Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

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Session Overview
2B - Shiny
Monday, 05/July/2021:
6:30pm - 8:00pm

Session Chair: Mohamed El Fodil Ihaddaden
Replacement Zoom Host: Juan Pablo Narváez-Gómez
Location: The Lounge #talk_shiny

Session Topics:
Web Applications (Shiny/Dash)

Session Sponsor: Open Analytics
Session Slide

6:30pm - 6:50pm
ID: 205 / ses-02-B: 1
Regular Talk
Topics: Web Applications (Shiny/Dash)
Keywords: Lateral Flow Assay, Smartphone-based Analysis, Point-of-care Diagnostics, R Shiny App, Image Analysis

All-in-one smartphone-based system for quantitative analysis of point-of-care diagnostics

Weronika Schary1,2, Filip Paskali1,2, Matthias Kohl1,2

1Furtwangen University, Medical and Life Sciences Faculty, Jakob-Kienzle Str. 17, D-78054, Villingen Schwenningen, Germany; 2Institute of Precision Medicine, Jakob-Kienzle Str. 17, D-78054, Villingen-Schwenningen, Germany

We propose a smartphone-based system for the quantification of various lateral flow assays for the detection and diagnosis of diseases. The proposed smartphone-based system consists of a 3D-printed photo box for standardized positioning and lighting, a smartphone for image acquisition and an R Shiny Software Package with modular, customizable applications for image editing, analysis, data extraction, calibration and quantification. This system is less expensive than commonly used hardware and software for analysis, so it could prove very beneficial for diagnostic testing in the context of pandemics, as well as low-resource countries, in which laboratory equipment as well as diagnostic facilities are scarce.

The proposed system is facilitated with R Shiny, an open-source package - free to use and modify. It can be used without extensive programming skills, which could further the development of diagnosis becoming simpler, quicker, more efficient and still cost-effective compared to the gold standard methods used in detection and diagnosis today. Also, the automatic documentation of all analysis steps implemented in the application via R Markdown allows for accurate reproducibility in research and clinical practice.

For further image analysis, package LFApp was created to enable image editing, cropping, segmentation, background correction, data analysis, calibration and quantification of extracted pixel intensity values from the image.

Besides Shiny, other major packages used are EBImage, ggplot2, DT, shinyjs, stats, shinyFiles, rmarkdown and shinythemes. Furthermore, we designed an additional version of the UI module, using ShinyMobile, to make the app more accessible on small touchscreens.

Our goal was to build a versatile free open-source system, that is scalable and extensible, and also modifiable to suit any research team requirements. It represents an all-in-one, portable, cost-efficient and easily reproducible system for full analysis, that works well on computers as well as portable devices, such as smartphones.

6:50pm - 7:10pm
ID: 226 / ses-02-B: 2
Regular Talk
Topics: Web Applications (Shiny/Dash)
Keywords: CI/CD

Unit Testing Shiny App Reactivity

Jonathan Sidi

Sage Therapeutics

When developing Shiny apps there are a lot of reactivity problems that can arise when one reactive or observe element triggers other elements. In some cases these can create cascading reactivity (the horror). The goal of reactor is to efficiently diagnose these reactivity problems and then plan unit tests to avert them during app development, making it a less painful and more robust experience. Reactor can improve the stability of shiny app development with many collaborators through its application in a version control and CI/CD framework.

Link to package or code repository.

7:10pm - 7:30pm
ID: 116 / ses-02-B: 3
Regular Talk
Topics: Web Applications (Shiny/Dash)
Keywords: Shiny, RStudio add-ins, dashboards, web application

ShinyQuickStarter: Build Shiny apps interactively with Drag & Drop

Leon Binder

Deggendorf Institute of Technology

The development of Shiny apps is often very time-consuming. This applies to the initial setup of the folder structure, but especially to the creation of the user interface and the implementation of the program logic. Many UI and logic elements are available and distributed across several packages.

To make the development process more efficient, we developed the RStudio addin ‘ShinyQuickStarter’. ‘ShinyQuickStarter’ is designed both for beginners who have acquired some basic knowledge of Shiny but have not gained much practical experience, and for advanced users who want to accelerate the process of developing new, powerful Shiny apps. It helps to setup the design of Shiny apps within a few minutes, so developers can start implementing the actual program logic almost immediately.

‘ShinyQuickStarter’ enables developers to create Shiny apps interactively using an intuitive drag and drop interface. A variety of page types and over 75 UI elements for navigation, layout, inputs, and outputs are supported. The options of these UI elements are interactively customizable, so developers can easily tailor Shiny apps towards their requirements and see the effect of an option immediately. Context-sensitive documentation furthermore supports especially beginners in orchestrating easy-to-use Shiny apps. ‘ShinyQuickStarter’ also creates the required folder structure for a new app and exports the source code of both the UI and the server component. Developers have the opportunity to organize the source code into Shiny modules. ‘ShinyQuickStarter’ solves the core problem of creating Shiny apps by streamlining the workflow of creating UI elements and corresponding server-side elements.

7:30pm - 7:50pm
ID: 348 / ses-02-B: 4
Sponsored Talk
Topics: Web Applications (Shiny/Dash)
Keywords: Shiny, enterprise computing, open source

ShinyProxy. The Good News Show.

Tobia De Koninck

Open Analytics

Interactive web applications have become standard data science artefacts. Since 5 years ShinyProxy offers a 100% open source enterprise solution to run and manage such applications. Whether you want to deploy Shiny, Dash, H2O Wave or Streamlit apps, ShinyProxy has your back. Whether you serve a small team or host internet-facing apps for thousands of users, ShinyProxy will scale and stand the load. Whether you use LDAP, ActiveDirectory, OpenID Connect, SAML 2.0 or Kerberos to authenticate / authorize users, ShinyProxy makes it happen. Want to mix in an IDE (e.g. RStudio) or notebook server (e.g. Jupyter or Zeppelin notebooks)? Look no further than ShinyProxy. Monitor your stack and gather usage statistics? Check. Embed the apps over APIs into other websites? Solved problem.

In this talk we provide technical detail to the good news and focus on the latest ShinyProxy refinements and developments.

Link to package or code repository.