@article {1303, title = {Machado: Open source genomics data integration framework.}, journal = {Gigascience}, volume = {9}, year = {2020}, month = {2020 09 14}, abstract = {

BACKGROUND: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD{\textquoteright}s (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it.

FINDINGS: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters.

CONCLUSION: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.

}, issn = {2047-217X}, doi = {10.1093/gigascience/giaa097}, author = {Mudadu, Mauricio de Alvarenga and Zerlotini, Adhemar} } @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 {1204, title = {The mobile sleep lab app: {An} open-source framework for mobile sleep assessment based on consumer-grade wearable devices}, journal = {Computers in Biology and Medicine}, volume = {103}, year = {2018}, pages = {8{\textendash}16}, abstract = {BACKGROUND: Sleep disorders have a prevalence of up to 50\% and are commonly diagnosed using polysomnography. However, polysomnography requires trained staff and specific equipment in a laboratory setting, which are expensive and limited resources are available. Mobile and wearable devices such as fitness wristbands can perform limited sleep monitoring but are not evaluated well. Here, the development and evaluation of a mobile application to record and synchronize data from consumer-grade sensors suitable for sleep monitoring is presented and evaluated for data collection capability in a clinical trial. METHODS: Wearable and ambient consumer-grade sensors were selected to mimic the functionalities of clinical sleep laboratories. Then, a modular application was developed for recording, processing and visualizing the sensor data. A validation was performed in three phases: (1) sensor functionalities were evaluated, (2) self-experiments were performed in full-night experiments, and (3) the application was tested for usability in a clinical trial on primary snoring. RESULTS: The evaluation of the sensors indicated their suitability for assessing basic sleep characteristics. Additionally, the application successfully recorded full-night sleep. The collected data was of sufficient quality to detect and measure body movements, cardiac activity, snoring and brightness. The ongoing clinical trial phase showed the successful deployment of the application by medical professionals. CONCLUSION: The proposed software demonstrated a strong potential for medical usage. With low costs, it can be proposed for screening, long-term monitoring or in resource-austere environments. However, further validations are needed, in particular the comparison to a clinical sleep laboratory.}, keywords = {Mobile sleep laboratory, Sleep screening, Smartphone, Telemedicine, Wearable technology}, issn = {1879-0534}, doi = {10.1016/j.compbiomed.2018.09.025}, author = {Burgdorf, Andreas and G{\"u}the, Inga and Jovanovi{\'c}, Marko and Kutafina, Ekaterina and Kohlschein, Christian and Bitsch, J{\'o} {\'A}gila and Jonas, Stephan M.} } @article {1267, title = {Mapping for Health in Cameroon: Polio Legacy and Beyond.}, journal = {J Infect Dis}, volume = {216}, year = {2017}, month = {2017 07 01}, pages = {S337-S342}, abstract = {

During the poliovirus outbreak in Cameroon from October 2013 to April 2015, the Ministry of Public Health{\textquoteright}s Expanded Program on Immunization requested technical support to improve mapping of health district boundaries and health facility locations for more effective planning and analysis of polio program data. In December 2015, teams collected data on settlements, health facilities, and other features using smartphones. These data, combined with high-resolution satellite imagery, were used to create new health area and health district boundaries, providing the most accurate health sector administrative boundaries to date for Cameroon. The new maps are useful to and used by the polio program as well as other public health programs within Cameroon such as the District Health Information System and the Emergency Operations Center, demonstrating the value of the Global Polio Eradication Initiative{\textquoteright}s legacy.

}, keywords = {Cameroon, Geographic Information Systems, Humans, Immunization Programs, Poliomyelitis, Public Health, Public Health Surveillance, Smartphone}, issn = {1537-6613}, doi = {10.1093/infdis/jix008}, author = {Rosencrans, Louie C and Sume, Gerald E and Kouontchou, Jean-Christian and Voorman, Arend and Anokwa, Yaw and Fezeu, Maurice and Seaman, Vincent Y} } @article {1276, title = {A Mobile-Based Community Health Management Information System for Community Health Workers and Their Supervisors in 2 Districts of Zambia.}, journal = {Glob Health Sci Pract}, volume = {5}, year = {2017}, month = {2017 09 27}, pages = {486-494}, abstract = {

INTRODUCTION: Effective community health management information systems (C-HMIS) are important in low-resource countries that rely heavily on community-based health care providers. Zambia currently lacks a functioning C-HMIS to provide real-time, community-based health information from community health workers (CHWs) to health center staff and higher levels of the health system.

