FranzEtAl-2017-SupplementaryMaterials-S2.txt

Franz N.M., Zhang C., Lee J. 2017. A logic approach to modeling nomenclatural change.
Manuscript in press with Cladistics.
Supplementary Materials S2: Instructions to run the “20 nomenclatural taxon use case”.

1. Ensure that the Java Platform (Java Runtime Enviroment; capable of executing .jar [Java Archive] file formats) is properly installed; see http://www.oracle.com/technetwork/java/javase/overview/index.html [optional if visualization is not needed]

2. Create a directory (e.g., "ASP-Nomenclature), and place the clingo code (Supplementary Materials S1) and .jar file (Supplementary Materials S2) into this directory.

3. Install clingo, version 3.0.5, into the new directory. Software available at https://sourceforge.net/projects/potassco/files/clingo/3.0.5/

4. Install GraphViz, version 1.0. Software available at http://www.graphviz.org/Download.php

5. Open a command line interface terminal (CLI).

6. Enter in ClI: cd ~ /ASP-Nomenclature/

7. To obtain the textual clingo output in the CLI, enter: ./clingo FranzEtAl-2016-SupplementaryMaterials-S1.txt 0

8. To obtain the output visualizations as GraphViz .dot files, enter: ./clingo FranzEtAl-2016-SupplementaryMaterials-S1.txt 0 | java -jar FranzEtAl-2016-SupplementaryMaterials-S4.jar

9. To convert the .dot files (step 8) into .png files, enter: dot *.dot -Tpng -O

10. Outputs from steps 8 and 9 are placed in the "ASP-Nomenclature" directory.