volume = {63}, year = {2016}, pages = {277{\textendash}294}, abstract = {BACKGROUND: Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. METHODS: We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. RESULTS: Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of \~{}2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. DISCUSSION: We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process.}, keywords = {Archetypes, Clinical data repository, clinical information systems, Data warehouse, Detailed clinical models, Healthcare analytics, i2b2, openEHR, Secondary use}, issn = {1532-0480}, doi = {10.1016/j.jbi.2016.08.007}, author = {Haarbrandt, Birger and Tute, Erik and Marschollek, Michael} } @article {1137, title = {How open science helps researchers succeed.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.

}, issn = {2050-084X}, doi = {10.7554/eLife.16800}, author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal} } @article {1135, title = {Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals.}, journal = {BMJ Glob Health}, volume = {1}, year = {2016}, month = {2016 May 24}, pages = {e000028}, abstract = {

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{\textquoteright} 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{\textquoteright} 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.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2016-000028}, author = {Tuti, Timothy and Bitok, Michael and Malla, Lucas and Paton, Chris and Muinga, Naomi and Gathara, David and Gachau, Susan and Mbevi, George and Nyachiro, Wycliffe and Ogero, Morris and Julius, Thomas and Irimu, Grace and English, Mike} } @article {1131, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jul 7}, abstract = {

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.

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, abstract = {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.}, keywords = {CellProfiler, continuous integration, high-content screening, high-performance computing}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {1170, title = {Open {Source} {Drug} {Discovery}: {Highly} {Potent} {Antimalarial} {Compounds} {Derived} from the {Tres} {Cantos} {Arylpyrroles}}, journal = {ACS central science}, volume = {2}, year = {2016}, pages = {687{\textendash}701}, abstract = {The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.}, issn = {2374-7943}, doi = {10.1021/acscentsci.6b00086}, author = {Williamson, Alice E. and Ylioja, Paul M. and Robertson, Murray N. and Antonova-Koch, Yevgeniya and Avery, Vicky and Baell, Jonathan B. and Batchu, Harikrishna and Batra, Sanjay and Burrows, Jeremy N. and Bhattacharyya, Soumya and Calderon, Felix and Charman, Susan A. and Clark, Julie and Crespo, Benigno and Dean, Matin and Debbert, Stefan L. and Delves, Michael and Dennis, Adelaide S. M. and Deroose, Frederik and Duffy, Sandra and Fletcher, Sabine and Giaever, Guri and Hallyburton, Irene and Gamo, Francisco-Javier and Gebbia, Marinella and Guy, R. Kiplin and Hungerford, Zoe and Kirk, Kiaran and Lafuente-Monasterio, Maria J. and Lee, Anna and Meister, Stephan and Nislow, Corey and Overington, John P. and Papadatos, George and Patiny, Luc and Pham, James and Ralph, Stuart A. and Ruecker, Andrea and Ryan, Eileen and Southan, Christopher and Srivastava, Kumkum and Swain, Chris and Tarnowski, Matthew J. and Thomson, Patrick and Turner, Peter and Wallace, Iain M. and Wells, Timothy N. C. and White, Karen and White, Laura and Willis, Paul and Winzeler, Elizabeth A. and Wittlin, Sergio and Todd, Matthew H.} } @article {1121, title = {Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.}, journal = {PLoS Pathog}, volume = {12}, year = {2016}, month = {2016 Jul}, pages = {e1005763}, abstract = {

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.

}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1005763}, author = {Van Voorhis, Wesley C and Adams, John H and Adelfio, Roberto and Ahyong, Vida and Akabas, Myles H and Alano, Pietro and Alday, Aintzane and Alem{\'a}n Resto, Yesmalie and Alsibaee, Aishah and Alzualde, Ainhoa and Andrews, Katherine T and Avery, Simon V and Avery, Vicky M and Ayong, Lawrence and Baker, Mark and Baker, Stephen and Ben Mamoun, Choukri and Bhatia, Sangeeta and Bickle, Quentin and Bounaadja, Lotfi and Bowling, Tana and Bosch, J{\"u}rgen and Boucher, Lauren E and Boyom, Fabrice F and Brea, Jose and Brennan, Marian and Burton, Audrey and Caffrey, Conor R and Camarda, Grazia and Carrasquilla, Manuela and Carter, Dee and Belen Cassera, Maria and Chih-Chien Cheng, Ken and Chindaudomsate, Worathad and Chubb, Anthony and Colon, Beatrice L and Col{\'o}n-L{\'o}pez, Daisy D and Corbett, Yolanda and Crowther, Gregory J and Cowan, Noemi and D{\textquoteright}Alessandro, Sarah and Le Dang, Na and Delves, Michael and DeRisi, Joseph L and Du, Alan Y and Duffy, Sandra and Abd El-Salam El-Sayed, Shimaa and Ferdig, Michael T and Fern{\'a}ndez Robledo, Jos{\'e} A and Fidock, David A and Florent, Isabelle and Fokou, Patrick V T and Galstian, Ani and Gamo, Francisco Javier and Gokool, Suzanne and Gold, Ben and Golub, Todd and Goldgof, Gregory M and Guha, Rajarshi and Guiguemde, W Armand and Gural, Nil and Guy, R Kiplin and Hansen, Michael A E and Hanson, Kirsten K and Hemphill, Andrew and Hooft van Huijsduijnen, Rob and Horii, Takaaki and Horrocks, Paul and Hughes, Tyler B and Huston, Christopher and Igarashi, Ikuo and Ingram-Sieber, Katrin and Itoe, Maurice A and Jadhav, Ajit and Naranuntarat Jensen, Amornrat and Jensen, Laran T and Jiang, Rays H Y and Kaiser, Annette and Keiser, Jennifer and Ketas, Thomas and Kicka, Sebastien and Kim, Sunyoung and Kirk, Kiaran and Kumar, Vidya P and Kyle, Dennis E and Lafuente, Maria Jose and Landfear, Scott and Lee, Nathan and Lee, Sukjun and Lehane, Adele M and Li, Fengwu and Little, David and Liu, Liqiong and Llin{\'a}s, Manuel and Loza, Maria I and Lubar, Aristea and Lucantoni, Leonardo and Lucet, Isabelle and Maes, Louis and Mancama, Dalu and Mansour, Nuha R and March, Sandra and McGowan, Sheena and Medina Vera, Iset and Meister, Stephan and Mercer, Luke and Mestres, Jordi and Mfopa, Alvine N and Misra, Raj N and Moon, Seunghyun and Moore, John P and Morais Rodrigues da Costa, Francielly and M{\"u}ller, Joachim and Muriana, Arantza and Nakazawa Hewitt, Stephen and Nare, Bakela and Nathan, Carl and Narraidoo, Nathalie and Nawaratna, Sujeevi and Ojo, Kayode K and Ortiz, Diana and Panic, Gordana and Papadatos, George and Parapini, Silvia and Patra, Kailash and Pham, Ngoc and Prats, Sarah and Plouffe, David M and Poulsen, Sally-Ann and Pradhan, Anupam and Quevedo, Celia and Quinn, Ronald J and Rice, Christopher A and Abdo Rizk, Mohamed and Ruecker, Andrea and St Onge, Robert and Salgado Ferreira, Rafaela and Samra, Jasmeet and Robinett, Natalie G and Schlecht, Ulrich and Schmitt, Marjorie and Silva Villela, Filipe and Silvestrini, Francesco and Sinden, Robert and Smith, Dennis A and Soldati, Thierry and Spitzm{\"u}ller, Andreas and Stamm, Serge Maximilian and Sullivan, David J and Sullivan, William and Suresh, Sundari and Suzuki, Brian M and Suzuki, Yo and Swamidass, S Joshua and Taramelli, Donatella and Tchokouaha, Lauve R Y and Theron, Anjo and Thomas, David and Tonissen, Kathryn F and Townson, Simon and Tripathi, Abhai K and Trofimov, Valentin and Udenze, Kenneth O and Ullah, Imran and Vallieres, Cindy and Vigil, Edgar and Vinetz, Joseph M and Voong Vinh, Phat and Vu, Hoan and Watanabe, Nao-Aki and Weatherby, Kate and White, Pamela M and Wilks, Andrew F and Winzeler, Elizabeth A and Wojcik, Edward and Wree, Melanie and Wu, Wesley and Yokoyama, Naoaki and Zollo, Paul H A and Abla, Nada and Blasco, Benjamin and Burrows, Jeremy and Laleu, Beno{\^\i}t and Leroy, Didier and Spangenberg, Thomas and Wells, Timothy and Willis, Paul A} } @article {1110, title = {Open-source hardware for medical devices.}, journal = {BMJ Innov}, volume = {2}, year = {2016}, month = {2016 Apr}, pages = {78-83}, abstract = {

