Feature Values Service

Overview

This KBase service provides a set of methods for manipulation and visualization of expression values organized as two-dimensional matrix and assigned to genome features on one dimension and to different sorts conditions on second dimension.

Notes for preparing test data

The Genome object test data is only needed to provide a list of feature ids that match the ids in the paired expression data files. The prepared test data is checked into the repository as .json files in specific test/data/ directories. These .json file will work for tests on as long as the Genome object does not incur backwards incompatible changes. The version of the checked in .json files is KBaseGenomes.Genome-17.0 from ci.kbase.us circa 2/10/2020/.

The tests require three different RefSeq Genomes with source .gbff files checked in to the appropriate test.data/upload directory. The genomes are: Desulfovibrio vulgaris Hildenborough, E. coli MG1655, and Rhodobacter sphaeroides. The steps to prepare new Genome .json test data are as follows:

• Load .gbff files into a narrative in target environment.
• Download the uploaded Genome object as a .json file.
• Remove all optional _ref and handle fields in the genome object: Assembly_ref, genbank_handle_ref, gff_handle_ref, taxon_ref.
• Place edited .json Genome files in the correct test/data/upload* directory.

Authors

Roman Sutormin, LBL (rsutormin@lbl.gov) Marcin Joachimiak, LBL (mjoachimiak@lbl.gov) Pavel Novichkov, LBL (psnovichkov@lbl.gov) Srividya Ramakrishnan, CSHL (srividya.ramki@gmail.com) Michael Sneddon, LBL (mwsneddon@lbl.gov)

Special deployment instructions

• There is a dependency to R-script command in both service and AWE-worker scripts
• Pyhton Scikit-learn package is not utilized yet but it's in short-term plans
• Follow the standard KBase deployment and testing procedures (you have to specify test user credentials in test/test.cfg file in order to be able to run "make test")

Starting/Stopping the service, and other notes

• to start and stop the service, use the 'start_service' and 'stop_service' scripts in (the default location) /kb/deployment/services/KBaseFeatureValues