This software was created by the WHONET development team to facilitate the interpretation of antibiotic measurements according to the published guidelines. For more information about the guidelines, please visit their websites: CLSI, EUCAST, SFM
You can install this software on Windows using the command winget install WHONET.AMRIE or by downloading the latest release from GitHub.
There are three different sets of needs that the solution aims to support:
- Interactive use
- Command line use
- Library integration
The library code is written in .NET 8 with no additional package dependencies. It can be directly integrated with other projects on any platform which supports .NET 8. The interactive and command line interfaces exercise various interpretation features.
The interactive system may be used to generate the interpretations for an entire data file, or explore ad hoc interpretations and view filtered resources.
Ad hoc queries allow you to select from lists of organisms and antibiotics, and provide an associated measurement to interpret.
To generate interpretations for an entire data file using the interface or command line application, the file must use WHONET naming conventions for the
data columns, measurements, organism codes, etc. Sample data and configuration files are provided in the installation package's Resources folder.
The command line interface is another option which can be used to generate interpretations without requiring knowledge of or integration with the library. Instead, the command line application can be called as needed (from another application, from a batch script, etc.). It should be possible to build the command line interface for platforms other than Windows with minimal changes.
We also provide SQL queries that demonstrate certain concepts, but which are not used by the code. These concepts are implemented in C# to assist others if they choose to make their own implementations, and also to eliminate any dependence on a certain database technology which could restrict cross-platform options.
To improve processing perfomance without the help of the database, the system has automatic breakpoint caching built in, and includes a way to "preheat" the breakpoint cache to maximize interpretation performance if additional information about the input data set can be provided ahead of time.