# News

#### Reference sequence database for Bacteria and Archaea v1.3 released

*2024-11-06*

The database for reference protein sequenes (bacteria and archaea) was updated. gapseq should automatically download the latest version. The sequences were retrieved from [UniProt](https://www.uniprot.org/) Release 2024_05.

DOI of Zenodo data set: https://doi.org/10.5281/zenodo.14046824

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#### gapseq version 1.4.0 now uses 'cobrar' instead of 'sybil'

*2024-10-25*

Prior to v1.4.0, gapseq used the R packages 'sybil' and 'sybilSBML' for constraint-based metabolic modelling, including FBA and SBML file export. In addition, the R package 'glpkAPI' was required to interface with GLPK as an LP solver. All these dependencies are now replaced by the single R package '**[cobrar](https://waschina.github.io/cobrar/)**'.

*What gapseq users need to know when updating from <=v1.3.1 to >=v1.4.0*:

You will need to install 'cobrar' with the following commands:

```R
install.packages("remotes") # only needed if 'remotes' is not installed yet
remotes::install_github("Waschina/cobrar")
```

Please make sure you have the system libraries 'libSBML' and 'glpk' installed before installing cobrar.

Detailed installation instructions for cobrar can be found in the [cobrar documentation](https://waschina.github.io/cobrar/). There you will also find reference documentation and tutorials on how to use cobrar to analyse genome-scale metabolic network models, including those generated by gapseq.

*Why this change?* The 'sybil' family packages seem to be no longer regularly maintained, which has caused some compatibility issues with the libSBML system library and some installation problems.

An official release of a new version that uses 'cobrar' instead of 'sybil' will be made via github after a short testing phase of the latest development version.