As mentioned previously, we (Colin Gillespie, Daniel Swan, Phillip Lord and I) have recently had some of our work on annotation quality accepted at the European Conference on Computational Biology (ECCB’12). Given this, I am due to give an oral presentation at ECCB’12 in Switzerland on the 11th September (ECCB’12 Schedule). I have made this [...]
As documented in numerous posts, a key aspect of my research has been the application of power laws to word occurrence in bulk biological annotation. A large portion of this work has recently been accepted at the European Conference on Computational Biology (ECCB) 2012 and the resulting paper will shortly appear in a special issue [...]
In the last blog post we looked at data parsing, and how Zipf’s law could possibly be used to detect parsing errors. Whilst reading a recent blog post by Ben Goldacre I was reminded of Benford’s law – which shares a number of similarities to Zipf’s – and considered how it may also be applicable [...]
The foundations for most of our work has been based on data parsed from text files. Extracted data has included single words and whole sentences from gigabytes of raw text. With such overwhelming amounts of data, how can we be confident that we have correctly parsed our data? Obviously some basic checking was performed. This [...]
During my analysis of Swiss-Prot and TrEMBL datasets I have extracted all the words from each version of each dataset and counted their occurrences. A neat way of looking at this data is to create word clouds. I have done this for all versions of Swiss-Prot and TrEMBL. These can be seen with common words [...]
Yesterday I attended the BCS and IET Turing Lecture in Glasgow. This year the lecture was given by Donald Knuth. Saying it was a lecture was slightly mis-leading, as it was basically a question and answer session. This was part 4 of the lectures, having also given the lecture at Manchester, Cardiff and London. I’d [...]