@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 {1220, title = {CODE STROKE ALERT-Concept and Development of a Novel Open-Source Platform to Streamline Acute Stroke Management.}, journal = {Front Neurol}, volume = {10}, year = {2019}, month = {2019}, pages = {725}, abstract = {

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

}, issn = {1664-2295}, doi = {10.3389/fneur.2019.00725}, author = {Seah, Huey Ming and Burney, Moe and Phan, Michael and Shell, Daniel and Wu, Jamin and Zhou, Kevin and Brooks, Owen and Coulton, Bronwyn and Maingard, Julian and Tang, Jennifer and Yazdabadi, Gohar and Tahayori, Bahman and Barras, Christen and Kok, Hong Kuan and Chandra, Ronil and Thijs, Vincent and Brooks, Duncan Mark and Asadi, Hamed} } @article {1211, title = {Open source software security vulnerability detection based on dynamic behavior features.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0221530}, abstract = {

Open source software has been widely used in various industries due to its openness and flexibility, but it also brings potential security problems. Therefore, security analysis is required before using open source software. The current mainstream open source software vulnerability analysis technology is based on source code, and there are problems such as false positives, false negatives and restatements. In order to solve the problems, based on the further study of behavior feature extraction and vulnerability detection technology, a method of using dynamic behavior features to detect open source software vulnerabilities is proposed. Firstly, the relationship between open source software vulnerability and API call sequence is studied. Then, the behavioral risk vulnerability database of open source software is proposed as a support for vulnerability detection. In addition, the CNN-IndRNN classification model is constructed by improving the Independently Recurrent Neural Net-work (IndRNN) algorithm and applies to open source software security vulnerability detection. The experimental results verify the effectiveness of the proposed open source software security vulnerability detection method based on dynamic behavior features.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0221530}, author = {Li, Yuancheng and Ma, Longqiang and Shen, Liang and Lv, Junfeng and Zhang, Pan} } @article {1274, title = {Development and Evaluation of a New Security and Privacy Track in a Health Informatics Graduate Program: Multidisciplinary Collaboration in Education.}, journal = {JMIR Med Educ}, volume = {4}, year = {2018}, month = {2018 Dec 21}, pages = {e19}, abstract = {

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

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

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

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

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

}, issn = {2369-3762}, doi = {10.2196/mededu.9081}, author = {Zhou, Leming and Parmanto, Bambang and Joshi, James} } @article {1205, title = {Open-{Source} {Electronic} {Health} {Record} {Systems} for {Low}-{Resource} {Settings}: {Systematic} {Review}}, journal = {JMIR Medical Informatics}, volume = {5}, year = {2017}, abstract = {Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings.}, issn = {2291-9694}, doi = {10.2196/medinform.8131}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703976/}, author = {Syzdykova, Assel and Malta, Andr{\'e} and Zolfo, Maria and Diro, Ermias and Oliveira, Jos{\'e} Lu{\'\i}s} } @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 {1169, title = {dot-app: a {Graphviz}-{Cytoscape} conversion plug-in}, journal = {F1000Research}, volume = {5}, year = {2016}, pages = {2543}, abstract = {dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.}, keywords = {attribute conversion, Cytoscape, Data visualization, DOT, export, format conversion, GraphViz, import, Network}, doi = {10.12688/f1000research.9751.1}, author = {Fitts, Braxton and Zhang, Ziran and Maher, Massoud and Demchak, Barry} } @article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, abstract = {High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.}, keywords = {CellProfiler, continuous integration, high-content screening, high-performance computing}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {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 {1147, title = {An open source solution for an in-house built dynamic platform for the validation of stereotactic ablative body radiotherapy for VMAT and IMRT.}, journal = {Australas Phys Eng Sci Med}, year = {2016}, month = {2016 Sep 15}, abstract = {

