scholarly journals SMART-on-FHIR implemented over i2b2

2016 ◽  
Vol 24 (2) ◽  
pp. 398-402 ◽  
Author(s):  
Kavishwar B Wagholikar ◽  
Joshua C Mandel ◽  
Jeffery G Klann ◽  
Nich Wattanasin ◽  
Michael Mendis ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Data Access ◽  
Patient Data ◽  
Third Party ◽  
Query Engine ◽  
Secure Data

We have developed an interface to serve patient data from Informatics for Integrating Biology and the Bedside (i2b2) repositories in the Fast Healthcare Interoperability Resources (FHIR) format, referred to as a SMART-on-FHIR cell. The cell serves FHIR resources on a per-patient basis, and supports the “substitutable” modular third-party applications (SMART) OAuth2 specification for authorization of client applications. It is implemented as an i2b2 server plug-in, consisting of 6 modules: authentication, REST, i2b2-to-FHIR converter, resource enrichment, query engine, and cache. The source code is freely available as open source. We tested the cell by accessing resources from a test i2b2 installation, demonstrating that a SMART app can be launched from the cell that accesses patient data stored in i2b2. We successfully retrieved demographics, medications, labs, and diagnoses for test patients. The SMART-on-FHIR cell will enable i2b2 sites to provide simplified but secure data access in FHIR format, and will spur innovation and interoperability. Further, it transforms i2b2 into an apps platform.

scholarly journals The Cambridge Cognitive and Psychiatric Assessment Kit (CamCOPS): A Secure Open-Source Client–Server System for Mobile Research and Clinical Data Capture

2021 ◽  
Vol 12 ◽  
Author(s):  
Rudolf N. Cardinal ◽  
Martin Burchell
Keyword(s):  
Open Source ◽  
Data Storage ◽  
Data Entry ◽  
Data Access ◽  
Data Capture ◽  
Third Party ◽  
Record System ◽  
Client Server ◽  
Network Connection ◽  
Server System

CamCOPS is a free, open-source client–server system for secure data capture in the domain of psychiatry, psychology, and the clinical neurosciences. The client is a cross-platform C++ application, suitable for mobile and offline (disconnected) use. It allows touchscreen data entry by subjects/patients, researchers/clinicians, or both together. It implements a large and extensible range of tasks, from simple questionnaires to complex animated tasks. The client uses encrypted data storage and sends data via an encrypted network connection to a CamCOPS server. Individual institutional users set up and run their own CamCOPS server, so no data is transferred outside the hosting institution's control. The server, written in Python, provides clinically oriented and research-oriented views of tasks, including the tracking of changes over time. It provides an audit trail, export facilities (such as to an institution's primary electronic health record system), and full structured data access subject to authorization. A single CamCOPS server can support multiple research/clinical groups, each having its own identity policy (e.g., fully identifiable for clinical use; de-identified/pseudonymised for research use). Intellectual property rules regarding third-party tasks vary and CamCOPS has several mechanisms to support compliance, including for tasks that may be permitted to some institutions but not others. CamCOPS supports task scheduling and home testing via a simplified user interface. We describe the software, report local information governance approvals within part of the UK National Health Service, and describe illustrative clinical and research uses.

scholarly journals ELIXIR Europe on the Road to Sustainable Research Software

2019 ◽  
Vol 3 ◽  
Author(s):  
Mateusz Kuzak ◽  
Jen Harrow ◽  
Paula Martinez ◽  
Fotis Psomopoulos ◽  
Allegra Via
Keyword(s):  
Best Practices ◽  
Software Development ◽  
Open Source ◽  
Life Science ◽  
Source Code ◽  
Management Plan ◽  
Third Party ◽  
Research Software ◽  
Communication Processes ◽  
Training Materials

ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas: Data, Tools, Interoperability, Compute and Training, each known as “platform”. The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. The Software Development Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, and promoting information standards and best practices relevant to the software development life cycle. We have published four (4OSS) simple recommendations to encourage best practices in research software (Jiménez et al. 2017) and the Top 10 metrics for recommended life science software practices (Artaza et al. 2016). The 4OSS simple recommendations are as follows: Develop a publicly accessible open source code from day one. Make software easy to discover by providing software metadata via a popular community registry. Adopt a license and comply with the licenses of third-party dependencies. Have clear and transparent contribution, governance and communication processes. Develop a publicly accessible open source code from day one. Make software easy to discover by providing software metadata via a popular community registry. Adopt a license and comply with the licenses of third-party dependencies. Have clear and transparent contribution, governance and communication processes. In order to encourage researchers and developers to adopt the 4OSS recommendations and build FAIR (Findable, Accessible, Interoperable and Reusable) software, the best practices group, in partnership with the ELIXIR Training platform, The Carpentries (Carpentries 2019, ELIXIR Europe 2019b), and other communities, are creating a collection of training materials (Kuzak et al. 2019). The next step is to adopt, promote, and recognise these information standards and best practices. The group will address this by (i) developing comprehensive guidelines for software curation, (ii) through training researchers and developers towards the adoption of software best practices and (iii) improvement of the usability of Tools Platform products. Additionally, a direct outcome of this task will be a software management plan template, connected to a concise description of the guidelines for open research software; and production of a white paper for the software development management plan for ELIXIR, which can be consequently used to produce training materials. We will work with the newly formed ReSA (Research Software Alliance) to facilitate the adoption of this plan for the broader community.

Towards a scalable, open-standards service for brokering cross-protocol data transfers across multiple sources and sinks

2010 ◽  
Vol 368 (1926) ◽  
pp. 4115-4131
Author(s):  
David Meredith ◽  
Stephen Crouch ◽  
Gerson Galang ◽  
Ming Jiang ◽  
Hung Nguyen ◽  
...  
Keyword(s):  
Open Source ◽  
Design Patterns ◽  
Data Transfer ◽  
Fault Tolerant ◽  
Data Access ◽  
Third Party ◽  
Multiple Sources ◽  
Wide Range ◽  
Bulk Data ◽  
Open Standards

Data Transfer Service (DTS) is an open-source project that is developing a document-centric message model for describing a bulk data transfer activity, with an accompanying set of loosely coupled and platform-independent components for brokering the transfer of data between a wide range of (potentially incompatible) storage resources as scheduled, fault-tolerant batch jobs. The architecture scales from small embedded deployments on a single computer to large distributed deployments through an expandable ‘worker-node pool’ controlled through message-orientated middleware. Data access and transfer efficiency are maximized through the strategic placement of worker nodes at or between particular data sources/sinks. The design is inherently asynchronous, and, when third-party transfer is not available, it side-steps the bandwidth, concurrency and scalability limitations associated with buffering bytes directly through intermediary client applications. It aims to address geographical–topological deployment concerns by allowing service hosting to be either centralized (as part of a shared service) or confined to a single institution or domain. Established design patterns and open-source components are coupled with a proposal for a document-centric and open-standards-based messaging protocol. As part of the development of the message protocol, a bulk data copy activity document is proposed for the first time.

THE TECHNOLOGY OF DETECTION INFORMATION ABOUT VULNERABILITY IN THIRD-PARTY OPEN SOURCE SOFTWARE

2020 ◽  
pp. 347-364
Author(s):  
Алексей Леонидович Сердечный ◽  
Игорь Васильевич Герасимов ◽  
Олег Юрьевич Макаров ◽  
Юрий Геннадьевич Пастернак ◽  
Николай Михайлович Тихомиров ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Open Source ◽  
Open Source Software ◽  
Rapid Detection ◽  
Source Code ◽  
Third Party ◽  
Version Control ◽  
Software Developers ◽  
Open Source Code

