Programming Language Interface Research Articles

МАТЕМАТИЧЕСКИЕ МОДЕЛИ И ЧИСЛЕННЫЕ МЕТОДЫ В КАРДИОЛОГИИ: СОБСТВЕННЫЙ ОПЫТ

Вackground. In the era of digital transformation in medicine, which is radically changing the way patient information is stored, processed and used, medical professionals need new tools and approaches that can efficiently process and interpret data for fast and accurate decision making. These methods also enable the creation of personalized treatment approaches, taking into account individual patient characteristics and risks. In this article, the authors share their own experience in applying numerical methods in cardiology. Purpose of the study. To develop methods of effective risk assessment of cardiovascular outcomes in different categories of patients. Characteristics of patients and methods of the study. Three variants of outcome prediction were included in the study. The 1st - assessment of the total risk of one-year cardiovascular outcomes after myocardial infarction with ST-segment elevation, the 2nd - assessment of the risk of postinfarction chronic heart failure, the 3rd – assessment of the risk of progressive course of atherosclerosis. Statistical analysis methods included the free cross-platform visual programming system Orange, the SPSS 22.0 package, and the C programming language console. Results and Conclusion. The conducted study has shown that the application of different approaches: regression analysis, machine learning, Excel programming capabilities, C programming language and console interface allows to develop models of cardiovascular outcomes prediction with high accuracy.

ImageNomer: Description of a functional connectivity and omics analysis tool and case study identifying a race confound

Most packages for the analysis of fMRI-based functional connectivity (FC) and genomic data are used with a programming language interface, lacking an easy-to-navigate GUI frontend. This exacerbates two problems found in these types of data: demographic confounds and quality control in the face of high dimensionality of features. The reason is that it is too slow and cumbersome to use a programming interface to create all the necessary visualizations required to identify all correlations, confounding effects, or quality control problems in a dataset. FC in particular usually contains tens of thousands of features per subject, and can only be summarized and efficiently explored using visualizations. To remedy this situation, we have developed ImageNomer, a data visualization and analysis tool that allows inspection of both subject-level and cohort-level demographic, genomic, and imaging features. The software is Python-based, runs in a self-contained Docker image, and contains a browser-based GUI frontend. We demonstrate the usefulness of ImageNomer by identifying an unexpected race confound when predicting achievement scores in the Philadelphia Neurodevelopmental Cohort (PNC) dataset, which contains multitask fMRI and single nucleotide polymorphism (SNP) data of healthy adolescents. In the past, many studies have attempted to use FC to identify achievement-related features in fMRI. Using ImageNomer to visualize trends in achievement scores between races, we find a clear potential for confounding effects if race can be predicted using FC. Using correlation analysis in the ImageNomer software, we show that FCs correlated with Wide Range Achievement Test (WRAT) score are in fact more highly correlated with race. Investigating further, we find that whereas both FC and SNP (genomic) features can account for 10-15% of WRAT score variation, this predictive ability disappears when controlling for race. We also use ImageNomer to investigate race-FC correlation in the Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP) dataset. In this work, we demonstrate the advantage of our ImageNomer GUI tool in data exploration and confound detection. Additionally, this work identifies race as a strong confound in FC data and casts doubt on the possibility of finding unbiased achievement-related features in fMRI and SNP data of healthy adolescents.

Prototyping an Online Patient Registration Based on a Smartphone App at the Malang Primary Health Care

Currently, the patient registration system at the Primary Health Care (PHC) in Malang City still uses a manual registration system with various existing problems, like the emergence of queues and patients jostling in the waiting room, so it takes longer for health services. This study aimed to design a prototype application for online patient registration at the Malang City Health Center. The method used is Research and Development Prototyping. The manufacturing stages start from (1) the identification of basic needs, (2) developing a working prototype, (3) using a prototype (trial), and (4) revising and improving the prototype. The instrument used in this study was an interview guide conducted with two Heads of PHC (Dinoyo and Rampal Celaket) and nine Registration Officers at two Health Centers to determine the need for designing a prototype online registration application. Observations were made regarding the existing IT systems (Hardware and Software) in both PHC, the facilities and infrastructure that support IT systems (rooms, internet networks, etc.) and the documents supporting the processes. The results of this prototype design were in the form of a list of functional and non-functional requirements, business process flow diagrams, data flow diagrams, Entity Relationship Diagrams, and Interface Design, including programming language and user interface. Based on the results of the online patient registration prototype design, it enters the initial stage of using a system design that is by user needs but has yet to reach the implementation stage. However, this prototype can be used as a reference in developing an integrated online registration system with existing information systems at the PHC.
 Keywords: Prototype, Online Registration, Smartphone, Primary Health Care, Patient

