@article {1230, title = {Data Migration from Operating EMRs to OpenEMR with Mirth Connect.}, journal = {Stud Health Technol Inform}, volume = {257}, year = {2019}, month = {2019}, pages = {288-292}, abstract = {

Electronic medical records (EMR) are integral to the functionality of day to day operations in a clinic. EMRs perform functions like scheduling or hosting medical records used by physicians and other staff [1]. A certain time comes when it is necessary to upgrade or change EMRs to maintain efficiency in a clinic. The most arduous part of changing a clinic{\textquoteright}s EMR is migrating the clinical data from the old EMR to the new. This paper explores the feasibility of data migration between two Electronic Medical Records using open source technologies. This enables smaller clinics to change EMRs when the need arises without incurring huge costs. Using Mirth Connect as a data integration engine and OpenEMR as the new EMR we successfully migrated data from our old EMR to OpenEMR.

}, keywords = {Ambulatory Care Facilities, electronic health records, Humans, Physicians, Software}, issn = {1879-8365}, author = {Lin, Jing and Ranslam, Kyle and Shi, Fang and Figurski, Mike and Liu, Zheng} } @article {1229, title = {Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0212463}, abstract = {

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

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

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0212463}, author = {Klann, Jeffrey G and Joss, Matthew A H and Embree, Kevin and Murphy, Shawn N} } @article {1222, title = {Data on security requirements in open-source software projects.}, journal = {Data Brief}, volume = {25}, year = {2019}, month = {2019 Aug}, pages = {103590}, abstract = {

The datasets presented in this article are related the research paper entitled "A Linear Classifier Approach for Identifying Security Requirements in Open Source Software Development" Wang et al. (2018) [1]. This article describes requirements collected from three open-source software (OSS) projects and labels of security requirements. The datasets are made available to support automated security requirements analyzing tools development as well as tools{\textquoteright} evaluation.

}, issn = {2352-3409}, doi = {10.1016/j.dib.2018.12.029}, author = {Wang, Wentao and Mahakala, Kavya Reddy and Gupta, Arushi and Hussein, Nesrin and Wang, Yinglin} } @article {1272, title = {Data for decision making: using a dashboard to strengthen routine immunisation in Nigeria.}, journal = {BMJ Glob Health}, volume = {3}, year = {2018}, month = {2018}, pages = {e000807}, abstract = {

Availability of reliable data has for a long time been a challenge for health programmes in Nigeria. Routine immunisation (RI) data have always been characterised by conflicting coverage figures for the same vaccine across different routine data reporting platforms. Following the adoption of District Health Information System version 2 (DHIS2) as a national electronic data management platform, the DHIS2 RI Dashboard Project was initiated to address the absence of some RI-specific indicators on DHIS2. The project was also intended to improve visibility and monitoring of RI indicators as well as strengthen the broader national health management information system by promoting the use of routine data for decision making at all governance levels. This paper documents the process, challenges and lessons learnt in implementing the project in Nigeria. A multistakeholder technical working group developed an implementation framework with clear preimplementation; implementation and postimplementation activities. Beginning with a pilot in Kano state in 2014, the project has been scaled up countrywide. Nearly 34 000 health workers at all administrative levels were trained on RI data tools and DHIS2 use. The project contributed to the improvement in completeness of reports on DHIS2 from 53 \% in first quarter 2014 to 81 \% in second quarter 2017. The project faced challenges relating to primary healthcare governance structures at the subnational level, infrastructure and human resource capacity. Our experience highlights the need for early and sustained advocacy to stakeholders in a decentralised health system to promote ownership and sustainability of a centrally coordinated systems strengthening initiative.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2018-000807}, author = {Etamesor, Sulaiman and Ottih, Chibuzo and Salihu, Ismail Ndalami and Okpani, Arnold Ikedichi} } @article {1293, title = {Designing mHealth for maternity services in primary health facilities in a low-income setting - lessons from a partially successful implementation.}, journal = {BMC Med Inform Decis Mak}, volume = {18}, year = {2018}, month = {2018 11 12}, pages = {96}, abstract = {

BACKGROUND: Increasing mobile phone ownership, functionality and access to mobile-broad band internet services has triggered growing interest to harness the potential of mobile phone technology to improve health services in low-income settings. The present project aimed at designing an mHealth system that assists midlevel health workers to provide better maternal health care services by automating the data collection and decision-making process. This paper describes the development process and technical aspects of the system considered critical for possible replication. It also highlights key lessons learned and challenges during implementation.

METHODS: The mHealth system had front-end and back-end components. The front-end component was implemented as a mobile based application while the back-end component was implemented as a web-based application that ran on a central server for data aggregation and report generation. The current mHealth system had four applications; namely, data collection/reporting, electronic health records, decision support, and provider education along the continuum of care including antenatal, delivery and postnatal care. The system was pilot-tested and deployed in selected health centers of North Shewa Zone, Amhara region, Ethiopia.

