Designing and modeling an IoT-based software system for land suitability assessment use case.

Assessing the quality of land is a very important step that precedes the planning of land use and taking management decisions; for example, in the agricultural field, it can be used to evaluate the suitability of the land for planting crops, determine the suitable irrigation system type, or adjust the agricultural inputs such as fertilizers and pesticides according to the requirements of each zone in the land. The spatial-temporal dynamic nature of land characteristics entails also updated evaluation process and updated management plan. The present paper tries to exploit the advances in information and communication technologies to develop a conceptual design of a dynamic system that accommodates the spatial-temporal dynamics of the agricultural soil characteristics to realize a land suitability assessment (LSA) based on a factor analysis method. The proposed design combines IoT technologies, web development, database, and digital mapping and tries to consolidate the system with other functionalities useful for decision support and suitable for different cases. The paper conducted a survey and made comparisons to select the best technologies that fit the current use case implementation and presents its reproducible conceptual modeling by developing the static and dynamic views through schemas, diagrams, message sequence charts, IoT messaging topic tree, pseudocode, etc. The functionality of the design was validated with a simple implementation of the system model. To our knowledge, there is no previous significant contribution that has addressed a LSA IoT use case. The proposed design automates the LSA process for more accurate decision-making, saving cost, time, and effort consumed in repeated field trips. It is characterized by flexibility and centralization in its offered services of spatial analysis, detection, visualizations, and status monitoring. The design also allows for remote control of field machinery.

Developing a More Responsive Radiology Resident Dashboard.

Residents have a limited time to be trained. Although having a highly variable caseload should be beneficial for resident training, residents do not necessarily get a uniform distribution of cases. By developing a dashboard where residents and their attendings can track the procedures they have done and cases that they have seen, we hope to give residents a greater insight into their training and into where gaps in their training may be occurring. By taking advantage of modern advances in NLP techniques, we process medical records and generate statistics describing each resident's progress so far. We have built the system described and its life within the NYP ecosystem. By creating better tracking, we hope that caseloads can be shifted to better close any individual gaps in training. One of the educational pain points for radiology residency is the assignment of cases to match a well-balanced curriculum. By illuminating the historical cases of a resident, we can better assign future cases for a better educational experience.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

BACKGROUND: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. RESULTS: We have developed WebGIVI, an interactive web-based visualization tool ( http://raven.anr.udel.edu/webgivi/ ) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. CONCLUSIONS: WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI . The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php .

Website Redesign: A Case Study.

A library website redesign is a complicated and at times arduous task, requiring many different steps including determining user needs, analyzing past user behavior, examining other websites, defining design preferences, testing, marketing, and launching the site. Many different types of expertise are required over the entire process. Lessons learned from the Norris Medical Library's experience with the redesign effort may be useful to others undertaking a similar project.

PhyloJS: Bridging phylogenetics and web development with a JavaScript utility library.

There is an increasing number of libraries devoted to parsing, manipulating and visualising phylogenetic trees in JavaScript. Many of these libraries bundle tree manipulation with visualisation, but have limited ability to manipulate trees and lack detailed documentation. As the number of web-based phylogenetic tools and the size of phylogenetics datasets increases, there is a need for a library that parses, writes and manipulates phylogenetic trees that is interoperable with other phylogenetic and data visualisation libraries. Here we introduce PhyloJS, a light zero-dependency TypeScript and JavaScript library for reading, writing and manipulating phylogenetic trees. PhyloJS allows for modification of and data-extraction from trees to integrate with other phylogenetics and data visualisation libraries. It can swiftly handle large trees, up to at least 10 6 tips in size, making it ideal for developing the next generation of more complex web-based phylogenetics applications handling ever larger datasets. The PhyloJS source code is available on GitHub (https://github.com/clockor2/phylojs) and can be installed via npm with the command npm install phylojs. Extensive documentation is available at https://clockor2.github.io/phylojs/.

Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server.

This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.

Characterizing browser-based medical imaging AI with serverless edge computing: towards addressing clinical data security constraints.