Tackling Data Quality Challenges in the Finnish Biodiversity Information Facility (FinBIF)

The Finnish Biodiversity Information Facility (FinBIF) Research Infrastructure (Schulman et al. 2021) is a national service with a broad coverage of the components of biodiversity informatics (Bingham et al. 2017). Data flows are managed under a single information technology (IT) architecture. Services are available in a single, branded on-line portal. Data are collated from all relevant sources e.g., research institutes, scientific collections, public authorities and citizen science projects, whose data represent a major contribution. The challenge is to analyse, classify and share good quality data in a way that the user understands its utility. Need for quality data The philosophy of FinBIF is that all observation records are important, and that all data are assessed for quality and able to be annotated. The challenge is that, in practice, many users desire data with 100% reliability. In our experience, most user concerns about data quality are related to citizen science data. Researchers are usually able to manage raw data to serve their purposes. However, decision-making authorities often have less capacity to analyse the data and thus require data that can be used instantly. Therefore, we need tools to provide users the data that are the most relevant and reliable for their specific use. For all users, standardized metadata (information about datasets) are key, when the user has doubts about the fitness-for-use of a particular dataset. There is also a need to provide data in different formats to serve various users. Finally, the service has to be machine-actionable (using an application programming interface (API) and R-package) as well as human-accessible for viewing and downloading data. Quality assignment FinBIF data accuracy varies significantly within and between datasets, and observers. Two quality-based classifications suitable for filtering are therefore applied. The dataset origin filter is based on the quality of a whole dataset (e.g. citizen science project) and includes three broad classes assigned with an appropriate quality label: Datasets by Professionals, by Specialists and by Citizen Scientists. The observation reliability filter is based on a single observation and on annotations by FinBIF users. This classification includes Expert verified, Community verified, Unassessed (default for all records), Uncertain, and Erroneous. The dataset origin does not necessarily determine the quality of the individual records in it. Observations made by citizen scientists are often accurate, while there may be errors in the professionally collected data. Records are frequently subject to annotation, which raises their quality over time (e.g., iNaturalist). Naturally, evidence (e.g., media, detailed descriptions, specimens) is needed for reliable identification. Annotating data When observations are compiled at FinBIF’s portal (Laji.fi), they are initially “Unassessed” (unless they have otherwise been assessed at the original source). When annotating occurrences, volunteers can make various entries using the tools provided. The aim of the commentary is to improve the quality of the observation data. Annotators are divided into two categories with two different roles: As a basic user, anyone who has logged in at Laji.fi can make comments or tag observations for review by experts. Users defined as experts have wider rights than basic users and their comments carry more weight. The most desired actions of expert users are to classify observations into confidence levels or to give them new or refined identifications. As a basic user, anyone who has logged in at Laji.fi can make comments or tag observations for review by experts. Users defined as experts have wider rights than basic users and their comments carry more weight. The most desired actions of expert users are to classify observations into confidence levels or to give them new or refined identifications. Information about new comments passes to the observer if the observation is recorded by using the FinBIF Observation Management System “Notebook”. However, comments cannot yet be automatically forwarded e.g., to the primary data management systems at the original source. Annotations add extra indications of quality. They do not replace or delete the original information. Nevertheless, annotations can change a record’s taxonomic identification, and by default, a record will be handled based on its latest identification. R-package for researchers and Public Authority Portal (PAP) for decision makers FinBIF has produced an R programming language interface to its API, which makes the publicly available data in FinBIF accessible from within R. For authorities, the PAP offers direct access to all available species information to authorised users, including sensitive and restricted-use data.

