In this research we present a method to develop a computerized tool, based on the ACT-R cognitive architecture, to evaluate the logical task flow in the EOPs, verifying if the timing assumptions for operator's actions contained in the procedure scripts can be accomplished by the human operators.
It has a specific procedure, scripts, file formats, criteria and images.
The complete mapping procedure, scripts, primary data, and PCA outputs are all available as a supplement to this mansucript or from the authors by request (Supporting Information, File S1).
The present experiments can be easily replicated using a standardized procedure (replication script) that is publicly available on the Open Science Framework.
During our effort to automate the attack and the system call auditing procedure, a script was written in Expect [43].
Sequences were demultiplexed and quality filtered using default QIIME parameters, and 16S rRNA operational taxonomic units (OTUs) were picked using a closed reference OTU picking procedure (QIIME script pick_reference_otus_through_otu_table.py).py
All participants provided written informed consent, and the procedures and script were approved by the Johns Hopkins University Institutional Review Board.> All FGDs were audio recorded, professionally transcribed verbatim, and coded for thematic content analysis in order to inductively derive concepts and core themes from the data.
Every in-silico discovery project is flooded with custom procedures and scripts to share data between programs.
Collection of procedures and scripts shown in Figure 2.
Extended Experimental Procedures All scripts were written in Perl (http://www.perl.org ), Python (http://www.python.org ), R (http://www.r-project.org ; R Development Core Team, 2008 ), or Bioconductor (http://www.bioconductor.org ; Gentleman et al., 2004 ), using the packages GenomicRanges, ShortRead, Sgenome, Biostrings, gtools, and gplots.
