@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 {1219, title = {Open Source HMIS Enabled Evaluation of Financial Burden of Disease and Patient Coverage in Three University Hospitals in Great Lakes Africa.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {969-973}, abstract = {

Since the eighties, case mix evaluation methods based on diagnosis-related groups (DRG) were gradually introduced in developed countries. These methods of assessing the costs of diseases to measure the productivity of the hospital have been introduced in management softwares that are not accessible to low-income countries. In this study, the authors applied these methods to an open source hospital management information system (HMIS) implemented in three university hospitals in Great Lakes Africa. A comparative study of the financial burden of five major diseases, monitored as part of a universal health coverage (UHC) analysis, was carried out. The level of coverage of patients in the hospitals was evaluated and the impact of UHC policies demonstrated. Although the financial protection of patients treated in the three hospitals had improved, HIV and tuberculosis treatments that ought to be free, remained a considerable financial burden for the patient.

}, issn = {1879-8365}, doi = {10.3233/SHTI190368}, author = {Karara, Gustave and Verbeke, Frank and Byiringiro, Jean-Claude and Nziza, Franck and Buyl, Ronald and Nyssen, Marc} } @article {1217, title = {STEM: An Open Source Tool for Disease Modeling.}, journal = {Health Secur}, volume = {17}, year = {2019}, month = {2019 Jul/Aug}, pages = {291-306}, abstract = {

The Spatiotemporal Epidemiologic Modeler (STEM) is an open source software project supported by the Eclipse Foundation and used by a global community of researchers and public health officials working to track and, when possible, control outbreaks of infectious disease in human and animal populations. STEM is not a model or a tool designed for a specific disease; it is a flexible, modular framework supporting exchange and integration of community models, reusable plug-in components, and denominator data, available to researchers worldwide at www.eclipse.org/stem. A review of multiple projects illustrates its capabilities. STEM has been used to study variations in transmission of seasonal influenza in Israel by strains; evaluate social distancing measures taken to curb the H1N1 epidemic in Mexico City; study measles outbreaks in part of London and inform local policy on immunization; and gain insights into H7N9 avian influenza transmission in China. A multistrain dengue fever model explored the roles of the mosquito vector, cross-strain immunity, and antibody response in the frequency of dengue outbreaks. STEM has also been used to study the impact of variations in climate on malaria incidence. During the Ebola epidemic, a weekly conference call supported the global modeling community; subsequent work modeled the impact of behavioral change and tested disease reintroduction via animal reservoirs. Work in Germany tracked salmonella in pork from farm to fork; and a recent doctoral dissertation used the air travel feature to compare the potential threats posed by weaponizing infectious diseases. Current projects include work in Great Britain to evaluate control strategies for parasitic disease in sheep, and in Germany and Hungary, to validate the model and inform policy decisions for African swine fever. STEM Version 4.0.0, released in early 2019, includes tools used in these projects and updates technical aspects of the framework to ease its use and re-use.

}, issn = {2326-5108}, doi = {10.1089/hs.2019.0018}, author = {Douglas, Judith V and Bianco, Simone and Edlund, Stefan and Engelhardt, Tekla and Filter, Matthias and G{\"u}nther, Taras and Hu, Kun Maggie and Nixon, Emily J and Sevilla, Nereyda L and Swaid, Ahmad and Kaufman, James H} } @article {1290, title = {mLearning in the Democratic Republic of the Congo: A Mixed-Methods Feasibility and Pilot Cluster Randomized Trial Using the Safe Delivery App.}, journal = {Glob Health Sci Pract}, volume = {6}, year = {2018}, month = {2018 12 27}, pages = {693-710}, abstract = {

BACKGROUND: Substandard delivery care has been widely documented as a major cause of maternal mortality in health facilities globally. Health worker learning via mobile devices is increasing rapidly; however, there is little evidence of mLearning effectiveness. This study sought to determine the feasibility, acceptability, and potential effect of the Safe Delivery App (SDA) on health workers{\textquoteright} practices in basic emergency obstetric and newborn care (BEmONC) in the Democratic Republic of the Congo (DRC). The Theoretical Domains Framework was used to guide this research.

METHODS: Eight BEmONC facilities in central DRC were randomized to either an mLearning intervention or to standard practice (control). Maternal and newborn health workers in intervention facilities (n=64) were trained on the use of smartphones and the French version of the SDA. The SDA is an evidence-based BEmONC training resource with visual guidance using animated videos and clinical management instructions developed by the Maternity Foundation and the Universities of Copenhagen and Southern Denmark. Knowledge on postpartum hemorrhage (PPH) and neonatal resuscitation (NR) and self-confidence in performing 12 BEmONC procedures were assessed at baseline and at 3 months post-intervention. Eighteen qualitative interviews were conducted with app users and key stakeholders to assess feasibility and acceptability of mLearning and the use of the SDA. Maternal mortality was compared in intervention and control facilities using a smartphone-based Open Data Kit (ODK) data application. One smartphone with SDA and ODK was entrusted to intervention facilities for the study period, whereas control facilities received smartphones with ODK only.

RESULTS: The analysis included 62 heath workers. Knowledge scores on postpartum hemorrhage and neonatal resuscitation increased significantly from baseline among intervention participants compared with controls at 3 months post-intervention (mean difference for PPH knowledge, 17.4 out of 100; 95\% confidence interval [CI]=10.7 to 24.0 and 19.4 for NR knowledge; 95\% CI=11.4 to 27.4), as did self-confidence scores on 12 essential BEmONC procedures (mean difference, 4.2 out of 48; CI=0.7 to 7.7). Increases were unaffected by health worker cadre and previous smartphone use. Qualitative interviews supported the feasibility and acceptability of the SDA and mLearning, and the potential for it to impact maternal and neonatal mortality in the DRC.

CONCLUSION: Use of the Safe Delivery App supported increased health worker knowledge and self-confidence in the management of obstetric and newborn emergencies after 3 months. SDA and mLearning were found to be feasible and acceptable to health workers and key stakeholders in the DRC.

