src

Data processing

Some of the primary files:

• load-files.scm - Load genomic/proteomic datasets into the AtomSpace
• cleanup-data.scm - Scrub datasets for cleaner results.
• bio-loop.scm - Data-mine triangular and pentagonal interactions.
• bio-tetra.scm - Data-mine tetrahedron interactions.
• data-export.scm - Export selected stats to CSV files for graphing.
• gene-pairs.scm - Provide a sparse-matrix API for data analysis.

The primary data-processing pipeline is to start up a guile shell, and then load each of the above files in turn. Review thier contents, and perform the "obvious" operations that each of them suggest. See also the graphs directory for assorted data-graphing scripts.

Some of the secondary files:

• performance-instrumentation.scm - measure performance stats.
• debug-wrapper.scm - Used for debugging the MOZI code-base.
• lmpd-genes.scm - a list of 1482 genes.
• mem-use.sh - log RAM usage statistics.
• grid.conf and path.conf - handy-dandy cogserver configs

Typical run

For info on typical data runs, see the files:

• graphs/loop-graphs/README.md
• graphs/pentagon-paths/README.md
• graphs/tetrahedra/README.md