Conveyor belt experiment setup for programmable logic controller education

Programmable logic controllers (PLC) have been one of the most widely used controllers in industry. They have a graphical programming language interface resambling the relay panels which they are intended to replace so that the transition from relay panels might be swift and smooth. Although learning this programming language is easy, real life experiments are essential for students to gain greater understanding of the logic behind the language. However, it is generally too expensive to provide an experimental set-up for students to test their theoretical knowledge. For this reason, a conveyor and feeder system was developed as a low cost 3D printable design using a CAD program and implemented for use in a control laboratory. Using this conveyor set-up, students can experience how to program a practical example of a PLC devices used in industry together with an introduction to actuators and sensors. Reading actual sensors and using actuators via the inputs and outputs of a PLC to control a real life system will be far more effective than simulator alternatives.

Implementation of Risk Analyzer Model for Undertaking the Risk Analysis of Proposed Building Projects for A Selected Client

The model of RISK ANALYZER was implemented as Knowledge-based System for the purpose of undertaking risk analysis for proposed construction projects in a selected domain. The Fuzzy Decision Variables (FDVs) that cause differences between initial and final contract sums of building projects were identified, the likelihood of the occurrence of the risks were determined and a Knowledge-Based System that would rank the risks was constructed using JAVA programming language and Graphic User Interface. The Knowledge-Based System is composed a Knowledge Base for storing data, an Inference Engine for controlling and directing the use of knowledge for problem-solution, and a User Interface that assists the user retrieve, use and alter data in the Knowledge Base. The developed Knowledge-Based System was compiled, implemented and validated with data of previously completed projects. The client could utilize the Knowledge-Based System to undertake proposed building projects.

Rapid Simulation of Optimally Responsive Façade during Schematic Design Phases: Use of a New Hybrid Metaheuristic Algorithm

Operation of environmentally responsive building components requires rapid prediction of the optimal adaptation of geometric shapes and positions, and such responsive configuration needs to be identified during the design process as early as possible. However, building simulation practices to characterize optimized shapes of various geometric design candidates are limited by complex simulation procedures, slow optimization, and lack of site information. This study suggests a practical approach to the design of responsive building façades by integrating on-site sensors, building performance simulation (BPS), machine-learning, and 3D geometry modeling on a unified design interface. To this end, a novel and efficient hybrid optimization algorithm, tabu-based adaptive pattern search simulated annealing (T-APSSA), was developed and integrated with wireless sensor data communication (using nRF24L01 and ESP8266 WiFi modules) on a parametric visual programming language (VPL) interface Rhino Grasshopper (0.9.0076, McNeel, Seattle, USA). The effectiveness of T-APSSA for early-stage BPS and optimal design is compared with other metaheuristic algorithms, and the proposed framework is validated by experimental optimal envelope (window shading) designs for single (daylight) and multiple (daylight and energy) objectives. Test results demonstrate the improved efficiency of T-APSSA in calculations (two to four times faster than other algorithms). This T-APSSA-integrated sensor-enabled design optimization practice supports rapid BPS and digital prototyping of responsive building façade design.

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

BackgroundCurrent high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read.In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection.ResultsWe have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes.In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel.ConclusionsIncreasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.

VPL-Based Big Data Analysis System: UDAS

Over the past five years, research on big data analysis has been actively conducted, and many services have been developed to find valuable data. However, low quality of raw data and data loss problem during data analysis make it difficult to perform accurate data analysis. With the enormous generation of both unstructured and structured data, refinement of data is becoming increasingly difficult. As a result, data refinement plays an important role in data analysis. In addition, as part of efforts to ensure research reproducibility, the importance of reuse of researcher data and research methods is increasing; however, the research on systems supporting such roles has not been conducted sufficiently. Therefore, in this paper, we propose a big data analysis system named the unified data analytics suite (UDAS) that focuses on data refinement. UDAS performs data refinement based on the big data platform and ensures the reusability and reproducibility of refinement and analysis through the visual programming language interface. It also recommends open source and visualization libraries to users for statistical analysis. The qualitative evaluation of UDAS using the functional evaluation factor of the big data analysis platform demonstrated that the average satisfaction of the users is significantly high.

