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

 

New SBML editors for 2014 :-)

Awesome news to end 2013 is that after a community vote I, together with Dagmar Waltemath, have been elected to serve as an SBML editors. This is a great opportunity to contribute to the development of standards in the Life Science community and I'm really looking forward to it.

Software and standards poster presented at NISB 2012

This is a poster I presented at the NISB meeting in 2012: NISB 2012 Poster