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Category Archives: science

At the end of last year I was commissioned to take some shots of the European Bioinformatics Institute (EBI) for their annual report. The EBI is a centre for research and services in bioinformatics (the subject of my PhD), part of European Molecular Biology Laboratory (EMBL), located on the Wellcome Trust Genome Campus in Hinxton near Cambridge. Here are a few of what I came up with.

I thought I’d better get a few of the oak tree that’s part of the EBI logo so I got as close as I could! I like the way the canopy covers so much of the image, it almost feels like you’re inside the tree. There’s a tree on Wimbledon common that I climbed then tried to take a planet but there were too many parallax issues and it wasn’t a good place for a tripod!


I’m really keen on interior shots with complex ceilings. I used my tripod and Nodal Ninja for this one so it wasn’t too hard to stitch; if I’d done it handheld I’m sure I’d have spent a while longer touching it up.


Here’s where all the science goes on. This is my friend Mark who I used to work with at Inpharmatica. He’s in John Overington’s chemoinformatics group. Big thanks to John (who was also at Inpharmatica) for getting me involved in this project.

I shot all of these with my Nodal Ninja, bracketed then Enfused, before finishing with some Topaz Adjust.

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In June I visited sunny Stockholm for the Intelligent Systems for Molecular Biology (ISMB) conference, a scientific meeting on the subjects of bioinformatics and computational biology that has been held annually since 1993, and has grown to the largest and most prestigious meetings in these fields. The conference and special interest groups went on for a week so I had quite a bit of free time to shoot some little planets. About 10 minutes walk from my hotel was this church which I think is called the Church of Riddarholmen – seems to be a pretty good match with this model that someone has created – which would make it one of the oldest buildings in Stockholm. I was a bit optimistic shooting this as stitching a nadir composed of cobblestones is usually a bit of a nightmare. I got lucky this time though and Hugin stitched it perfectly first time.

church_topaz

Close by is an area know as Gamla stan which means ‘Old City’. Gamla stan consists primarily of the island Stadsholmen and is home to Stockholm Cathedral, the Nobel Museum and Sweden’s baroque Royal Palace. Here are two of my partners in crime for the trip, Daniel and Tracey, who assisted me in conducting a thorough analysis of Stockholm’s nightlife.

gamblastan_topaz

One of the conference receptions was held in Stockholm City Hall. It stands on the eastern tip of Kungsholmen island, next to Riddarfjärden’s northern shore and facing the islands of Riddarholmen and Södermalm. It houses offices and conference rooms as well as ceremonial blue and golden halls. It is the venue of the Nobel Prize banquet and one of Stockholm’s major tourist attractions.

nobel_3_topaz

One of the strangest things about Stockholm in summer is that night seems to last only a few hours. It was dark by about midnight, but then light again by about 2.30am. If you’re out drinking until this sort of time then you face an inevitable walk of shame home without the cover of darkness. Not particulaly fair, but in winter I imagine the situation is reversed so things probably even out. This was taken using ISO 1600 at just before 3am.

waterfront_topaz

I didn’t have my tripod with me for this trip so all these planets were handheld, so no bracketing, enfusing or HDR. I’ve recently reinstalled Windows XP and am having lots of fun with CS4 and a plugin called Topaz Adjust, which produces HDR/enfuse-like effects via adaptive exposure adjustments – perfect for handheld panoramas. There’s a free trial but it’s quite cheap anyway.

Every year at UCL, the graduate school holds the Research Images as Art competition. I’m happy to announce that, out of about 250 entries, my mosaic of Charles Darwin was runner-up in this year’s competition!

My image is based on a photograph of Charles Darwin by Julia Margaret. I’ve turned it into a 1.2 gigapixel mosaic using images of protein structures from the Protein Data Bank (PDB), generated from X-ray crystallography and nuclear magnetic resonance data. The mosaic is composed of image tiles from a pool of about 19000 non-identical PDB structures and so represents the current content of the entire PDB. To produce the image I used a mosaic generator called Metapixel.

At the moment I’m struggling to embed the flash applet into (free) WordPress, so to explore the image using the flash applet click here. If you zoom in using the flash controls (the triangular slider works best), you should be able to make out one or two crystal structures. If you can’t view the flash applet, you can see the various levels of zoom here.

charles darwin pdb mosaic

As Darwin’s 200th birthday is rapidly approaching, I’ve had some very enthusiastic feedback from my department who are keen to display a large print of this image in the entrance hall as part of a celebratory Darwin exhibit.  This is pretty exciting for me – I just hope they can afford to do it justice and print it at a scale where you can make the proteins out. At 300DPI you could print it at 9×11 feet though I dread to think how much that would cost. For more large scale science images you may want to check out some of Ben Fry’s projects. His image of chromosome 13 is very big.

My other entry in the competition is an image of a potassium channel. Due to the use of detergents in protein crystallography, transmembrane proteins are rarely visualised in their natural state – embedded in a lipid bilayer. However, computational approaches now allow us to predict the position of such proteins within the membrane and reconstruct the ensemble. This image shows a bacterial inward rectifying potassium channel [pdb code 1p7b] embedded in the inner membrane, with potassium ions flowing through it into the cell. It was generated using Pymol, taking about 4 hours to render due to the huge number of atoms that make up the membrane. The potassium ions were added afterwards using Gimp.

potassium channel 1p7b

Unfortunately I didn’t win anything for this one, which actually took a lot longer to produce than the Darwin one. However, I’ve got some ideas to expand it into a more panoramic view of the plasma membrane, with a large number of membrane proteins embedded inside it. Roll on the 2009 competition..