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device.

}, issn = {2055-642X}, doi = {10.1136/bmjinnov-2015-000080}, author = {Niezen, Gerrit and Eslambolchilar, Parisa and Thimbleby, Harold} } @article {1163, title = {{RABIX}: {AN} {OPEN}-{SOURCE} {WORKFLOW} {EXECUTOR} {SUPPORTING} {RECOMPUTABILITY} {AND} {INTEROPERABILITY} {OF} {WORKFLOW} {DESCRIPTIONS}}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {22}, year = {2016}, pages = {154{\textendash}165}, abstract = {As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.}, issn = {2335-6936}, author = {Kaushik, Gaurav and Ivkovic, Sinisa and Simonovic, Janko and Tijanic, Nebojsa and Davis-Dusenbery, Brandi and Kural, Deniz} } @article {1125, title = {TREMOR12: An Open-Source Mobile App for Tremor Quantification.}, journal = {Stereotact Funct Neurosurg}, volume = {94}, year = {2016}, month = {2016}, pages = {182-186}, abstract = {

BACKGROUND: Evaluating the effect of treatment of tremor is mostly performed with clinical rating scales. Mobile applications facilitate a more rapid, objective, and quantitative evaluation of treatment effect. Existing mobile apps do not offer raw data access, which limits algorithm development.

OBJECTIVE: To develop a novel open-source mobile app for tremor quantification.

METHODS: TREMOR12 is an open-source mobile app that samples acceleration, rotation, rotation speed, and gravity, each in 3 axes and time-stamped in a frequency up to 100 Hz. The raw measurement data can be exported as a comma-separated value file for further analysis in the TREMOR12P data processing module. The app was evaluated with 3 patients suffering from essential tremor, who were between 55 and 71 years of age.

RESULTS: This proof-of-concept study shows that the TREMOR12 app is able to detect and register tremor characteristics such as acceleration, rotation, rotation speed, and gravity in a simple and nonburdensome way. The app is compatible with current regulatory oversight by the European Union (MEDDEV regulations) and the Food and Drug Administration (FDA) guidance on mobile medical applications.

CONCLUSION: TREMOR12 offers low-cost tremor quantification for research purposes and algorithm development, and may help to improve treatment evaluation.

}, issn = {1423-0372}, doi = {10.1159/000446610}, author = {Kubben, Pieter L and Kuijf, Mark L and Ackermans, Linda P C M and Leentjes, Albert F G and Temel, Yasin} } @article {1008, title = {Design and development of an EMR for Ebola Treatment Centers in Sierra Leone using OpenMRS.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {916}, abstract = {

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.

}, issn = {0926-9630}, author = {Jazayeri, Darius and Oza, Shefali and Ramos, Glauber and Fraser, Hamish and Teich, Jonathan M and Kanter, Andrew S and Ball, Ellen} } @article {1145, title = {A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.}, journal = {Methods Inf Med}, volume = {54}, year = {2015}, month = {2015}, pages = {455-60}, abstract = {

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

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

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

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

}, issn = {0026-1270}, doi = {10.3414/ME14-02-0030}, author = {Firnkorn, D and Ganzinger, M and Muley, T and Thomas, M and Knaup, P} } @article {997, title = {Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Jun 10}, abstract = {

OBJECTIVE: To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice.

MATERIALS AND METHODS: The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals{\textquoteright} pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals.

RESULTS: In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use.

CONCLUSION: A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv028}, author = {Tuti, Timothy and Bitok, Michael and Paton, Chris and Makone, Boniface and Malla, Lucas and Muinga, Naomi and Gathara, David and English, Mike} } @article {1292, title = {Innovative Technological Approach to Ebola Virus Disease Outbreak Response in Nigeria Using the Open Data Kit and Form Hub Technology.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0131000}, abstract = {

The recent outbreak of Ebola Virus Disease (EVD) in West Africa has ravaged many lives. Effective containment of this outbreak relies on prompt and effective coordination and communication across various interventions; early detection and response being critical to successful control. The use of information and communications technology (ICT) in active surveillance has proved to be effective but its use in Ebola outbreak response has been limited. Due to the need for timeliness in reporting and communication for early discovery of new EVD cases and promptness in response; it became imperative to empower the response team members with technologies and solutions which would enable smooth and rapid data flow. The Open Data Kit and Form Hub technology were used in combination with the Dashboard technology and ArcGIS mapping for follow up of contacts, identification of cases, case investigation and management and also for strategic planning during the response. A remarkable improvement was recorded in the reporting of daily follow-up of contacts after the deployment of the integrated real time technology. The turnaround time between identification of symptomatic contacts and evacuation to the isolation facility and also for receipt of laboratory results was reduced and informed decisions could be taken by all concerned. Accountability in contact tracing was ensured by the use of a GPS enabled device. The use of innovative technologies in the response of the EVD outbreak in Nigeria contributed significantly to the prompt control of the outbreak and containment of the disease by providing a valuable platform for early warning and guiding early actions.