An HLA-Based Distributed Cosimulation Framework in Mixed-Signal System-on-Chip Design

In mixed-signal system-on-chip (SoC) design, distributed cosimulation is one of the practical approaches for unifying various abstracted hardware models using different description languages. Conventional ad hoc distributed cosimulation solutions do not have formal theoretical backgrounds of simulator integration into their solutions. In this brief, we propose a general cosimulation framework based on the high-level architecture (HLA) and newly defined programming language interface for interoperation (PLI-I) as a formal simulator interface. Based on the PLI-I and HLA, we propose formal integration and interoperation procedures. To reduce integration costs, the procedures have been developed into a common library and then merged with model-dependent signal-event converter to handle differently abstracted in/out signals. During the interoperation, to resolve the different time-advance mechanisms of the digital and analog simulators, the adapter executes an advanced HLA-based synchronization based on the presimulation concepts. The case study shows the reduced design effort in integrating and validating the heterogeneous models and simulators using the proposed framework in mixed-signal SoC design.

BioBIKE: A Web-based, programmable, integrated biological knowledge base

BioBIKE (biobike.csbc.vcu.edu) is a web-based environment enabling biologists with little programming expertise to combine tools, data, and knowledge in novel and possibly complex ways, as demanded by the biological problem at hand. BioBIKE is composed of three integrated components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Each of the five current BioBIKE instances provides all available information (genomic, metabolic, experimental) appropriate to a given research community. The BioBIKE programming language and graphical programming interface employ familiar operations to help users combine functions and information to conduct biologically meaningful analyses. Many commonly used tools, such as Blast and PHYLIP, are built-in, allowing users to access them within the same interface and to pass results from one to another. Users may also invent their own tools, packaging complex expressions under a single name, which is immediately made accessible through the graphical interface. BioBIKE represents a partial solution to the difficult question of how to enable those with no background in computer programming to work directly and creatively with mass biological information. BioBIKE is distributed under the MIT Open Source license. A description of the underlying language and other technical matters is available at www.Biobike.org.

Design de componentes construtivos personalizados usando um método de desenho baseado nas restrições

This article describes a systematic implementation of an explored technology-transfer model, looking for an optimization of building, enlargement or equipments processes in the housing industry. For achieving that optimization, a heterogeneous group of manufacturing activities are studied according to the UN Classifications Registry (UN 2007), and their application in the chilean industry is evaluated. The explored model has been formulated according to Senn’s (1992) method of prototype design, and the method of information systems development based on its life-cycle. Finally, by using a Visual Programming Language (VPL) interface, the model is applied for the formulation of the design problem of a customized constructive component. In this case, the component is a sanitary services pack. The proposal includes an experimental Graphic-User Interface (GUI), where each client configures the constructive components according to his particular requirements.

A transaction-based unified architecture for simulation and emulation

The availability of millions of transistors on a single chip has allowed the creation of complex on-chip systems. The functional verification of such systems has become a challenge. Simulation run times are increasing, and emulation is now a necessity. Creating separate verification environments for simulation and emulation slows the design cycle and it requires additional human efforts. This paper describes a layered architecture suitable for both simulation and emulation. The architecture uses transactions for communication and synchronization between the driving environment (DE) and the device under test (DUT). Transactions provide synchronization only as needed and cycle and event-based synchronization common in emulators. The result is more efficient development of the DE and 100% portability when moving from simulation to emulation. We give an overview of our layered architecture and describe its implementation. Our results show that, by using emulation, the register-transfer level (RTL) implementation of an industrial design can be verified in the same amount of time it takes to run a C-based simulation. We also show two orders of magnitude speeds up over simulations of C and RTL through a programming language interface

VHDL standards

Provides a brief overview of VHDL-related standards. The IEEE approved the original VHDL standard (IEEE Std 1076) in 1987, then revised and significantly enhanced it in 1993. In 2000, an interim edition added concurrency control features for shared variables. The new features, called protected types, are based on the idea of monitors seen in concurrent programming languages. The standard is now nearing the final stages of a further revision process, and is headed for approval later this year. This new version is essentially a maintenance revision, with no new language features. The VHDL working group has started collecting requirements for language enhancements to be included in the next revision. A task group within the VHDL working group is also writing a standard for a programming language interface for VHDL simulators and should have a draft ready toward the end of this year.