В статье приведены результаты разработки технологии выявления сведений об уязвимостях сторонних компонентов программного обеспечения (ПО), позволяющей своевременно обнаруживать проблемы безопасности, связанные с использованием заимствованных компонентов с открытым исходным кодом. Технология отличается процедурами оперативного обнаружения, ранжирования и подтверждения достоверности первоисточников сообщений о таких проблемах. Разработанная технология основана на проведении сбора и семантического анализа сведений об ошибках и средствах (алгоритмах) эксплуатации уязвимостей ПО, содержащихся в сообщениях, публикуемых на информационных ресурсах разработчиков ПО с открытым исходным кодом. Технология включает процедуру подтверждения сведений о наиболее опасных уязвимостях с последующей оценкой рисков для подтверждённых уязвимостей. В статье также приводятся результаты реализации предлагаемой технологии в виде средства сбора и интерактивного анализа сообщений о ошибках в ПО с открытым исходным кодом, размещаемым на платформах для совместной разработки GitHub и GitLab. Технология выявления сведений об уязвимостях сторонних компонентов позволяет повысить защищённость ПО, использующего в своём составе общедоступные компоненты с открытым исходным кодом. The article presents the results of the development the technology of detection information about vulnerability in third-party open source software, which allows timely detection of security problems associated with the use of borrowed components provided with open source code. The technology is characterized by procedures for rapid detection, ranking, and confirmation of the authenticity sources of primary reports about such problems. The technology is based on collecting and mining information about bugs, vulnerabilities and exploits contained in messages that published in sources of open source software developers. The technology includes a procedure for confirming information about the most dangerous vulnerabilities, followed by a risk assessment for confirmed vulnerabilities. The article also presents the results of implementing the proposed technology as a tool for collecting and interactively analyzing bug messages in open source software hosted on the GitHub and GitLab collaborative version control platforms. The technology for detecting information about vulnerabilities of third-party components allows you to increase the security of software that uses publicly available open source components.

scholarly journals Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform

2018 ◽  
Vol 10 ◽  
pp. 117822261877774 ◽  
Author(s):  
Kavishwar B Wagholikar ◽  
Michael Mendis ◽  
Pralav Dessai ◽  
Javier Sanz ◽  
Sindy Law ◽  
...  
Keyword(s):  
Open Source ◽  
Clinical Data ◽  
Data Analytics ◽  
Source Code ◽  
Patient Data ◽  
Extensive Documentation ◽  
Starting Point ◽  
Reference Implementation ◽  
Automated Installation ◽  
Complex Architecture

Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at more than 150 institutions for querying patient data. An i2b2 installation (called hive) comprises several i2b2 cells that provide different functionalities. Given the complex architecture of i2b2 installation, creating a working installation of the platform is challenging for new users. This is despite the availability of extensive documentation for i2b2 and access to a large and active mailing list community of i2b2 users. To address this problem, we have created an automated installation package, called i2b2-quickstart, which automatically downloads the latest i2b2 source code and dependencies, and compiles and configures the i2b2 cells to create a functional i2b2 hive installation. This package will serve as a convenient starting point and reference implementation that will facilitate researchers in the installation and exploration of the i2b2 platform.

Impact of Clone Refactoring on External Quality Attributes of Open Source Softwares

2018 ◽  
pp. 86-94
Author(s):  
Himanshi Vashisht ◽  
Sanjay Bharadwaj ◽  
Sushma Sharma
Keyword(s):  
Open Source ◽  
Internal Structure ◽  
Software Quality ◽  
Source Code ◽  
Quality Attributes ◽  
Software Component ◽  
External Quality ◽  
Code Refactoring ◽  
Observable Behaviour

Code refactoring is a “Process of restructuring an existing source code.”. It also helps in improving the internal structure of the code without really affecting its external behaviour”. It changes a source code in such a way that it does not alter the external behaviour yet still it improves its internal structure. It is a way to clean up code that minimizes the chances of introducing bugs. Refactoring is a change made to the internal structure of a software component to make it easier to understand and cheaper to modify, without changing the observable behaviour of that software component. Bad smells indicate that there is something wrong in the code that have to refactor. There are different tools that are available to identify and emove these bad smells. A software has two types of quality attributes- Internal and external. In this paper we will study the effect of clone refactoring on software quality attributes.

AN OPEN-SOURCE CODE FOR NUMERICAL SIMULATION OF DRAINAGE BASIN DEVELOPMENT

2017 ◽  
Author(s):  
George H. Shaw ◽  
◽  
Howard D. Mooers ◽  
Josef Smrz ◽  
Zdenek Papez ◽  
...  
Keyword(s):  
Numerical Simulation ◽  
Open Source ◽  
Drainage Basin ◽  
Source Code ◽  
Open Source Code ◽  
Basin Development

Secure Data Access and Sharing Scheme for Cloud Storage

2016 ◽  
Vol 96 (4) ◽  
pp. 5295-5314 ◽  
Author(s):  
Xiong Li ◽  
Saru Kumari ◽  
Jian Shen ◽  
Fan Wu ◽  
Caisen Chen ◽  
...  
Keyword(s):  
Cloud Storage ◽  
Data Access ◽  
Sharing Scheme ◽  
Secure Data
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