}, keywords = {Disease Outbreaks, Ebolavirus, Epidemiological Monitoring, Female, Hemorrhagic Fever, Ebola, Humans, Male, Medical Informatics, Nigeria}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131000}, author = {Tom-Aba, Daniel and Olaleye, Adeniyi and Olayinka, Adebola Tolulope and Nguku, Patrick and Waziri, Ndadilnasiya and Adewuyi, Peter and Adeoye, Olawunmi and Oladele, Saliu and Adeseye, Aderonke and Oguntimehin, Olukayode and Shuaib, Faisal} } @article {980, title = {Virtualization of Open-Source Secure Web Services to Support Data Exchange in a Pediatric Critical Care Research Network.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Mar 21}, abstract = {

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.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv009}, author = {Frey, Lewis J and Sward, Katherine A and Newth, Christopher Jl and Khemani, Robinder G and Cryer, Martin E and Thelen, Julie L and Enriquez, Rene and Shaoyu, Su and Pollack, Murray M and Harrison, Rick E and Meert, Kathleen L and Berg, Robert A and Wessel, David L and Shanley, Thomas P and Dalton, Heidi and Carcillo, Joseph and Jenkins, Tammara L and Dean, J Michael} } @article {1031, title = {Evaluation of software maintain ability with open EHR - a comparison of architectures.}, journal = {Int J Med Inform}, volume = {83}, year = {2014}, month = {2014 Nov}, pages = {849-59}, abstract = {

PURPOSE: To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods.

METHODS: A new open source application (GastrOS) has been developed following open EHR{\textquoteright}s multi-level modelling approach using .Net/C$\#$ based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request.

RESULTS: Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests.

CONCLUSIONS: The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible.

}, keywords = {Data Curation, electronic health records, Information Dissemination, Information Storage and Retrieval, Meaningful Use, Software, Software Design}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2014.07.006}, author = {Atalag, Koray and Yang, Hong Yul and Tempero, Ewan and Warren, James R} } @article {1034, title = {Telecytological diagnosis of space-occupying lesions of the liver.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {174-81}, abstract = {

OBJECTIVE: In this study, the efficiency of telemedical consulting with regard to fine needle aspirates from space-occupying lesions (SOLs) of the liver is investigated for the first time.

STUDY DESIGN: The study includes fine needle aspirations from 62 patients, 33 with hepatocellular carcinoma (HCC) and 29 with non-hepatic tumors. Using the Internet-based iPath system, the initial pathologist submitted 1-8 images from smears and cell block sections. One consultant assessed the cytological and another one the histological images. Both made their diagnoses independent of each other. A final diagnosis was made by immunochemistry of cell block sections. The cytological images were analyzed retrospectively for the occurrence of the most typical HCC indicators. The number of these indicators was related to the initial diagnoses of the three pathologists, and possible reasons for diagnostic errors were analyzed based on this analysis.

RESULTS: The accuracy of the preliminary telemedical diagnoses regarding HCC was 82.0\% for the cytological images and 87.7\% for the histological images. Most of the false diagnoses occurred in tumors with unusual cytological and histological patterns.

CONCLUSIONS: Telemedical consulting is a valuable tool to obtain a second opinion. However, for improvement of the diagnosis of HCC, supplementary immunochemical tests are necessary.

}, keywords = {Adult, Aged, Aged, 80 and over, Carcinoma, Hepatocellular, Female, Humans, Image-Guided Biopsy, Liver, Liver Neoplasms, Male, Middle Aged, Retrospective Studies, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000357195}, author = {Mostafa, Mohammad Golam and Dalquen, Peter and Kunze, Dietmar and Terracciano, Luigi} } @article {1010, title = {E-health systems for management of MDR-TB in resource-poor environments: a decade of experience and recommendations for future work.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {627-31}, abstract = {

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.