}, keywords = {Congo, Feasibility Studies, Female, Humans, Infant Care, Infant, Newborn, Interviews as Topic, Male, Maternal Mortality, Mobile Applications, Obstetrics, Pilot Projects, qualitative research, Quality of Health Care}, issn = {2169-575X}, doi = {10.9745/GHSP-D-18-00275}, author = {Bolan, Nancy E and Sthreshley, Larry and Ngoy, Bernard and Ledy, Faustin and Ntayingi, Mano and Makasy, Davis and Mbuyi, Marie-Claude and Lowa, Gisele and Nemeth, Lynne and Newman, Susan} } @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 {1206, title = {Health care consumer{\textquoteright}s perception of the {Electronic} {Medical} {Record} ({EMR}) system within a referral hospital in {Kigali}, {Rwanda}}, journal = {Rwanda Journal}, volume = {4}, year = {2017}, pages = {48{\textendash}53{\textendash}53}, abstract = {Background: Worldwide Electronic Medical Records (EMR) when compared to a paper-based system has been proven to improve service delivering numerous health care facilities. However, no research has been described in the literature regarding the user{\textquoteright}s perception of the clinical electronic medical record (EMR) system in Rwanda. The objective of this study is to evaluate the health care consumer{\textquoteright}s perception of the Electronic Medical Record (EMR) OpenClinic regarding improving the quality of health care delivery within the hospital setting. How does the OpenClinic system affect the patients{\textquoteright} waiting time? How complete is the information obtained from OpenClinic as compared to paper medical records, and the level of satisfaction of the users of OpenClinic.Method: A structured questionnaire was developed, validated and utilized in this quantitative research project. Quantitative data were collected from 170 participants while an interview guide was used to collect qualitative data from 6 key informants at a referral hospital in Kigali. The SPSS version 20.0 was used to analyze the quantitative data. The interviews transcribed verbatim; the data were thematically analyzed and categorized by pre-determined themes. Permission to conduct the study was approved from the ethics committee of the University of Rwanda, College of Health Sciences and the hospital.Results: The majority of the participants were satisfied with OpenClinic, (90\%), while only a few (10\%) did not perceive any advantage of a computer-based EMR and preferred paper based records.Conclusion: Openclinc EMR was seen to be an improvement in the data collection involving health care delivery in Kigali, Rwanda.Keywords: Electronic Medical Records, OpenClinic and Perceptions}, keywords = {Electronic medical records, OpenClinic and Perceptions}, issn = {2305-2678}, doi = {10.4314/rj.v4i1.7F}, url = {https://www.ajol.info/index.php/rj/article/view/156412}, author = {Uwambaye, Peace and Njunwa, Kato and Nuhu, Assouman and Kumurenzi, Anne and Isyagi, Moses and Murererehe, Julienne and Ngarambe, Donart} } @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 {1189, title = {Orchestrating differential data access for translational research: a pilot implementation}, journal = {BMC Medical Informatics and Decision Making}, volume = {17}, year = {2017}, month = {2017}, pages = {30}, abstract = {BACKGROUND: Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data. METHODS: In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements. RESULTS: Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility. CONCLUSIONS: Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.}, isbn = {1472-6947}, doi = {10.1186/s12911-017-0424-6}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363029/}, author = {Brandizi, Marco and Melnichuk, Olga and Bild, Raffael and Kohlmayer, Florian and Rodriguez-Castro, Benedicto and Spengler, Helmut and Kuhn, Klaus A and Kuchinke, Wolfgang and Ohmann, Christian and Mustonen, Timo and Linden, Mikael and Nyr{\"o}nen, Tommi and Lappalainen, Ilkka and Brazma, Alvis and Sarkans, Ugis} } @article {1134, title = {Assessment of four common underfive children illnesses Routine Health Management Information System data for decision making at Ilemela Municipal Council, Northwest Tanzania: A case series analysis.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {85-91}, abstract = {

BACKGROUND: In 2012, The Tanzania Ministry Of Health introduced the revised Routine Health Management Information System (RHMIS) modules and registers, and introduced the open source software for data collection at the district council level. Despite a series of data collection tools revisions, the quality of data collated from both public and private primary health care facilities has not been investigated.

METHODS: A case series study design was conducted on underfive children outpatient registers and monthly reports on malaria, acute respiratory infections, acute diarrhoea and pneumonia from 10 randomly selected health facilities. The data was entered into excel software and exported to stata version 11 for analysis. The data was analyzed for completeness, timely report submission and reporting accuracy.

RESULTS: The Study found that 62\% of the expected data was complete. Around 40\% of the facilities submitted reports on time. Private health facilities submitted monthly reports late compared to the public facilities (p-value=0.039). There was 26\% over-reporting of diagnosis. Health centres tended to over-report more diagnoses by 11 times higher than the dispensaries. In addition, private owned health facilities tended to over-report more diagnoses by 6 times higher than public owned health facilities.

CONCLUSION: The RHMIS data collected through out patients department (OPD) registers on four common underfive children{\textquoteright}s illnesses at ilemela municipality were of unsatisfactory quality in light of allocation of resource allocations in the comprehensive council health plan.

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.003}, author = {Kabakama, Severin and Ngallaba, Sospatro and Musto, Richard and Montesanti, Stephanie and Konje, Eveline and Kishamawe, Coleman} } @inbook {1119, title = {BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets}, booktitle = {Biomedical Data Management and Graph Online Querying: VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 {\textendash} September 4, 2015, Revised Selected Papers}, year = {2016}, pages = {89{\textendash}105}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.}, isbn = {978-3-319-41576-5}, doi = {10.1007/978-3-319-41576-5_7}, url = {http://dx.doi.org/10.1007/978-3-319-41576-5_7}, author = {Bessani, Alysson and Brandt, J{\"o}rgen and Bux, Marc and Cogo, Vinicius and Dimitrova, Lora and Dowling, Jim and Gholami, Ali and Hakimzadeh, Kamal and Hummel, Micheal and Ismail, Mahmoud and Laure, Erwin and Leser, Ulf and Litton, Jan-Eric and Martinez, Roxanna and Niazi, Salman and Reichel, Jane and Zimmermann, Karin}, editor = {Wang, Fusheng and Luo, Gang and Weng, Chunhua and Khan, Arijit and Mitra, Prasenjit and Yu, Cong} } @article {1106, title = {Health figures: an open source JavaScript library for health data visualization.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {38}, abstract = {

BACKGROUND: The way we look at data has a great impact on how we can understand it, particularly when the data is related to health and wellness. Due to the increased use of self-tracking devices and the ongoing shift towards preventive medicine, better understanding of our health data is an important part of improving the general welfare of the citizens. Electronic Health Records, self-tracking devices and mobile applications provide a rich variety of data but it often becomes difficult to understand. We implemented the hFigures library inspired on the hGraph visualization with additional improvements. The purpose of the library is to provide a visual representation of the evolution of health measurements in a complete and useful manner.

RESULTS: We researched the usefulness and usability of the library by building an application for health data visualization in a health coaching program. We performed a user evaluation with Heuristic Evaluation, Controlled User Testing and Usability Questionnaires. In the Heuristics Evaluation the average response was 6.3 out of 7 points and the Cognitive Walkthrough done by usability experts indicated no design or mismatch errors. In the CSUQ usability test the system obtained an average score of 6.13 out of 7, and in the ASQ usability test the overall satisfaction score was 6.64 out of 7.

CONCLUSIONS: We developed hFigures, an open source library for visualizing a complete, accurate and normalized graphical representation of health data. The idea is based on the concept of the hGraph but it provides additional key features, including a comparison of multiple health measurements over time. We conducted a usability evaluation of the library as a key component of an application for health and wellness monitoring. The results indicate that the data visualization library was helpful in assisting users in understanding health data and its evolution over time.

