A methodology for interfacing open source SystemC with a third party software

The proliferation of modern data processing tools has given rise to open-source columnar data formats. These formats help organizations avoid repeated conversion of data to a new format for each application. However, these formats are read-only, and organizations must use a heavy-weight transformation process to load data from on-line transactional processing (OLTP) systems. As a result, DBMSs often fail to take advantage of full network bandwidth when transferring data. We aim to reduce or even eliminate this overhead by developing a storage architecture for in-memory database management systems (DBMSs) that is aware of the eventual usage of its data and emits columnar storage blocks in a universal open-source format. We introduce relaxations to common analytical data formats to efficiently update records and rely on a lightweight transformation process to convert blocks to a read-optimized layout when they are cold. We also describe how to access data from third-party analytical tools with minimal serialization overhead. We implemented our storage engine based on the Apache Arrow format and integrated it into the NoisePage DBMS to evaluate our work. Our experiments show that our approach achieves comparable performance with dedicated OLTP DBMSs while enabling orders-of-magnitude faster data exports to external data science and machine learning tools than existing methods.

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Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics

Earth Surface Dynamics ◽

10.5194/esurf-5-21-2017 ◽

2017 ◽

Vol 5 (1) ◽

pp. 21-46 ◽

Cited By ~ 63

Author(s):

Daniel E. J. Hobley ◽

Jordan M. Adams ◽

Sai Siddhartha Nudurupati ◽

Eric W. H. Hutton ◽

Nicole M. Gasparini ◽

...

Keyword(s):

Open Source ◽

Numerical Models ◽

Epistemic Uncertainty ◽

Process Models ◽

Third Party ◽

Sensitivity Analyses ◽

Surface Dynamics ◽

New Process ◽

Creative Computing ◽

Classroom Use

Abstract. The ability to model surface processes and to couple them to both subsurface and atmospheric regimes has proven invaluable to research in the Earth and planetary sciences. However, creating a new model typically demands a very large investment of time, and modifying an existing model to address a new problem typically means the new work is constrained to its detriment by model adaptations for a different problem. Landlab is an open-source software framework explicitly designed to accelerate the development of new process models by providing (1) a set of tools and existing grid structures – including both regular and irregular grids – to make it faster and easier to develop new process components, or numerical implementations of physical processes; (2) a suite of stable, modular, and interoperable process components that can be combined to create an integrated model; and (3) a set of tools for data input, output, manipulation, and visualization. A set of example models built with these components is also provided. Landlab's structure makes it ideal not only for fully developed modelling applications but also for model prototyping and classroom use. Because of its modular nature, it can also act as a platform for model intercomparison and epistemic uncertainty and sensitivity analyses. Landlab exposes a standardized model interoperability interface, and is able to couple to third-party models and software. Landlab also offers tools to allow the creation of cellular automata, and allows native coupling of such models to more traditional continuous differential equation-based modules. We illustrate the principles of component coupling in Landlab using a model of landform evolution, a cellular ecohydrologic model, and a flood-wave routing model.

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Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics

10.5194/esurf-2016-45 ◽

2016 ◽

Author(s):

Daniel E. J. Hobley ◽

Jordan M. Adams ◽

Sai Siddhartha Nudurupati ◽

Eric W. H. Hutton ◽

Nicole M. Gasparini ◽

...

Keyword(s):

Open Source ◽

Numerical Models ◽

Epistemic Uncertainty ◽

Process Models ◽

Third Party ◽

Sensitivity Analyses ◽

Surface Dynamics ◽

New Process ◽

Creative Computing ◽

Classroom Use

Abstract. The ability to model surface processes and to couple them to both subsurface and atmospheric regimes has proven invaluable to research in the Earth and planetary sciences. However, creating a new model typically demands a very large investment of time, and modifying an existing model to address a new problem typically means the new work is constrained to its detriment by model adaptations for a different problem. Landlab is an open-source software framework explicitly designed to accelerate the development of new process models by providing: (1) a set of tools and existing grid structures – including both regular and irregular grids – to make it faster and easier to develop new process components, or numerical implementations of physical processes; (2) a suite of stable, modular, and interoperable process components that can be combined to create an integrated model; and (3) a set of tools for data input, output, manipulation, and visualization. A set of example models built with these components is also provided. Landlab's structure makes it ideal not only for fully developed modelling applications, but also for model prototyping and classroom use. Because of its modular nature, it can also act as a platform for model intercomparison and epistemic uncertainty and sensitivity analyses. Landlab exposes a standardized model interoperability interface, and is able to couple to third party models and software. Landlab also offers tools to allow the creation of cellular automata, and allows native coupling of such models to more traditional continuous differential equation-based modules. We illustrate the principles of component coupling in Landlab using a model of landform evolution, a cellular ecohydrologic model, and a flood-wave routing model.