PROGRAM DESCRIPTION: We developed a C-HMIS mobile platform for use by CHWs providing integrated community case management (iCCM) services and their supervisors to address challenges of frequent stock-outs and inadequate supportive supervision of iCCM-trained CHWs. The platform used simple feature mobile phones on which were loaded the District Health Information System version 2 (DHIS2) software and Java 2 platform micro edition (J2ME) aggregation and tracker applications. This project was implemented in Chipata and Chadiza districts, which supported previous mHealth programs and had cellular coverage from all 3 major network carriers in Zambia. A total of 40 CHWs and 20 CHW supervisors received mobile phones with data bundles and training in the mobile application, after which they implemented the program over a period of 5.5 months, from February to mid-July 2016. CHWs used the mobile phones to submit data on iCCM cases seen, managed, and referred, as well as iCCM medical and diagnostic supplies received and dispensed. Using their mobile phones, the supervisors tracked CHWs{\textquoteright} reported cases with medicine consumption, sent CHWs feedback on their referrals, and received SMS reminders to set up mentorship sessions.

OBSERVATIONS: CHWs were able to use the mobile application to send weekly reports to health center supervisors on disease caseloads and medical commodities consumed, to make drug and supply requisitions, and to send pre-referral notices to health centers. Health center staff used the mobile system to provide feedback to CHWs on the case outcomes of referred patients and to receive automated monthly SMS reminders to invite CHWs to the facility for mentorship. District- and central-level staff were able to access community-level health data in real time using passwords.

LESSONS LEARNED: C-HMIS, using simple feature phones, was feasible and viable for the provision of real-time community-based health information to all levels of the health care system in Zambia, but smartphones, laptops, or desktop computers are needed to perform data analysis and visualization. Ongoing technical support is needed to address the hardware and software challenges CHWs face in their day-to-day interaction with the application on their mobile phones.

}, keywords = {Community Health Services, Community Health Workers, Delivery of Health Care, Health information systems, Humans, Mobile Applications, Referral and Consultation, Zambia}, issn = {2169-575X}, doi = {10.9745/GHSP-D-16-00275}, author = {Biemba, Godfrey and Chiluba, Boniface and Yeboah-Antwi, Kojo and Silavwe, Vichaels and Lunze, Karsten and Mwale, Rodgers K and Russpatrick, Scott and Hamer, Davidson H} } @article {1168, title = {Methods for {Specifying} {Scientific} {Data} {Standards} and {Modeling} {Relationships} with {Applications} to {Neuroscience}}, journal = {Frontiers in Neuroinformatics}, volume = {10}, year = {2016}, pages = {48}, abstract = {Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.}, keywords = {data format specification, electrophysiology, neuroscience, relationship modeling}, doi = {10.3389/fninf.2016.00048}, author = {R{\"u}bel, Oliver and Dougherty, Max and Prabhat, null and Denes, Peter and Conant, David and Chang, Edward F. and Bouchard, Kristofer} } @article {979, title = {medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0121760}, abstract = {

In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user{\textquoteright}s computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0121760}, author = {Ahlin, {\v C}rt and Stupica, Da{\v s}a and Strle, Franc and Lusa, Lara} } @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 {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 {931, title = {Managing multicentre clinical trials with open source.}, journal = {Inform Health Soc Care}, volume = {39}, year = {2014}, month = {2014 Mar}, pages = {67-80}, abstract = {

Background: Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. Objective: The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. Methods: We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. Results: This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Conclusion: Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

}, issn = {1753-8165}, doi = {10.3109/17538157.2013.812647}, author = {Raptis, Dimitri Aristotle and Mettler, Tobias and Fischer, Michael Alexander and Patak, Michael and Lesurtel, Mickael and Eshmuminov, Dilmurodjon and de Rougemont, Olivier and Graf, Rolf and Clavien, Pierre-Alain and Breitenstein, Stefan} } @article {1096, title = {Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.}, journal = {Stud Health Technol Inform}, volume = {202}, year = {2014}, month = {2014}, pages = {157-60}, abstract = {

The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

}, issn = {0926-9630}, author = {Marc, David T and Khairat, Saif 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 {862, title = {MRIdb: Medical Image Management for Biobank Research.}, journal = {J Digit Imaging}, year = {2013}, month = {2013 Apr 26}, abstract = {

Clinical picture archiving and communications systems provide convenient, efficient access to digital medical images from multiple modalities but can prove challenging to deploy, configure and use. MRIdb is a self-contained image database, particularly suited to the storage and management of magnetic resonance imaging data sets for population phenotyping. It integrates a mature image archival system with an intuitive web-based user interface that provides visualisation and export functionality. In addition, utilities for auditing, data migration and system monitoring are included in a virtual machine image that is easily deployed with minimal configuration. The result is a freely available turnkey solution, designed to support epidemiological and imaging genetics research. It allows the management of patient data sets in a secure, scalable manner without requiring the installation of any bespoke software on end users{\textquoteright} workstations. MRIdb is an open-source software, available for download at http://www3.imperial.ac.uk/bioinfsupport/resources/software/mridb .

