RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but ...still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.
We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility.
ideal is distributed as an R package in the Bioconductor project ( http://bioconductor.org/packages/ideal/ ), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.
Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high ...throughput data analysis.
In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica's query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application.
The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica .
Over 90 recipes to help you build and run automated tests for your web applications with Selenium WebDriverAbout This Book• Learn to leverage the power of Selenium WebDriver with simple examples that ...illustrate real-world problems and their workarounds• Explains the testing of mobile applications with Appium for mobile platforms such as iOS and Android• A pragmatic manual with engaging recipes and attractive screenshots to test your web applications efficientlyWho This Book Is ForThis book is intended for software quality assurance/testing professionals, software project managers, or software developers with prior experience in using Selenium and Java to test web-based applications. This books also provides examples for C#, Python and Ruby users.What You Will Learn• Understand how the locators work and use various locator methods to build reliable tests• Build reliable and maintainable tests with the Selenium WebDriver API• Use the PageFactory pattern to build a robust and easy to maintain test framework• Build data-driven tests and extend Selenium API to implement custom steps and checks• Integrate and use ATDD/BDD tools such as Cucumber, SpecFlow, Capybara, and Behave with the Selenium WebDriver API• Set up iPhone/iPad and Android simulators and devices to test your mobile web application with Appium• Set up Selenium Grid for faster and parallel running of tests, increasing test coverage and reducing test execution time for cross-browser testing• Build extended Selenium WebDriver tests for additional coverageIn DetailThis book is an incremental guide that will help you learn and use the advanced features of the Selenium toolset including the WebDriver API in various situations to build a reliable test automation. You start off by setting up the test development environment and gain tips on the advanced locater strategy and the effective use of the Selenium WebDriver API.After that, the use of design patterns such as data - driven tests and PageFactory are demonstrated. You will then be familiarised with extending Selenium WebDriver API by implementing custom tasks and setting up your own distributed environment to run tests in parallel for cross-browser testing.Finally, we give you some tips on integrating Selenium WebDriver with other popular tools and testing mobile applications. By the end of this book, you will have learned enough to solve complex testing issues on your own.Style and approachThis recipe-based guide covers real-life scenarios of testing your web apps with Selenium. Each recipe begins with a short introduction and key concepts along with illustrated examples of use cases, and ends with detailed but informative descriptions of the inner workings of the example.
The study adapted an existing Web-based intervention, the Family Gene Toolkit, for Swiss and Korean families that harbor the genetic changes associated with hereditary breast and ovarian cancer ...syndrome. The Family Gene Toolkit encourages family communication of genetic testing results and cascade genetic testing among at-risk relatives. Feedback from 68 women with genetic changes and 31 clinicians informed the culturally sensitive adaptation of the content. The Information Technology team developed the web application that will host the intervention. Finally, a new sample of 18 women from families with hereditary breast and ovarian cancer reviewed and evaluated the adapted content and the functions of the web application. Findings support that overall, the adapted Family Gene Toolkit is well-designed, has useful information for these families, and provides interactive content and illustrative stories. The research team will test if it can increase rates of cascade testing among at-risk relatives in a subsequent randomized trial. The study adapted the Family Gene Toolkit and developed a customized web application for Swiss and Korean families harboring BRCA1 or BRCA2 pathogenic variants to support family communication of genetic testing results and promote cascade genetic testing among at-risk relatives. In the first step, narrative data from 68 women with BRCA1/BRCA2 pathogenic variants and clinician feedback informed a culturally sensitive adaptation of the content consistent with current risk management guidelines. In the second step, the Information Technology team developed the functions and the interface of the web application that will host the intervention. In the third step, a new sample of 18 women from families harboring BRCA1/BRCA2 pathogenic variants tested the acceptability and usability of the intervention using “think-aloud” interviews and a questionnaire. Participants expressed high levels of satisfaction with the intervention. They provided positive feedback for the information regarding active coping, strategies to enhance family communication, interactive elements, and illustrative stories. They reported that the information was useful and the web application was easy to navigate. Findings suggest that the Family Gene Toolkit is well-designed and can increase rates of cascade testing among at-risk relatives. Its efficacy will be tested in a subsequent randomized trial.
Evaluation of a mobile application tool Sampurna, Mahendra T. A; Ratnasari, Kinanti A; Irawan, Zahra S ...
