Protein ROA Band Assignments

When I was working with Ewan Blanch on protein Raman Optical Activity spectroscopy, one of the key problems was the lack of a central resource describing the band assignments (the signatures in the spectra that indicate the presence of a particular substructure). I did a bit of simple work towards bringing this together, but never really put it into action.

If you don't know what I'm talking about this probably isn't your cup of tea. It's things like the presence of a peak between X and Y indicates the presence of beta sheet, for example. If this information was all centralised it would be a lot easier to utilise and validate.

With this in mind, I've set up a little form to collate things. If you want to contribute do (but you probably won't). Two important points. 1) I'm only really interested in ROA bands (not Raman), and 2) I want to capture the provenance of the assignment, so at the very least I'd like a Traceable Author Statement.

UPDATE: you can see currently entered assignments (albeit in an unpretty form) here.

Don't bother spamming, it only takes about half a second to get rid of it.

Text Mining Paper

I'm a paper machine this month! I have a second paper out, in collaboration with the National Centre for Text Mining (NaCTeM) and friends from Japan. You can find it here.

It's about linking a text mining-specific workflow system called U-Compare to the more generic Taverna workflow environment to make it easier to apply text mining methods to your textual data, whatever it may be.

Text Mining Meets Workflow: Linking U-Compare with Taverna

Yoshinobu Kano, Paul Dobson, Mio Nakanishi, Jun’ichi Tsujii and Sophia Ananiadou

Bioinformatics. 2010;(Advance access)

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Abstract

Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community.

Arabidopsis metabolic network

We have a new paper out about the reconstruction of metabolic networks. Find it here.

Here I put my cheminformatics tools into action towards a new reconstruction for Arabidopsis thaliana, or mouse-ear cress, a popular model organism for plant biology and genetics.

Image source: Wikipedia

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Karin Radrich, Yoshimasa Tsuruoka, Paul Dobson, Albert Gevorgyan, Neil Swainston, Gino Baart and Jean-Marc Schwartz

BMC Systems Biology. 2010;4:114

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Abstract

Background
Genome-scale metabolic reconstructions have been recognised as a valuable tool for a variety of applications ranging from metabolic engineering to evolutionary studies. However, the reconstruction of such networks remains an arduous process requiring a high level of human intervention. This process is further complicated by occurrences of missing or conflicting information and the absence of common annotation standards between different data sources.

Results
In this article, we report a semi-automated methodology aimed at streamlining the process of metabolic network reconstruction by enabling the integration of different genome-wide databases of metabolic reactions. We present results obtained by applying this methodology to the metabolic network of the plant Arabidopsis thaliana. A systematic comparison of compounds and reactions between two genome-wide databases allowed us to obtain a high-quality core consensus reconstruction, which was validated for stoichiometric consistency. A lower level of consensus led to a larger reconstruction, which has a lower quality standard but provides a baseline for further manual curation.

Conclusion
This semi-automated methodology may be applied to other organisms and help to streamline the process of genome-scale network reconstruction in order to accelerate the transfer of such models to applications.

Every Inch the Gardener

In the Sir Robert Hadfield building in Sheffield (where I now work) there is a green roof space - a sort of garden up in the air - designed by Dr Nigel Dunnett of the Green Roof Centre. I like the hidden surprise of roof and vertical gardens, and suspect they will become increasingly common.

Musée du quai Branly

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The Sir Robert Hadfield garden is one of a growing number of green roof spaces in Sheffield built to demonstrate their potential. They are so much more than parks in the sky to relax in, although this is justification enough. On a practical level green roofing also has a role in managing storm run-off as plants hold back water and slowly trickle it into the drainage system to prevent flooding.

In Paris there are a number of vertical gardens, where walls have been adapted to allow them to be planted (above). Just imagine how greatly this will change how our cities look and feel as it becomes more widespread. With walls of foliage replacing hard surfaces city sounds will become softer and gentler, while plants capable of trapping pollutants will improve air quality. With all the extra space I'm sure people will look to grow food, probably on a small scale initially, but later on will farms be multi-storey?

The shape of things to come? There were goats on the roof when I was there.

Old Country Market, Coombs BC, Canada

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Walking around the Sir Robert Hadfield green space with it's handsome green oak and larch lodge, I thought some more about my dream lab - a shed for experiments and a garden to grow medicinal plants. I'm rather sceptical of herbal medicines as often they are nonsense and sometimes extremely dangerous, but I keep returning to the fact that many of our current medicines derive from plants and, contrary to what Dara O'Briain says, we haven't tested them all.

I can think of a number of relatively simple but useful experiments to investigate interactions between plant extracts and specific proteins that might lead to new drugs. The first step towards this is a well-stocked medicines garden, which I feel would be an interesting and fitting way to use the green space on a science department's roof. Perhaps I'll take my trowel to work.