Learn how to secure your ASP.NET Core web app through robust and secure codeKey FeaturesDiscover the different types of security weaknesses in ASP.NET Core web applications and learn how to fix ...themUnderstand what code makes an ASP.NET Core web app unsafeBuild your secure coding knowledge by following straightforward recipesBook DescriptionASP.NET Core developers are often presented with security test results showing the vulnerabilities found in their web apps. While the report may provide some high-level fix suggestions, it does not specify the exact steps that you need to take to resolve or fix weaknesses discovered by these tests. In ASP.NET Secure Coding Cookbook, you'll start by learning the fundamental concepts of secure coding and then gradually progress to identifying common web app vulnerabilities in code. As you progress, you'll cover recipes for fixing security misconfigurations in ASP.NET Core web apps. The book further demonstrates how you can resolve different types of Cross-Site Scripting. A dedicated section also takes you through fixing miscellaneous vulnerabilities that are no longer in the OWASP Top 10 list. This book features a recipe-style format, with each recipe containing sample unsecure code that presents the problem and corresponding solutions to eliminate the security bug. You'll be able to follow along with each step of the exercise and use the accompanying sample ASP.NET Core solution to practice writing secure code. By the end of this book, you'll be able to identify unsecure code causing different security flaws in ASP.NET Core web apps and you'll have gained hands-on experience in removing vulnerabilities and security defects from your code.What you will learnUnderstand techniques for squashing an ASP.NET Core web app security bugDiscover different types of injection attacks and understand how you can prevent this vulnerability from being exploitedFix security issues in code relating to broken authentication and authorizationEliminate the risks of sensitive data exposure by getting up to speed with numerous protection techniquesPrevent security misconfiguration by enabling ASP.NET Core web application security featuresExplore other ASP.NET web application vulnerabilities and secure coding best practicesWho this book is forThis ASP.NET Core book is for intermediate-level ASP.NET Core web developers and software engineers who use the framework to develop web applications and are looking to focus on their security using coding best practices. The book is also for application security engineers, analysts, and specialists who want to know more about securing ASP.NET Core using code and understand how to resolve issues identified by the security tests they perform daily.
The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and accurate protein structure prediction, powered by deep learning and Rosetta. With the input of a protein's ...amino acid sequence, a deep neural network is first used to predict the inter-residue geometries, including distance and orientations. The predicted geometries are then transformed as restraints to guide the structure prediction on the basis of direct energy minimization, which is implemented under the framework of Rosetta. The trRosetta server distinguishes itself from other similar structure prediction servers in terms of rapid and accurate de novo structure prediction. As an illustration, trRosetta was applied to two Pfam families with unknown structures, for which the predicted de novo models were estimated to have high accuracy. Nevertheless, to take advantage of homology modeling, homologous templates are used as additional inputs to the network automatically. In general, it takes ~1 h to predict the final structure for a typical protein with ~300 amino acids, using a maximum of 10 CPU cores in parallel in our cluster system. To enable large-scale structure modeling, a downloadable package of trRosetta with open-source codes is available as well. A detailed guidance for using the package is also available in this protocol. The server and the package are available at https://yanglab.nankai.edu.cn/trRosetta/ and https://yanglab.nankai.edu.cn/trRosetta/download/ , respectively.
Cell-cell communication mediated by ligand-receptor complexes is critical to coordinating diverse biological processes, such as development, differentiation and inflammation. To investigate how the ...context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions. In contrast to other repositories, our database takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, provide procedures for inferring cell-cell communication networks from single-cell RNA sequencing data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v.2.0 is an updated version of our resource that incorporates additional functionalities to enable users to introduce new interacting molecules and reduces the time and resources needed to interrogate large datasets. CellPhoneDB v.2.0 is publicly available, both as code and as a user-friendly web interface; it can be used by both experts and researchers with little experience in computational genomics. In our protocol, we demonstrate how to evaluate meaningful biological interactions with CellPhoneDB v.2.0 using published datasets. This protocol typically takes ~2 h to complete, from installation to statistical analysis and visualization, for a dataset of ~10 GB, 10,000 cells and 19 cell types, and using five threads.