}, keywords = {Developing Countries, electronic health records, Electronic Prescribing, Extensively Drug-Resistant Tuberculosis, Haiti, Health Information Management, Humans, Medication Systems, Hospital, Pakistan, Remote Consultation}, issn = {0926-9630}, author = {Fraser, Hamish S F and Habib, Ali and Goodrich, Mark and Thomas, David and Blaya, Joaquin A and Fils-Aime, Joseph Reginald and Jazayeri, Darius and Seaton, Michael and Khan, Aamir J and Choi, Sharon S and Kerrison, Foster and Falzon, Dennis and Becerra, Mercedes C} } @article {892, title = {Integration of advanced 3D SPECT modeling into the open-source STIR framework}, journal = {Medical Physics}, volume = {40}, year = {2013}, pages = {092502}, keywords = {C++ language, image reconstruction, medical image processing, object-oriented programming, public domain software, single photon emission computed tomography, software libraries, software packages}, doi = {10.1118/1.4816676}, url = {http://link.aip.org/link/?MPH/40/092502/1}, author = {Berta Marti Fuster and Carles Falcon and Charalampos Tsoumpas and Lefteris Livieratos and Pablo Aguiar and Albert Cot and Domenec Ros and Kris Thielemans} } @inbook {866, title = {MITK-US: Echtzeitverarbeitung von Ultraschallbildern in MITK}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2013}, series = {Informatik aktuell}, year = {2013}, pages = {302-307}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Ultraschall (US) als bildgebendes Verfahren in der Medizin ist nicht invasiv, schnell, vielerorts verf{\"u}gbar, kommt ohne Strahlenbelastung aus und liefert kontinuierlich Daten in Echtzeit. Die Nutzung von US f{\"u}r computerassistierte Interventionen (CAI) stellt jedoch nicht nur extrem hohe Anforderungen an die Methoden zur Bildverarbeitung aufgrund der beschr{\"a}nkten Bildqualit{\"a}t, sondern bedeutet auch einen betr{\"a}chtlichen Integrationsaufwand wenn die Daten in Echtzeit weiterverarbeitet werden sollen. Mit MITK-US stellen wir in dieser Arbeit ein neues Modul f{\"u}r das Open Source verf{\"u}gbare Medical Imaging Interaction Toolkit (MITK) vor, welches die einheitliche Einbindung und Weiterverarbeitung von Echtzeitultraschalldaten erm{\"o}glicht und somit den Aufwand f{\"u}r die Integration von US in CAI Systeme verringert. Da die Verwendung von Echtzeitdaten insbesondere im Bereich der CAI zahlreiche neue M{\"o}glichkeiten bietet, erwarten wir einen hohen Nutzen dieses Moduls f{\"u}r k{\"u}nftige Projekte.}, isbn = {978-3-642-36479-2}, doi = {10.1007/978-3-642-36480-8_53}, url = {http://dx.doi.org/10.1007/978-3-642-36480-8_53}, author = {Franz, AlfredMichael and M{\"a}rz, Keno and Seitel, Alexander and M{\"u}ller, Michael and Zelzer, Sascha and Nodeln, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena}, editor = {Meinzer, Hans-Peter and Deserno, Thomas Martin and Handels, Heinz and Tolxdorff, Thomas} } @article {837, title = {Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {125}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched. RESULTS: Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers. CONCLUSIONS: The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-125}, author = {Fraser, Hamish S F and Thomas, David and Tomaylla, Juan and Garcia, Nadia and Lecca, Leonid and Murray, Megan and Becerra, Mercedes C} } @article {813, title = {ADDIS: a decision support system for evidence-based medicine}, journal = {Decision Support Systems}, volume = {in press}, year = {2012}, abstract = {Clinical trials are the main source of information for the efficacy and safety evaluation of medical treatments. Al- though they are of pivotal importance in evidence-based medicine, there is a lack of usable information systems providing data-analysis and decision support capabilities for aggregate clinical trial results. This is partly caused by unavailability (i) of trial data in a structured format suitable for re-analysis, and (ii) of a complete data model for ag- gregate level results. In this paper, we develop a unifying data model that enables the development of evidence-based decision support in the absence of a complete data model. We describe the supported decision processes and show how these are implemented in the open source ADDIS software. ADDIS enables semi-automated construction of meta-analyses, network meta-analyses and benefit-risk decision models, and provides visualization of all results.}, keywords = {clinicaltrial, datamodel, decisionanalysis, Evidence-basedmedicine, evidencesynthesis}, doi = {10.1016/j.dss.2012.10.005}, author = {van Valkenhoef, G. and Tervonen, T. and Zwinkels, T. and de Brock, B. and Hillege, H.} } @article {795, title = {BioImageXD: an open, general-purpose and high-throughput image-processing platform.}, journal = {Nat Methods}, volume = {9}, year = {2012}, month = {2012}, pages = {683-9}, abstract = {BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.}, issn = {1548-7105}, doi = {10.1038/nmeth.2047}, author = {Kankaanp{\"a}{\"a}, Pasi and Paavolainen, Lassi and Tiitta, Silja and Karjalainen, Mikko and P{\"a}iv{\"a}rinne, Joacim and Nieminen, Jonna and Marjom{\"a}ki, Varpu and Heino, Jyrki and White, Daniel J} } @article {776, title = {Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project.}, journal = {J Biomed Inform}, year = {2012}, month = {2012 Feb 4}, abstract = {The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) will enable the use of the electronic health record (EHR) for secondary purposes, such as care process and outcomes improvement, biomedical research and epidemiologic monitoring of the nation{\textquoteright}s health. One of the primary informatics problem areas in this endeavor is the standardization of disparate health data from the nation{\textquoteright}s many health care organizations and providers. The SHARPn team is developing open source services and components to support the ubiquitous exchange, sharing and reuse or {\textquoteright}liquidity{\textquoteright} of operational clinical data stored in electronic health records. One year into the design and development of the SHARPn framework, we demonstrated end to end data flow and a prototype SHARPn platform, using thousands of patient electronic records sourced from two large healthcare organizations: Mayo Clinic and Intermountain Healthcare. The platform was deployed to (1) receive source EHR data in several formats, (2) generate structured data from EHR narrative text, and (3) normalize the EHR data using common detailed clinical models and Consolidated Health Informatics standard terminologies, which were (4) accessed by a phenotyping service using normalized data specifications. The architecture of this prototype SHARPn platform is presented. The EHR data throughput demonstration showed success in normalizing native EHR data, both structured and narrative, from two independent organizations and EHR systems. Based on the demonstration, observed challenges for standardization of EHR data for interoperable secondary use are discussed.}, issn = {1532-0480}, doi = {10.1016/j.jbi.2012.01.009}, author = {Rea, Susan and Pathak, Jyotishman and Savova, Guergana and Oniki, Thomas A and Westberg, Les and Beebe, Calvin E and Tao, Cui and Parker, Craig G and Haug, Peter J and Huff, Stanley M and Chute, Christopher G} } @inbook {1080, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @inbook {851, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Diabetes is one of the foremost causes of death in many countries and a leading cause of blindness, renal failure, and non-traumatic amputation. Therefore, diabetic foot ulceration and amputation cause extensive burden on individuals and health care systems in developed and developing countries. Due to the multi-disciplinary requirements for the treatment of diabetic foot ulceration, telemedicine has been introduced to facilitate the access of the patients to specialized health professionals. In this paper the development of an open source mobile health platform is presented, able to support diagnostic algorithms, with the use of a smartphone.}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @article {799, title = {A framework for mapping, visualisation and automatic model creation of signal-transduction networks.}, journal = {Mol Syst Biol}, volume = {8}, year = {2012}, month = {2012}, pages = {578}, abstract = {Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.}, issn = {1744-4292}, doi = {10.1038/msb.2012.12}, author = {Tiger, Carl-Fredrik and Krause, Falko and Cedersund, Gunnar and Palm{\'e}r, Robert and Klipp, Edda and Hohmann, Stefan and Kitano, Hiroaki and Krantz, Marcus} } @article {815, title = {Free and open-source software application for the evaluation of coronary computed tomography angiography images.}, journal = {Arq Bras Cardiol}, year = {2012}, month = {2012 Oct 2}, abstract = {BACKGROUND: The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. OBJECTIVE: To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. METHODS: We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. RESULTS: The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. CONCLUSION: The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50\% in the LMCA and < 70\% in the ADA. The agreement for lesions > 70\% in the ADA was lower, but this is also observed when the anatomical reference standard is used.}, issn = {1678-4170}, author = {Hadlich, Marcelo Souza and Oliveira, Gl{\'a}ucia Maria Moraes and Feij{\'o}o, Ra{\'u}l A and Azevedo, Clerio F and Tura, Bernardo Rangel and Ziemer, Paulo Gustavo Portela and Blanco, Pablo Javier and Pina, Gustavo and Meira, M{\'a}rcio and Souza E Silva, Nelson Albuquerque de} } @conference {838, title = {Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA}, booktitle = {VPH 2012}, year = {2012}, address = {Londres, United Kingdom}, abstract = {The contributions of this work are twofold. First, we developed an electrophysiological training simulator in SOFA which tackles the interactive issue in the context of cardiac arrhythmias. Coupled with this electrophysiology, we developed a mechanical model of the heart that can be personalized from MRI datasets. Our simulations are based on the SOFA platform. SOFA is an open-source framework targeted at real-time simulation with an emphasis on medical simulation, mainly developed at Inria. A large choice of efficient solvers, hyperelastic or viscous material laws are already implemented in SOFA. Moreover, it enables interactivity during the simulation (pacing, surgery planning, ...) and gives a good trade-off between accuracy and computational efficiency.}, url = {http://hal.inria.fr/hal-00751537}, author = {Talbot, Hugo and Marchesseau, St{\'e}phanie and Duriez, Christian and Courtecuisse, Hadrien and Relan, Jatin and Sermesant, Maxime and Cotin, St{\'e}phane and Delingette, Herv{\'e}} } @inbook {789, title = {SOFA: A Multi-Model Framework for Interactive Physical Simulation}, booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery}, series = {Studies in Mechanobiology, Tissue Engineering and Biomaterials}, volume = {11}, year = {2012}, pages = {283-321}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Simulation Open Framework Architecture (SOFA) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, SOFA can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.}, isbn = {978-3-642-29013-8}, doi = {10.1007/8415_2012_125}, url = {http://dx.doi.org/10.1007/8415_2012_125}, author = {Faure, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Allard, J{\'e}r{\'e}mie and Gilles, Benjamin and Marchesseau, St{\'e}phanie and Talbot, Hugo and Courtecuisse, Hadrien and Bousquet, Guillaume and Peterlik, Igor and Cotin, St{\'e}phane}, editor = {Payan, Yohan} } @article {779, title = {STIR: software for tomographic image reconstruction release 2.}, journal = {Phys Med Biol}, volume = {57}, year = {2012}, month = {2012 Feb 21}, pages = {867-83}, abstract = {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.}, keywords = {Algorithms, Animals, Computers, Image Processing, Computer-Assisted, Mice, Software, Tomography}, issn = {1361-6560}, doi = {10.1088/0031-9155/57/4/867}, author = {Thielemans, Kris and Tsoumpas, Charalampos and Mustafovic, Sanida and Beisel, Tobias and Aguiar, Pablo and Dikaios, Nikolaos and Jacobson, Matthew W} } @article {575, title = {Brainstorm: A User-Friendly Application for MEG/EEG Analysis}, journal = {Computational Intelligence and Neuroscience}, volume = {2011}, year = {2011}, month = {01/2011}, abstract = {Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI).}, doi = {10.1155/2011/879716}, url = {http://www.hindawi.com/journals/cin/2011/879716/}, author = {Fran{\c c}ois Tadel and Sylvain Baillet and John C. Mosher and Dimitrios Pantazis} } @article {868, title = {The caBIG{\textregistered} Life Science Business Architecture Model.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 May 15}, pages = {1429-35}, abstract = {