Abstract Interpretation for Termination Analysis in Functional Active Databases

An active database consists of a traditional database supplemented by a set of Event-Condition-Action (ECA) rules. One of the key questions for active database designers is that of termination of the ECA rules. The behaviour of the ECA rules may be obscure and their semantics is often not specified formally. Consequently, developing termination analysis algorithms and proving their correctness is a challenging task. In this paper we address this problem for functional active databases by adopting an abstract interpretation approach. By “functional active databases” we mean active databases whose transaction execution semantics have been expressed in a purely functional language. Although we demonstrate our techniques for a specific active DBMS which supports a functional database programming language interface, these techniques are directly applicable to other active DBMSs whose execution semantics have been specified using a functional or a denotational approach.

From object-process analysis to object-process design

The object-process methodology incorporates the system static-structural and dynamic-procedural aspects into a single, unified model. This unification bridges the gap that separates the static, “object” model from the dynamic, behavior, state, or function-oriented models found in many current object oriented methodologies. In this work we concentrate on the transition from object-process analysis to design within the development of information systems. We use a detailed case study as a running example throughout the paper to demonstrate how the structure-behavior unification, which characterizes object-process analysis, is carried on to object-process design. The case study first applies object-process analysis to perform the analysis stage. The sequence of steps that constitutes the design is then discussed and demonstrated through the case study. The design is divided into two phases: the analysis refinement phase and the implementation-dependent phase. Analysis refinement is concerned with adding details to the analysis results which are beyond the interest of the analysis itself, yet they are not related with a particular implementation. The implementation-dependent phase is concerned with code-level design, which takes place after specific implementation details, such as programming language, data organization, and user interface, have been made during the strategic design.

Designing and prototyping data-intensive applications in the Logres and Algres programming environment

The authors present an environment and a methodology for the design and rapid prototyping of data-intensive software applications, i.e., applications which perform substantial retrieval and update activity on persistent data. In the approach, the application is formally specified using Logres, a database language which combines object-oriented data modeling and rule-based programming. These specifications are translated into Algres, an extended relational algebra, thus yielding a rapid executable prototype. Algres programs embedded into a conventional programming language interface may be converted to conventional programs operating on a commercial relational system. This methodology helps automate the conversion from declarative requirements to imperative code, performing several tasks fully automatically and reducing the probability of human errors, while integrity constraints and application specifications are expressed in a declarative language, at a very high level of abstraction. >

A precision measurement system for use in underwater acoustics measurements.

A Precision Measurement System (PMS) has been developed at NRL-USRD to serve both as a production measurement system and as a platform for ongoing research in new signal generation and measurement techniques. This system is intended as a single-platform solution to most of USRD’s underwater acoustic test needs. Calibration of transducers and measurements of acoustic coatings are included in the tests performed by the PMS. The precision measurement system offers the following features: wide range in both frequency and amplitude; built-in calibration for traceability to NIST; multiple channels for simultaneous signal measurements; a flexible combination of analog gain and filtering stages; digital technology to allow generation of complex waveforms as well as sophisticated processing of measured data; an integrated programming language interface based on VAX/VMS workstations; a variety of signal processing algorithms for wideband versus narrow band, continuous versus transient, parametric versus nonparametric signal processing techniques. Four copies of the system have been built to insure uniformity of measurements across all USRD measurement facilities. Because the system is based on VAX/VMS, a variety of software is available for plotting and reporting as well as more sophisticated offline mathematical analysis.

The design of POSTGRES

This paper presents the preliminary design of a new database management system, called POSTGRES, that is the successor to the INGRES relational database system. The main design goals of the new system are to provide better support for complex objects, provide user extendibility for data types, operators and access methods, provide facilities for active databases (i.e., alerters and triggers) and inferencing including forward- and backward-chaining, simplify the DBMS code for crash recovery, produce a design that can take advantage of optical disks, workstations composed of multiple tightly-coupled processors, and custom designed VLSI chips, and make as few changes as possible (preferably none) to the relational model. The paper describes the query language, programming language interface, system architecture, query processing strategy, and storage system for the new system.