}, issn = {1618-727X}, doi = {10.1007/s10278-013-9604-9}, author = {Woodbridge, Mark and Fagiolo, Gianlorenzo and O{\textquoteright}Regan, Declan P} } @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 {573, title = {mantisGRID: A Grid Platform for DICOM Medical Images Management in Colombia and Latin America.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Apr}, pages = {271-83}, abstract = {This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.}, issn = {1618-727X}, author = {Garcia Ruiz, Manuel and Garcia Chaves, Alvin and Ruiz Iba{\~n}ez, Carlos and Gutierrez Mazo, Jorge Mario and Ramirez Giraldo, Juan Carlos and Pelaez Echavarria, Alejandro and Valencia Diaz, Edison and Pelaez Restrepo, Gustavo and Montoya Munera, Edwin Nelson and Garcia Loaiza, Bernardo and Gomez Gonzalez, Sebastian} } @inbook {springerlink:10.1007/978-1-4419-8204-9_9, title = {Medical Image Registration}, booktitle = {Multi Modality State-of-the-Art Medical Image Segmentation and Registration Methodologies}, year = {2011}, note = {10.1007/978-1-4419-8204-9_9}, pages = {227-245}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {In this chapter, we cover the necessary background information required to understand medical image registration, the basic tools required to implement registration algorithms, and demonstrate a complete application for various types of registration between different modalities using freely available and maintained software.}, isbn = {978-1-4419-8204-9}, url = {http://dx.doi.org/10.1007/978-1-4419-8204-9_9}, author = {Aladl, Usaf E. and Peters, Terry}, editor = {El-Baz, Ayman S. and Acharya U, Rajendra and Laine, Andrew F. and Suri, Jasjit S.} } @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 {20646816, title = {Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.}, journal = {Annales de chirurgie plastique et esthetique}, year = {2010}, month = {2010 Jun 18}, abstract = {The techniques of free tissue transfers are mainly used for mandibular reconstruction by specialized surgical teams. This type of reconstruction is mostly realized in matters of head and neck cancers affecting mandibular bone and requiring a wide surgical resection and interruption of the mandible. To decrease the duration of the operation, surgical procedure involves generally two teams, one devoted to cancer resection and the other one to raise the fibular flap and making the reconstruction. For a better preparation of this surgical procedure, we propose here the use of a medical imaging software enabling mandibular reconstructions in three dimensions using the CT-scan done during the initial disease-staging checkup. The software used is Osirix((R)), developed since 2004 by a team of radiologists from Geneva and UCLA, working on Apple((R)) computers and downloadable free of charge in its basic version. We report here our experience of this software in 17 patients, with a preoperative modelling in three dimensions of the mandible, of the segment of mandible to be removed. It also forecasts the numbers of fragments of fibula needed and the location of osteotomies.}, author = {Albert, S and Cristofari, J-P and Cox, A and Bensimon, J-L and Guedon, C and Barry, B} } @article {847, title = {Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.}, journal = {J Am Med Inform Assoc}, volume = {17}, year = {2010}, month = {2010 Sep-Oct}, pages = {507-13}, abstract = {

We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source technologies-the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text.