RESULTS: The system was used in 5 health centers since Jan 2014 and later expanded to additional 10 health centers in June 2016 with a total of 5927 electronic forms submitted to the back-end system. The submissions through the mHealth system were slightly lower compared to the actual number of clients who visited those facilities as verified by record reviews. Regarding timeliness, only 11\% of the electronic forms were submitted on the day of the client visit, while an additional 17\% of the forms were submitted within 10~days of clients{\textquoteright} visit. On average forms were submitted 39~days after the day of clients visit with a range of 0 to 150~days.

CONCLUSIONS: In conclusion, the study illustrated that an effective mHealth intervention can be developed using an open source platform and local resources. The system impacted key health outcomes and contributed to timely and complete data submission. Lessons learned through the process including success factors and challenges are discussed.

}, keywords = {Cell Phone, Delivery of Health Care, electronic health records, Ethiopia, Female, Health Facilities, Humans, Maternal Health Services, Mobile Applications, Poverty, Pregnancy, Telemedicine}, issn = {1472-6947}, doi = {10.1186/s12911-018-0704-9}, author = {Shiferaw, Solomon and Workneh, Andualem and Yirgu, Robel and Dinant, Geert-Jan and Spigt, Mark} } @article {1274, title = {Development and Evaluation of a New Security and Privacy Track in a Health Informatics Graduate Program: Multidisciplinary Collaboration in Education.}, journal = {JMIR Med Educ}, volume = {4}, year = {2018}, month = {2018 Dec 21}, pages = {e19}, abstract = {

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

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

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

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

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

}, issn = {2369-3762}, doi = {10.2196/mededu.9081}, author = {Zhou, Leming and Parmanto, Bambang and Joshi, James} } @article {1203, title = {The {District} {Health} {Information} {System} ({DHIS}2): {A} literature review and meta-synthesis of its strengths and operational challenges based on the experiences of 11 countries}, journal = {Health Information Management: Journal of the Health Information Management Association of Australia}, year = {2018}, pages = {1833358318777713}, abstract = {BACKGROUND: Health information systems offer many potential benefits for healthcare, including financial benefits and for improving the quality of patient care. The purpose of District Health Information Systems (DHIS) is to document data that are routinely collected in all public health facilities in a country using the system. OBJECTIVE: The aim of this study was to examine the strengths and operational challenges of DHIS2, with a goal to enable decision makers in different counties to more accurately evaluate the outcomes of introducing DHIS2 into their particular country. METHOD: A review of the literature combined with the method of meta-synthesis was used to source information and interpret results relating to the strengths and operational challenges of DHIS2. Databases (Embase, PubMed, Scopus and Google Scholar) were searched for documents related to strengths and operational challenges of DHIS2, with no time limit up to 8 April 2017. The review and evaluation of selected studies was conducted in three stages: title, abstract and full text. Each of the selected studies was reviewed carefully and key concepts extracted. These key concepts were divided into two categories of strengths and operational challenges of DHIS2. Then, each category was grouped based on conceptual similarity to achieve the main themes and sub-themes. Content analysis was used to analyse extracted data. RESULTS: Of 766 identified citations, 20 studies from 11 countries were included and analysed in this study. Identified strengths in the DHIS were represented in seven themes (with 21 categories): technical features of software, proper management of data, application flexibility, networking and increasing the satisfaction of stakeholders, development of data management, increasing access to information and economic benefits. Operational challenges were identified and captured in 11 themes (with 18 categories): funds; appropriate communication infrastructure; the need for the existence of appropriate data; political, cultural, social and structural infrastructure; manpower; senior managers; training; using academic potentials; definition and standardising the deployment processes; neglect to application of criteria and clinical guidelines in the use of system; data security; stakeholder communications challenges and the necessity to establish a pilot system. CONCLUSION: This study highlighted specific strengths in the technical and functional aspects of DHIS2 and also drew attention to particular challenges and concerns. These results provide a sound evidence base for decision makers and policymakers to enable them to make more accurate decisions about whether or not to use the DHIS2 in the health system of their country.}, keywords = {content analysis, District Health Information System, health information system, health information technology, information technology, meta-synthesis, qualitative research}, issn = {1322-4913}, doi = {10.1177/1833358318777713}, author = {Dehnavieh, Reza and Haghdoost, AliAkbar and Khosravi, Ardeshir and Hoseinabadi, Fahime and Rahimi, Hamed and Poursheikhali, Atousa and Khajehpour, Nahid and Khajeh, Zahra and Mirshekari, Nadia and Hasani, Marziyeh and Radmerikhi, Samera and Haghighi, Hajar and Mehrolhassani, Mohammad Hossain and Kazemi, Elaheh and Aghamohamadi, Saeide} } @article {1238, title = {Design and implementation of an affordable, public sector electronic medical record in rural Nepal.}, journal = {J Innov Health Inform}, volume = {24}, year = {2017}, month = {2017 Jun 23}, pages = {862}, abstract = {

INTRODUCTION: Globally, electronic medical records are central to the infrastructure of modern healthcare systems. Yet the vast majority of electronic medical records have been designed for resource-rich environments and are not feasible in settings of poverty. Here we describe the design and implementation of an electronic medical record at a public sector district hospital in rural Nepal, and its subsequent expansion to an additional public sector facility.DevelopmentThe electronic medical record was designed to solve for the following elements of public sector healthcare delivery: 1) integration of the systems across inpatient, surgical, outpatient, emergency, laboratory, radiology, and pharmacy sites of care; 2) effective data extraction for impact evaluation and government regulation; 3) optimization for longitudinal care provision and patient tracking; and 4) effectiveness for quality improvement initiatives.

