docs/index.md

In a-kramer/SBtabVFGEN: Converts from SBtab to vf,mod,[sbml]

SBtabVFGEN

This is an R package which converts a Model written in SBtab, saved as a series of tsv files or alternatively an Open Document Spreadsheet ods to a VFGEN vector field file vf.

Install

Using remotes (R):

remotes::install_github("a-kramer/SBtabVFGEN")

You may have to check .libPaths() to verify that it includes a path that you have permission to write to (this is just generally the case, not just for this package).

Usage Example

Within an interactive R session called from the folder that contains the tsv files:

library(SBtabVFGEN)
model.tsv <- dir(pattern=".*[.]tsv$");
model.sbtab <- sbtab_from_tsv(model.tsv)
sbtab_to_vfgen(model.sbtab)

SBtab (Systems Biology Tables)

This format is human readable and writable. We use the standard as we understand it, but use our own code to process the files, using a subset of named columns. These files can hold a great variety of content.

Systems Biology Markup Language (SBML level 2 version 4)

The program in sbtab_to_vfgen.R also produces an .xml file in the Systems Biology Markup Language (SBML). This is only done, if libsbml is installed with R bindings, like this:

$ R CMD INSTALL libSBML_5.18.0.tar.gz

If this check: if (require(libSBML)) succeeds, then the scripts attempts to make an sbml file. SBML is a format that has units. The units found in the SBtab document (strings) are forwarded to SBML (nested, structured xml-elements). The formats are very different with regard to unit handling and math generally. The method we use to parse the common (human readble) text units is described in units.md.

There is an official guide on sbml.org that we used to write the SBML output part of this program. The guide contains some examples. But, the libSBML R bindings are not documented yet and there is some guesswork involved (on our side).

Here is a small (incomplete) list of libsbml functions in R that we use to create SBML files.

a-kramer/SBtabVFGEN documentation built on Nov. 14, 2024, 8:41 p.m.