An in-house solution for the verification of dose delivered to a moving phantom as required for the clinical implementation of lung stereotactic ablative body radiation therapy was developed. The superior-inferior movement required to simulate tumour motion during a normal breathing cycle was achieved via the novel use of an Arduino Uno{\texttrademark}, a low-cost open-source microcontroller board connected to a high torque servo motor. Slow CT imaging was used to acquire the image set and a 4D cone beam CT (4D-CBCT) verified the efficacy of contoured margins before treatment on the moving phantom. Treatment fields were delivered to a section of a CIRS{\texttrademark} anthropomorphic phantom. Dose verification to the dynamic phantom with Gafchromic EBT3 film using 3~\%-1~mm gamma analysis acceptance criteria registered an absolute dose pass rate for IMRT and VMAT of 98 and 96.6~\%, respectively. It was verified that 100~\% of the PTV received the prescribed dose of 12~Gy per fraction using the dynamic phantom, and no major discrepancy between planned and measured results due to interplay between multileaf collimator sequences and target motion was observed. This study confirmed that the use of an in-house solution using open source hardware and software with existing quality assurance equipment was appropriate in validating a new treatment technique.

}, issn = {1879-5447}, doi = {10.1007/s13246-016-0484-4}, author = {Munoz, Luis and Ziebell, Amy and Morton, Jason and Bhat, Madhava} } @article {1002, title = {Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.}, journal = {J Biomed Inform}, volume = {53}, year = {2015}, month = {2015 Feb}, pages = {390-404}, abstract = {

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2014.11.012}, author = {Zaidan, A A and Zaidan, B B and Al-Haiqi, Ahmed and Kiah, M L M and Hussain, Muzammil and Abdulnabi, Mohamed} } @article {977, title = {Implementation, reliability, and feasibility test of an Open-Source PACS.}, journal = {Radiol Med}, year = {2015}, month = {2015 Jun 19}, abstract = {

PURPOSE: To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment.

MATERIALS AND METHODS: A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed.

RESULTS: The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS.

CONCLUSIONS: An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

}, issn = {1826-6983}, doi = {10.1007/s11547-015-0560-y}, author = {Valeri, Gianluca and Zuccaccia, Matteo and Badaloni, Andrea and Ciriaci, Damiano and La Riccia, Luigi and Mazzoni, Giovanni and Maggi, Stefania and Giovagnoni, Andrea} } @article {976, title = {Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.}, journal = {J Cheminform}, volume = {7}, year = {2015}, month = {2015}, pages = {26}, abstract = {

BACKGROUND: There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software.

RESULTS: The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery.

CONCLUSION: Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT{\textquoteright}s source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

}, issn = {1758-2946}, doi = {10.1186/s13321-015-0078-2}, author = {W{\'o}jcikowski, Maciej and Zielenkiewicz, Piotr and Siedlecki, Pawel} } @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 {946, title = {An Albanian open source telemedicine platform.}, journal = {Telemed J E Health}, volume = {20}, year = {2014}, month = {2014 Jul}, pages = {673-7}, abstract = {

INTRODUCTION: The use of open source technologies to create collaboration platforms can produce huge advantages with small investment.

MATERIALS AND METHODS: We set up a telemedicine network for a healthcare district with typical centralization issues of developing countries. Our network was built using broadband Internet connection, and the digital divide in rural areas was reduced by means of wireless Internet connection. A software infrastructure was deployed on the network to implement the collaboration platform among different healthcare facilities.

RESULTS: We obtained an integrated platform with modest investment in hardware and operating systems and no costs for application software. Messaging, content management, information sharing, and videoconferencing are among the available services of the infrastructure. Furthermore, open source software is managed and continuously updated by active communities, making it possible to obtain systems similar to commercial ones in terms of quality and reliability.

CONCLUSIONS: As the use of free software in public administration is being widely promoted across the European Union, our experience may provide an example to implement similar infrastructures in the field of healthcare and welfare.

