Summary: Studying biological systems generally relies on computational modeling and simulation, e.g., for model-driven discovery and hypothesis testing. Progress in standardization efforts led to the development of interrelated file formats to exchange and reuse models in systems biology, such as SBML, the Simulation Experiment Description Markup Language (SED-ML), or the Open Modeling EXchange format (OMEX). Conducting simulation experiments based on these formats requires efficient and reusable implementations to make them accessible to the broader scientific community and to ensure the reproducibility of the results. The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in Java™. The library simulates even complex bio-models and supports deterministic Ordinary Differential Equations (ODEs); Stochastic Differential Equations (SDEs); constraint-based analyses; recent SBML and SED-ML versions; exchange of results, and visualization of in silico experiments; open modeling exchange formats (COMBINE archives); hierarchically structured models; and compatibility with standard testing systems, including the Systems Biology Test Suite and published models from the BioModels and BiGG databases. Availability and implementation: SBSCL is freely available at https://draeger-lab.github.io/SBSCL/.

The multidisciplinary nature of the work required for research in the Covid-19 pandemic has created new challenges for health professionals in the battle against the virus. They need to be equipped with novel tools and resources ---that have emerged during the pandemic--- to gain access to breakthrough findings, know the latest developments, and to address their specific needs for rapid data acquisition, analysis, evaluation, and reporting. Because of the complex nature of the virus, the healthcare systems worldwide are severely impacted as the treatment and the vaccine for Covid-19 disease are not yet discovered. This leads to frequent changes in regulations and policies by governments and international organizations. Our analysis suggests that given the abundance of information sources, finding the most suitable tool for a given task is one of such challenges. But health professionals and policymakers need access to the most relevant, reliable, trusted, and latest information and tools that can be used in their day-to-day tasks of Covid-19 research and analysis. In this article, we present our analysis of various novel and important tools that have been specifically developed during the Covid-19 pandemic and that can be used by the health professionals community to help in advancing their analysis and research. These tools comprise of search engines, information repositories for literature and clinical trials, data sources, dashboards, and forecasting models. We present list of the minimally essential tools to serve a multitude of purposes, from hundreds of those developed since the beginning of the pandemic. A critical analysis is provided for the selected tools based on 17 parameters that can be useful for researchers and analysts for their evaluations. These parameters make up our evaluation framework and have not been used previously for analysis and evaluation. Hence, knowledge of the tools will not only increase the productivity but will also allow to explore new dimensions for using existing tools with more control, better management, and greater outcome of their research. In addition, the parameters used in our framework can be applied for future evaluations of similar tools and health professionals can adapt them for evaluation of other tools not covered in this analysis.

This proposal describes the design and development of an interoperable application that supports green open access with long-term sustainability and improved user experience of article deposit. Introduction: The lack of library resources and unfriendly repository user interface are two significant barriers that hinder green open access. Tasked to implement the open access mandate, librarians at an American research university developed a comprehensive system called Easy Deposit 2 to automate the support workflow of green open access. Implementation: Easy Deposit 2 is a web application that is able to harvest newly publications, outreach for manuscript on behalf of the library, and facilitate self-archiving to IR. It is developed and maintained by the library and integrated with the IR. Results and Discussion: The article deposit rate is about 25% with Easy Deposit 2, which increases significantly comparing to the previous period. It also serves as a local database for faculty publications with open access status. The lesson learned is that library cannot rely on a single commercial provider for publication data due to mismatched priorities. Conclusion: Recent IT developments provides new opportunities of innovation like Easy Deposit 2 in supporting open access. Academic librarians are vital in promoting "openness" in scholarly communication such as transparency and diversity in the sharing of publication data.

