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Visualizing multidimensional cancer genomics data

GENOME MEDICINE 2013年第1期5卷 9-9页

作者： Schroeder, Michael P. Gonzalez-Perez, Abel Lopez-Bigas, Nuria UPF Res Program Biomed Informat GRIB E-08003 Barcelona Spain ICREA Barcelona Spain

Cancer genomics projects employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Examples include projects carried out by the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). A crucial step in the extraction of knowledge from the data is the exploration by experts of the different alterations, as well as the multiple relationships between them. To that end, the use of intuitive visualization tools that can integrate different types of alterations with clinical data is essential to the field of cancer genomics. Here, we review effective and common visualization techniques for exploring oncogenomics data and discuss a selection of tools that allow researchers to effectively visualize multidimensional oncogenomics datasets. The review covers visualization methods employed by tools such as Circos, Gitools, the Integrative Genomics Viewer, Cytoscape, Savant Genome Browser, StratomeX and platforms such as cBio Cancer Genomics Portal, IntOGen, the UCSC Cancer Genomics Browser, the Regulome Explorer and the Cancer Genome Workbench.

关键词： application programming interface Visualization Tool Visual Exploration Somatic Alteration Cancer Driver

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APIs for EU Governments: A Landscape Analysis on Policy Instruments, Standards, Strategies and Best Practices

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DATA 2021年第6期6卷 59-59页

作者： Vaccari, Lorenzino Posada, Monica Boyd, Mark Santoro, Mattia European Commiss Joint Res Ctr JRC I-21017 Ispra Italy Natl Res Council Italy CNR IIA Inst Atmospher Pollut Res I-50019 Sesto Fiorentino Italy

application programming interfaces (APIs) could greatly facilitate the exchange of data and functionalities between software applications in a flexible, controlled and secure way, especially on the web. Private companies, from startups to enterprises, have been using APIs for several years now, but it is only recently that APIs have seen increased interest in the public sector. API adoption in the public sector faces organisational, technical, legal and economic obstacles, and to overcome these barriers, proposed methods from the private sector and early adopters in the public sector provide a way forward. The available documentation is often sparse, difficult to find and to reuse for new contexts. No past efforts to collect and analyse these resources have been made. To address this shortcoming, this paper describes a landscape analysis in four areas: the main European Commission policy instruments on the adoption of APIs, the available web API standards, a set of European government API strategies and cases, and a list of government proposed methods distilled from more than 3900 documents. Our results reveal that European policy legislation and associated instruments promote, and in some cases mandate, the use of APIs, and that governments' API strategies in the European Union are rather young but also that there are well known web APIs standards and proposed methods ready to support the digital transformation of governments through rapid, harmonised and successful adoption of APIs.

关键词： digital government eGovernment application programming interface API interoperability Digital Single Market digital transformation

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Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer

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EPIGENETICS & CHROMATIN 2015年第1期8卷 22-22页

作者： Diez-Villanueva, Anna Mallona, Izaskun Peinado, Miguel A. Inst Predict & Personalized Med Canc IMPPC Badalona 08916 Spain Hlth Res Inst Germans Trias & Pujol IGTP Badalona 08916 Spain

Background: The Cancer Genome Atlas (TCGA) offers a multilayered view of genomics and epigenomics data of many human cancer types. However, the retrieval of expression and methylation data from TCGA is a cumbersome and time-consuming task. Results: Wanderer is an intuitive Web tool allowing real time access and visualization of gene expression and DNA methylation profiles from TCGA. Given a gene query and selection of a TCGA dataset (e.g., colon adenocarcinomas), the Web resource provides the expression profile, at the single exon level, and the DNA methylation levels of HumanMethylation450 BeadChip loci inside or in the vicinity of the queried gene. Graphic and table outputs include individual and summary data as well as statistical tests, allowing the comparison of tumor and normal profiles and the exploration along the genomic locus and across tumor collections. Conclusions: Wanderer offers a simple interface to straightforward access to TCGA data, amenable to experimentalists and clinicians without bioinformatics expertise. Wanderer may be accessed at http://***/wanderer.

