slv-utils
v0.5.1
Published
Utilities for working with SLV and DAT files.
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slv-utils
Utilities for transformation of DBSolve files (.SLV, .RCT and .DAT). It can be used as node package as well as command line tool.
DBSolveOptimum is modeling software for systems biology and systems pharmacology modeling developed by InSysBio, see http://insysbio.com/en/software/db-solve-optimum.
Installation
Required nodejs
installed. Recommended version is >= 10.0.0.
npm install --global slv-utils
slv --version
Help
See list of commands
slv -h
See help for particular command
slv help [command]
Transformation of .SLV files
Parse SLV file and save in SLVJS format (JSON).
slv parse -o output.json model.slv
Export SLV file to Heta module file (.HETA).
slv slv2heta -o output.heta model.slv
Note. Conversion of SLV to Heta modules is intended for learning purposes and should NOT be used for modeling workflow. After creating Heta file one should check and manually fix update file for proper structure. Known restrictions are:
- slv-utils does not transform slv functions to Heta supported list.
- All SLV ODE variables are transformed to species.
- slv-utils ignores Pools and if/else statements.
- slv-utils throw error when Initial Values includes expressions.
Export SLV file to Heta JSON file.
slv slv2heta --json -o output.json model.slv
Transformation of .RCT files
Parse and save RCT in RCTJS format (JSON).
slv rct-parse -o output.json structure.rct
Serialize RCT from RCTJS format (reverse to slv rct-parse).
slv rct-serialize -o output.rct input.json
Transformation of .DAT files
Parse and save DAT file in DATJS format (JSON).
slv dat-parse -o output.json data.dat
Serialize DAT from DATJS format (reverse to slv dat-parse).
slv dat-serialize -o output.dat input.json
Transformations available in previous versions
Convert XLSX file with specific structure to DAT.
slv excel2dat -o output.dat input.xlsx
Convert XLSX file with specific structure to DATJS (JSON).
slv excel2json -o output.json input.xlsx
Convert DATJS file to XLSX.
slv json2excel -o output.xlsx input.json
Usage for git
The tool can be used to display changes in Git diff command. It represents .SLV as text file based on RHS and Initial Values part.
Try
slv clear model.slv >> out.txt
For implementation in all git repositories use
git config --global diff.slv.textconv "slv clear"
In particular project include lines in .gitattributes
*.slv diff=slv
Git settings
Developers
- Evgeny Metelkin @metelkin
- Viktoria Tkachenko @vetedde