Therefore, to execute the tool, the users must first execute the AspectJ weaver to instrument the target code with the aspects provided by the tool's implementation.
XML files were written for each integrated SBRT and in-house tool which include all the information required to execute the tool.
Additional Perl scripts were also written that take input from Galaxy and generate plots in MetaNET using R. XML files were written for each integrated SBRT and in-house tool which include all the information required to execute the tool.
JC developed or executed the tools that generate structures, templates, domains, DNA binding sites, and multiple sequence alignments.
Every time, OSSperf is executed, the tool prints out a line of data, which informs the user about the date (column 1) and time (column 2) when the execution was finished, the number of created objects (column 3), the size of the single objects in bytes (column 4), as well as the required time in seconds to execute the single steps 1 6 (columns 5 10).
BioDEAL provides a Web browser tab to an NLP interface where users may execute NLP tools on publications to populate the BioDEAL database with automatically annotated evidence that is presented to the user through the User Frontend Interface.
Moreover, our system can automatically execute bioinformatics tools and generate annotations, link to other well-known protein databases, construct MySQL databases, and generate PHP scripts to build its website.
The bioKepler module is an extension for Kepler that integrates bioinformatics components in order to execute bioinformatics tools (e.g., BLAST [ 46] and HMMER [ 47]) and to facilitate the development of workflows for execution in distributed environments (grid platforms or cloud).
GenomeSpace allows the user to store data in a common repository and the same web interface guides users to execute the integrated tools, load data, and store results.
Multiple sequence alignment and subsequent calculation of pair-wise amino acid conservation within individual domain superfamilies were executed using tools provided by ClustalW2 (http://simgene.com/ClustalW).com/ClustalW