APPLICATION: For these purposes, we adapted Bahmni, a product built with open-source components for patient tracking, clinical protocols, pharmacy, laboratory, imaging, financial management, and supply logistics. In close partnership with government officials, we deployed the system in February of 2015, added on additional functionality, and iteratively improved the system over the following year. This experience enabled us then to deploy the system at an additional district-level hospital in a different part of the country in under four weeks. We discuss the implementation challenges and the strategies we pursued to build an electronic medical record for the public sector in rural Nepal.DiscussionOver the course of 18 months, we were able to develop, deploy and iterate upon the electronic medical record, and then deploy the refined product at an additional facility within only four weeks. Our experience suggests the feasibility of an integrated electronic medical record for public sector care delivery even in settings of rural poverty.

}, keywords = {Delivery of Health Care, Integrated, electronic health records, Global Health, Health Plan Implementation, Hospitals, Public, Humans, Nepal, Public Sector, Rural Population}, issn = {2058-4563}, doi = {10.14236/jhi.v24i2.862}, author = {Raut, Anant and Yarbrough, Chase and Singh, Vivek and Gauchan, Bikash and Citrin, David and Verma, Varun and Hawley, Jessica and Schwarz, Dan and Harsha Bangura, Alex and Shrestha, Biplav and Schwarz, Ryan and Adhikari, Mukesh and Maru, Duncan} } @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 {1129, title = {Development of an Open Source Educational Resource: "Clinical Procedures for Safer Patient Care".}, journal = {Stud Health Technol Inform}, volume = {225}, year = {2016}, month = {2016}, pages = {979-80}, abstract = {

An Open Education Resource (OER) has been developed by two nurse educators to address inconsistencies in how clinical health care skills are taught and practiced in the clinical setting, and to ensure best practice and quality care based on the latest evidence. A checklist approach aims to provide clear steps and rationale for procedures, standardized processes for clinical skills and to assist nursing schools and clinical practice partners in teaching clinical skills, and keeping procedural practice current. The format is logical, organized and focused on patient safety, and will provide information retrieval opportunities at the point of care to support decisions and plan patient care. This poster discusses the development of this resource, the framework used, and the process from conception to distribution.

}, issn = {0926-9630}, author = {Doyle, Glynda and McCutcheon, Jodie} } @article {1130, title = {Development of an open technology sensor suite for assisted living: a student-led research project.}, journal = {Interface Focus}, volume = {6}, year = {2016}, month = {2016 Aug 6}, pages = {20160018}, abstract = {

Many countries have a rapidly ageing population, placing strain on health services and creating a growing market for assistive technology for older people. We have, through a student-led, 12-week project for 10 students from a variety of science and engineering backgrounds, developed an integrated sensor system to enable older people, or those at risk, to live independently in their own homes for longer, while providing reassurance for their family and carers. We provide details on the design procedure and performance of our sensor system and the management and execution of a short-term, student-led research project. Detailed information on the design and use of our devices, including a door sensor, power monitor, fall detector, general in-house sensor unit and easy-to-use location-aware communications device, is given, with our open designs being contrasted with closed proprietary systems. A case study is presented for the use of our devices in a real-world context, along with a comparison with commercially available systems. We discuss how the system could lead to improvements in the quality of life of older users and increase the effectiveness of their associated care network. We reflect on how recent developments in open source technology and rapid prototyping increase the scope and potential for the development of powerful sensor systems and, finally, conclude with a student perspective on this team effort and highlight learning outcomes, arguing that open technologies will revolutionize the way in which technology will be deployed in academic research in the future.

}, issn = {2042-8898}, doi = {10.1098/rsfs.2016.0018}, author = {Manton, James D and Hughes, Josephine A E and Bonner, Oliver and Amjad, Omar A and Mair, Philip and Miele, Isabella and Wang, Tiesheng and Levdik, Vitaly and Hall, Richard D and Baekelandt, G{\'e}raldine and Vasconcellos, Fernando da Cruz and Hadeler, Oliver and Hutter, Tanya and Kaminski, Clemens F} } @article {1120, title = {Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {103}, abstract = {

BACKGROUND: Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention.

RESULTS: The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English.