MOTIVATION: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG{\textregistered}) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research.

RESULTS: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model{\textquoteright}s current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

}, keywords = {Biomedical Research, Computational Biology, Computer Systems, National Cancer Institute (U.S.), Neoplasms, Software, United States, Vocabulary, Controlled}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr141}, author = {Boyd, Lauren Becnel and Hunicke-Smith, Scott P and Stafford, Grace A and Freund, Elaine T and Ehlman, Michele and Chandran, Uma and Dennis, Robert and Fernandez, Anna T and Goldstein, Stephen and Steffen, David and Tycko, Benjamin and Klemm, Juli D} } @article {909, title = {Common characteristics of open source software development and applicability for drug discovery: A systematic review}, journal = {Health Research Policy and Systems}, volume = {9}, year = {2011}, abstract = {Background: Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery.Methods: A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project.Results: Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined.Conclusions: We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. {\textcopyright} 2011 {\r A}rdal et al; licensee BioMed Central Ltd.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-80053368637\&partnerID=40\&md5=758353a8f6509a3198a8d06164bdec37}, author = {{\r A}rdal, C.a and Alstads{\ae} ter, A.b and R{\o}ttingen, J.-A.b} } @article {869, title = {DDN: a caBIG{\textregistered} analytical tool for differential network analysis.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Apr 1}, pages = {1036-8}, abstract = {

UNLABELLED: Differential dependency network (DDN) is a caBIG{\textregistered} (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG{\textregistered}{\textquoteright}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{\textquoteright} web site http://www.cbil.ece.vt.edu/software.htm.

}, keywords = {Animals, Computational Biology, Epigenesis, Genetic, Female, Gene Regulatory Networks, Mammary Glands, Animal, Rats, Software, Systems Biology}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr052}, author = {Zhang, Bai and Tian, Ye and Jin, Lu and Li, Huai and Shih, Ie-Ming and Madhavan, Subha and Clarke, Robert and Hoffman, Eric P and Xuan, Jianhua and Hilakivi-Clarke, Leena and Wang, Yue} } @article {doi:10.3109/17538157.2011.590257, title = {A novel open-source web-based platform promoting collaboration of healthcare professionals and biostatisticians: A design science approach}, journal = {Informatics for Health and Social Care}, year = {2011}, pages = {1-15}, abstract = {Collaboration among clinicians and statisticians is relatively poor, with many cases leading to poor quality research, reflected by low level of evidence studies published in the literature, thus affecting the overall quality of healthcare. We have developed a novel open-source web-based platform aiming in reinforcing the clinician{\textendash}statistician relationship, using an iterative design research process by involving all end-users. Evaluation of this platform by healthcare professionals and biostatisticians was highly positive, as we first identified the pitfalls of their relationship and overcame them through the use of this platform. We are hoping that this will strengthen the clinician{\textendash}statistician relationship in the short term and ultimately improve the quality of research and hence the quality of healthcare in the long term.}, keywords = {clinician, collaboration, design science research, open source, quality of research, relationship, statisticians, user-centred}, doi = {10.3109/17538157.2011.590257}, url = {http://informahealthcare.com/doi/abs/10.3109/17538157.2011.590257}, author = {Raptis, Dimitri A. and Mettler, Tobias and Tzanas, Kostas and Graf, Rolf} } @inbook {springerlink:10.1007/978-1-4419-7046-6_68, title = {Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research}, booktitle = {Software Tools and Algorithms for Biological Systems}, series = {Advances in Experimental Medicine and Biology}, volume = {696}, year = {2011}, note = {10.1007/978-1-4419-7046-6_68}, pages = {667-677}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system{\textquoteright}s porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal{\textquoteright}s patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.}, isbn = {978-1-4419-7046-6}, url = {http://dx.doi.org/10.1007/978-1-4419-7046-6_68}, author = {Locatelli, Paolo and Baj, Emanuele and Restifo, Nicola and Origgi, Gianni and Bragagia, Silvia}, editor = {Arabnia, Hamid R. R. and Tran, Quoc-Nam} } @article {599, title = {Wikipedia: a key tool for global public health promotion.}, journal = {Journal of medical Internet research}, volume = {13}, year = {2011}, month = {2011}, pages = {e14}, abstract = {The Internet has become an important health information resource for patients and the general public. Wikipedia, a collaboratively written Web-based encyclopedia, has become the dominant online reference work. It is usually among the top results of search engine queries, including when medical information is sought. Since April 2004, editors have formed a group called WikiProject Medicine to coordinate and discuss the English-language Wikipedia{\textquoteright}s medical content. This paper, written by members of the WikiProject Medicine, discusses the intricacies, strengths, and weaknesses of Wikipedia as a source of health information and compares it with other medical wikis. Medical professionals, their societies, patient groups, and institutions can help improve Wikipedia{\textquoteright}s health-related entries. Several examples of partnerships already show that there is enthusiasm to strengthen Wikipedia{\textquoteright}s biomedical content. Given its unique global reach, we believe its possibilities for use as a tool for worldwide health promotion are underestimated. We invite the medical community to join in editing Wikipedia, with the goal of providing people with free access to reliable, understandable, and up-to-date health information.}, keywords = {Consumer Health Information, Encyclopedias as Topic, Health Promotion, Humans, Information Dissemination, Information Services, Internet, Patient Education as Topic, Public Health, World Health}, issn = {1438-8871}, author = {Heilman, James M and Kemmann, Eckhard and Bonert, Michael and Chatterjee, Anwesh and Ragar, Brent and Beards, Graham M and Iberri, David J and Harvey, Matthew and Thomas, Brendan and Stomp, Wouter and Martone, Michael F and Lodge, Daniel J and Vondracek, Andrea and de Wolff, Jacob F and Liber, Casimir and Grover, Samir C and Vickers, Tim J and Mesk{\'o}, Bertalan and Laurent, Micha{\"e}l R} } @article {600, title = {WikiProject Medicine.}, journal = {BMJ (Clinical research ed.)}, volume = {342}, year = {2011}, month = {2011}, pages = {d3387}, issn = {1468-5833}, doi = {10.1136/bmj.d3387}, author = {Trevena, Lyndal} } @article {1015, title = {Experience implementing OpenMRS to support maternal and reproductive health in Northern Nigeria.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {332-6}, abstract = {

