JC developed or executed the tools that generate structures, templates, domains, DNA binding sites, and multiple sequence alignments.
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.
LK implemented and executed the computational tools for motif discovery and promoter enrichment analyses; AB performed the gene expression and clustering analysis; CK, LM and XX designed and coordinated the project; all authors wrote the paper; all authors read and approved the final manuscript.
The tester can also provide a test data (or a test data set) in XML format to be executed by the tool, to check the score, as well as, to set a mutant as equivalent.
To measure power consumption, a workstation executing the AMALGHMA tool is connected to an Agilent DSO03202A oscilloscope, which captures the platform-drained current by measuring the voltage drop across a 1 Ohm sense resistor (average microcontroller impedance is order of magnitude higher than this).
A pipeline framework executes the pipeline tools on a cluster or cloud using a big data processing engine or a supercomputer job scheduler.
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.
We executed the above searches with Biopython tools [ 70] which allowed accessing and querying of PubMed repository, and PMC online facilities to search through the PMC collection.
