libSBML C++ API
5.11.0
|
To begin, please use the following table to find the appropriate instructions for your situation:
The installation packages in the libSBML SourceForge download site contain interfaces for C, C++, C#, Java, MATLAB, Perl, Python, and Ruby in the same package. (However, there are better ways to get the Python interface, as explained below.) The download area has two subdirectories: one for stable releases of libSBML, and one for experimental releases. The stable releases contain support for only the accepted parts of SBML, while the experimental releases contain code for SBML Level 3 packages still in development.
Screenshot of the SourceForge download page for libSBML.
Click on either stable or experimental, and then
navigate to a subdirectory matching your operating system platform. Download
the appropriate installer or package file for your platform, and use the
appropriate platform-specific approach to install the software. (E.g., if you
downloaded a Mac .dmg
file, double-click the file in the Mac
Finder to mount the disk image, open the image contents in the Finder,
and finally, double-click the .pkg
file contained inside.)
We provide three easy options for obtaining the libSBML Python interface:
(1) packages available from the Python Package Index (PyPI), to be used with
pip
, (2) for Linux only, installers for use with the standard
operating system installation tools such as yum
and
apt-get
, and (3) for Windows only, standalone Windows
installers. The following paragraphs provide more information about each.
If you have pip installed on
your Windows, Mac OS X or Linux system, you can use it to install
the latest releases of libSBML. First, make sure you have installed the
following prerequisite software packages on your operating system: python-dev
, libxml2-dev
, libz-dev
, and
libbz2-dev
. (Those are for Linux; for
other operating systems, please find the appropriate software distributions.)
Then, to get the stable release of libSBML, execute the following
command:
sudo pip install python-libsbml
For the experimental release of libSBML, use the following command instead:
sudo pip install python-libsbml-experimental
If all goes well, the command above should result in pip
printing many messages while it builds libSBML on your computer, ultimately
ending in the following message to tell you it finished successfully:
[... much text omitted ...]
Successfully installed python-libsbml
Cleaning up...
After this, you should be able to access the Python language interface
for libSBML on your computer directly from your Python interpreter by
importing it like any other Python module. In other words,
import libsbml
apt-get
and yum
together with online
repositories If you are running Linux, and you prefer to use the standard over-the-air
installation tools provided by your operating system (e.g., yum
and apt-get
), you can take advantage of binary packages we
provide using the OpenSUSE Build System (OBS) for many
different flavors of Linux including CentOS, Fedora, Ubuntu, and others:
python-libsbml
.
python-libsbml-experimental
.
As an example, the following is a screenshot of the page currently found at the python-libsbml page. From this page, clicking on the name of an operating system will display the instructions for what to do:
Screenshot of the OBS python-libsbml page for different Linux systems.
After following the instructions to install the appropriate binary
distribution on your computer, you should be able to access the Python
language interface for libSBML on your computer directly from your Python
interpreter. In other words, import libsbml
If you are running Windows, you can take advantage of executable installers that we make available for that platform. They can be found in a subdirectory named python within each of the Windows subdirectories (stable and experimental) in the libSBML area on SourceForge. There are different installers for different versions of Python. The following screenshot shows an example.
Screenshot of the SourceForge download page for the Windows libSBML installers.
After you download an appropriate .exe
file for your system,
run the installer. The installer will lead you through the installation
process.
We provide installers for the libSBML R language interface for Linux,
Mac OS X and Windows. You can download the installer archive file
from the SourceForge download
page mentioned below. This file will have a name of the form
libSBML_5.11.0.tgz
on Mac OS X,
libSBML_5.11.0.zip
on Windows, and
libSBML_5.11.0_R_i686-pc-linux-gnu.tar.gz
or
libSBML_5.11.0_R_x86_64-pc-linux-gnu.tar.gz
on Linux
systems.
Once you have downloaded the appropriate version of the installer for your operating system, one more step is required to install the libSBML R interface. You can do this step in one of two ways: either using the R graphical interface, or using a terminal/shell command. These approaches are explained below.
From the R menu "Packages" or "Packages & Data" (depending on your operating system), select the "Package Installer" item. You will be presented with an interface that lets you install a local binary package. Use that interface to navigate to the directory where you copied the libSBML archive file, and select the archive file for installation.
Suppose that the path to the libSBML R archive on your computer is archive. Execute the following command in a terminal/shell window (note: not in the R command line interpreter!):
R CMD INSTALL archive
If all goes well, you should see R print messages such as the following (the paths on your computer may differ):
* installing to library '/Library/Frameworks/R.framework/Versions/3.1/Resources/library' * installing *binary* package 'libSBML' ... * DONE (libSBML)
In the command above, R
is the executable for the
command-line version of R. We assume it is accessible from your shell's
command line, but if it is not accessible by simply typingR
, you
may need to supply the full path to R
.
If you need to use Octave, or no installation package is available for your particular platform, or you have special requirements for libSBML's configuration, you can always build libSBML from sources. The process for doing that is the topic a separate section, Building and installing libSBML .