}, keywords = {Data visualization, Health data, Health informatics, Javascript}, issn = {1472-6947}, doi = {10.1186/s12911-016-0275-6}, author = {Ledesma, Andres and Al-Musawi, Mohammed and Nieminen, Hannu} } @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 {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 {1124, title = {Open-source LIMS in Vietnam: The path toward sustainability and host country ownership.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {92-102}, abstract = {

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

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

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

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

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.010}, author = {Landgraf, Kenneth M and Kakkar, Reshma and Meigs, Michelle and Jankauskas, Paul T and Phan, Thi Thu Huong and Nguyen, Viet Nga and Nguyen, Duy Thai and Duong, Thanh Tung and Nguyen, Thi Hoa and Bond, Kyle B} } @article {1122, title = {PACS for Bhutan: a cost effective open source architecture for emerging countries.}, journal = {Insights Imaging}, year = {2016}, month = {2016 Jul 28}, abstract = {

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three~days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer.

MESSAGES/TEACHING POINTS: {\textbullet} Open source imaging informatics platforms can provide cost-effective alternatives for PACS {\textbullet} Robust and cost-effective open architecture can provide adequate solutions for emerging countries {\textbullet} Imaging informatics is often lacking in hospitals equipped with digital modalities.

}, issn = {1869-4101}, doi = {10.1007/s13244-016-0512-7}, author = {Ratib, Osman and Roduit, Nicolas and Nidup, Dechen and De Geer, Gerard and Rosset, Antoine and Geissbuhler, Antoine} } @article {992, title = {A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Sep 2}, abstract = {

OBJECTIVE: Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management.

MATERIALS AND METHODS: An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software.

RESULTS: Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool{\textquoteright}s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security.

DISCUSSION: By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use.

CONCLUSION: The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool{\textquoteright}s open source, cloud model for health data interoperability is applicable to other healthcare use cases.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv104}, author = {Neinstein, Aaron and Wong, Jenise and Look, Howard and Arbiter, Brandon and Quirk, Kent and McCanne, Steve and Sun, Yao and Blum, Michael and Adi, Saleh} } @article {1190, title = {caTissue Suite to OpenSpecimen: developing an extensible, open source, web-based biobanking management system}, journal = {Journal of biomedical informatics}, volume = {57}, year = {2015}, month = {2015/10/}, pages = {456 - 464}, abstract = {The National Cancer Institute (NCI) Cancer Biomedical Informatics Grid({\textregistered}) (caBIG({\textregistered})) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions.}, isbn = {1532-04641532-0480}, doi = {10.1016/j.jbi.2015.08.020}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772150/}, author = {McIntosh, Leslie D and Sharma, Mukesh K and Mulvihill, David and Gupta, Snehil and Juehne, Anthony and George, Bijoy and Khot, Suhas B and Kaushal, Atul and Watson, Mark A and Nagarajan, Rakesh} } @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} } @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 {972, title = {MzJava: An open source library for mass spectrometry data processing.}, journal = {J Proteomics}, year = {2015}, month = {2015 Jun 30}, abstract = {

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library{\textquoteright}s API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava.

}, issn = {1876-7737}, doi = {10.1016/j.jprot.2015.06.013}, author = {Horlacher, Oliver and Nikitin, Frederic and Alocci, Davide and Mariethoz, Julien and M{\"u}ller, Markus and Lisacek, Frederique} } @article {1065, title = {OpenFDA: an innovative platform providing access to a wealth of FDA{\textquoteright}s publicly available data.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Dec 7}, abstract = {

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

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

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

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

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv153}, author = {Kass-Hout, Taha A and Xu, Zhiheng and Mohebbi, Matthew and Nelsen, Hans and Baker, Adam and Levine, Jonathan and Johanson, Elaine and Bright, Roselie A} } @article {995, title = {OpenHELP (Heidelberg laparoscopy phantom): development of an open-source surgical evaluation and training tool.}, journal = {Surg Endosc}, year = {2015}, month = {2015 Feb 12}, abstract = {

BACKGROUND: Apart from animal testing and clinical trials, surgical research and laparoscopic training mainly rely on phantoms. The aim of this project was to design a phantom with realistic anatomy and haptic characteristics, modular design and easy reproducibility. The phantom was named open-source Heidelberg laparoscopic phantom (OpenHELP) and serves as an open-source platform.

METHODS: The phantom was based on an anonymized CT scan of a male patient. The anatomical structures were segmented to obtain digital three-dimensional models of the torso and the organs. The digital models were materialized via rapid prototyping. One flexible, using an elastic abdominal wall, and one rigid method, using a plastic shell, to simulate pneumoperitoneum were developed. Artificial organ production was carried out sequentially starting from raw gypsum models to silicone molds to final silicone casts. The reproduction accuracy was exemplarily evaluated for ten silicone rectum models by comparing the digital 3D surface of the original rectum with CT scan by calculating the root mean square error of surface variations. Haptic realism was also evaluated to find the most realistic silicone compositions on a visual analog scale (VAS, 0-10).

RESULTS: The rigid and durable plastic torso and soft silicone organs of the abdominal cavity were successfully produced. A simulation of pneumoperitoneum could be created successfully by both methods. The reproduction accuracy of ten silicone rectum models showed an average root mean square error of 2.26 (0-11.48) mm. Haptic realism revealed an average value on a VAS of 7.25 (5.2-9.6) for the most realistic rectum.

CONCLUSION: The OpenHELP phantom proved to be feasible and accurate. The phantom was consecutively applied frequently in the field of computer-assisted surgery at our institutions and is accessible as an open-source project at www.open-cas.org for the academic community.

}, issn = {1432-2218}, doi = {10.1007/s00464-015-4094-0}, author = {Kenngott, H G and W{\"u}nscher, J J and Wagner, M and Preukschas, A and Wekerle, A L and Neher, P and Suwelack, S and Speidel, S and Nickel, F and Oladokun, D and Maier-Hein, L and Dillmann, R and Meinzer, H P and M{\"u}ller-Stich, B P} } @article {1045, title = {The Role of Hospital Information Systems in Universal Health Coverage Monitoring in Rwanda.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {193-7}, abstract = {

In this retrospective study, the authors monitored the patient health coverage in 6 Rwandan hospitals in the period between 2011 and 2014. Among the 6 hospitals, 2 are third level hospitals, 2 district hospitals and 2 private hospitals. Patient insurance and financial data were extracted and analyzed from OpenClinic GA, an open source hospital information system (HIS) used in those 6 hospitals. The percentage of patients who had no health insurer globally decreased from 35\% in 2011 to 15\% in 2014. The rate of health insurance coverage in hospitals varied between 75\% in private hospitals and 84\% in public hospitals. The amounts paid by the patients for health services decreased in private hospitals to 25\% of the total costs in 2014 (-7.4\%) and vary between 14\% and 19\% in public hospitals. Although the number of insured patients has increased and the patient share decreased over the four years of study, the patients{\textquoteright} out-of-pocket payments increased especially for in-patients. This study emphasizes the value of integrated hospital information systems for this kind of health economics research in developing countries.