}, issn = {1556-3669}, doi = {10.1089/tmj.2013.0239}, author = {Zangara, Gianluca and Valentino, Francesca and Spinelli, Gaetano and Valenza, Mario and Marcheggiani, Angelo and Di Blasi, Francesco} } @article {944, title = {Open source EMR software: Profiling, insights and hands-on analysis.}, journal = {Comput Methods Programs Biomed}, year = {2014}, month = {2014 Jul 17}, abstract = {

BACKGROUND: The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects.

OBJECTIVE: The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records.

METHODS: The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors.

RESULTS: The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the literature landscape more perceivable. Nevertheless, the surveyed articles fall short of fulfilling the targeted objective of providing clear reference to potential implementers. The hands-on study contributed a more detailed comparative guide relative to our set of assessment measures. Overall, no system seems to satisfy an industry-standard measure, particularly in security and interoperability. The systems, as software applications, feel similar from a usability perspective and share a common set of functionality, though they vary considerably in community support and activity.

CONCLUSION: More detailed analysis of popular open source software can benefit the potential implementers of electronic health/medical records systems. The number of examined systems and the measures by which to compare them vary across studies, but still rewarding insights start to emerge. Our work is one step toward that goal. Our overall conclusion is that open source options in the medical field are still far behind the highly acknowledged open source products in other domains, e.g. operating systems market share.

}, issn = {1872-7565}, doi = {10.1016/j.cmpb.2014.07.002}, author = {Kiah, M L M and Haiqi, Ahmed and Zaidan, B B and Zaidan, A A} } @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 {813, title = {ADDIS: a decision support system for evidence-based medicine}, journal = {Decision Support Systems}, volume = {in press}, year = {2012}, abstract = {Clinical trials are the main source of information for the efficacy and safety evaluation of medical treatments. Al- though they are of pivotal importance in evidence-based medicine, there is a lack of usable information systems providing data-analysis and decision support capabilities for aggregate clinical trial results. This is partly caused by unavailability (i) of trial data in a structured format suitable for re-analysis, and (ii) of a complete data model for ag- gregate level results. In this paper, we develop a unifying data model that enables the development of evidence-based decision support in the absence of a complete data model. We describe the supported decision processes and show how these are implemented in the open source ADDIS software. ADDIS enables semi-automated construction of meta-analyses, network meta-analyses and benefit-risk decision models, and provides visualization of all results.}, keywords = {clinicaltrial, datamodel, decisionanalysis, Evidence-basedmedicine, evidencesynthesis}, doi = {10.1016/j.dss.2012.10.005}, author = {van Valkenhoef, G. and Tervonen, T. and Zwinkels, T. and de Brock, B. and Hillege, H.} } @booklet {814, title = {ADDIS: an automated way to do network meta-analysis}, year = {2012}, author = {Zhao, J. and van Valkenhoef, G. and de Brock, B. and Hillege, H.} } @article {804, title = {Development of a Next-Generation Automated DICOM Processing System in a PACS-Less Research Environment.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 May 1}, abstract = {The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve{\textregistered}, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8~months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9482-6}, author = {Ziegler, Scott E} } @article {815, title = {Free and open-source software application for the evaluation of coronary computed tomography angiography images.}, journal = {Arq Bras Cardiol}, year = {2012}, month = {2012 Oct 2}, abstract = {BACKGROUND: The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. OBJECTIVE: To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. METHODS: We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. RESULTS: The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. CONCLUSION: The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50\% in the LMCA and < 70\% in the ADA. The agreement for lesions > 70\% in the ADA was lower, but this is also observed when the anatomical reference standard is used.}, issn = {1678-4170}, author = {Hadlich, Marcelo Souza and Oliveira, Gl{\'a}ucia Maria Moraes and Feij{\'o}o, Ra{\'u}l A and Azevedo, Clerio F and Tura, Bernardo Rangel and Ziemer, Paulo Gustavo Portela and Blanco, Pablo Javier and Pina, Gustavo and Meira, M{\'a}rcio and Souza E Silva, Nelson Albuquerque de} } @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} } @article {791, title = {Navigated laparoscopy - liver shift and deformation due to pneumoperitoneum in an animal model.}, journal = {Minim Invasive Ther Allied Technol}, volume = {21}, year = {2012}, month = {2012 May}, pages = {241-8}, abstract = {Abstract Background: Precise laparoscopic liver resection requires accurate planning and visualization of important anatomy such as vessels and tumors. Combining laparoscopic ultrasound with navigation technology could provide this. Preoperative images are valuable for planning and overview of the procedure, while intraoperative images provide an updated view of the surgical field. Purpose: To validate the accuracy of navigation technology based on preoperative images, we need to understand how much the liver shifts and deforms due to heartbeat, breathing, surgical manipulation and pneumoperitoneum. In this study, we evaluated liver tumor shift and deformation due to pneumoperitoneum in an animal model. Methods: Tumor models were injected into the liver of the animal, and 3D CT images were acquired before and after insufflation. Tumor shifts and deformation were determined. Results: The results showed significant tumor position shift due to pneumoperitoneum, with a maximum of 28 mm in cranio-caudal direction. No significant tumor deformation was detected. Small standard deviations suggest rigid body transformation of the liver as a whole, but this needs further investigation. Conclusion: The findings indicate a need for anatomic shift correction of preoperative images before they are used in combination with LUS guidance during a laparoscopic liver resection procedure.}, issn = {1365-2931}, doi = {10.3109/13645706.2012.665805}, author = {Zijlmans, Mariken and Lang{\o}, Thomas and Hofstad, Erlend Fagertun and Van Swol, Christiaan F P and Rethy, Anna} } @article {869, title = {DDN: a caBIG{\textregistered} analytical tool for differential network analysis.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Apr 1}, pages = {1036-8}, abstract = {