PloS one,
06/2022, Volume:
17, Issue:
6
Journal Article
Peer reviewed
Severe hyperbilirubinemia is more frequent in low- and middle-income countries such as Indonesia than in high-income countries. One of the contributing factors might be the lack of adherence to ...existing guidelines on the diagnosis and treatment of hyperbilirubinemia. We developed a new national guideline for hyperbilirubinemia management in Indonesia. To help healthcare workers use this guideline, a web-based decision support tool application may improve both the adherence to the guideline and the care for infants with hyperbilirubinemia. We developed a web-based application (BiliNorm) to be used on a smartphone that displays the bilirubin level of the patient on the nomogram and advises about the treatment that should be started. Healthcare workers of two teaching hospitals in East Java, Indonesia, were trained on the use of BiliNorm. At 6 months after the introduction, a questionnaire was sent to those who worked with the application enquiring about their experiences. An observational study was conducted in two time epochs. A chart review of infants with hyperbilirubinemia in the two hospitals was sent. The appropriateness of hyperbilirubinemia management during a 6-month period before BiliNorm introduction was compared to that during a 7-month period after its introduction. A total of 43 participants filled in the questionnaire, the majority (72%) of them indicated that BiliNorm was well received and easy to use. Moreover, 84% indicated that BiliNorm was helpful for the decision to start phototherapy. Chart review of 255 infants before BiliNorm introduction and that of 181 infants after its introduction indicated that significantly more infants had received treatment according to the guideline (38% vs 51%, p = 0.006). Few infants received phototherapy, but bilirubin level was not measured (14% vs 7%, p = 0.024). There was no difference in the proportion of infants who were over- and under-treated (34% vs 32% and 14% vs 10%, respectively). The web-based decision tool BiliNorm appears to be a valuable application. It is easy to use for healthcare workers and helps them adhere to the guideline. It improves the care for infants with hyperbilirubinemia and may help reduce the incidence of severe hyperbilirubinemia in Indonesia.
Covidence and Rayyan Kellermeyer, Liz; Harnke, Ben; Knight, Shandra
Journal of the Medical Library Association,
10/2018, Volume:
106, Issue:
4
Journal Article
Peer reviewed
Open access
Health sciences librarians from two institutions conducted an assessment of Covidence, a subscription-based systematic review tool, and Rayyan, a free competitor, for abilities, strengths, and ...limitations. Covidence mirrors the multiphase review process, including data extraction, directly in its design. Rayyan, on the other hand, does not easily mirror this process and really only aids with the reference screening phases. Rayyan takes a minimalist approach, placing more of the logistical and workflow burden on the users themselves. Many of the peripheral features (e.g., highlighting, tagging, etc.) are comparable. Covidence works well and is well suited for more rigorous systematic reviews, where methodology must be adhered to and documented at each stage. In spite of some limited functionality and clunky features, Rayyan is a good free alternative for article screening and works as a viable upgrade from a workflow using only EndNote and/or Excel.
A rich source: Calculated reaction and activation energies for elementary coupling reactions occurring on metal surfaces can be found by using a web application. This tool provides access to data for ...reactions of molecules with up to three C, N, or O atoms on a number of different transition‐metal surfaces. The underlying dataset is generated from a consistent set of DFT calculations and extrapolations based on linear scaling relations.
Many transactions in web applications are constructed ad hoc in the application code. For example, developers might explicitly use locking primitives or validation procedures to coordinate critical ...code fragments. We refer to database operations coordinated by application code as ad hoc transactions. Until now, little is known about them. This paper presents the first comprehensive study on ad hoc transactions. By studying 91 ad hoc transactions among eight popular open-source web applications, we found that (i) every studied application uses ad hoc transactions (up to 16 per application), 71 of which play critical roles; (ii) compared with database transactions, concurrency control of ad hoc transactions is much more flexible; (iii) ad hoc transactions are error-prone—53 of them have correctness issues, and 33 of them are confirmed by developers; and (iv) ad hoc transactions have the potential for improving performance in contentious workloads by utilizing application semantics such as access patterns. Based on these findings, we discuss the implications of ad hoc transactions to the database research community.
Background Adaptive interventions are often used in individualized health care to meet the unique needs of clients. Recently, more researchers have adopted the Sequential Multiple Assignment ...Randomized Trial (SMART), a type of research design, to build optimal adaptive interventions. SMART requires research participants to be randomized multiple times over time, depending upon their response to earlier interventions. Despite the increasing popularity of SMART designs, conducting a successful SMART study poses unique technological and logistical challenges (e.g., effectively concealing and masking allocation sequence to investigators, involved health care providers, and subjects) in addition to other challenges common to all study designs (e.g., study invitations, eligibility screening, consenting procedures, and data confidentiality protocols). Research Electronic Data Capture (REDCap) is a secure, browser-based web application widely used by researchers for data collection. REDCap offers unique features that support researchers' ability to conduct rigorous SMARTs. This manuscript provides an effective strategy for performing automatic double randomization for SMARTs using REDCap. Methods Between January and March 2022, we conducted a SMART using a sample of adult (age 18 and older) New Jersey residents to optimize an adaptive intervention to increase COVID-19 testing uptake. In the current report, we discuss how we used REDCap for our SMART, which required double randomization. Further, we share our REDCap project XML file for future investigators to use when designing and conducting SMARTs. Results We report on the randomization feature that REDCap offers and describe how the study team automated an additional randomization that was required for our SMART. An application programming interface was used to automate the double randomizations in conjunction with the randomization feature provided by REDCap. Conclusions REDCap offers powerful tools to facilitate the implementation of longitudinal data collection and SMARTs. Investigators can make use of this electronic data capturing system to reduce errors and bias in the implementation of their SMARTs by automating double randomization. Trial registration The SMART study was prospectively registered at Clinicaltrials.gov; registration number: NCT04757298, date of registration: 17/02/2021. Keywords: Research Electronic Data capture (REDCap), Randomized controlled trials (RCT), Adaptive interventions, Sequential multiple assignment Randomized Trial (SMART), Randomization, Experimental design, Reducing human errors, Automation
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