}, issn = {0926-9630}, author = {Karara, Gustave and Verbeke, Frank and Nyssen, Marc} } @article {999, title = {Role of OpenEHR as an open source solution for the regional modelling of patient data in obstetrics.}, journal = {J Biomed Inform}, volume = {55}, year = {2015}, month = {2015 Jun}, pages = {174-87}, abstract = {

This work investigates, whether openEHR with its reference model, archetypes and templates is suitable for the digital representation of demographic as well as clinical data. Moreover, it elaborates openEHR as a tool for modelling Hospital Information Systems on a regional level based on a national logical infrastructure. OpenEHR is a dual model approach developed for the modelling of Hospital Information Systems enabling semantic interoperability. A holistic solution to this represents the use of dual model based Electronic Healthcare Record systems. Modelling data in the field of obstetrics is a challenge, since different regions demand locally specific information for the process of treatment. Smaller health units in developing countries like Brazil or Malaysia, which until recently handled automatable processes like the storage of sensitive patient data in paper form, start organizational reconstruction processes. This archetype proof-of-concept investigation has tried out some elements of the openEHR methodology in cooperation with a health unit in Colombo, Brazil. Two legal forms provided by the Brazilian Ministry of Health have been analyzed and classified into demographic and clinical data. LinkEHR-Ed editor was used to read, edit and create archetypes. Results show that 33 clinical and demographic concepts, which are necessary to cover data demanded by the Unified National Health System, were identified. Out of the concepts 61\% were reused and 39\% modified to cover domain requirements. The detailed process of reuse, modification and creation of archetypes is shown. We conclude that, although a major part of demographic and clinical patient data were already represented by existing archetypes, a significant part required major modifications. In this study openEHR proved to be a highly suitable tool in the modelling of complex health data. In combination with LinkEHR-Ed software it offers user-friendly and highly applicable tools, although the complexity built by the vast specifications requires expert networks to define generally excepted clinical models. Finally, this project has pointed out main benefits enclosing high coverage of obstetrics data on the Clinical Knowledge Manager, simple modelling, and wide network and support using openEHR. Moreover, barriers described are enclosing the allocation of clinical content to respective archetypes, as well as stagnant adaption of changes on the Clinical Knowledge Manager leading to redundant efforts in data contribution that need to be addressed in future works.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2015.04.004}, author = {Pahl, Christina and Zare, Mojtaba and Nilashi, Mehrbakhsh and de Faria Borges, Marco Aur{\'e}lio and Weingaertner, Daniel and Detschew, Vesselin and Supriyanto, Eko and Ibrahim, Othman} } @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 {1025, title = {Experience of using an open source clinical trials data management software system in Kenya.}, journal = {BMC Res Notes}, volume = {7}, year = {2014}, month = {2014}, pages = {845}, abstract = {

BACKGROUND: Clinical trials data management (CTDM) remains one of the many challenges in running state of the art trials in resource-poor settings since most trials do not allocate, or have available, sufficient resources for CTDM and because of poor internet connectivity. Open-source software like OpenClinica could be a solution in such scenarios.

FINDINGS: In 2007, the KEMRI-Wellcome Trust Research Programme (KWTRP) adopted OpenClinica (OC) community edition, an open-source software system and we share our experience and lessons learnt since its adoption. We have used OC in three different modes; direct remote data entry from sites through Global System for Mobile Communications (GSM) modems, a centralized data centre approach where all data from paper records were entered at a central location and an off-line approach where data entry was done from a copy of database hosted on a field-site server laptop, then data uploaded to a centralized server later. We have used OC in eleven trials/studies with a cumulative number of participants in excess of 6000. These include large and complex trials, with multiple sites recruiting in different regions of East Africa. In the process, we have developed substantial local capacity through hands-on training and mentorship, which we have now begun to share with other institutions in the region.

CONCLUSIONS: Our experience demonstrates that an open source data management system to manage trials{\textquoteright} data can be utilized to international industry standards in resource-poor countries.

}, issn = {1756-0500}, doi = {10.1186/1756-0500-7-845}, author = {Ngari, Moses M and Waithira, Naomi and Chilengi, Roma and Njuguna, Patricia and Lang, Trudie and Fegan, Greg} } @article {1033, title = {Making cytological diagnoses on digital images using the iPath network.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {453-60}, abstract = {

BACKGROUND: The iPath telemedicine platform Basel is mainly used for histological and cytological consultations, but also serves as a valuable learning tool.

AIM: To study the level of accuracy in making diagnoses based on still images achieved by experienced cytopathologists, to identify limiting factors, and to provide a cytological image series as a learning set.

METHOD: Images from 167 consecutive cytological specimens of different origin were uploaded on the iPath platform and evaluated by four cytopathologists. Only wet-fixed and well-stained specimens were used. The consultants made specific diagnoses and categorized each as benign, suspicious or malignant.

RESULTS: For all consultants, specificity and sensitivity regarding categorized diagnoses were 83-92 and 85-93\%, respectively; the overall accuracy was 88-90\%. The interobserver agreement was substantial (κ = 0.791). The lowest rate of concordance was achieved in urine and bladder washings and in the identification of benign lesions.

CONCLUSION: Using a digital image set for diagnostic purposes implies that even under optimal conditions the accuracy rate will not exceed to 80-90\%, mainly because of lacking supportive immunocytochemical or molecular tests. This limitation does not disqualify digital images for teleconsulting or as a learning aid. The series of images used for the study are open to the public at http://pathorama.wordpress.com/extragenital-cytology-2013/.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Computers, Handheld, Cytodiagnosis, Diagnosis, Differential, Female, Humans, Hyperplasia, Infant, Male, Metaplasia, Middle Aged, Neoplasms, Observer Variation, Reproducibility of Results, Sensitivity and Specificity, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000369241}, author = {Dalquen, Peter and Savic Prince, Spasenija and Spieler, Peter and Kunze, Dietmar and Neumann, Heinrich and Eppenberger-Castori, Serenella and Adams, Heiner and Glatz, Katharina and Bubendorf, Lukas} } @article {865, title = {GBM volumetry using the 3D Slicer medical image computing platform.}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {1364}, abstract = {

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

}, issn = {2045-2322}, doi = {10.1038/srep01364}, author = {Egger, Jan and Kapur, Tina and Fedorov, Andriy and Pieper, Steve and Miller, James V and Veeraraghavan, Harini and Freisleben, Bernd and Golby, Alexandra J and Nimsky, Christopher and Kikinis, Ron} } @article {1035, title = {A hybrid approach to telepathology in Cambodia.}, journal = {J Telemed Telecare}, volume = {19}, year = {2013}, month = {2013 Dec}, pages = {475-8}, abstract = {