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

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

}, keywords = {Animals, Computational Biology, Epigenesis, Genetic, Female, Gene Regulatory Networks, Mammary Glands, Animal, Rats, Software, Systems Biology}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr052}, author = {Zhang, Bai and Tian, Ye and Jin, Lu and Li, Huai and Shih, Ie-Ming and Madhavan, Subha and Clarke, Robert and Hoffman, Eric P and Xuan, Jianhua and Hilakivi-Clarke, Leena and Wang, Yue} } @article {1746-1596-6-S1-S16, title = {Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images}, journal = {Diagnostic Pathology}, volume = {6}, number = {Suppl 1}, year = {2011}, pages = {S16}, abstract = {BACKGROUND:Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.METHODS:We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.RESULTS:Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.CONCLUSIONS:Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.}, issn = {1746-1596}, doi = {10.1186/1746-1596-6-S1-S16}, url = {http://www.diagnosticpathology.org/content/6/S1/S16}, author = {Zerbe, Norman and Hufnagl, Peter and Schluns, Karsten} } @conference {558, title = {xDAuth: A Scalable and Lightweight Framework for Cross Domain Access Control and Delegation}, booktitle = {SACMAT{\textquoteright}11}, year = {2011}, publisher = {ACM}, organization = {ACM}, address = {Innsbruck, Austria}, abstract = {Cross domain resource sharing and collaborations have be- come pervasive in today{\textquoteright}s service oriented organizations. Existing approaches for the realization of cross domain ac- cess control are either focused on the model level only with- out concrete implementation mechanisms, or not general enough to provide a exible framework for enterprise web applications. In this paper, we present xDAuth, a frame- work for the realization of cross domain access control and delegation with RESTful web service architecture. While focusing on real issues under the context of cross domain access scenarios such as no prede ned trust relationship be- tween a service provider domain and service requestor do- main, xDAuth leverages existing web technologies to real- ize desired security requirements while supporting exible and scalable security policies and privacy protection with low performance overhead. We have implemented xDAuth in a medical module in OpenERP, an open source ERP sys- tem. Our evaluation demonstrates that xDAuth is a feasible framework towards general cross domain access control for service oriented architectures.}, url = {http://profsandhu.com/zhang/pub/sacmat11-xdauth.pdf}, author = {Masoom Alam and Xinwen Zhang and Kamran H Khan and Gohar Ali} } @article {904, title = {Electronic data capture for registries and clinical trials in orthopaedic surgery: Open source versus commercial systems}, journal = {Clinical Orthopaedics and Related Research}, volume = {468}, year = {2010}, pages = {2664{\textendash}2671}, abstract = {Background: Collection and analysis of clinical data can help orthopaedic surgeons to practice evidence based medicine. Spreadsheets and offline relational databases are prevalent, but not flexible, secure, workflow friendly and do not support the generation of standardized and interoperable data. Additionally these data collection applications usually do not follow a structured and planned approach which may result in failure to achieve the intended goal. Questions/purposes: Our purposes are (1) to provide a brief overview of EDC systems, their types, and related pros and cons as well as to describe commonly used EDC platforms and their features; and (2) describe simple steps involved in designing a registry/clinical study in DADOS P, an open source EDC system. Where are we now?: Electronic data capture systems aimed at addressing these issues are widely being adopted at an institutional/national/ international level but are lacking at an individual level. A wide array of features, relative pros and cons and different business models cause confusion and indecision among orthopaedic surgeons interested in implementing EDC systems. Where do we need to go?: To answer clinical questions and actively participate in clinical studies, orthopaedic surgeons should collect data in parallel to their clinical activities. Adopting a simple, user-friendly, and robust EDC system can facilitate the data collection process. How do we get there?: Conducting a balanced evaluation of available options and comparing them with intended goals and requirements can help orthopaedic surgeons to make an informed choice. {\textcopyright} 2010 The Association of Bone and Joint Surgeons{\textregistered}.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77957336660\&partnerID=40\&md5=dec3706be86215e9656a06f82265cb28}, author = {Shah, J.a b and Rajgor, D.a b and Pradhan, S.a b and McCready, M.c and Zaveri, A.a d and Pietrobon, R.c} } @proceedings {512, title = {Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform}, year = {2010}, month = {11/2010}, abstract = {To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients{\textquoteright} online records, ultimately building a fully customizable experience for diverse patient needs.}, url = {http://proceedings.amia.org/127eoo}, author = {Adida, Ben and Sanyal, Arjun and Zabak, Steve and Kohane, Isaac S. and Mandl, Kenneth D} } @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 {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 {19745435, title = {Reversible anonymization of DICOM images using automatically generated policies.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {861-5}, abstract = {Many real-world applications in the area of medical imaging like case study databases require separation of identifying (IDATA) and non-identifying (MDATA) data, specifically those offering Internet-based data access. These kinds of projects also must provide a role-based access system, controlling, how patient data must be organized and how it can be accessed. On DICOM image level, different image types support different kind of information, intermixing IDATA and MDATA in a single object. To separate them, it is possible to reversibly anonymize DICOM objects by substituting IDATA by a unique anonymous token. In case that later an authenticated user needs full access to an image, this token can be used for re-linking formerly separated IDATA and MDATA, thus resulting in a dynamically generated, exact copy of the original image. The approach described in this paper is based on the automatic generation of anonymization policies from the DICOM standard text, providing specific support for all kinds of DICOM images. The policies are executed by a newly developed framework based on the DICOM toolkit DCMTK and offer a reliable approach to reversible anonymization. The implementation is evaluated in a German BMBF-supported expert network in the area of skeletal dysplasias, SKELNET, but may generally be applicable to related projects, enormously improving quality and integrity of diagnostics in a field focused on images. It performs effectively and efficiently on real-world test images from the project and other kind of DICOM images.}, author = {Onken, Michael and Riesmeier, J{\"o}rg and Engel, Marcel and Yabanci, Adem and Zabel, Bernhard and Despr{\'e}s, Stefan} } @article {18366760, title = {OpenMS - an open-source software framework for mass spectrometry.}, journal = {BMC bioinformatics}, volume = {9}, year = {2008}, month = {2008}, pages = {163}, abstract = {BACKGROUND: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. RESULTS: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. CONCLUSION: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.