关键词： application programming interface Glyph Epigenomics Data Bioinformatics Skill Zinc Transporter ZIP14

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Blackboard-based software framework and tool for mobile device context awareness

VTT Publications

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VTT Publications 2005年第579期 3-225页

作者： Korpipää, Panu VTT Electronics Finland

The usage needs of a mobile device vary according to context. Mobile context awareness research aims at providing the device user with a way of usage that suits the situation. Interaction based on context requires acquiring, abstracting and delivering information from multiple sources, such as sensors, to the application or application control. A generic software framework and tool for facilitating the rapid development of mobile device context-aware applications were developed in this work. The blackboard-based framework supports all tasks that are required for context-based application control, where contexts can be any events that are relevant to user interaction with the application, including explicit inputs. The core component of the framework, Context Manager, provides a publish and subscribe mechanism and a database for the applications and application control. The framework provides an application programming interface (API) for developers. As a higher abstraction-level programming interface, a customization tool enables easy end-user development of context-aware features into existing applications without changing them. An extensible ontology is used as a uniform context representation within the framework. The purpose of the ontology, together with the API, is to enable easy access, use and reuse of human-understandable context information. Context information sources, such as sensors, often produce a continuous stream of low abstraction-level data. The framework supports the transformation of a continuous data stream into abstracted context events, described in the ontology. Context information is delivered to applications or application control as abstracted events. The main result of the dissertation is a software framework, ontology and tool, which facilitate the customization of sensor-based human-computer interaction in mobile devices. The practical applicability, scope, and computational efficiency of the implemented framework and customization too

关键词： application control application programming interface Blackboard-based architecture Context management Context-aware computing Customization End-user development Information model Mobile computing Mobile context awareness Mobile interaction Personalization Sensor-based interaction Software framework

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Design and implementation of the first nationwide, web-based Chinese Renal Data System (CNRDS)

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BMC MEDICAL INFORMATICS AND DECISION MAKING 2012年第1期12卷 11-11页

作者： Xie, Fengbo Zhang, Dong Wu, Jinzhao Zhang, Yunfeng Yang, Qing Sun, Xuefeng Cheng, Jing Chen, Xiangmei Tsinghua Univ Sch Med Dept Biomed Engn Med Syst Biol Res Ctr Beijing 100084 Peoples R China Natl Engn Res Ctr Beijing Biochip Technol Beijing 102206 Peoples R China Chinese Gen Hosp PLA Dept Nephrol State Key Lab Kidney Dis Beijing 100853 Peoples R China Tsinghua Univ State Key Lab Biomembrane & Membrane Biotechnol Beijing 100084 Peoples R China

Background: In April 2010, with an endorsement from the Ministry of Health of the People's Republic of China, the Chinese Society of Nephrology launched the first nationwide, web-based prospective renal data registration platform, the Chinese Renal Data System (CNRDS), to collect structured demographic, clinical, and laboratory data for dialysis cases, as well as to establish a kidney disease database for researchers and policy makers. Methods: The CNRDS program uses information technology to facilitate healthcare professionals to create a blood purification registry and to deliver an evidence-based care and education protocol tailored to chronic kidney disease, as well as online forum for communication between nephrologists. The online portal https://*** is implemented as a Java web application using an Apache Tomcat web server and a MySQL database. All data are stored in a central databank to establish a Chinese renal database for research and publication purposes. Results: Currently, over 270,000 clinical cases, including general patient information, diagnostics, therapies, medications, and laboratory tests, have been registered in CNRDS by 3,669 healthcare institutions qualified for hemodialysis therapy. At the 2011 annual blood purification forum of the Chinese Society of Nephrology, the CNRDS 2010 annual report was reviewed and accepted by the society members and government representatives. Conclusions: CNRDS is the first national, web-based application for collecting and managing electronic medical records of patients with dialysis in China. It provides both an easily accessible platform for nephrologists to store and organize their patient data and acts as a communication platform among participating doctors. Moreover, it is the largest database for treatment and patient care of end-stage renal disease (ESRD) patients in China, which will be beneficial for scientific research and epidemiological investigations aimed at improving the quality of life

关键词： Chronic Kidney Disease application programming interface Case Report Form United States Renal Data System Renal Registry

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BIM AIDED INFORMATION AND VISUALIZATION REPOSITORY FOR MANAGING CONSTRUCTION DELAY CLAIMS

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JOURNAL OF INFORMATION TECHNOLOGY IN CONSTRUCTION 2021年 26卷 1023-1040页

作者： Ali, Babar Zahoor, Hafiz Aibinu, Ajibade Nasir, Abdur Rehman Tariq, Ali Imran, Umair Khan, Rashid Mehmood Univ Melbourne Melbourne Sch Design Fac Architecture Bldg & Planning Melbourne Vic Australia Natl Univ Sci & Technol NUST Coll Civil Engn Dept Construct Engn & Management Risalpur Campus Risalpur 24080 Pakistan Natl Univ Sci & Technol SCEE Dept Construct Engn & Management Islamabad 44000 Pakistan Abasyn Univ Fac Civil Engn Islamabad Campus Islamabad 45710 Pakistan Natl Univ Modern Languages Dept Management Sci Islamabad 44000 Pakistan

