Book chapter now online

Last year Maciej Swat, Martijn Mone and I contributed a chapter to a book on "Systems Medicine" in the Methods in Molecular Biology series. This is now available as an epub and should be in print soon, our chapter is titled "Modeling and Simulation Tools: From Systems Biology to Systems Medicine".

Installing libSBML Python bindings on Ubuntu 14.04 LTS

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)!

Modelling with Python

I rediscovered this paper the other day, as far as I know, one of the first published uses of Python/SciPy for modelling cellular metabolism (a.k.a systems biology). Today it looks trivial but considering the time it was written/published it's not too bad.

Modelling cellular processes with Python and Scipy
BG Olivier, JM Rohwer, JHS Hofmeyr - Molecular biology reports, 2002

Unfortunately, the PDF was published as a bitmap so the next step is to transcribe the code contained in the paper and see if it still works ... reproducible research in the life sciences with a paper over 10 years old? Watch this space ...

Fun and games with Win 8.1 pro, VirtualBox and HyperV

Just having bought a new machine that came pre-loaded with Windows 8.1pro I have been spending time getting to grips with Redmonds latest. Metro aside, one of the only major issues was running Virtualbox which turned into a saga that went something like this:

1. Installed VirtualBox 4.3.14
2. Installed ok, virtual machine crashed on startup with some Vbox error
3. Web search ... found a single post on a forum that this was a known 8.1 issue with 4.3.14 and to use 4.3.12 instead.
4. Downgraded to 4.3.12 which installed ok, however, vt-x extensions not detected (only single CPU VM's! and bad performance)
5. Web search ... found a forum posting that explained how Virtualbox behaved like this when Hyper-V is installed, recommended action uninstall Hyper-V
6. Clicked over to windows components ... Hyper V not installed!
7. ...
8. ...
9. The next day a new strategy crystallised ...
10. Installed Hyper-V via system components
11. Rebooted a few times to be sure
12. Uninstalled Hyper-V and rebooted a few times
13. Installed VirtualBox 4.3.12 and voila ... vt-x is now available
14. !!!!!

Conclusion. For some or other reason Win 8.1 pro only enabled support for vt-x after installing Hyper-V even though it was enabled in the BIOS. The next chapter in this saga will be to compare VirtualBox and HyperV.

Final work discussion for this season

Had a great time presenting the design and implementation of CBMPy and how it can be used for model driven media design. Python, object-oriented programming, biochemistry, microbiology and algorithms all unleashed on an amazingly awake audience. Especially considering this happened the night before :-)

Small core SBML L3+FBC model published in Biotechnology Journal

The first SBML3+FBC model (a small core model) published in support of this paper:

Basic concepts and principles of stoichiometric modeling of metabolic networks

Timo R. Maarleveld, Ruchir A. Khandelwal et. al

Biotechnology Journal, Volume 8, Issue 9, pages 997–1008, September 2013