In Northern Nigeria a deteriorating health system has resulted in one of the World{\textquoteright}s highest rates of maternal and infant deaths. The dire situation in Northern Nigeria is only amplified by the lack of an effective health information system, leaving hospitals and clinics to make decisions about patient care with only uninformed guesses about medical history and access to unreliable and unintelligible patient registers and summary reports. In 2009 we implemented an electronic medical records system using OpenMRS for the Family Health Unit of the Shehu Idris College. The three-month process resulted in electronic forms for all clinical areas, greatly reduced data duplication and a monthly reporting process that takes minutes instead of days. This system provides not only access to the first patient-based health indicators in Nigeria (as opposed to previously error-prone aggregate data) but is also an example of the potential to overcome the harsh computing environment in Nigeria to implement eHealth systems that will improve the quality of patient care.

}, keywords = {Delivery of Health Care, electronic health records, Maternal Health Services, Maternal Welfare, Models, Organizational, Needs Assessment, Nigeria, Reproductive Medicine, Utilization Review}, issn = {0926-9630}, author = {Thompson, Adam and Castle, Evelyn and Lubeck, Paul and Makarfi, Provost Shehu} } @article {20663165, title = {Heterogeneity prevails: the state of clinical trial data management in Europe - results of a survey of ECRIN centres.}, journal = {Trials}, volume = {11}, year = {2010}, month = {2010 Jul 21}, pages = {79}, abstract = {ABSTRACT: BACKGROUND: The use of Clinical Data Management Systems (CDMS) has become essential in clinical trials to handle the increasing amount of data that must be collected and analyzed. With a CDMS trial data are captured at investigator sites with "electronic Case Report Forms". Although more and more of these electronic data management systems are used in academic research centres an overview of CDMS products and of available data management and quality management resources for academic clinical trials in Europe is missing. METHODS: The ECRIN (European Clinical Research Infrastructure Network) data management working group conducted a two-part standardized survey on data management, software tools, and quality management for clinical trials. The questionnaires were answered by nearly 80 centres / units (with an overall response rate of 47\% and 43\%) from 12 European countries and EORTC. RESULTS: Our survey shows that about 90\% of centres have a CDMS in routine use. Of these CDMS nearly 50\% are commercial systems; Open Source solutions don{\textquoteright}t play a major role. In general, solutions used for clinical data management are very heterogeneous: 20 different commercial CDMS products (7 Open Source solutions) in addition to 17/18 proprietary systems are in use. The most widely employed CDMS products are MACRO TM and Capture System TM, followed by solutions that are used in at least 3 centres: eResearch Network TM, CleanWeb TM, GCP Base TM and SAS TM. Although quality management systems for data management are in place in most centres / units, there exist some deficits in the area of system validation. CONCLUSIONS: Because the considerable heterogeneity of data management software solutions may be a hindrance to cooperation based on trial data exchange, standards like CDISC (Clinical Data Interchange Standard Consortium) should be implemented more widely. In a heterogeneous environment the use of data standards can simplify data exchange, increase the quality of data and prepare centres for new developments (e.g. the use of EHR for clinical research). Because data management and the use of electronic data capture systems in clinical trials are characterized by the impact of regulations and guidelines, ethical concerns are discussed. In this context quality management becomes an important part of compliant data management. To address these issues ECRIN will establish certified data centres to support electronic data management and associated compliance needs of clinical trial centres in Europe.}, url = {http://www.trialsjournal.com/content/11/1/79}, author = {Kuchinke, Wolfgang and Ohmann, Christian and Yang, Qin and Salas, Nader and Lauritsen, Jens and Gueyffier, Francois and Leizorovicz, Alan and Schade-Brittinger, Carmen and Wittenberg, Michael and Voko, Zoltan and Gaynor, Siobhan and Cooney, Margaret and Doran, Peter and Maggioni, Aldo and Lorimer, Andrea and Torres, Ferran and McPherson, Gladys and Charvill, Jim and Hellstrom, Mats and Lejeune, Stephane} } @article {20663194, title = {ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.}, journal = {Breast cancer research : BCR}, volume = {12}, year = {2010}, month = {2010 Jul 27}, pages = {R56}, abstract = {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.}, author = {Tuominen, Vilppu J and Ruotoistenmaki, Sanna and Viitanen, Arttu and Jumppanen, Mervi and Isola, Jorma} } @article {10.1371/journal.pone.0014094, title = {JULIDE: A Software Tool for 3D Reconstruction and Statistical Analysis of Autoradiographic Mouse Brain Sections}, journal = {PLoS ONE}, volume = {5}, number = {11}, year = {2010}, month = {11}, pages = {e14094}, publisher = {Public Library of Science}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, doi = {10.1371/journal.pone.0014094}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J. and Thiran, Jean-Philippe} } @article {1042, title = {JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010}, pages = {e14094}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, keywords = {Animals, Autoradiography, Brain, Carbon Radioisotopes, Deoxyglucose, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Male, Maze Learning, Mice, Mice, Inbred C57BL, Reproducibility of Results, Software}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J and Thiran, Jean-Philippe} } @article {19910667, title = {The medical exploration toolkit: an efficient support for visual computing in surgical planning and training.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {16}, year = {2010}, month = {2010 Jan-Feb}, pages = {133-46}, abstract = {Application development is often guided by the usage of software libraries and toolkits. For medical applications, the toolkits currently available focus on image analysis and volume rendering. Advance interactive visualizations and user interface issues are not adequately supported. Hence, we present a toolkit for application development in the field of medical intervention planning, training, and presentation--the MEDICALEXPLORATIONTOOLKIT (METK). The METK is based on the rapid prototyping platform MeVisLab and offers a large variety of facilities for an easy and efficient application development process. We present dedicated techniques for advanced medical visualizations, exploration, standardized documentation, adn interface widgets for common tasks. These include, e.g., advanced animation facilities, viewpoint selection, several illustrative rendering techniques, and new techniques for object selection in 3D surface models. No extended programming skills are needed for application building, since a graphical programming approach can be used. the toolkit is freely available and well documented to facilitate the use and extension of the toolkit.}, author = {M{\"u}hler, Konrad and Tietjen, Christian and Ritter, Felix and Preim, Bernhard} } @article {20482787, title = {Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.}, journal = {BMC bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {260}, abstract = {BACKGROUND: Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. RESULTS: We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. CONCLUSIONS: The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.}, author = {Tolopko, Andrew N and Sullivan, John P and Erickson, Sean D and Wrobel, David and Chiang, Su L and Rudnicki, Katrina and Rudnicki, Stewart and Nale, Jennifer and Selfors, Laura M and Greenhouse, Dara and Muhlich, Jeremy L and Shamu, Caroline E} } @article {803, title = {Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience.}, journal = {Int J Comput Assist Radiol Surg}, volume = {3}, year = {2008}, month = {2008 Nov 1}, pages = {395-403}, abstract = {OBJECTIVE: Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. METHODS: IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. RESULTS: The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. CONCLUSION: With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community.}, issn = {1861-6429}, doi = {10.1007/s11548-008-0243-4}, author = {Enquobahrie, Andinet and Gobbi, David and Turek, Matt and Cheng, Patrick and Yaniv, Ziv and Lindseth, Frank and Cleary, Kevin} } @article {17947615, title = {Early experiences with personal health records.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Jan-Feb}, pages = {1-7}, abstract = {Over the past year, several payers, employers, and commercial vendors have announced personal health record projects. Few of these are widely deployed and few are fully integrated into ambulatory or hospital-based electronic record systems. The earliest adopters of personal health records have many lessons learned that can inform these new initiatives. We present three case studies--MyChart at Palo Alto Medical Foundation, PatientSite at Beth Israel Deaconess Medical Center, and Indivo at Children{\textquoteright}s Hospital Boston. We describe our implementation challenges from 1999 to 2007 and postulate the evolving challenges we will face over the next five years.