We established a hybrid telepathology network at the Children{\textquoteright}s Surgical Centre (CSC) in Cambodia, based on store-and-forward communication using iPATH and videoconferencing using Skype. We retrospectively analysed all data from the CSC stored on the iPATH server and reviewed the patient notes over an 8-month period. Of 115 patients for histopathology diagnosis during the study period, 38 cases were uploaded onto iPATH for further telemedicine discussion. The median number of days it took a specialist, other than the local one, to comment on the case on iPATH was 5 days (range 0-15). In three cases (8\%) there was no reply from a specialist on iPATH. During the study period, seven clinical conferences were held, with an average of 6 cases (range 4-7) discussed at each conference. All 38 cases discussed had a final agreed diagnosis and firm management plans were made. Of the 24 cases where proactive management was advised, 17 patients followed through with the recommendations. Although the combination of video consultations and store-and-forward communication has not been used much before in the developing world, it has benefited patient care and outcomes at the CSC.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Cambodia, Child, Child, Preschool, Female, Humans, Internet, Male, Middle Aged, Remote Consultation, Retrospective Studies, Surgical Procedures, Operative, telepathology, Videoconferencing, Young Adult}, issn = {1758-1109}, doi = {10.1177/1357633X13512071}, author = {Kadaba, Varsha and Ly, Tho and Noor, Saqib and Chhut, Serey V and Hinsch, Nora and Stauch, Gerhard and Gollogly, James} } @article {1011, title = {Informatics lessons from using a novel immunization information system.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {589-93}, abstract = {

In the 1990s, NewYork-Presbyterian Hospital began developing a comprehensive, standards-based immunization information system. The system, known as EzVac, has been operational since 1998 and now includes information on 2 million immunizations administered to more than 260,000 individuals. The system exchanges data with multiple electronic health records, a public health immunization registry, and a standalone personal health record. EzVac modules have recently been incorporated into the OpenMRS application and are being used to enhance immunization efforts in developing nations. We report on our experience with developing and using the EzVac system for 1) clinical care, both in local and global settings, 2) public health reporting, 3) consumer engagement, and 4) clinical and informatics research. We emphasize the advantages of using health IT standards to facilitate immunization information exchange in each of these domains.

}, keywords = {electronic health records, Health Information Management, Immunization, Internet, Medical Record Linkage, New York, Registries, Software}, issn = {0926-9630}, author = {Vawdrey, David K and Natarajan, Karthik and Kanter, Andrew S and Hripcsak, George and Kuperman, Gilad J and Stockwell, Melissa S} } @article {852, title = {The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.}, journal = {Int J Comput Assist Radiol Surg}, year = {2013}, month = {2013 Apr 16}, abstract = {

PURPOSE: ~~~The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. METHODS: ~~~MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. RESULTS: ~~~MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. CONCLUSIONS: ~~~MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today{\textquoteright}s and tomorrow{\textquoteright}s clinically motivated research.

}, issn = {1861-6429}, doi = {10.1007/s11548-013-0840-8}, author = {Nolden, Marco and Zelzer, Sascha and Seitel, Alexander and Wald, Diana and M{\"u}ller, Michael and Franz, Alfred M and Maleike, Daniel and Fangerau, Markus and Baumhauer, Matthias and Maier-Hein, Lena and Maier-Hein, Klaus H and Meinzer, Hans -Peter and Wolf, Ivo} } @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 {858, title = {Open source electronic health records and chronic disease management.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 29}, abstract = {

OBJECTIVE: To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC).

METHODS AND MATERIALS: The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR.

RESULTS: Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients.

DISCUSSION: The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems.

CONCLUSIONS: The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001672}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @article {899, title = {SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows}, journal = {International Journal of Biomedical Imaging}, volume = {2013}, year = {2013}, abstract = {Quantitative analysis of magnetic resonance spectroscopic imaging (MRSI) data provides maps of metabolic parameters that show promise for improving medical diagnosis and therapeutic monitoring. While anatomical images are routinely reconstructed on the scanner, formatted using the DICOM standard, and interpreted using PACS workstations, this is not the case for MRSI data. The evaluation of MRSI data is made more complex because files are typically encoded with vendor-specific file formats and there is a lack of standardized tools for reconstruction, processing, and visualization. SIVIC is a flexible open-source software framework and application suite that enables a complete scanner-to-PACS workflow for evaluation and interpretation of MRSI data. It supports conversion of vendor-specific formats into the DICOM MR spectroscopy (MRS) standard, provides modular and extensible reconstruction and analysis pipelines, and provides tools to support the unique visualization requirements associated with such data. Workflows are presented which demonstrate the routine use of SIVIC to support the acquisition, analysis, and delivery to PACS of clinical 1H MRSI datasets at UCSF. {\textcopyright} 2013 Jason C. Crane et al.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84881398824\&partnerID=40\&md5=dbbc0d09b4153fd2609d0bb01b37bb30}, author = {Crane, J C and Olson, M P and Nelson, S J} } @article {859, title = {The use of open source electronic health records within the federal safety net.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 6}, abstract = {

OBJECTIVE: To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). METHODS AND MATERIALS: The study was conducted by the National Opinion Research Center (NORC) at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to West Virginia, California and Arizona FQHC that were currently using an open source EHR. RESULTS: Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. DISCUSSION: Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. CONCLUSIONS: An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001671}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @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 {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} } @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 {820, title = {MITK Diffusion Imaging.}, journal = {Methods Inf Med}, volume = {51}, year = {2012}, month = {2012 Oct 11}, pages = {441-8}, abstract = {Background: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets. Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field. Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITK-DI, are demonstrated using in-vivo datasets. Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use installable application. Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.}, issn = {0026-1270}, doi = {10.3414/ME11-02-0031}, author = {Fritzsche, K H and Neher, P F and Reicht, I and van Bruggen, T and Goch, C and Reisert, M and Nolden, M and Zelzer, S and Meinzer, H-P and Stieltjes, B} } @conference {785, title = {MITK global tractography}, booktitle = {Medical Imaging 2012: Image Processing}, year = {2012}, publisher = {SPIE}, organization = {SPIE}, abstract = {Fiber tracking algorithms yield valuable information for neurosurgery as well as automated diagnostic approaches. However, they have not yet arrived in the daily clinical practice. In this paper we present an open source integration of the global tractography algorithm proposed by Reisert et.al.1 into the open source Medical Imaging Interaction Toolkit (MITK) developed and maintained by the Division of Medical and Biological Informatics at the German Cancer Research Center (DKFZ). The integration of this algorithm into a standardized and open development environment like MITK enriches accessibility of tractography algorithms for the science community and is an important step towards bringing neuronal tractography closer to a clinical application. The MITK diffusion imaging application, downloadable from www.mitk.org, combines all the steps necessary for a successful tractography: preprocessing, reconstruction of the images, the actual tracking, live monitoring of intermediate results, postprocessing and visualization of the final tracking results. This paper presents typical tracking results and demonstrates the steps for pre- and post-processing of the images.}, doi = {10.1117/12.911215}, url = {http://link.aip.org/link/?PSI/8314/83144D/1}, author = {Peter F. Neher and Bram Stieltjes and Marco Reisert and Ignaz Reicht and Meinzer, Hans-Peter and Klaus H. Fritzsche}, editor = {David R. Haynor and Sebastien Ourselin} } @article {1055, title = {The NIH National Center for Integrative Biomedical Informatics (NCIBI).}, journal = {J Am Med Inform Assoc}, volume = {19}, year = {2012}, month = {2012 Mar-Apr}, pages = {166-70}, abstract = {