CONCLUSIONS: The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

}, issn = {1472-6947}, doi = {10.1186/s12911-016-0339-7}, author = {Gomide, H P and Bernardino, H S and Richter, K and Martins, L F and Ronzani, T M} } @article {1169, title = {dot-app: a {Graphviz}-{Cytoscape} conversion plug-in}, journal = {F1000Research}, volume = {5}, year = {2016}, pages = {2543}, abstract = {dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.}, keywords = {attribute conversion, Cytoscape, Data visualization, DOT, export, format conversion, GraphViz, import, Network}, doi = {10.12688/f1000research.9751.1}, author = {Fitts, Braxton and Zhang, Ziran and Maher, Massoud and Demchak, Barry} } @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 {978, title = {DICOM for Clinical Research: PACS-Integrated Electronic Data Capture in Multi-Center Trials.}, journal = {J Digit Imaging}, year = {2015}, month = {2015 May 23}, abstract = {

Providing surrogate endpoints in clinical trials, medical imaging has become increasingly important in human-centered research. Nowadays, electronic data capture systems (EDCS) are used but binary image data is integrated insufficiently. There exists no structured way, neither to manage digital imaging and communications in medicine (DICOM) data in EDCS nor to interconnect EDCS with picture archiving and communication systems (PACS). Manual detours in the trial workflow yield errors, delays, and costs. In this paper, requirements for a DICOM-based system interconnection of EDCS and research PACS are analysed. Several workflow architectures are compared. Optimized for multi-center trials, we propose an entirely web-based solution integrating EDCS, PACS, and DICOM viewer, which has been implemented using the open source projects OpenClinica, DCM4CHEE, and Weasis, respectively. The EDCS forms the primary access point. EDCS to PACS interchange is integrated seamlessly on the data and the context levels. DICOM data is viewed directly from the electronic case report form (eCRF), while PACS-based management is hidden from the user. Data privacy is ensured by automatic de-identification and re-labelling with study identifiers. Our concept is evaluated on a variety of 13 DICOM modalities and transfer syntaxes. We have implemented the system in an ongoing investigator-initiated trial (IIT), where five centers have recruited 24 patients so far, performing decentralized computed tomography (CT) screening. Using our system, the chief radiologist is reading DICOM data directly from the eCRF. Errors and workflow processing time are reduced. Furthermore, an imaging database is built that may support future research.

}, issn = {1618-727X}, doi = {10.1007/s10278-015-9802-8}, author = {Haak, Daniel and Page, Charles-E and Reinartz, Sebastian and Kr{\"u}ger, Thilo and Deserno, Thomas M} } @article {1022, title = {Digital Imaging and Electronic Data Capture in Multi-Center Clinical Trials.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {930}, abstract = {

While medical image data is managed in picture archiving and communication systems (PACS) via the digital imaging and communications in medicine (DICOM) protocol, electronic data capture systems (EDCS) in clinical trials lack PACS interfacing. This complicates the trial workflow and increases errors, time, and costs. In this work, four system architectures of image integration for multi-center trials are analyzed with respect to data, function, visual, and context integration levels. We propose an open source-based architecture composed of OpenClinica, DCM4CHE, and Weasis for EDCS, PACS, and Viewer, respectively.

}, issn = {0926-9630}, author = {Deserno, Thomas M and Deserno, Verena and Haak, Daniel and Kabino, Klaus} } @article {1030, title = {Do interoperable national information systems enhance availability of data to assess the effect of scale-up of HIV services on health workforce deployment in resource-limited countries?}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {677-81}, abstract = {

Sub-Saharan Africa (SSA) bears the heaviest burden of the HIV epidemic. Health workers play a critical role in the scale-up of HIV programs. SSA also has the weakest information and communication technology (ICT) infrastructure globally. Implementing interoperable national health information systems (HIS) is a challenge, even in developed countries. Countries in resource-limited settings have yet to demonstrate that interoperable systems can be achieved, and can improve quality of healthcare through enhanced data availability and use in the deployment of the health workforce. We established interoperable HIS integrating a Master Facility List (MFL), District Health Information Software (DHIS2), and Human Resources Information Systems (HRIS) through application programmers interfaces (API). We abstracted data on HIV care, health workers deployment, and health facilities geo-coordinates. Over 95\% of data elements were exchanged between the MFL-DHIS and HRIS-DHIS. The correlation between the number of HIV-positive clients and nurses and clinical officers in 2013 was R2=0.251 and R2=0.261 respectively. Wrong MFL codes, data type mis-match and hyphens in legacy data were key causes of data transmission errors. Lack of information exchange standards for aggregate data made programming time-consuming.