Background: Process mining (PM) exploits event logs to obtain meaningful information about the processes that produced them. As the number of applications developed on cloud infrastructures is increasing, it becomes important to study and discover their underlying processes. However, many current PM technologies face challenges in dealing with complex and large event logs from cloud applications, especially when they have little structure (e.g., clickstreams). Methods: Using Design Science Research, this paper introduces a new method, called Cloud Pattern API – Process Mining (CPA-PM), that enables discovering and analyzing cloud-based application processes using PM in a way that addresses many of these challenges. CPA-PM exploits a new application programming interface (API), with an R implementation, for creating repeatable scripts that preprocess event logs collected from such applications. Results: Applying CPA-PM to a case with real and evolving event logs related to the trial process of a Software-as-a-Service cloud application led to useful analyses and insights, with reusable scripts. Conclusion: CPA-PM helps producing executable scripts for filtering event logs from clickstream and cloud-based applications, where the scripts can be used in pipelines while minimizing the need for error-prone and time-consuming manual filtering.

The world tsunami hazard map is developed to understand the pattern of occurrence of tsunami across the globe and for using this database for preparing effective evacuation plan and rescue operations. It has been developed by using Web GIS tools. HTML, CSS, Java Script, JQuery, IIS and Maps API are utilized to develop hazard map. These data can be even used by government authorities as well as by other nodal agencies.

We present a methodology to enable users to interact with statistical information owned by an institution and stored in a cloud infrastructure. Mainly based on R, this approach was developed following the open-data philosophy. Also, since we use R, the implementation is mainly based on open-source software. R gives several advantages from the point of view of data management and acquisition, as it becomes a common framework that can be used to structure the processes involved in any statistical operation. This simplifies the access to the data and enable to use all the power of R in the cloud information. This methodology was applied successfully to develop a tool to manage the data of the Centre d’Estudis d’Opinió, but it can be applied to other institutions to enable open access to its data. The infrastructure also was deployed to a cloud infrastructure, to assure the scalability and a 24/7 access.

Apigenin (API) possesses excellent antitumor properties, but its limited water solubility and low bioavailability restrict its therapeutic impact. Thus, a suitable delivery systems is needed to overcome these limitations and improve the therapeutic efficiency. Poly (lactic-co-glycolic acid) (PLGA) is a copolymer extensively utilized in drug delivery. Hyaluronic acid (HA) is a major extracellular matrix and can specifically bind with CD44 on colon cancer cells. Chitosan (CS) can serve as an intermediate binding with HA and PLGA. Herein, we aimed to perpare receptor-selective HA-coated PLGA nanoparticles (NPs) for colon cancer with high expression of CD44. Firstly, API was encapsulated in PLGA to obtain PLGA-API-NPs, which were then sequentially combined with CS and HA to form HA-coated PLGA NPs. HA coated PLGA NPs had a stronger sustained-release capability. Cellular uptake of HA coated PLGA NPs was enhanced in HT-29 cells with high expression of CD44. HA-PLGA-DiR-NPs can target specificity towards the HT-29 ectopic tumor model. Overall, HA coated PLGA NPs was an effectively drug deliver platform for API in treatment of colon cancer with high expression of CD44.

The rapid development of technology has led to the implementation of data-driven systems whose performance heavily relies on the amount and type of the data itself. In the latest decades, in the fields of bioengineering data management, among others, eye-tracking data has become one of the most interesting and essential components for many medical, psychological, and engineering research applications. However, despite the large usage of eye-tracking data in many studies and applications, a strong gap is still present in the literature regarding real-time data collection and management, which led to strong constraints for the reliability and accuracy of on-time results. To address this gap, this study aims to introduce a system that enables the collection, processing, real-time streaming, and storage of eye-tracking data. The system is developed by using Java programming language, WebSocket protocol, and Representational State Transfer (REST), improving the efficiency in transferring and managing eye-tracking data. Results were computed in two test conditions, i.e., local and online scenarios, within a time window of 100 seconds. The experiments conducted for this study were carried out by comparing the time delay between two different scenarios. Even if preliminary, results showed a significantly improved performance of data management systems in managing real-time data transfer. Overall, this system can significantly benefit the research community by providing real-time data transfer and storing the data, enabling more extensive studies using eye-tracking data.

