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pvm_xstar is a software tool which fosters concurrent execution of the XSTAR command line application on independent sets of parameters.
It has been implemented to work with NetCDF and CSV file formats as a command line application, in the ArcGIS ModelBuilder environment, and as part of a web-based data exploration tool.
The server is a command line application that listens for client connections on a specific port.
The generator project is a simple command line application which serves the purpose of computing the background hierarchy.
For the command line application - NET 4.0 for Windows based systems, Mono framework 3.10 or newer (http://www.mono-project.com) for other OS.
The most common use of Open Babel is through the obabel command line application (or the corresponding graphical user interface) for the interconversion of chemical file formats.
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This paper focuses on standards and usability within the context of the Fraunhofer Resource Grid that implements a simple, Petri net-based graph model for orchestrating Grid Services and legacy command line applications on OGSI-compatible middleware.
Five methods: the Bootstrap, the Jackknife, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building are included as separate classes and may be used in user-written Perl scripts or through stand-alone command line applications.
The three applications presented above and many other command line applications have been in use at Genentech for many years with high impact on small molecule drug discovery projects.
All sequence similarity searches were carried out using the BLAST+ command line applications, v.2.2.27 [ 52].
Initially, probe sequences were blasted against a local non-redundant Viridiplantae protein database using BLAST+ command line applications, v.2.2.27 [ 56] at an e-value of 10−6.
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