}, issn = {0926-9630}, author = {Oluoch, Tom and Muturi, David and Kiriinya, Rose and Waruru, Anthony and Lanyo, Kevin and Nguni, Robert and Ojwang, James and Waters, Keith P and Richards, Janise} } @mastersthesis {1197, title = {Design and Development of a Web-Based Clinical Trial Management System}, year = {2014}, month = {05/2014}, school = {Graz University of Technology}, abstract = {Clinical trials represent a compulsory and labour-intensive part in the course of the approval process of new diagnostic or therapeutic measures. Trials are conducted by specialized staff at trial sites such as the Clinical Research Center (CRC), a dedicated facility for Phase I and II clinical trials of the Medical University of Graz. Clinical Trial Management System (CTMS) is a term for enterprise applications, which map the particular processes of trial sites. This work introduces the Phoenix CTMS, a tailored Java web application of medium size, which covers all major processes at the CRC. Its mutli-tiered architecture is based on a Spring/Hibernate/JSF technology stack. While a model-driven approach is used for backend layers, generated artefacts are avoided for the extensive Rich Internet Application (RIA) presentation layer, which utilizes a state-of-the-art JSF component suite. Elaborated user requirements are implemented in multiple modules and range from group-ware features such as web calendars, document management and creation up to complete Electronic Data Capture (EDC) capabilities with input form composition and scripting plus editors for ad-hoc queries, allowing to formulate subject eligibility criteria. Compliance with relevant regulations (Good Clinical Practice, Data Privacy Act) is considered by an exceptional number of data security measures, including: subject de-identification and application-level encryption of data at rest, audit trail and digital signatures, configurable user privileges and host-based access restriction. It is shown how this business-critical application was designed, implemeted and rolled out at the level of commercial software products, while keeping costs minimal. The Phoenix CTMS is realeased under LGPLv2.1, www.phoenixctms.org, ISBN 978-3-200-04054-0. Design and Development of a Web-Based Clinical Trial Management System (PDF Download Available). Available from: https://www.researchgate.net/publication/263412137_Design_and_Development_of_a_Web-Based_Clinical_Trial_Management_System [accessed Nov 05 2017].}, doi = {10.13140/2.1.4306.2723 }, url = {https://www.researchgate.net/publication/263412137_Design_and_Development_of_a_Web-Based_Clinical_Trial_Management_System}, author = {Krenn, Rene} } @article {1044, title = {The development of an application for data privacy by applying an audit repository based on IHE ATNA.}, journal = {Stud Health Technol Inform}, volume = {198}, year = {2014}, month = {2014}, pages = {219-25}, abstract = {

It is necessary to optimize workflows and communication between institutions involved in patients{\textquoteright} treatment to improve quality and efficiency of the German healthcare. To achieve these in the Metropolregion Rhein-Neckar, a personal, cross-institutional patient record (PEPA) is used. Given the immense sensitivity of health-related information saved in the PEPA, it is imperative to obey the data protection regulations in Germany. One important aspect is the logging of access to personal health data and all other safety-related events. For gathering audit information, the IHE profile ATNA can be used, because it provides a flexible and standardized infrastructure. There are already existing solutions for gathering the audit information based on ATNA. In this article one solution (OpenATNA) is evaluated, which uses the method of evaluation defined by Peter Baumgartner. In addition, a user interface for a privacy officer is necessary to support the examination of the audit information. Therefore, we will describe a method to develop an application in Liferay (an OpenSource enterprise portal project) which supports examinations on the gathered audit information.

}, keywords = {Computer Security, Confidentiality, Data Curation, Databases, Factual, electronic health records, Guideline Adherence, Guidelines as Topic, Information Storage and Retrieval, Internationality, Medical Audit, Medical Record Linkage, Software, Software Design}, issn = {0926-9630}, author = {Bresser, Laura and K{\"o}hler, Steffen and Schwaab, Christoph} } @inbook {1091, title = {Designing Sustainable Open Source Systems: The Cuban National Health Care Network and Portal (INFOMED)}, booktitle = {Grand Successes and Failures in IT. Public and Private Sectors}, series = {IFIP Advances in Information and Communication Technology}, volume = {402}, year = {2013}, pages = {451-466}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {Cuba, INFOMED, national health care systems, open source software, qualitative research methods, virtual infrastructures}, isbn = {978-3-642-38861-3}, doi = {10.1007/978-3-642-38862-0_28}, url = {http://dx.doi.org/10.1007/978-3-642-38862-0_28}, author = {S{\'e}ror, Ann}, editor = {Dwivedi, YogeshK. and Henriksen, HelleZinner and Wastell, David and De{\textquoteright}, Rahul} } @article {863, title = {DICOM RIS/PACS Telemedicine Network Implementation using Free Open Source Software}, journal = {Latin America Transactions, IEEE (Revista IEEE America Latina)}, volume = {11}, year = {2013}, pages = {168-171}, abstract = {The increasing incorporation of modern medical imaging equipment requires the operation of systems that store, transmit and display images, PACS (Picture Archiving and Communication System) via digital networks to provide health services with higher quality. These revolutionized radiology systems based on digital techniques, communications, visualization and information technologies. One of the major problems that arise in institutions working with Imaging Diagnosis (Dx) in the interconnection network or equipment, are the "bottlenecks" caused by the high flow of network data. This flux is given by the transfer of images in DICOM (Digital Imaging and Communications in Medicine) to the various devices that make up a DICOM network, called Service Class Users (SCU) and Service Class Providers (SCP). This paper describes the development and implementation of a network of medical images using free software and its compatibility with its own data network of a RIS (Radiology Information System). Describes techniques used for the interconnection of local nodes on a LAN (Local Area Network) remote WAN Wide Area Network) via Internet and WLAN (Wireless Area Network.}, keywords = {DICOM, Free Software, Medical Imaging, Telemedicine}, issn = {1548-0992}, doi = {10.1109/TLA.2013.6502797}, author = {Alvarez, Luis R. and Vargas Solis, Roberto} } @article {797, title = {Deformable three-dimensional model architecture for interactive augmented reality in minimally invasive surgery.}, journal = {Surg Endosc}, year = {2012}, month = {2012 Jun 27}, abstract = {BACKGROUND: Surgical procedures have undergone considerable advancement during the last few decades. More recently, the availability of some imaging methods intraoperatively has added a new dimension to minimally invasive techniques. Augmented reality in surgery has been a topic of intense interest and research. METHODS: Augmented reality involves usage of computer vision algorithms on video from endoscopic cameras or cameras mounted in the operating room to provide the surgeon additional information that he or she otherwise would have to recognize intuitively. One of the techniques combines a virtual preoperative model of the patient with the endoscope camera using natural or artificial landmarks to provide an augmented reality view in the operating room. The authors{\textquoteright} approach is to provide this with the least number of changes to the operating room. Software architecture is presented to provide interactive adjustment in the registration of a three-dimensional (3D) model and endoscope video. RESULTS: Augmented reality including adrenalectomy, ureteropelvic junction obstruction, and retrocaval ureter and pancreas was used to perform 12 surgeries. The general feedback from the surgeons has been very positive not only in terms of deciding the positions for inserting points but also in knowing the least change in anatomy. CONCLUSIONS: The approach involves providing a deformable 3D model architecture and its application to the operating room. A 3D model with a deformable structure is needed to show the shape change of soft tissue during the surgery. The software architecture to provide interactive adjustment in registration of the 3D model and endoscope video with adjustability of every 3D model is presented.}, issn = {1432-2218}, doi = {10.1007/s00464-012-2395-0}, author = {Vemuri, Anant S and Wu, Jungle Chi-Hsiang and Liu, Kai-Che and Wu, Hurng-Sheng} } @article {1049, title = {Designing and Implementing an Innovative SMS-based alert system (RapidSMS-MCH) to monitor pregnancy and reduce maternal and child deaths in Rwanda.}, journal = {Pan Afr Med J}, volume = {13}, year = {2012}, month = {2012}, pages = {31}, abstract = {

