Category Archives: bioinformatics

Exploring pathway data

I’ve added a document on
exploring pathway data to blipdoc. I’ll highlight some of the salient points on this blog at a later date.

ICLP 2009

My invited talk from ICLP-2009 is available from slideshare:

experiences-with-logic-programming-in-bioinformatics

Unfortunately I didn’t get to go into detail in some sections, particularly Thea.

Overall I had an excellent time, good to meet many LP luminaries and users.

intervaldb now on github

intervaldb has moved from blipkit svn to githib.

intervaldb is an SWI-Prolog wrapper for the nested containment list (NCList) C library distributed as part of PyGR. Query time is O(n+logN) where N is the size of the database and n is the size of the result set. It is primarily intended for indexing genomic data, but can be used for any kind of intervals, e.g. temporal data

See: http://bioinformatics.oxfordjournals.org/cgi/reprint/btl647v1

Robot Scientist

This story received a bit of coverage last month:
http://news.bbc.co.uk/2/hi/science/nature/7979113.stm [BBC]

There are more details in the Science publication, “the automation of science”:

The system generates scientific hypotheses about gene functions, then devises and carries out experiments to test these hypotheses. The system appears to be written in Prolog, with the hypothesis generation using Inductive/Abductive Logic Programming, in particular the ProGol system.

More details can be found on the group’s website.