Delays in construction result in a multitude of negative effects on project performance, and severe dismays among participating parties. This study aims to digitize the traditional process of recording and managing the construction delays using Building Information Modeling (BIM). Extensive literature review followed by semi structure interviews of 21 industry experts were carried out to identify the issues faced by construction stakeholders in managing construction delays. To resolve these issues, a plugin named BIM-based Construction Delays Recorder (BIM-CDR) is developed using application programming interface (API) of the most commonly used BIM software i.e. Autodesk Revit. BIM-CDR provides a centralized repository, encompassing detailed information related to delays, which can be retrieved and visualized to analyze their impact on delay claims. To assess the effectiveness of BIM-CDR, a feasibility study is conducted with the experts' review panel. The results revealed that BIM-CDR can record wide-ranging information related to all the significant issues causing delays on construction sites, and can help in effectively managing their corresponding claims. The advantages of the developed prototype include visualization of delays' location, facilitation of delay analysis and effective delays management. Moreover, it also promotes transparency and speedy settlement of delay related claims without any unwanted disputes.

关键词： Construction delays Building Information Modeling application programming interface Plugin Delay analysis Claims

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Computed tomography-based automated measurement of abdominal aortic aneurysm using semantic segmentation with active learning

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SCIENTIFIC REPORTS 2024年第1期14卷 1-13页

作者： Kim, Taehun On, Sungchul Gwon, Jun Gyo Kim, Namkug Univ Ulsan Asan Med Inst Convergence Sci & Technol Asan Med Ctr Dept Convergence MedColl Med 88Olympic Ro 43 Gil Seoul 05505 South Korea Korea Inst Sci & Technol Artificial Intelligence & Robot Inst Seoul South Korea Univ Ulsan Asan Med Inst Convergence Sci & Technol Asan Med Ctr Dept Biomed EngnColl Med Seoul South Korea Univ Ulsan Coll Med Asan Med Ctr Div Vasc SurgDept Surg 88Olympic Ro 43 Gil Seoul 05505 South Korea Univ Ulsan Coll Med Asan Med Ctr Dept Radiol Seoul South Korea

Accurate measurement of abdominal aortic aneurysm is essential for selecting suitable stent-grafts to avoid complications of endovascular aneurysm repair. However, the conventional image-based measurements are inaccurate and time-consuming. We introduce the automated workflow including semantic segmentation with active learning (AL) and measurement using an application programming interface of computer-aided design. 300 patients underwent CT scans, and semantic segmentation for aorta, thrombus, calcification, and vessels was performed in 60-300 cases with AL across five stages using UNETR, SwinUNETR, and nnU-Net consisted of 2D, 3D U-Net, 2D-3D U-Net ensemble, and cascaded 3D U-Net. 7 clinical landmarks were automatically measured for 96 patients. In AL stage 5, 3D U-Net achieved the highest dice similarity coefficient (DSC) with statistically significant differences (p < 0.01) except from the 2D-3D U-Net ensemble and cascade 3D U-Net. SwinUNETR excelled in 95% Hausdorff distance (HD95) with significant differences (p < 0.01) except from UNETR and 3D U-Net. DSC of aorta and calcification were saturated at stage 1 and 4, whereas thrombus and vessels were continuously improved at stage 5. The segmentation time between the manual and AL-corrected segmentation using the best model (3D U-Net) was reduced to 9.51 +/- 1.02, 2.09 +/- 1.06, 1.07 +/- 1.10, and 1.07 +/- 0.97 min for the aorta, thrombus, calcification, and vessels, respectively (p < 0.001). All measurement and tortuosity ratio measured - 1.71 +/- 6.53 mm and - 0.15 +/- 0.25. We developed an automated workflow with semantic segmentation and measurement, demonstrating its efficiency compared to conventional methods.

关键词： Abdominal aortic aneurysm Active learning application programming interface Computer-aided design Deep learning Endovascular abdominal repair stent graft

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Cutting through complexity: Coordinated demand response and future directions in global communication technologies

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ELECTRICITY JOURNAL 2023年第9-10期36卷

作者： Mohseni, Soheil Brent, Alan C. Victoria Univ Wellington Wellington Fac Engn Sustainable Energy Syst Wellington 6140 New Zealand Ausgrid Sydney 2000 Australia Univ Technol Sydney Inst Sustainable Futures Sydney NSW 2007 Australia Univ Stellenbosch Dept Ind Engn ZA-7600 Stellenbosch South Africa Stellenbosch Univ Ctr Renewable & Sustainable Energy Studies ZA-7600 Stellenbosch South Africa