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

}, keywords = {Biomedical Research, Databases as Topic, Forecasting, Goals, Information Dissemination, Integrative Medicine, Medical Informatics, National Institutes of Health (U.S.), United States}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000552}, author = {Athey, Brian D and Cavalcoli, James D and Jagadish, H V and Omenn, Gilbert S and Mirel, Barbara and Kretzler, Matthias and Burant, Charles and Isokpehi, Raphael D and DeLisi, Charles} } @conference {774, title = {Research and implementation of Electronic Medical Records Editing System based on CDA}, booktitle = {Consumer Electronics, Communications and Networks (CECNet), 2012 2nd International Conference on}, year = {2012}, month = {april}, abstract = {It is difficult to exchange information between heterogeneous Hospital Information Systems (HIS). It becomes the obstacle of regional medical system establishment. The coming forth of HL7 (Health Level 7) CDA (Clinical Document Architecture) standard provides the technical basic conditions. This paper describes CDA standards and CDA document structure. Through a complete analysis of Electronic Medical Record (EMR), the model of Electronic Medical Records Editing Subsystem is given. Based on this model, functional modules of Electronic Medical Records Editing Subsystem are designed and implemented. Through Electronic Medical Records Editing Subsystem, clinical documents can effectively produce, parse, validate and view. It provides a technical support for exchanges of medical and health information.}, keywords = {CDA document structure, CDA standards, clinical document architecture, document handling, electronic medical records editing system, EMR, health level 7, HIS, HL7, hospital information systems, information exchange, medical information systems, regional medical system establishment}, doi = {10.1109/CECNet.2012.6201451}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=\&arnumber=6201451\&contentType=Conference+Publications\&queryText\%3DResearch+and+implementation+of+Electronic+Medical+Records+Editing+System+based+on+CDA}, author = {Lu Xiaoqi and Yu Ning and Gu Yu and Jia Weitao} } @article {1036, title = {A static-image telepathology system for dermatopathology consultation in East Africa: the Massachusetts General Hospital Experience.}, journal = {J Am Acad Dermatol}, volume = {67}, year = {2012}, month = {2012 Nov}, pages = {997-1007}, abstract = {

BACKGROUND: The histologic diagnosis of skin lesions in the developing world is complicated by the shortage of pathologists with subspecialty training in dermatopathology, limited access to ancillary diagnostic testing, and costly referrals for expert glass slide consultation in challenging cases.

OBJECTIVE: In this study we evaluate the feasibility of a static-image telepathology platform in Africa for performing accurate dermatopathology consultations.

METHODS: A static-image telepathology platform using the iPath server was utilized by referring pathologists in 4 African hospitals. Diagnostic interpretations were provided by Massachusetts General Hospital dermatopathologists at no cost. The diagnostic accuracy and interobserver correlation was evaluated.

RESULTS: The static histopathologic images were diagnostic in 22 of 29 (76\%) cases. Diagnostic accuracy between static image and glass slide diagnosis in 22 cases was 91\%, ranging from 86\% to 95\% according to years of dermatopathology subspecialty expertise. Comparison with the glass slides showed that the telepathology diagnosis was limited by inappropriate field selection in only one case. Interobserver concordance between two pathologists was high (K = 0.86) suggesting that this platform is easy to use with minimal training of both referring and consulting pathologists.

LIMITATIONS: Concordance between conventional microscopy and static image telepathology was performed in 22 of 29 cases for which glass slides were received. Interobserver concordance was performed for two pathologists.

CONCLUSION: Static-image telepathology is a feasible means of rendering diagnoses on dermatopathology cases and is a cost-effective technology for obtaining much-needed second opinions in resource-poor settings.

}, keywords = {Africa, Eastern, Cost-Benefit Analysis, Feasibility Studies, Hospitals, General, Humans, Massachusetts, Microscopy, Observer Variation, Pathology, Clinical, Remote Consultation, Skin Diseases, Skin Neoplasms, telepathology}, issn = {1097-6787}, doi = {10.1016/j.jaad.2011.12.036}, author = {Gimbel, Devon C and Sohani, Aliyah R and Prasad Busarla, Satya Vara and Kirimi, Jesca Muthoni and Sayed, Shahin and Okiro, Patricia and Nazarian, Rosalynn M} } @article {1037, title = {A telemedicine network to support paediatric care in small hospitals in rural Tanzania.}, journal = {J Telemed Telecare}, volume = {18}, year = {2012}, month = {2012 Jan}, pages = {59-62}, abstract = {

We reviewed our experience with the Tanzanian Telemedicine Network in supporting paediatric care at 40 small, rural hospitals in the country. The network began operating in 2008. Store and forward telemedicine was provided via the open source software iPath. The 33 volunteer consultants were based in several countries, although most of them had practical experience in Tanzania. During the first three years of network operation there were 533 referrals. There were 159 paediatric cases (median age five years). Three paediatric specialists provided most consultations (64\%), but other specialists provided recommendations when required. The response time was usually less than two days (median 6 h; inter-quartile range 2-24 h). A precise recommendation was not always provided, but since all consultants had an intimate knowledge of the state of health services in Tanzania, their advice was usually well adapted to the local circumstances of the hospitals. Referral to a higher level of care was recommended in 26 cases (16\%). A simple web-based telemedicine system combined with email alerts is feasible in remote locations in Tanzania, even where fast Internet connections are not available.