While Twitter has been touted to provide up-to-date information about hazard events, the reliability of tweets is still a concern. Our previous publication extracted relevant tweets containing information about the 2013 Colorado flood event and its impacts. Using the relevant tweets, this research further examined the reliability (accuracy and trueness) of the tweets by examining the text and image content and comparing them to other publicly available data sources. Both manual identification of text information and automated (Google Cloud Vision API) extraction of images were implemented to balance accurate information verification and efficient processing time. The results showed that both the text and images contained useful information about damaged/flooded roads/street networks. This information will help emergency response coordination efforts and informed allocation of resources when enough tweets contain geocoordinates or locations/venue names. This research will help identify reliable crowdsourced risk information to enable near-real time emergency response through better use of crowdsourced risk communication platforms.

In recent years, Web APIs have become a de facto standard for exchanging machine-readable data on the Web. Despite this success though, they often fail in making resource descriptions interoperable due to the fact that they rely on proprietary vocabularies that lack formal semantics. The Linked Data principles similarly seek the massive publication of data on the Web, yet with the specific goal of ensuring semantic interoperability. Given their complementary goals, it is commonly admitted that cross-fertilization could stem from the automatic combination of Linked Data and Web APIs. Towards this goal, in this paper we leverage the micro-service architectural principles to define a SPARQL Micro-Service architecture, aimed at querying Web APIs using SPARQL. A SPARQL micro-service is a lightweight SPARQL endpoint that provides access to a small, resource-centric, virtual graph. In this context, we argue that full SPARQL Query expressiveness can be supported efficiently without jeopardizing servers availability. Furthermore, we demonstrate how this architecture can be used to dynamically assign dereferenceable URIs to Web API resources that do not have URIs beforehand, thus literally ``bringing'' Web APIs into the Web of Data. We believe that the emergence of an ecosystem of SPARQL micro-services published by independent providers would enable Linked Data-based applications to easily glean pieces of data from a wealth of distributed, scalable and reliable services. We describe a working prototype implementation and we finally illustrate the use of SPARQL micro-services in the context of two real-life use cases related to the biodiversity domain, developed in collaboration with the French National Museum of Natural History.

The established classical method of treating oil refinery effluent is flotation followed by biological treatment. Membrane bioreactors (MBRs) offer more advanced treatment, producing a clarified and potentially reusable treated effluent, but demand robust pretreatment to remove oil and grease (O&G) down to consistent, reliably low levels. An analysis of a full-scale conventional oil refinery ETP based on flotation alone, coupled with projected performance, energy consumption and costs associated with a downstream MBR, have demonstrated satisfactory performance of flotation-based pre-treatment. The flotation processes, comprising an API separator followed by dissolved air flotation (DAF), provided ~90% removal of both total suspended solids (TSS) and O&G coupled with 75% COD removal. The relative energy consumption and cost of the pretreatment, normalised against both the volume treated and COD removed, was considerably less for the API-DAF sequence compared to the MBR. The combined flotation specific energy consumption in kWh was found to be almost an order of magnitude lower than for the MBR (0.091 vs 0.86 kWh per m3 effluent treated), and the total cost (in terms of the net present value) around one sixth that of the MBR. However, the nature of the respective waste streams generated and end disposal of waste solids differs significantly between the pretreatment and MBR stages.

Spatial Data Infrastructures (SDI) established during the past two decades ’unlocked’ heterogeneous geospatial datasets. The European Union INSPIRE Directive laid down the foundation of a pan-European SDI where thousands of public sector data providers make their data available for cross-border and cross-domain reuse. At the same time, SDIs should inevitably adopt new technology and standards in order to remain fit for purpose and address in the best possible way the needs of different stakeholders (government, businesses and citizens). Some of the recurring technical requirements raised by SDI stakeholders include (i) the need for adoption of RESTful architectures, together with (ii) alternative (to GML) data encodings, such as JavaScript Object Notation (JSON) and binary exchange formats, and (iii) adoption of asynchronous publish-subscribe-based messaging protocols. The newly established OGC standard SensorThings API is particularly interesting to investigate for INSPIRE, as it addresses together all three topics. In this manuscript, we provide our synthesised perspective on the necessary steps for the OGC SensorThings API standard to be considered as a solution that meets the legal obligations stemming out of the INSPIRE Directive. We share our perspective on what should be done concerning (i) data encoding, and (ii) the use of SensorThings API as a download service.