INTRODUCTION: With the continuous growth of mobile network coverage and unprecedented penetration of mobile devices in the developing world, several mHealth initiatives are being implemented in developing countries. This paper aims to describe requirements for designing and implementing a mobile phone-based communication system aiming at monitoring pregnancy and reducing bottlenecks in communication associated with maternal and newborn deaths; and document challenges and lessons learned.

METHODS: An SMS-based system was developed to improve maternal and child health (MCH) using RapidSMS({\textregistered}), a free and open-sourced software development framework. To achieve the expected results, the RapidSMS-MCH system was customized to allow interactive communication between a community health worker (CHW)following mother-infant pairs in their community, a national centralized database, the health facility and in case of an emergency alert, the ambulance driver. The RapidSMS-MCH system was piloted in Musanze district, Nothern province of Rwanda over a 12-month period.

RESULTS: A total of 432 CHW were trained and equipped with mobile phones. A total of 35,734 SMS were sent by 432 CHW from May 2010 to April 2011. A total of 11,502 pregnancies were monitored. A total of 362 SMS alerts for urgent and life threatening events were registered. We registered a 27\% increase in facility based delivery from 72\% twelve months before to 92\% at the end of the twelve months pilot phase. Major challenges were telephone maintenance and replacement. Disctrict heath team capacity to manage and supervise the system was strengthened by the end of pilot phase. Highly committed CHWs and effective coordination by the District health team were critical enablers.

CONCLUSION: We successully designed and implemented a mobile phone SMS-based system to track pregnancy and maternal and child outcomes in limited resources setting. Implementation of mobile-phone systems at community level could contribute to improving emergency obstetric and neonatal care, yet it requires a well-organized community health structure in limited resource settings.