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COMPARATIVE FEATURES OF OPEN SOURCE SOFTWARE PRODUCTS FOR THE DEVELOPMENT OF AN AUTOMATED BREAST CANCER DIAGNOSTIC PROGRAM

Eastern Ukrainian Medical Journal ◽

10.21272/eumj.2019;7(4):377-385 ◽

2019 ◽

Vol 7 (4) ◽

pp. 377-385

Author(s):

V. Kovalev ◽

Y. Diachenko ◽

V. Malyshev ◽

S. Rjabceva ◽

O. Kolomiets ◽

...

Keyword(s):

Breast Cancer ◽

Open Source ◽

Cancer Diagnosis ◽

Open Source Software ◽

Imaging Techniques ◽

Digital Pathology ◽

Third Party ◽

Histopathological Diagnosis ◽

Histological Verification ◽

Whole Slide Images

Breast cancer is one of the most common cancer diseases in the world among women. The reliability of histological verification of breast cancer depends on pathologist’s experience, knowledge, his willingness to self-improve and study specialized literature. Digital pathology is also widely used for educational purposes, in telepathology, teleconsultation and research projects. Recently developed Whole Slide Image (WSI) system opens great opportunities in the histopathological diagnosis quality improvement. Digital whole-slide images provide the effective use of morphometry and various imaging techniques to assist pathologists in quantitative and qualitative evaluation of histopathological preparations. The development of software for morphological diagnosis is important for improving the quality of histological verification of diagnosis in oncopathology. The purpose of this work is to find and benchmark existing open-source software for the whole-slide histological images processing. Choosing an open source program is an important step in developing an automated breast cancer diagnosis program. The result is a detailed study of open-source software: ASAP, Orbit, Cytomine and QuPath. Their features and methods of image processing were analyzed. QuPath software has the best characteristics for extending it with an automated module for the cancer diagnosis. QuPath combines a user-friendly, easy-to-use interface, customizable functionality, and moderate computing power requirements. Besides, QuPath works with whole-slide images with immunohistochemical markers; features implemented in this software allow making a morphometric analysis. QuPath saves time for a graphical user interface development and provides a scalable system to add new key features. QuPath supports third-party MATLAB and Python extensions.

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Executing Distributed Healthcare and Research Processes – The HiGHmed Data Sharing Framework

German Medical Data Sciences: Bringing Data to Life - Studies in Health Technology and Informatics ◽

10.3233/shti210060 ◽

2021 ◽

Author(s):

Hauke Hund ◽

Reto Wettstein ◽

Christian M. Heidt ◽

Christian Fegeler

Keyword(s):

Open Source ◽

Data Sharing ◽

Record Linkage ◽

Healthcare Delivery ◽

Third Party ◽

Size Estimation ◽

University Hospitals ◽

Reference Implementation ◽

Healthcare Processes ◽

Process Engine

Several standards and frameworks have been described in existing literature and technical manuals that contribute to solving the interoperability problem. Their data models usually focus on clinical data and only support healthcare delivery processes. Research processes including cross organizational cohort size estimation, approvals and reviews of research proposals, consent checks, record linkage and pseudonymization need to be supported within the HiGHmed medical informatics consortium. The open source HiGHmed Data Sharing Framework implements a distributed business process engine for executing arbitrary biomedical research and healthcare processes modeled and executed using BPMN 2.0 while exchanging information using FHIR R4 resources. The proposed reference implementation is currently being rolled out to eight university hospitals in Germany as well as a trusted third party and available open source under the Apache 2.0 license.

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

Frontiers in Psychiatry ◽

10.3389/fpsyt.2021.578298 ◽

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.

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Blockchain Technology and It’s Applications in E-Governance Services

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.d8599.118419 ◽

2019 ◽

Vol 8 (4) ◽

pp. 5795-5802

Keyword(s):

Supply Chain ◽

Data Structure ◽

Open Source ◽

Smart Cities ◽

Third Party ◽

Technical Aspects ◽

Blockchain Technology ◽

Smart Contract ◽

Peer Network ◽

Peer To Peer Network

Blockchain Technology is one of the most popular technologies of present days. This technology has the capability to eliminate the requirement of third party to validate the transactions over the Peer-to-Peer network. Due to various features of Blockchain like smart contract, consensus mechanism, network transactions are completed securely, efficiently and timely. This technology is very useful in many areas including medical, IoT, e-Governance services, smart cities, taxation, supply chain, banking etc. In this paper, we discuss the Blockchain Technology in detail, its data structure, open source platform like Ethereum and Hyperledger, technical aspects of this technology, possible applications of this technology, challenges and limitations in adaptation of this technology.