}, author = {Halamka, John D and Mandl, Kenneth D and Tang, Paul C} } @article {18570554, title = {Standards-based, open-source electronic health record systems: a desirable future for the U.S. health industry.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {14}, year = {2008}, month = {2008 Apr}, pages = {284-8}, abstract = {Many healthcare systems are moving toward a fully electronic health record (EHR) in order to better manage patient care. Unfortunately, in the United States, many current EHR systems leave much to be desired. Among well-documented criticisms are that they tend to be inflexible, proprietary, nonintuitive, expensive, difficult to maintain and rarely interoperable across health systems. From the clinician{\textquoteright}s perspective, these flaws sometimes make having an EHR system seem no better than retaining a paper-based system. Open-source software, a great success in other information-intensive industries, is one possible solution to these problems, and may help integrate a functional EHR system into, and across, more health systems and clinics because of the greater potential for local customization. We believe that the advantages of an open-source EHR system outweigh the costs of a more traditional, proprietary EHR system, and recommend that more work be done to advance an interoperable open-source EHR system in the United States. Open-source EHR systems have the potential to improve healthcare in the United States as they have done in many other areas around the world.}, author = {Yellowlees, Peter M and Marks, Shayna L and Hogarth, Michael and Turner, Stuart} } @article {18755989, title = {Whose personal control? Creating private, personally controlled health records for pediatric and adolescent patients.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Nov-Dec}, pages = {737-43}, abstract = {Personally controlled health records (PCHRs) enable patients to store, manage, and share their own health data, and promise unprecedented consumer access to medical information. To deploy a PCHR in the pediatric population requires crafting of access and security policies, tailored to a record that is not only under patient control, but one that may also be accessed by parents, guardians, and third-party entities. Such hybrid control of health information requires careful consideration of both the PCHR vendor{\textquoteright}s access policies, as well as institutional policies regulating data feeds to the PCHR, to ensure that the privacy and confidentiality of each user is preserved. Such policies must ensure compliance with legal mandates to prevent unintended disclosures and must preserve the complex interactions of the patient-provider relationship. Informed by our own operational involvement in the implementation of the Indivo PCHR, we provide a framework for understanding and addressing the challenges posed by child, adolescent, and family access to PCHRs.}, author = {Bourgeois, Fabienne C and Taylor, Patrick L and Emans, S Jean and Nigrin, Daniel J and Mandl, Kenneth D} } @article {17917780, title = {Benefits of using the DCM4CHE DICOM archive.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {125-9}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2039778}, author = {Warnock, Max J and Toland, Christopher and Evans, Damien and Wallace, Bill and Nagy, Paul} } @article {17680308, title = {Mastering DICOM with DVTk.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {47-62}, abstract = {The Digital Imaging and Communications in Medicine (DICOM) Validation Toolkit (DVTk) is an open-source framework with potential value for anyone working with the DICOM standard. DICOM{\textquoteright}s flexibility requires hands-on experience in understanding ways in which the standard{\textquoteright}s interpretation may vary among vendors. DVTk was developed as a clinical engineering tool to aid and accelerate DICOM integration at clinical sites. DVTk is used to provide an independent measurement of the accuracy of a product{\textquoteright}s DICOM interface, according to both the DICOM standard and the product{\textquoteright}s conformance statement. DVTk has stand-alone tools and a framework with which developers can create new tools. We provide an overview of the architecture of the toolkit, sample scenarios of its utility, and evidence of its relative ease of use. Our goal is to encourage involvement in this open-source project and attract developers to build off and further enrich this platform for DICOM integration testing.}, url = {http://www.springerlink.com/content/r17t75244k2376n0/}, author = {Potter, Glenn and Busbridge, Rick and Toland, Michael and Nagy, Paul} } @article {17846835, title = {Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {94-100}, abstract = {The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.}, author = {Prior, Fred W and Erickson, Bradley J and Tarbox, Lawrence} } @article {18074196, title = {Open-source, low-cost, high-reliability solutions for digital imaging systems: example of a "dicom router".}, journal = {La Radiologia medica}, volume = {112}, year = {2007}, month = {2007 Dec}, pages = {1252-9}, abstract = {PURPOSE: The purpose of this article is to illustrate a case where acquisition of digital imaging know-how by a modern radiotherapy division has helped to solve a technical problem while allowing substantial savings through the use of free and open-source resources. The problem was related to the necessity to route, with complex policies, the images produced by different digital imaging and communications in medicine (DICOM) sources within the department or in other divisions and/or hospitals. MATERIALS AND METHODS: The problem was solved by using completely free, well-tested and stable technologies (PHP, Apache, MySQL, DCMTK OFFIS, Red Hat Linux 9A and Linux Fedora Core 4) and low-cost hardware to contain costs. In the development, we also considered integration of the routed images with the existing electronic clinical records. RESULTS: The system developed, called the dicom router, implemented two kinds of routing: manual and automatic, both oriented to link the images acquired with the existing electronic clinical records. System stability was enhanced in a second phase by using a low-cost hardware redundancy solution. The system has now been operating for 1 year and has proved the value of the technologies used. CONCLUSIONS: The need to operate with more than one provider creates a series of integration issues, so that it becomes economically appealing to acquire internally the knowledge needed to interact more precisely with providers of big information technology (IT) solutions. This need is well catered for by open-source technologies, which are well documented and available to everyone. By using them, in-house IT technicians are able to implement valuable technical solutions for small-to medium-sized informatization problems, which would otherwise remain unsolved except with great economic efforts.}, author = {Gatta, R and Abeni, F and Buglione, M and Peveri, A and Barbera, F and Tonoli, S and Fratta, P and Magrini, S M} } @article {17249408, title = {OpenSourcePACS: an extensible infrastructure for medical image management.}, journal = {IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {11}, year = {2007}, month = {2007 Jan}, pages = {94-109}, abstract = {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.}, url = {http://escholarship.org/uc/item/186368fv}, author = {Bui, Alex A T and Morioka, Craig and Dionisio, John David N and Johnson, David B and Sinha, Usha and Ardekani, Siamak and Taira, Ricky K and Aberle, Denise R and El-Saden, Suzie and Kangarloo, Hooshang} } @article {17238397, title = {Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {529-33}, abstract = {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.}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638}, author = {Mamlin, Burke W and Biondich, Paul G and Wolfe, Ben A and Fraser, Hamish and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @article {17018156, title = {Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow.}, journal = {BMC bioinformatics}, volume = {7}, year = {2006}, month = {2006}, pages = {430}, abstract = {BACKGROUND: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. RESULTS: We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. CONCLUSION: Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.}, author = {Morisawa, Hiraku and Hirota, Mikako and Toda, Tosifusa} } @article {17238765, title = {The OpenMRS system: collaborating toward an open source EMR for developing countries.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {1146}, abstract = {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.}, author = {Wolfe, Benjamin A and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @article {16160381, title = {Linking primary care information systems and public health information networks: lessons from the Philippines.}, journal = {Studies in health technology and informatics}, volume = {116}, year = {2005}, month = {2005}, pages = {955-60}, abstract = {Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed "health information system islands" connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of "information work" in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.}, author = {Tolentino, Herman and Marcelo, Alvin and Marcelo, Portia and Maramba, Inocencio} } @article {1262, title = {A study of clinically related open source software projects.}, journal = {AMIA Annu Symp Proc}, year = {2005}, month = {2005}, pages = {330-4}, abstract = {