}, url = {http://www.biomedcentral.com/1471-2105/9/163}, author = {Sturm, Marc and Bertsch, Andreas and Gr{\"o}pl, Clemens and Hildebrandt, Andreas and Hussong, Rene and Lange, Eva and Pfeifer, Nico and Schulz-Trieglaff, Ole and Zerck, Alexandra and Reinert, Knut and Kohlbacher, Oliver} } @inbook {springerlink:10.1007/978-3-540-73044-6_189, title = {O3-RWS: a Java-based, IHE-compliant open-source radiology workstation}, booktitle = {11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007}, series = {IFMBE Proceedings}, volume = {16}, year = {2007}, note = {10.1007/978-3-540-73044-6_189}, pages = {727-731}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Within the Open Three Consortium (O3) an open source radiological reporting workstation, called O3- RWS, has been studied, developed and experimented in the routine of European and US hospitals. The O3 Consortium is an international open-source project constituted in 2005 by Higher Education in Clinical Engineering (HECE) of the University of Trieste; it deals with the multi-centric integration of hospitals, RHIOs and citizen (care at home and on the move, and ambient assisted living). O3-RWS has been studied and developed with the goal to give a solution for the needs of the physician, who wants to have an easy-to-use, light and complete solution for the radiology reporting and report creation. O3-RWS, a very versatile platform-independent radiology workstation, providing user authentication and being easy to use also for private users, is able to retrieve, visualize and manage medical images; in an universal version, it is going to be able to deal with vital signs like ECG, hemodynamical and pneumological data.}, isbn = {978-3-540-73044-6}, url = {http://dx.doi.org/10.1007/978-3-540-73044-6_189}, author = {Faustini, Giorgio and Inchingolo, P.}, editor = {Magjarevic, Ratko and Jarm, Tomaz and Kramar, Peter and Zupanic, Anze} } @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} } @article {15361001, title = {The RODS Open Source Project: removing a barrier to syndromic surveillance.}, journal = {Studies in health technology and informatics}, volume = {107}, year = {2004}, month = {2004}, pages = {1192-6}, abstract = {The goal of the Real-time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate deployment of computer-based syndromic surveillance. To this end, the project has released the RODS software under the GNU General Public License and created an organizational structure to catalyze its development. This paper describes the design of the software, requested extensions, and the structure of the development effort.}, author = {Espino, Jeremy U and Wagner, Michael M and Tsui, Fu-Chang and Su, Hoah-Der and Olszewski, Robert T and Lie, Zhen and Chapman, Wendy and Zeng, Xiaoming and Ma, Lili and Lu, Zhong Wei and Dara, Jagan} } @article {11679206, title = {LIPSIA - a new software system for the evaluation of functional magnetic resonance images of the human brain.}, journal = {Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society}, volume = {25}, year = {2001}, month = {2001 Nov-Dec}, pages = {449-57}, abstract = {This paper describes the non-commercial software system LIPSIA that was developed for the processing of functional magnetic resonance images (fMRI) of the human brain. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. In LIPSIA, particular emphasis was placed on the development of new visualization and segmentation techniques that support visualizations of individual brain anatomy so that experts can assess the exact location of activation patterns in individual brains. As the amount of data that must be handled is enormous, another important aspect in the development LIPSIA was the efficiency of the software implementation. Well established statistical techniques were used whenever possible.}, author = {Lohmann, G and M{\"u}ller, K and Bosch, V and Mentzel, H and Hessler, S and Chen, L and Zysset, S and von Cramon, D Y} }