}, keywords = {Child, Child, Preschool, Electronic Mail, Female, Hospitals, Rural, Humans, Internet, Male, Pediatrics, Physician{\textquoteright}s Practice Patterns, Referral and Consultation, Retrospective Studies, Rural Health Services, Tanzania, Telemedicine}, issn = {1758-1109}, doi = {10.1258/jtt.2011.110312}, author = {Kr{\"u}ger, Carsten and Niemi, Mauri} } @article {591, title = {MITK-ToF-Range data within MITK.}, journal = {International journal of computer assisted radiology and surgery}, year = {2011}, month = {2011 May 31}, abstract = {PURPOSE: The time-of-flight (ToF) technique is an emerging technique for rapidly acquiring distance information and is becoming increasingly popular for intra-operative surface acquisition. Using the ToF technique as an intra-operative imaging modality requires seamless integration into the clinical workflow. We thus aim to integrate ToF support in an existing framework for medical image processing. METHODS: MITK-ToF was implemented as an extension of the open-source C++ Medical Imaging Interaction Toolkit (MITK) and provides the basic functionality needed for rapid prototyping and development of image-guided therapy (IGT) applications that utilize range data for intra-operative surface acquisition. This framework was designed with a module-based architecture separating the hardware-dependent image acquisition task from the processing of the range data. RESULTS: The first version of MITK-ToF has been released as an open-source toolkit and supports several ToF cameras and basic processing algorithms. The toolkit, a sample application, and a tutorial are available from http://mitk.org . CONCLUSIONS: With the increased popularity of time-of-flight cameras for intra-operative surface acquisition, integration of range data supports into medical image processing toolkits such as MITK is a necessary step. Handling acquisition of range data from different cameras and processing of the data requires the establishment and use of software design principles that emphasize flexibility, extendibility, robustness, performance, and portability. The open-source toolkit MITK-ToF satisfies these requirements for the image-guided therapy community and was already used in several research projects.}, issn = {1861-6429}, author = {Seitel, Alexander and Yung, Kwong and Mersmann, Sven and Kilgus, Thomas and Groch, Anja and Dos Santos, Thiago R and Franz, Alfred M and Nolden, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena} } @article {10.1109/ESEM.2011.11, title = {A Qualitative Study of Open Source Software Development: The Open EMR Project}, journal = {Empirical Software Engineering and Measurement, International Symposium on}, year = {2011}, pages = {30-39}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Open Source software is competing successfully in many areas. The commercial sector is recognizing the benefits offered by Open Source development methods that lead to high quality software. Can these benefits be realized in specialized domains where expertise is rare? This study examined discussion forums of an Open Source project in a particular specialized application domain -- electronic medical records -- to see how development roles are carried out, and by whom. We found through a qualitative analysis that the core developers in this system include doctors and clinicians who also use the product. We also found that the size of the community associated with the project is an order of magnitude smaller than predicted, yet still maintains a high degree of responsiveness to issues raised by users. The implication is that a few experts and a small core of dedicated programmers can achieve success using an Open Source approach in a specialized domain.}, isbn = {978-0-7695-4604-9}, doi = {http://doi.ieeecomputersociety.org/10.1109/ESEM.2011.11}, author = {John Noll and Sarah Beecham and Dominik Seichter} } @article {531, title = {Building a open source framework for virtual medical training.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {23}, year = {2010}, month = {2010 Dec}, pages = {706-20}, abstract = {This paper presents a framework to build medical training applications by using virtual reality and a tool that helps the class instantiation of this framework. The main purpose is to make easier the building of virtual reality applications in the medical training area, considering systems to simulate biopsy exams and make available deformation, collision detection, and stereoscopy functionalities. The instantiation of the classes allows quick implementation of the tools for such a purpose, thus reducing errors and offering low cost due to the use of open source tools. Using the instantiation tool, the process of building applications is fast and easy. Therefore, computer programmers can obtain an initial application and adapt it to their needs. This tool allows the user to include, delete, and edit parameters in the functionalities chosen as well as storing these parameters for future use. In order to verify the efficiency of the framework, some case studies are presented.}, issn = {1618-727X}, author = {de Oliveira, Ana Cl{\'a}udia Melo Tiessi Gomes and Nunes, F{\'a}tima de Lourdes dos Santos} } @article {1013, title = {Combining vital events registration, verbal autopsy and electronic medical records in rural Ghana for improved health services delivery.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {416-20}, abstract = {

This paper describes the process of implementing a low-cost {\textquoteright}real-time{\textquoteright} vital registration and verbal autopsy system integrated within an electronic medical record within the Millennium Village cluster in rural Ghana. Using MGV-Net, an open source health information architecture built around the OpenMRS platform, a total of 2378 births were registered between January 2007 and June 2009. The percentage of births registered in the health facility under supervision of a skilled attendant increased substantially over the course of the project from median of 35\% in 2007 to 64\% in 2008 and 85\% midway through 2009. Building additional clinics to reduce distance to facility and using the CHEWs to refer women for delivery in the clinics are possible explanations for the success in the vital registration. The integration of vital registration and verbal autopsies with the MGV-Net information system makes it possible for rapid assessment of effectiveness and provides important feedback to local providers and the Millennium Villages Project.

}, keywords = {Cause of Death, Database Management Systems, Delivery of Health Care, electronic health records, Ghana, Medical Record Linkage, Quality Assurance, Health Care, Quality Improvement, Registries, Rural Health Services, Vital Statistics}, issn = {0926-9630}, author = {Ohemeng-Dapaah, Seth and Pronyk, Paul and Akosa, Eric and Nemser, Bennett and Kanter, Andrew S} } @article {586, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, volume = {100}, year = {2010}, month = {2010 Oct}, pages = {79-86}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, keywords = {Computers, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1872-7565}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @article {20409608, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, year = {2010}, month = {2010 Apr 19}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @article {1014, title = {Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {411-5}, abstract = {