Fintech facilitates financial inclusion by introducing new sustainable and accessible business models in developing countries. Open banking API technology is used by various fintech businesses in both developing and developed countries, with varying effects on financial markets. It changes the financial market distribution structure by separating financial product manufacturing and distribution and intensifying competition between traditional financial institutions and fintech companies. Fintech companies innovate by using this tool to create new business models. In December 2019, Korea established a standardized "open banking API platform," sharing an interbank payment network with fintech companies. It has since shown explosive growth, surpassing the trading volume of the UK, the country that introduced open banking APIs for the first time. This study analyzes new business models fintech companies created using this API technology. Based on existing literature, statistics from the platform operator (the Korea Financial Telecommunications and Clearings Institute), and investigations of 30 Korean fintech mobile applications, this study analyzes new fintech business models that provide financial services using this platform. These companies create sustainable business models by combining multiple APIs. Four representative business models (simple funds transfer, simple payment, cross-border remittance, and asset management) are analyzed to reveal how fintech companies create business models with open APIs.

The role of the databases is to allow persisting data, no matter if they are of the SQL or NoSQL type. In SQL databases, data is structured in a set of tables in the relational database model, grouped in rows and columns. The CRUD operations (create, read, update, and delete) are used to manage the information contained in the relational databases. Several dialects of the SQL language exist, as well as frameworks for mapping Java classes (models) to a relational database. The question is what we should choose for our Java application and why. A comparison between the most used relational database management systems, mixed with the most used frameworks should give us some guidance about when to use what. The evaluation is done on timing for each CRUD operation, from thousands to millions of entries, using the possible combinations between the relational database system and the framework. The experiments included the possibilities to warm up the Java Virtual Machine before the execution of the queries. Also, the research investigated the time spent inside different methods of the code, to determine the critical regions. Thus, the conclusions provide a comprehensive overview of the performances of Java applications accessing databases depending on the suite of decisions considering the database type, the framework in use, the type of operation, and supporting architects and developers for their technological decisions and for improving the speed of their programs.

Air passenger traffic prediction is crucial for the effective operation of civil aviation airports. Despite some progress in this field, the prediction accuracy and methods need further improvement. This paper proposes an integrated approach to the prediction of air passenger index as follows. Firstly, the air passenger index is defined and classified by the K-means clustering method. Based on the mutual information (MI) principle, the information entropy is used to analyze and select the key influencing factors of air passenger travel. By incorporating the MI principle into the support vector regression (SVR) framework, this paper presents an innovative MI-SVR machine learning model used to predict the air passenger index. Finally, the proposed model is validated by passenger throughput data of the Shanghai Pudong International Airport, China. The experimental results prove the model feasibility and effectiveness by comparing them with conventional methods, such as ARIMA, LSTM, and other machine learning models, outperformed by the MI-SVR model. Besides, it is shown that the prediction effect of each model could be improved by introducing influencing factors based on mutual information. The main findings are considered instrumental to the airport operation and air traffic optimization.

Air passenger traffic prediction is crucial for the effective operation of civil aviation airports. Despite some progress in this field, the prediction accuracy and methods need further improvement. This paper proposes an integrated approach to the prediction of air passenger index as follows. Firstly, the air passenger index is defined and classified by the K-means clustering method. Based on the mutual information (MI) principle, the information entropy is used to analyze and select the key influencing factors of air passenger travel. By incorporating the MI principle into the support vector regression (SVR) framework, this paper presents an innovative MI-SVR machine learning model used to predict the air passenger index. Finally, the proposed model is validated by passenger throughput data of the Shanghai Pudong International Airport, China. The experimental results prove the model feasibility and effectiveness by comparing them with conventional methods, such as ARIMA, LSTM, and other machine learning models, outperformed by the MI-SVR model. Besides, it is shown that the prediction effect of each model could be improved by introducing influencing factors based on mutual information. The main findings are considered instrumental to the airport operation and air traffic optimization.