}, keywords = {Cell Phones, Child Mortality, Child, Preschool, Emergency Medical Services, Female, Fetal Death, Health Plan Implementation, Humans, Infant, Newborn, Maternal Death, Maternal Health Services, Maternal-Child Health Centers, Monitoring, Physiologic, Pregnancy, Prenatal Care, Program Development, Rwanda, Telemedicine}, issn = {1937-8688}, author = {Ngabo, Fidele and Nguimfack, Judith and Nwaigwe, Friday and Mugeni, Catherine and Muhoza, Denis and Wilson, David R and Kalach, John and Gakuba, Richard and Karema, Corrine and Binagwaho, Agnes} } @article {816, title = {Developing open source, self-contained disease surveillance software applications for use in resource-limited settings.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {99}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness. METHODS: As components of its Suite for Automated Global bioSurveillance (SAGES) program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies. RESULTS: ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system. CONCLUSIONS: OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-99}, author = {Campbell, Timothy C and Hodanics, Charles J and Babin, Steven M and Poku, Adjoa M and Wojcik, Richard A and Skora, Joseph F and Coberly, Jacqueline S and Mistry, Zarna S and Lewis, Sheri H} } @inbook {792, title = {Development of a Laparoscopic Surgical Training System with Simulation Open Framework Architecture (SOFA)}, booktitle = {Computer Aided Surgery}, series = {Proceedings in Information and Communications Technology}, volume = {3}, year = {2012}, pages = {83-91}, publisher = {Springer Japan}, organization = {Springer Japan}, abstract = {With a number of advantages over traditional laparotomy, laparoscopic surgery is a successful minimally invasive surgical procedure. However, laparoscopy demands high surgical skill. For efficient and safe training, virtual surgery simulation systems have been developed recently. In this paper, we describe the development of a laparoscopic surgery training system using Simulation Open Framework Architecture (SOFA). The simulation software was integrated with a two-hand haptic device specially developed for laparoscopic surgical training. As an example, we focused on the simulation of gallbladder removal surgery using laparoscopic instruments. Gallbladder removal was successfully simulated by the proposed methods. We expect this training system to be similarly successful in simulating a number of other surgical procedures.}, isbn = {978-4-431-54094-6}, url = {http://dx.doi.org/10.1007/978-4-431-54094-6_10}, author = {Kim, Youngjun and Kim, Kyunghwan and Roy, Fr{\'e}d{\'e}rick and Park, Sehyung}, editor = {Dohi, Takeyoshi and Liao, Hongen} } @article {804, title = {Development of a Next-Generation Automated DICOM Processing System in a PACS-Less Research Environment.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 May 1}, abstract = {The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve{\textregistered}, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8~months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9482-6}, author = {Ziegler, Scott E} } @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} } @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} } @article {784, title = {DicomBrowser: Software for Viewing and Modifying DICOM Metadata.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Feb 15}, abstract = {Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at http://nrg.wustl.edu/software/dicom-browser .}, issn = {1618-727X}, doi = {10.1007/s10278-012-9462-x}, author = {Archie, Kevin A and Marcus, Daniel S} } @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 {Ferranti23092011, title = {The design and implementation of an open-source, data-driven cohort recruitment system: the Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN)}, journal = {Journal of the American Medical Informatics Association}, year = {2011}, abstract = {Objective Failure to reach research subject recruitment goals is a significant impediment to the success of many clinical trials. Implementation of health-information technology has allowed retrospective analysis of data for cohort identification and recruitment, but few institutions have also leveraged real-time streams to support such activities.Design Duke Medicine has deployed a hybrid solution, The Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN), that combines both retrospective warehouse data and clinical events contained in prospective Health Level 7 (HL7) messages to immediately alert study personnel of potential recruits as they become eligible.Results DISCERN analyzes more than 500{\quotesinglbase}{\"A}{\`a}000 messages daily in service of 12 projects. Users may receive results via email, text pages, or on-demand reports. Preliminary results suggest DISCERN{\textquoteright}s unique ability to reason over both retrospective and real-time data increases study enrollment rates while reducing the time required to complete recruitment-related tasks. The authors have introduced a preconfigured DISCERN function as a self-service feature for users.Limitations The DISCERN framework is adoptable primarily by organizations using both HL7 message streams and a data warehouse. More efficient recruitment may exacerbate competition for research subjects, and investigators uncomfortable with new technology may find themselves at a competitive disadvantage in recruitment.Conclusion DISCERN{\textquoteright}s hybrid framework for identifying real-time clinical events housed in HL7 messages complements the traditional approach of using retrospective warehoused data. DISCERN is helpful in instances when the required clinical data may not be loaded into the warehouse and thus must be captured contemporaneously during patient care. Use of an open-source tool supports generalizability to other institutions at minimal cost.}, doi = {10.1136/amiajnl-2011-000115}, url = {http://jamia.bmj.com/content/early/2011/09/23/amiajnl-2011-000115.abstract}, author = {Ferranti, Jeffrey M and Gilbert, William and McCall, Jonathan and Shang, Howard and Barros, Tanya and Horvath, Monica M} } @article {660, title = {Dicoogle - an Open Source Peer-to-Peer PACS.