Artificial intelligence (AI) has been widely introduced to various medical imaging applications ranging from disease visualization to medical decision support. However, data privacy has become an essential concern in clinical practice of deploying the deep learning algorithms through cloud computing. The sensitivity of patient health information (PHI) commonly limits network transfer, installation of bespoke desktop software, and access to computing resources. Serverless edge-computing shed light on privacy preserved model distribution maintaining both high flexibility (as cloud computing) and security (as local deployment). In this paper, we propose a browser-based, cross-platform, and privacy preserved medical imaging AI deployment system working on consumer-level hardware via serverless edge-computing. Briefly we implement this system by deploying a 3D medical image segmentation model for computed tomography (CT) based lung cancer screening. We further curate tradeoffs in model complexity and data size by characterizing the speed, memory usage, and limitations across various operating systems and browsers. Our implementation achieves a deployment with (1) a 3D convolutional neural network (CNN) on CT volumes (256×256×256 resolution), (2) an average runtime of 80 seconds across Firefox v.102.0.1/Chrome v.103.0.5060.114/Microsoft Edge v.103.0.1264.44 and 210 seconds on Safari v.14.1.1, and (3) an average memory usage of 1.5 GB on Microsoft Windows laptops, Linux workstation, and Apple Mac laptops. In conclusion, this work presents a privacy-preserved solution for medical imaging AI applications that minimizes the risk of PHI exposure. We characterize the tools, architectures, and parameters of our framework to facilitate the translation of modern deep learning methods into routine clinical care.

Development of an interactive web dashboard to facilitate the reexamination of pathology reports for instances of underbilling of CPT codes.

Current Procedural Terminology Codes is a numerical coding system used to bill for medical procedures and services and crucially, represents a major reimbursement pathway. Given that pathology services represent a consequential source of hospital revenue, understanding instances where codes may have been misassigned or underbilled is critical. Several algorithms have been proposed that can identify improperly billed CPT codes in existing datasets of pathology reports. Estimation of the fiscal impacts of these reports requires a coder (i.e., billing staff) to review the original reports and manually code them again. As the re-assignment of codes using machine learning algorithms can be done quickly, the bottleneck in validating these reassignments is in this manual re-coding process, which can prove cumbersome. This work documents the development of a rapidly deployable dashboard for examination of reports that the original coder may have misbilled. Our dashboard features the following main components: (1) a bar plot to show the predicted probabilities for each CPT code, (2) an interpretation plot showing how each word in the report combines to form the overall prediction, and (3) a place for the user to input the CPT code they have chosen to assign. This dashboard utilizes the algorithms developed to accurately identify CPT codes to highlight the codes missed by the original coders. In order to demonstrate the function of this web application, we recruited pathologists to utilize it to highlight reports that had codes incorrectly assigned. We expect this application to accelerate the validation of re-assigned codes through facilitating rapid review of false-positive pathology reports. In the future, we will use this technology to review thousands of past cases in order to estimate the impact of underbilling has on departmental revenue.

COVID-BIOCHIP: A Web Tool to Analyse COVID-19 Antigen Microarrays.

During the COVID-19 pandemic, there was a growing need to characterise the disease. A very important aspect is the ability to measure the immunisation extent, which can be achieved using antigen microarrays that quantitively measure the presence of COVID-related antibodies. A significant limitation for these tests was the complexity of manually analysing the results, and the limited availability of software for its analysis. In this paper, we describe the development of COVID-BIOCHIP, an ad-hoc web-based solution for the automatic analysis and visualisation of COVID-19 antigen microarray data results.

Development of a Website for a Living Network Meta-analysis of Atopic Dermatitis Treatments Using a User-Centered Design: Multimethod Study.

BACKGROUND: A rapid expansion of systemic immunological treatment options for atopic dermatitis (AD) has created a need for clinically relevant and understandable comparative efficacy and safety information for patients and clinicians. Given the scarcity of head-to-head trials, network meta-analysis (NMA) is an alternative way to enable robust comparisons among treatment options; however, NMA results are often complex and difficult to directly implement in shared decision-making. OBJECTIVE: The aim of this study is to develop a website that effectively presents the results of a living systematic review and NMA on AD treatments to patient and clinician users. METHODS: We conducted a multimethod study using iterative feedback from adults with AD, adult caregivers of children with AD, dermatologists, and allergists within a user-centered design framework. We used questionnaires followed by workshops among patients and clinicians to develop and improve the website interface. Usability testing was done with a caregiver of a patient with eczema. RESULTS: Questionnaires were completed by 31 adults with AD or caregivers and 94 clinicians. Patients and caregivers felt it was very important to know about new treatments (20/31, 65%). Clinicians felt the lack of evidence-based comparisons between treatments was a barrier to care (55/93, 59%). "Avoiding dangerous side effects" was ranked as the most important priority for patients (weighted ranking 5.2/7, with higher ranking being more important), and "improving patients' overall symptoms" was the most important priority for clinicians (weighted ranking 5.0/6). A total of 4 patients and 7 clinicians participated in workshops; they appreciated visualizations of the NMA results and found the website valuable for comparing different treatments. The patients suggested changes to simplify the interface and clarify terminology related to comparative efficacy. The user in the usability testing found the website intuitive to navigate. CONCLUSIONS: We developed a website, "eczematherapies.com," with a user-centered design approach. Visualizations of NMA results enable users to compare treatments as part of their shared decision-making process.