Recording and analyzing microbial growth is a routine task in the life sciences. Microplate readers that record dozens to hundreds of growth curves simultaneously are increasingly used for this task ...raising the demand for their rapid and reliable analysis.
Here, we present Dashing Growth Curves, an interactive web application ( http://dashing-growth-curves.ethz.ch/ ) that enables researchers to quickly visualize and analyze growth curves without the requirement for coding knowledge and independent of operating system. Growth curves can be fitted with parametric and non-parametric models or manually. The application extracts maximum growth rates as well as other features such as lag time, length of exponential growth phase and maximum population size among others. Furthermore, Dashing Growth Curves automatically groups replicate samples and generates downloadable summary plots for of all growth parameters.
Dashing Growth Curves is an open-source web application that reduces the time required to analyze microbial growth curves from hours to minutes.
In this work, a computer program is developed which allows to find and graph the phase velocities, group velocities and the slowness of a solid from its physical characteristics, namely the stiffness ...tensor and the volumetric density of the material that composes it. The graphs are also made in such a way that it is possible to obtain the magnitudes according to the angle and the coordinate plane of a specific propagation direction, which are given to the program as inputs. Keywords: Stress, strain, stiffness tensor, Christoffel tensor, phase velocity, group velocity, slowness, polarization vectors
External quality assessment is the process of evaluating the performance of a laboratory and the competence of professionals. Participation in EQA and standardizing the quality of laboratory services ...are a mandatory requirements for accreditation. This review is aimed at identifying and discussing challenges that hinder the effective implementation of an EQA program in countries with resource limited setting. To obtain abundant information, articles were identified by searching the literature published in English using the National Library of Medicine, PubMed, Science Direct and AMC digital library databases. The articles identified in the references were manually searched and included. After the article was identified, it was imported to Endnote version 8.1 and exported to Microsoft Word for citation. Based on this review, the major identified challenges that hinder the implementation of an EQA program include the high cost of control materials, malfunction and lack of maintenance for equipment failure and breakdown, a knowledge gap among laboratory professionals, noncommutability of control samples, and difficulty in assigning target values. In addition, failing to participate in EQA and failing to take corrective action are the major challenges identified. As a result, applying to an EQA program in resource-limited counties was highly challenging. To attain high performance in the laboratory and to provide quality laboratory service for patient care, the EQA supplier and the user laboratory must pay attention to these issues and take appropriate corrective actions for ongoing quality improvement and accreditation. Keywords: external quality assessment, proficiency testing, challenge, resource-limited countries
Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. ...They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.
jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams.
jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.
This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines. SCENIC ...reconstructs regulons (i.e., transcription factors and their target genes) assesses the activity of these discovered regulons in individual cells and uses these cellular activity patterns to find meaningful clusters of cells. Here we present an improved version of SCENIC with several advances. SCENIC has been refactored and reimplemented in Python (pySCENIC), resulting in a tenfold increase in speed, and has been packaged into containers for ease of use. It is now also possible to use epigenomic track databases, as well as motifs, to refine regulons. In this protocol, we explain the different steps of SCENIC: the workflow starts from the count matrix depicting the gene abundances for all cells and consists of three stages. First, coexpression modules are inferred using a regression per-target approach (GRNBoost2). Next, the indirect targets are pruned from these modules using cis-regulatory motif discovery (cisTarget). Lastly, the activity of these regulons is quantified via an enrichment score for the regulon's target genes (AUCell). Nonlinear projection methods can be used to display visual groupings of cells based on the cellular activity patterns of these regulons. The results can be exported as a loom file and visualized in the SCope web application. This protocol is illustrated on two use cases: a peripheral blood mononuclear cell data set and a panel of single-cell RNA-sequencing cancer experiments. For a data set of 10,000 genes and 50,000 cells, the pipeline runs in <2 h.
Abstract
Background
Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically ...involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.
Results
Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at
http://shaman.pasteur.fr/
, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at
https://github.com/aghozlane/shaman
. Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis.
Conclusions
With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.
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