Now that Ubuntu 14.04 has been around a bit now and I have started upgrading my development machines.
One of the first things that always gets installed is the libSBML and its Python bindings which then gives me access to the best library for reading/writing/manipulating Systems Biology Markup Language (SBML) files out there and is critical for my work.
Thanks to the fantastic work done by the development team installation is this easy:
# Python development packages and Pip install system
sudo apt-get install python-dev python-pip
# libSBML dependencies and development libraries
sudo apt-get install libxml2 libxml2-dev
sudo apt-get install zlib1g zlib1g-dev
sudo apt-get install bzip2 libbz2-dev
# libSBML
sudo pip install python-libsbml
That's it, happy modelling (please look up the above packages, before installing them, if you don't know what they are)!
Hi ! just a quick question right on spot: after doing this I have a py script whose author has put the following line:
ReplyDeletefrom libsbml import *
therefore, after installing python-libsbml as you suggest (I didn't install the dependencies, but I guess that should show up in another way, if troublesome),
I still get:
ImportError: No module named libsbml
If I modify the script to:
from python-libsbml import *
I get:
from python-libsbml import *
^
SyntaxError: invalid syntax
Same behaviour if I just try to import python-libsbml or import libsml
Any Ideas ??
Thanks In advance ! and best regards
Claudio (a great fan of your flux network module related work, and FAME user)
This was really helpful ! Thanks for posting this !
ReplyDeleteGreetings
Claudio
(Please ignore my previous comment [except for the part I like your work on modularization], I'm already on my way to using the library )
Hi Claudio
ReplyDeleteGlad this helped. Let me know if you have any other questions regarding the enumeration pipelines etc.
b.