Usability Design in Medical Informatics: A Prospective Research Project.

This short paper aims to raise awareness of good usability design in medical computer sciences. We present a research plan about developing usability design guidelines for web application development in medical informatics. Following a nimble creation process we shall create a guideline tailored for software developers, that aims to improve communication between the developer and the medical professional. Results are therefore expected to impact the way applications are being developed within the medical sector.

Trends in access of plant biodiversity data revealed by Google Analytics.

The amount of plant biodiversity data available via the web has exploded in the last decade, but making these data available requires a considerable investment of time and work, both vital considerations for organizations and institutions looking to validate the impact factors of these online works. Here we used Google Analytics (GA), to measure the value of this digital presence. In this paper we examine usage trends using 15 different GA accounts, spread across 451 institutions or botanical projects that comprise over five percent of the world's herbaria. They were studied at both one year and total years. User data from the sample reveal: 1) over 17 million web sessions, 2) on five primary operating systems, 3) search and direct traffic dominates with minimal impact from social media, 4) mobile and new device types have doubled each year for the past three years, 5) and web browsers, the tools we use to interact with the web, are changing. Server-side analytics differ from site to site making the comparison of their data sets difficult. However, use of Google Analytics erases the reporting heterogeneity of unique server-side analytics, as they can now be examined with a standard that provides a clarity for data-driven decisions. The knowledge gained here empowers any collection-based environment regardless of size, with metrics about usability, design, and possible directions for future development.

Contribución de la planeación al desarrollo Web: los wireframes / Contribution of planning to Web development: wireframes

La planeación de un Web es una tarea intensa e insoslayable cuando se trata de un esfuerzo serio en busca de un sitio que cumpla con las expectativas de sus solicitantes y visitantes. Sin embargo, con frecuencia, no se concede a esta actividad su verdadero valor y ello provoca numerosos problemas durante el desarrollo del trabajo y que se llegue al final de la tarea con deficiencias difíciles de eliminar con vistas a cumplir con las expectativas de los clientes, las condiciones del tráfico, las necesidades de perfeccionamiento y la credibilidad requerida, todo esto reduce las posibilidades de éxito ante la competencia, entre otras dificultades. El desarrollo, tratamiento y gestión de los contenidos requieren de un manejo preferencial desde la dimensión humana si realmente se desea alcanzar una relación beneficiosa con sus destinatarios. La coherencia del trabajo en equipo, el pensamiento socializador y una mentalidad abierta para escuchar y permitir que ideas diferentes se presenten y se abran paso, superen o fertilicen las de otros, incluidas las propias, forman parte de un grupo de aspectos esenciales en el trabajo, en este caso, para el desarrollo Web, que hacen más integral, válida, segura y placentera la tarea, todo lo cual redunda en mejores resultados.

Planning a Web is an intense and unavoidable task, when a serious effort is made to create a site that satisfies the expectations of its clients. Nevertheless, the real value of this activity is frequently underestimated, causing numerous problems during the development of the work and deficiencies that are difficult to eliminate at the end of the task in order to meet the expectations of the clients, the traffic conditions, the improvement needs and the required credibility; thus reducing the probability of success before competence, among other difficulties. The development, processing and management of the contents require a preferential management from the human dimension if you really want to achieve a beneficial relation with its users. The teamwork coherence, the socializing thought and an open mind to listen and to allow different ideas to come up and develop, and to surpass or improve those of others, included one's own ideas; are part of a group of essential aspects for Web development, that make this task more integral, valid, secure and pleasant, and allow to have better results.