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Oct}, pages = {848-56}, abstract = {Picture Archiving and Communication Systems (PACS) have been widely deployed in healthcare institutions, and they now constitute a normal commodity for practitioners. However, its installation, maintenance, and utilization are still a burden due to their heavy structures, typically supported by centralized computational solutions. In this paper, we present Dicoogle, a PACS archive supported by a document-based indexing system and by peer-to-peer (P2P) protocols. Replacing the traditional database storage (RDBMS) by a documental organization permits gathering and indexing data from file-based repositories, which allows searching the archive through free text queries. As a direct result of this strategy, more information can be extracted from medical imaging repositories, which clearly increases flexibility when compared with current query and retrieval DICOM services. The inclusion of P2P features allows PACS internetworking without the need for a central management framework. Moreover, Dicoogle is easy to install, manage, and use, and it maintains full interoperability with standard DICOM services.}, issn = {1618-727X}, doi = {10.1007/s10278-010-9347-9}, author = {Costa, Carlos and Ferreira, Carlos and Basti{\~a}o, Lu{\'\i}s and Ribeiro, Lu{\'\i}s and Silva, Augusto and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {1746-1596-6-S1-S16, title = {Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images}, journal = {Diagnostic Pathology}, volume = {6}, number = {Suppl 1}, year = {2011}, pages = {S16}, abstract = {BACKGROUND:Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.METHODS:We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.RESULTS:Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.CONCLUSIONS:Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.}, issn = {1746-1596}, doi = {10.1186/1746-1596-6-S1-S16}, url = {http://www.diagnosticpathology.org/content/6/S1/S16}, author = {Zerbe, Norman and Hufnagl, Peter and Schluns, Karsten} } @article {20335647, title = {The development and design of an electronic patient record using open source web-based technology.}, journal = {The HIM journal}, volume = {39}, year = {2010}, month = {2010}, pages = {30-5}, abstract = {This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour.}, author = {Syed-Mohamad, Sharifa Mastura and Ali, Siti Hawa and Mat-Husin, Mohd Nazri} } @article {19352444, title = {DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.}, journal = {Frontiers in neuroinformatics}, volume = {3}, year = {2009}, month = {2009}, pages = {9}, abstract = {Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK{\textquoteright}s low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user{\textquoteright}s operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.}, author = {Gouws, Andr{\'e} and Woods, Will and Millman, Rebecca and Morland, Antony and Green, Gary} } @article {19230726, title = {Demonstration of the Adamkiewicz artery by multidetector computed tomography angiography analysed with the open-source software OsiriX.}, journal = {European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {395-400}, abstract = {OBJECTIVE: To evaluate the feasibility of the Adamkiewicz artery (AKA) detection by multidetector computed tomography (CT) data analysis without the need of a dedicated workstation, using low-cost hardware and the freeware OsiriX. METHODS: CT scans of 67 patients undergoing a thoracic or thoraco-abdominal aortic procedure between April 2006 and August 2008 were evaluated with respect to detection rate and AKA level and side using the OsiriX software version 3.2 on Mac OS X computer and compared to results obtained by standard workstation analysis, in a fully blinded analysis. The results were also compared with data compiled from a review of the English-language literature on this topic. RESULTS: (1) AKA identification showed a substantial agreement of 85.07\% between the methods (k=0.636). (2) The comparison of AKA level showed a substantial agreement (weighted k=0.661), with consensus in 70.14\%. (3) From the literature review, we found that recognition of the AKA was achieved in 466 of 555 cases (83.96\%). (4) In 384 (83.3\%) cases the AKA originated from a left intercostal artery. (5) The proposed method and literature-compiled data showed a similar AKA level distribution. CONCLUSIONS: Noninvasive AKA location with open-source software and low-cost hardware is feasible. The OsiriX software allows to effectively navigate through CT data not only to study the aorta, but also to detect the AKA, as in the case of the standard method and the literature data. Its availability and ease of use may contribute to make identification of the AKA part of the routine evaluation of CT scans in patients with aortic disease, even where dedicated workstations are not available, with potential benefits for planning therapeutic procedures.}, author = {Melissano, G and Bertoglio, L and Civelli, V and Amato, A C Moraes and Coppi, G and Civilini, E and Calori, G and De Cobelli, F and Del Maschio, A and Chiesa, R} } @article {19056288, title = {Dimensional error of selective laser sintering, three-dimensional printing and PolyJet models in the reproduction of mandibular anatomy.}, journal = {Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {167-73}, abstract = {BACKGROUND: Selective laser sintering (SLS), three-dimensional printing (3DP) and PolyJet are rapid prototyping (RP) techniques to fabricate prototypes from virtual biomedical images. To be used in maxillofacial surgery, these models must accurately reproduce the craniofacial skeleton. PURPOSE: To analyze the capacity of SLS, 3DP and PolyJet models to reproduce mandibular anatomy and their dimensional error. MATERIAL: Dry mandible, helical CT images, SLS, 3DP and PolyJet prototypes, and digital electronic caliper. METHODS: Helical CT images were acquired from a dry mandible (criterion standard) and manipulated with the InVesalius software. Prototypes were produced using SLS, 3DP and PolyJet techniques. Thirteen linear measurements of each prototype were made and compared with the dry mandible measurements. RESULTS: The results showed a dimensional error of 1.79\%, 3.14\% and 2.14\% for SLS, 3DP and PolyJet models, respectively. The models satisfactorily reproduced anatomic details and the SLS and PolyJet prototypes showed greater dimensional precision and reproduced mandibular anatomy more accurately than the 3DP model. CONCLUSIONS: The SLS prototype had a greater dimensional accuracy than the PolyJet and 3DP models. The PolyJet technique reproduced anatomic details of the mandible more accurately.}, author = {Ibrahim, Danilo and Broilo, Tiago Leonardo and Heitz, Claiton and Gerhardt de Oliveira, Mar{\'\i}lia and de Oliveira, Helena Willhelm and Nobre, Stella Maris Wanderlei and Dos Santos Filho, Jos{\'e} Henrique Gomes and Silva, Daniela Nascimento} } @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 {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} }