The global electricity market is undergoing a transformative shift, envisioning a future resembling commodity trading platforms. Enabled by mature communication technologies, this evolution empowers energy consumers worldwide to actively engage in the energy market, negotiating arrangements for adjusting energy demand during grid stress and optimizing costs. In this era of technological advancements, this vision is materializing globally. Commercial and industrial entities are playing active roles in ancillary services markets, providing crucial grid support. Efforts are expanding to engage smaller users through third-party aggregators. However, many initiatives retain opt-in structures, limiting customer engagement. A promising solution is local energy markets, integrating modest flexibility reserves globally. This empowers small-scale users to choose services aligned with their preferences. This paper delves into the essential components facilitating the transition to globally applicable, aggregator-mediated demand-side management markets. Anchored in dynamic consumer engagement and nurtured by reciprocal information flows, this shift signals a fundamental reshaping of the global energy landscape. The paper introduces a universally adaptable demand response aggregation framework for energy enterprises to systematically devise consumer-centric programs. This framework serves as a foundational structure, fostering a strategic and flexible approach to meet evolving consumer preferences in demand response initiatives worldwide.

关键词： AMI advanced metering infrastructure ANSI American National Standards Institute API application programming interface CPN customer premises network DCU data concentrator unit DR demand response DRA demand response aggregator DSM demand-side management ETSI European Telecommunications Standards Institute HAN home area network HVAC heating, ventilation, and air conditioning IAN industrial area network ISO independent system operator IoT Internet of Things LAN local area network M2M machine-to-machine MQTT message queuing telemetry transport NAN neighborhood area network NIST U.S. National Institute of Standards and Technology Open ADR Open Automated Demand Response PLC power line communication TCP/IP Transmission Control Protocol/Internet Protocol WAN wide area network

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Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon

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JOURNAL OF BIOMEDICAL INFORMATICS 2019年 100卷 103325-000页

作者： Fecho, Karamarie Ahalt, Stanley C. Arunachalam, Saravanan Champion, James Chute, Christopher G. Davis, Sarah Gersing, Kenneth Glusman, Gustavo Hadlock, Jennifer Lee, Jewel Pfaff, Emily Robinson, Max Sid, Eric Ta, Casey Xu, Hao Zhu, Richard Zhu, Qian Peden, David B. Univ North Carolina Chapel Hill Renaissance Comp Inst Chapel Hill NC 27599 USA Univ North Carolina Chapel Hill Inst Environm Chapel Hill NC USA Univ North Carolina Chapel Hill North Carolina Translat & Clin Sci Inst Chapel Hill NC USA Johns Hopkins Univ Baltimore MD USA NIH Natl Ctr Advancing Translat Sci Bldg 10 Bethesda MD 20892 USA Inst Syst Biol Seattle WA USA Columbia Univ New York NY USA Univ North Carolina Chapel Hill Ctr Environm Med Asthma & Lung Biol Chapel Hill NC USA Univ North Carolina Chapel Hill Dept Pediat Div Allergy Immunol & Rheumatol Sch Med Chapel Hill NC USA

This special communication describes activities, products, and lessons learned from a recent hackathon that was funded by the National Center for Advancing Translational Sciences via the Biomedical Data Translator program (`Translator'). Specifically, Translator team members self-organized and worked together to conceptualize and execute, over a five-day period, a multi-institutional clinical research study that aimed to examine, using open clinical data sources, relationships between sex, obesity, diabetes, and exposure to airborne fine particulate matter among patients with severe asthma. The goal was to develop a proof of concept that this new model of collaboration and data sharing could effectively produce meaningful scientific results and generate new scientific hypotheses. Three Translator Clinical Knowledge Sources, each of which provides open access (via application programming interfaces) to data derived from the electronic health record systems of major academic institutions, served as the source of study data. Jupyter Python notebooks, shared in GitHub repositories, were used to call the knowledge sources and analyze and integrate the results. The results replicated established or suspected relationships between sex, obesity, diabetes, exposure to airborne fine particulate matter, and severe asthma. In addition, the results demonstrated specific differences across the three Translator Clinical Knowledge Sources, suggesting cohort- and/or environment-specific factors related to the services themselves or the catchment area from which each service derives patient data. Collectively, this special communication demonstrates the power and utility of intense, team-oriented hackathons and offers general technical, organizational, and scientific lessons learned.

关键词： Hackathon Open data Clinical data Team science application programming interface Multi-institutional collaboration

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A knowledge discovery object model API for Java

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BMC BIOINFORMATICS 2003年第1期4卷 51-51页

作者： Zuyderduyn, SD Jones, SJM British Columbia Canc Agcy Canadas Michael Smith Genome Sci Ctr Vancouver BC V5Z 4E6 Canada

Background: Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results: This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions: The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at http://***/bioinfo/software.

关键词： Biological Data Resource Description Framework application programming interface Software Project Biological Knowledge

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