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the {\textquoteright}fit{\textquoteright} of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects.

}, keywords = {Clinical Medicine, Information Dissemination, Intellectual Property, Software}, issn = {1942-597X}, author = {Hogarth, Michael A and Turner, Stuart} } @article {15361001, title = {The RODS Open Source Project: removing a barrier to syndromic surveillance.}, journal = {Studies in health technology and informatics}, volume = {107}, year = {2004}, month = {2004}, pages = {1192-6}, abstract = {The goal of the Real-time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate deployment of computer-based syndromic surveillance. To this end, the project has released the RODS software under the GNU General Public License and created an organizational structure to catalyze its development. This paper describes the design of the software, requested extensions, and the structure of the development effort.}, author = {Espino, Jeremy U and Wagner, Michael M and Tsui, Fu-Chang and Su, Hoah-Der and Olszewski, Robert T and Lie, Zhen and Chapman, Wendy and Zeng, Xiaoming and Ma, Lili and Lu, Zhong Wei and Dara, Jagan} } @article {494, title = {PropeR: a multi disciplinary EPR system.}, journal = {International journal of medical informatics}, volume = {70}, year = {2003}, month = {2003 Jul}, pages = {149-60}, abstract = {This article describes the architecture of an EPR system developed for the PropeR project. This EPR system not only aims at supporting home care of stroke patients, but is also designed in such a way that it can be ported to other medical services without much effort. We will briefly describe the Stroke Service and the related PropeR project. Starting from a list of requirements to construct a generic EPR system we will outline the architecture and describe the standards and methods used. Subsequently we describe the implementation and the problems encountered. In the discussion, we will go into the advantages and disadvantages of the tools and techniques we have used.}, keywords = {Computer Systems, Delivery of Health Care, Integrated, Humans, Interprofessional Relations, Medical Records Systems, Computerized, Stroke}, issn = {1386-5056}, author = {van der Linden, Helma and Boers, Gerrit and Tange, Huibert and Talmon, Jan and Hasman, Arie} } @article {12807803, title = {Technical description of RODS: a real-time public health surveillance system.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {10}, year = {2003}, month = {2003 Sep-Oct}, pages = {399-408}, abstract = {This report describes the design and implementation of the Real-time Outbreak and Disease Surveillance (RODS) system, a computer-based public health surveillance system for early detection of disease outbreaks. Hospitals send RODS data from clinical encounters over virtual private networks and leased lines using the Health Level 7 (HL7) message protocol. The data are sent in real time. RODS automatically classifies the registration chief complaint from the visit into one of seven syndrome categories using Bayesian classifiers. It stores the data in a relational database, aggregates the data for analysis using data warehousing techniques, applies univariate and multivariate statistical detection algorithms to the data, and alerts users of when the algorithms identify anomalous patterns in the syndrome counts. RODS also has a Web-based user interface that supports temporal and spatial analyses. RODS processes sales of over-the-counter health care products in a similar manner but receives such data in batch mode on a daily basis. RODS was used during the 2002 Winter Olympics and currently operates in two states-Pennsylvania and Utah. It has been and continues to be a resource for implementing, evaluating, and applying new methods of public health surveillance.}, author = {Tsui, Fu-Chiang and Espino, Jeremy U and Dato, Virginia M and Gesteland, Per H and Hutman, Judith and Wagner, Michael M} }