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Tools4MSP: an open source software package to support Maritime Spatial Planning

PeerJ Computer Science ◽

10.7717/peerj-cs.165 ◽

2018 ◽

Vol 4 ◽

pp. e165 ◽

Cited By ~ 10

Author(s):

Stefano Menegon ◽

Alessandro Sarretta ◽

Daniel Depellegrin ◽

Giulio Farella ◽

Chiara Venier ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Spatial Planning ◽

Software Package ◽

Integrated System ◽

Third Party ◽

Data Repositories ◽

Open Source Software Package ◽

Geospatial Datasets ◽

Maritime Spatial Planning

This paper presents the Tools4MSP software package, a Python-based Free and Open Source Software (FOSS) for geospatial analysis in support of Maritime Spatial Planning (MSP) and marine environmental management. The suite was initially developed within the ADRIPLAN data portal, that has been recently upgraded into the Tools4MSP Geoplatform (data.tools4msp.eu), an integrated web platform that supports MSP through the application of different tools, e.g., collaborative geospatial modelling of cumulative effects assessment (CEA) and marine use conflict (MUC) analysis. The package can be used as stand-alone library or as collaborative webtool, providing user-friendly interfaces appropriate to decision-makers, regional authorities, academics and MSP stakeholders. An effective MSP-oriented integrated system of web-based software, users and services is proposed. It includes four components: the Tools4MSP Geoplatform for interoperable and collaborative sharing of geospatial datasets and for MSP-oriented analysis, the Tools4MSP package as stand-alone library for advanced geospatial and statistical analysis, the desktop applications to simplify data curation and the third party data repositories for multidisciplinary and multilevel geospatial datasets integration. The paper presents an application example of the Tools4MSP GeoNode plugin and an example of Tools4MSP stand-alone library for CEA in the Adriatic Sea. The Tools4MSP and the developed software have been released as FOSS under the GPL 3 license and are currently under further development.

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Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research

JCO Clinical Cancer Informatics ◽

10.1200/cci.19.00131 ◽

2020 ◽

pp. 336-345 ◽

Cited By ~ 2

Author(s):

Erik Ziegler ◽

Trinity Urban ◽

Danny Brown ◽

James Petts ◽

Steve D. Pieper ◽

...

Keyword(s):

Cancer Research ◽

Open Source ◽

Web Application ◽

Data Exchange ◽

Quantitative Imaging ◽

Third Party ◽

Web Based ◽

Web Architecture ◽

Imaging Research ◽

Commercial Applications

PURPOSE Zero-footprint Web architecture enables imaging applications to be deployed on premise or in the cloud without requiring installation of custom software on the user’s computer. Benefits include decreased costs and information technology support requirements, as well as improved accessibility across sites. The Open Health Imaging Foundation (OHIF) Viewer is an extensible platform developed to leverage these benefits and address the demand for open-source Web-based imaging applications. The platform can be modified to support site-specific workflows and accommodate evolving research requirements. MATERIALS AND METHODS The OHIF Viewer provides basic image review functionality (eg, image manipulation and measurement) as well as advanced visualization (eg, multiplanar reformatting). It is written as a client-only, single-page Web application that can easily be embedded into third-party applications or hosted as a standalone Web site. The platform provides extension points for software developers to include custom tools and adapt the system for their workflows. It is standards compliant and relies on DICOMweb for data exchange and OpenID Connect for authentication, but it can be configured to use any data source or authentication flow. Additionally, the user interface components are provided in a standalone component library so that developers can create custom extensions. RESULTS The OHIF Viewer and its underlying components have been widely adopted and integrated into multiple clinical research platforms (e,g Precision Imaging Metrics, XNAT, LabCAS, ISB-CGC) and commercial applications (eg, Osirix). It has also been used to build custom imaging applications (eg, ProstateCancer.ai, Crowds Cure Cancer [presented as a case study]). CONCLUSION The OHIF Viewer provides a flexible framework for building applications to support imaging research. Its adoption could reduce redundancies in software development for National Cancer Institute–funded projects, including Informatics Technology for Cancer Research and the Quantitative Imaging Network.

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Utilizing Readily Available and Open Source Libraries to Create a 3D Game Engine

International Journal of Gaming and Computer-Mediated Simulations ◽

10.4018/jgcms.2009091502 ◽

2009 ◽

Vol 1 (4) ◽

pp. 20-49 ◽

Cited By ~ 3

Author(s):

Tim Stowell ◽

Jon Scoresby ◽

Michael R. Capell ◽

Brett E. Shelton

Keyword(s):

Open Source ◽

Third Party ◽

Game Engine ◽

Application Development ◽

Development Environment ◽

Checks And Balances ◽

Development Platform ◽

Making Choices ◽

Game Engines ◽

Fully Functioning

Market 3D engines have all the capabilities needed for developing full-featured 3D simulation and game environments. However, for those in education and small business, it remains a formidable task to acquire the resources needed to purchase or create a development platform with cutting-edge capabilities. Leveraging existing and open-source software libraries can greatly enhance the main application development, freeing developers to focus more on the application concept itself rather than the needed supporting pieces. This article explores the nuances of successfully mixing core code with these third-party libraries in creating a fully functioning development environment. Many steps with accompanying checks-and-balances are involved in creating a game engine, including making choices of which libraries to use, and integrating the core code with third-party libraries. By offering insights into our open source driven process, we help inform the understanding of how game engines may be generated for other educational and small-budget projects.

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