}, keywords = {Biomedical Research, electronic health records, Information Storage and Retrieval, Natural Language Processing}, issn = {1527-974X}, doi = {10.1136/jamia.2009.001560}, author = {Savova, Guergana K and Masanz, James J and Ogren, Philip V and Zheng, Jiaping and Sohn, Sunghwan and Kipper-Schuler, Karin C and Chute, Christopher G} } @article {19910667, title = {The medical exploration toolkit: an efficient support for visual computing in surgical planning and training.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {16}, year = {2010}, month = {2010 Jan-Feb}, pages = {133-46}, abstract = {Application development is often guided by the usage of software libraries and toolkits. For medical applications, the toolkits currently available focus on image analysis and volume rendering. Advance interactive visualizations and user interface issues are not adequately supported. Hence, we present a toolkit for application development in the field of medical intervention planning, training, and presentation--the MEDICALEXPLORATIONTOOLKIT (METK). The METK is based on the rapid prototyping platform MeVisLab and offers a large variety of facilities for an easy and efficient application development process. We present dedicated techniques for advanced medical visualizations, exploration, standardized documentation, adn interface widgets for common tasks. These include, e.g., advanced animation facilities, viewpoint selection, several illustrative rendering techniques, and new techniques for object selection in 3D surface models. No extended programming skills are needed for application building, since a graphical programming approach can be used. the toolkit is freely available and well documented to facilitate the use and extension of the toolkit.}, author = {M{\"u}hler, Konrad and Tietjen, Christian and Ritter, Felix and Preim, Bernhard} } @conference {1085, title = {MediGrid {\textendash} Facilitating Semantic-Based processing of Biomedical Data and Knowledge}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828500180021}, author = {Jan Vejvalka and Petr Lesn{\'y} and Tom{\'a}{\v s} Hole{\v c}ek and Kry{\v s}tof Slab{\'y} and Ad{\'e}la Jarol{\'\i}mkov{\'a} and Helena Bouzkov{\'a}} } @article {872, title = {Metadata mapping and reuse in caBIG.}, journal = {BMC Bioinformatics}, volume = {10 Suppl 2}, year = {2009}, month = {2009}, pages = {S4}, abstract = {

BACKGROUND: This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI){\textquoteright}s cancer Biomedical Informatics Grid (caBIG). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG framework or other frameworks that use metadata repositories.

RESULTS: The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG framework and potentially any framework that uses a metadata repository.

CONCLUSION: This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG. This effort contributes to facilitating the development of interoperable systems within caBIG as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

}, keywords = {Algorithms, Computational Biology, Database Management Systems, Databases, Factual, Medical Informatics, Software, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/1471-2105-10-S2-S4}, author = {Kunz, Isaac and Lin, Ming-Chin and Frey, Lewis} } @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 {1018, title = {Mobile Care (Moca) for Remote Diagnosis and Screening.}, journal = {J Health Inform Dev Ctries}, volume = {3}, year = {2009}, month = {2009 Jan 1}, pages = {17-21}, abstract = {

Moca is a cell phone-facilitated clinical information system to improve diagnostic, screening and therapeutic capabilities in remote resource-poor settings. The software allows transmission of any medical file, whether a photo, x-ray, audio or video file, through a cell phone to (1) a central server for archiving and incorporation into an electronic medical record (to facilitate longitudinal care, quality control, and data mining), and (2) a remote specialist for real-time decision support (to leverage expertise). The open source software is designed as an end-to-end clinical information system that seamlessly connects health care workers to medical professionals. It is integrated with OpenMRS, an existing open source medical records system commonly used in developing countries.

}, issn = {1178-4407}, author = {Celi, Leo Anthony and Sarmenta, Luis and Rotberg, Jhonathan and Marcelo, Alvin and Clifford, Gari} } @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 {Jahnke-weber_makingavailable, title = {Making available Clinical Decision Support in Service-Oriented Architectures}, journal = {Journal on Information Technology in Healthcare}, volume = {6}, year = {2008}, pages = {54}, chapter = {42}, abstract = {Computer-based clinical decision support (CDS) has great potential for cost savings and for increasing patient safety and quality of care. The cost of owning and particularly maintaining CDS systems is significant. Therefore, it makes good economic sense to share a CDS service installation among a larger set of client systems. The emerging paradigm of serviceoriented architectures (SOAs) embraces the idea of sharing and interaction between loosely coupled, co-operative services. Canada has based its planned architecture for realizing the electronic medical record (EMR) on the SOA paradigm. While CDS components are currently not in the set of services to be constructed for Canada{\textquoteright}s health information infrastructure, they seems to be growing interest in adding them in the future, after the more essential services have been implemented. In this paper, we discuss the status of clinical decision support systems today and some challenges of making them available in SOA-based infrastructures. We report on design choices and solutions we have selected during the construction of the EGADSS (Electronic Guideline and Decision Support System) component. Our design decisions are based on domainspecific challenges such as knowledge, data and workflow interoperability as well as on technical considerations about construction high quality services for SOA-based infrastructures. EGADSS has been released under open-source license and is freely available.}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.5385\&rep=rep1\&type=pdf}, author = {Jens H. Jahnke-Weber and Morgan Price and Glen McCallum} } @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 {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} }