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

}, keywords = {Database Management Systems, Delivery of Health Care, electronic health records, HIV Infections, Information Storage and Retrieval, Medical Record Linkage, Mozambique, Population Surveillance, Rural Health Services}, issn = {0926-9630}, author = {Manders, Eric-Jan and Jos{\'e}, Eurico and Solis, Manuel and Burlison, Janeen and Nhampossa, Jos{\'e} Leopoldo and Moon, Troy} } @inbook {springerlink:10.1007/978-3-642-12197-5_85, title = {rtMEG: A Real-Time Software Toolbox for Brain-Machine Interfaces Using Magnetoencephelography}, booktitle = {17th International Conference on Biomagnetism Advances in Biomagnetism {\textendash} Biomag2010}, series = {IFMBE Proceedings}, volume = {28}, year = {2010}, note = {10.1007/978-3-642-12197-5_85}, pages = {362-365}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-642-12197-5}, url = {http://dx.doi.org/10.1007/978-3-642-12197-5_85}, author = {Sudre, Gustavo and Wang, Wei and Song, Tao and Kajola, Matti and Vinjamuri, Ramana and Collinger, Jennifer and Degenhart, Alan and Bagic, Anto and Weber, Doug J.}, editor = {Magjarevic, R. and Nagel, J. H. and Supek, Selma and Su{\v s}ac, Ana} } @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 {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} } @inbook {springerlink:10.1007/978-3-642-01932-6_45, title = {GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes}, booktitle = {Functional Imaging and Modeling of the Heart}, series = {Lecture Notes in Computer Science}, volume = {5528}, year = {2009}, note = {10.1007/978-3-642-01932-6_45}, pages = {417-426}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computational models, which is extensible through the development of application-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and commercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart.}, url = {http://dx.doi.org/10.1007/978-3-642-01932-6_45}, author = {Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and Bijnens, Bart and Frangi, Alejandro}, editor = {Ayache, Nicholas and Delingette, Herv{\'e} and Sermesant, Maxime} } @article {20044607, title = {Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model.}, journal = {Anticancer research}, volume = {29}, year = {2009}, month = {2009 Dec}, pages = {4995-8}, abstract = {BACKGROUND: Image analysis of tissue sections using RGB image profiling is a modern accepted technique. MATERIALS AND METHODS: A new method of RGB analysis, using the freeware ImageJ, is presented which can be applied to sections with either nuclear or cytoplasmic staining. The step-by-step process is presented and the method is tested using breast cancer specimens immunostained for CK-19 and estrogen receptors. RESULTS: This image analysis easily discriminates CK-19 and estrogen receptor positivity in prepared breast cancer specimens. The method is easy to perform, without the need for previous image transformations. CONCLUSION: Compared to previous methods, this method proved more accurate in estimating the actual colours that an observer recognizes as positive after immunostaining. Further studies are needed to evaluate whether this method is efficient enough to be applied in clinical practice.}, author = {Vrekoussis, T and Chaniotis, V and Navrozoglou, I and Dousias, V and Pavlakis, K and Stathopoulos, E N and Zoras, O} } @article {870, title = {Infrastructure for a learning health care system: CaBIG.}, journal = {Health Aff (Millwood)}, volume = {28}, year = {2009}, month = {2009 May-Jun}, pages = {923-4; author reply 924-5}, keywords = {Cooperative Behavior, Delivery of Health Care, Diffusion of Innovation, Humans, Medical Informatics Applications, Medical Informatics Computing, National Cancer Institute (U.S.), United States, United States Food and Drug Administration}, issn = {1544-5208}, doi = {10.1377/hlthaff.28.3.923-a}, author = {Buetow, Kenneth H and Niederhuber, John} } @article {19439392, title = {Interactive segmentation framework of the Medical Imaging Interaction Toolkit.}, journal = {Computer methods and programs in biomedicine}, volume = {96}, year = {2009}, month = {2009 Oct}, pages = {72-83}, abstract = {Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.}, author = {Maleike, D and Nolden, M and Meinzer, H-P and Wolf, I} } @article {1017, title = {Millennium Global Village-Net: bringing together Millennium Villages throughout sub-Saharan Africa.}, journal = {Int J Med Inform}, volume = {78}, year = {2009}, month = {2009 Dec}, pages = {802-7}, abstract = {

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

}, keywords = {Africa South of the Sahara, Community Health Services, Developing Countries, Healthy People Programs, Humans, Poverty}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2009.08.002}, author = {Kanter, Andrew S and Negin, Joel and Olayo, Bernard and Bukachi, Frederick and Johnson, Edward and Sachs, Sonia Ehrlich} } @article {20351824, title = {Mychildren{\textquoteright}s: integration of a personally controlled health record with a tethered patient portal for a pediatric and adolescent population.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2009}, year = {2009}, month = {2009}, pages = {65-9}, abstract = {Personally controlled health records (PCHRs) and patient portals are increasingly being offered by healthcare institutions, employers, insurance companies and commercial entities to allow patients access to their health information. Both applications offer unique services to provide patients with tools to manage their health. While PCHRs allow users ubiquitous, portable, patient controlled access to their health information, traditional patient portals provide provider-tethered applications allowing patients access, but not control of, certain healthcare information, as well as communication and administrative functions, such as secure messaging, appointment management and prescription refill requests, facilitating care at a specific healthcare facility.We describe our approach for the design, content creation, policy development, and implementation of MyChildren{\textquoteright}s, a unique web-based application leveraging the advantages of both a provider-tethered patient portal and a PCHR to allow patients and their guardians access to the functionality and convenience of a traditional patient portal, as well as the portability and flexibility of a PCHR.}, author = {Bourgeois, Fabienne C and Mandl, Kenneth D and Shaw, Danny and Flemming, Daisy and Nigrin, Daniel J} } @article {18999296, title = {caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2008}, month = {2008}, pages = {197-201}, abstract = {The caBIG Compatibility Review System (CRS) is a web-based application to support compatibility reviews, which certify that software applications that pass the review meet a specific set of criteria that allow them to interoperate. The CRS contains workflows that support both semantic and syntactic reviews, which are performed by the caBIG Vocabularies and Common Data Elements (VCDE) and Architecture workspaces, respectively. The CRS increases the efficiency of compatibility reviews by reducing administrative overhead and it improves uniformity by ensuring that each review is conducted according to a standard process. The CRS provides metrics that allow the review team to evaluate the level of data element reuse in an application, a first step towards quantifying the extent of harmonization between applications. Finally, functionality is being added that will provide automated validation of checklist criteria, which will further simplify the review process.}, author = {Freimuth, Robert R and Schauer, Michael W and Lodha, Preeti and Govindrao, Poornima and Nagarajan, Rakesh and Chute, Christopher G} } @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 {17674101, title = {Open source in imaging informatics.}, 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 = {1-10}, abstract = {The open source community within radiology is a vibrant collection of developers and users working on scores of collaborative projects with the goal of promoting the use of information technology within radiology for education, clinical, and research purposes. This community, which includes many commercial partners, has a rich history in supporting the success of the digital imaging and communication in medicine (DICOM) standard and today is pioneering interoperability limits by embracing the Integrating the Healthcare Enterprise. This article describes only a small portion of the more successful open source applications and is written to help end users see these projects as practical aids for the imaging informaticist and picture archiving and communication system (PACS) administrator.}, url = {http://www.springerlink.com/content/ux777t47g638k402/}, author = {Nagy, Paul} } @article {587, title = {The medical imaging interaction toolkit.}, journal = {Medical image analysis}, volume = {9}, year = {2005}, month = {2005 Dec}, pages = {594-604}, abstract = {Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org).}, keywords = {Algorithms, Artificial Intelligence, Computer Graphics, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1361-8415}, author = {Wolf, Ivo and Vetter, Marcus and Wegner, Ingmar and B{\"o}ttger, Thomas and Nolden, Marco and Sch{\"o}binger, Max and Hastenteufel, Mark and Kunert, Tobias and Meinzer, Hans-Peter} } @article {500, title = {Advances in functional and structural MR image analysis and implementation as FSL.}, journal = {NeuroImage}, volume = {23 Suppl 1}, year = {2004}, month = {2004}, pages = {S208-19}, abstract = {The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB{\textquoteright}s Software Library (FSL).}, keywords = {Bayes Theorem, Brain, Databases, Factual, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Neurological, Models, Statistical, Software}, issn = {1053-8119}, author = {Smith, Stephen M and Jenkinson, Mark and Woolrich, Mark W and Beckmann, Christian F and Behrens, Timothy E J and Johansen-Berg, Heidi and Bannister, Peter R and De Luca, Marilena and Drobnjak, Ivana and Flitney, David E and Niazy, Rami K and Saunders, James and Vickers, John and Zhang, Yongyue and De Stefano, Nicola and Brady, J Michael and Matthews, Paul M} }