https://github.com/sysbiochalmers/sybil-sbml
SBML (Systems Biology Markup Language) integration in sybil
https://github.com/sysbiochalmers/sybil-sbml
Last synced: 11 months ago
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SBML (Systems Biology Markup Language) integration in sybil
- Host: GitHub
- URL: https://github.com/sysbiochalmers/sybil-sbml
- Owner: SysBioChalmers
- License: gpl-3.0
- Created: 2022-02-17T13:46:48.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2023-08-01T19:31:34.000Z (almost 3 years ago)
- Last Synced: 2025-04-05T08:51:15.332Z (about 1 year ago)
- Language: R
- Homepage:
- Size: 314 KB
- Stars: 4
- Watchers: 3
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# sybil-SBML
This SBML (Systems Biology Markup Language) integration provides SBML support for [sybil](https://github.com/SysBioChalmers/sybil).
If you're facing any problems, please open an [issue](issues/new) or a [discussion](/discusions/new).
### Installation
> The guide below has worked with R 4.1.2 on Linux Mint 21, which is based on Ubuntu 22.04 LTS.
Start by installing the dependencies. Follow the [installation instructions from libSBML](https://github.com/sbmlteam/libsbml#installation). Below is a shortcut of the instructions adapted to Ubuntu, thus might require some tweaking for your system.
Start by fetching the latest libSBML and R interface from the official location:
```bash
wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Linux/64-bit/libSBML-5.18.0-Linux-x64.deb
wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/R%20interface/libSBML_5.18.0.tar.gz
```
Then install libSBML as a system library:
```bash
sudo apt install ./libSBML-5.18.0-Linux-x64.deb
```
If the previous step failed, it might be that some libSBML dependencies (such as lixbml2) might need for the previous step to work:
```bash
sudo yum install libxml2-devel
```
Finally, proceed to install the R interface to libSBML (will take a while):
```bash
R CMD INSTALL libSBML_5.18.0.tar.gz
```
For various reasons, `sybil-SBML` is temporarily not available on CRAN anymore. Until then, it needs to be installed straight from this GitHub repository:
Use the following commands in the R console to install this package:
```R
install.packages("remotes")
remotes::install_github("SysBioChalmers/sybil-SBML")
```
If the above fails because of failing to load `libsbml.so`, try adding the path to this file before starting R:
```bash
LD_LIBRARY_PATH=/usr/lib64 R
```
If the fix worked, make this permanent by changing this variable in your `.bashrc` file.
Remove the installation files::
```bash
rm libSBML-5.18.0-Linux-x64.deb libSBML_5.18.0.tar.gz
```
_Note_: This repository was previously hosted at https://gitlab.cs.uni-duesseldorf.de/general/ccb/sybilSBML .