Category: bioinformatics
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DORIS on the high seas
Yesterday was the first test of the full DORIS marine mapping system I’m developing with Amber Teacher and David Hodgson at Exeter University. We went out on a fishing boat from Mylor harbour for a 5 hour trip along the Cornish coast. It’s a quiet season for lobsters at the moment, so this was an…
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Doris: Lobster mapping
A new project, coming from Borrowed Scenery’s Zizim project, converted into a scientific research tool in collaboration with the College of Life and Environmental Sciences at Exeter University and Helsinki University. Doris is named after the sea nymph from Greek mythology, and will be used for mapping Lobster catches on fishing boats so researchers working…
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Hapstar graphs in the wild
Some examples of graphs that scientists have created and published using Hapstar, all these images were taken from the papers that cite the hapstar publication, with links to them below. I think the range of representations of this genetic information indicate some exciting new directions we can take the software in. There are also some…
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Hapstar version 0.7
Hapstar has achieved some popularity in the genetics community, the paper has currently racked up 13 citations, including one for it’s use to create a figure for a Nature paper. This version addresses some requests from users, including the ability to save graphs midway though balancing. This means it’s easier to run them for long…
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Hapstar in Molecular Ecology Resources
Our hapstar paper has been published (actually a few weeks back): Teacher AGF. Griffiths DJ (2010) HapStar: automated haplotype network layout and visualization. Molecular Ecology Resources There is a preprint version available on the foam site.
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Hapstar 0.5
Hapstar is released, and now has it’s own website. Here’s a screenshot of an example haplotype network of human and neanderthal DNA sequences.
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HapStar
Hapstar is the new name for my little bioinformatics project, visualising population structure from differences between genetic sequences. The last few days I’ve done a lot of work on the GUI, allowing you to drag nodes around by hand, zoom in and out and navigate the graph. Also quite a bit of graph theory, validating…
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Hapnet
A small bioinformatics project in progress: Haplotype networks and Minimum Spanning Networks are commonly used for representing associations between sequences. HapNet is a tool for viewing both types of networks, using the output data generated from Arlequin. HapNet automatically formats the network in the optimal layout for easy visualisation, and publication-ready figures can be exported…