External Configuration Files Research Articles

APACHE LOG4J SHELL VULNERABILITY ANALYSIS

The Apache log4j implementation provides a logging framework that is extremely scalable, reliable, and configurable. This API makes it easier to write logging code within an application while also allowing you to regulate logging activity from an external configuration file. It also enables us to publish logging information at the required granularity based on the specifics of the logging information for each application. Almost every major program has its own logging or tracing API. After several improvements, various iterations, and a lot of hard work, that API has developed into log4j, a popular logging package for Java. The Apache Software License, a fullfledged open source license recognized by the open source effort, is used to distribute the program.

GfaViz: flexible and interactive visualization of GFA sequence graphs.

The graphical fragment assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. Although GFA 1 was primarily targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images. GfaViz is available at https://github.com/ggonnella/gfaviz. Supplementary data are available at Bioinformatics online.

AnnaBot: A Static Verifier for Java Annotation Usage

This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 and have become widely used in recent years due to their introduction in the Java Enterprise Edition 5, the Hibernate object-relational mapping API, the Spring Framework, and elsewhere. Despite that, mainstream development tools have not yet produced a widely-used verification tool to confirm correct configuration and placement of annotations external to the particular runtime component. While most of the examples in this paper use the Java Persistence API, AnnaBot is capable of verifying anyannotation-based API for which “claims”—description of annotation usage—are available. These claims can be written in Java or using a proposed Domain-Specific Language, which has been designed and a parser (but not the code generator) have been written.

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

BackgroundRecent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists.ResultsWe have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures.ConclusionOur results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.

Small program for fast DAQ in windows environment

A new data acquisition program for personal computers with the Windows operating system has been built at Charles University van de Graaff laboratory. It allows fast data acquisition from VME, CAMAC, and other PC interface cards using an interrupt or polling mode via several types of crate controllers. The program also facilitates basic on-line analysis and visualization of acquired data in graphs and histograms. The program is written as a combination of MSVC6.0++ and ROOT macros and offers easy customization to individual user requirements via external configuration files, without need of recompilation. A driver interface supports PCI bus devices (W-IE-NE-R PCI-CC32) or older ISA bus devices with internal drivers. In this paper, a description of the program concepts and features is given. The program was extensively tested with several combinations of hardware and software, and results of the tests are shown.