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Circuitscape Protects Endangered Species Using PyAMG
Scientists map the “current” of mountain lions moving between mountain ranges. Blue shows areas of low current density, which are expected to have low densities of dispersing mountain lions; yellow designates movement bottlenecks, which are most vulnerable to habitat destruction. Destroying high-flow habitat can isolate populations and endanger their survival.
Image: Brad McRae and Brett Dickson
PyAMG is an open-source numerical package of multigrid and Krylov solvers for sparse matrices in Python. One of the biggest users of PyAMG is Circuitscape. This open-source software program borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes. Circuit theory complements least-cost path approaches because it considers effects of all possible pathways across a landscape simultaneously.
Circuitscape was written by Brad McRae and Viral Shah. Brad is an Ecologist with the The Nature Conservancy in Seattle. He works on habitat connectivity conservation, climate change, and landscape genetics. Viral is a Senior Scientist with Interactive Supercomputing and a Visiting Scientist at the University of California, Santa Barbara. He develops systems for scientific computing for work and for fun.
For additional information on Circuitscape:
The authors presentation at SciPy 2008: http://www.circuitscape.org/Circuitscape/Pubs_files/Shah_McRae_Circuitscape_Python_Scipy08.pdf.
Conservation Magazine: Circuitous Routes: Circuit Theory Guides Wildlife Corridor Design by Eric Wagner
Convergence Magazine: Where the Wild Things Are by Anna Davison
Python in Astronomy
On 28 March, NASA’s Swift satellite observed a flash of gamma rays brighter than anything astronomers had seen before. It soon became evident that the event wasn’t a typical gamma ray burst, an emission of high-energy radiation that often accompanies a supernova explosion. The flash didn’t die out but was sustained for weeks, and although it has faded in intensity, it is still going strong 2½ months later. Two papers published online today in Science provide an explanation for this luminous surprise. The flare is in fact a high-energy jet of radiation produced by a star falling into a black hole at the center of a galaxy 4 billion light-years away. The reason the flare is so bright is that the jet is pointed straight in the direction of Earth. And it’s sustained becausethe black hole is consuming the star gradually. “That’s because as the black hole rips the star apart, the mass swirls around like water going down a drain, and this swirling process releases a lot of energy,” says Joshua Bloom, an astronomer at the University of California, Berkeley, and lead author of one of the two papers. Bloom expects the flare to fade out over the next year.
by Yudhijit Bhattacharjee on 16 June 2011, 2:00 PM
For related story and photo, http://discovermagazine.com/2012/jan-feb/14.
Chairman of NumFOCUS’ Board of Director’s,Travis Oliphant, spoke at the March meeting of Tokyo SciPy via live webcast. Topics he covered included the history of SciPy, where NumPy should go next, and Numba. Questions were asked regarding sparse matrix integration with NumPy, and packaging.
Tokyo SciPy member, Syoyo, gave Travis the link to his code for simulating smoke, http://code.google.com/p/smoke3d/. Perhaps at some point, Syoyo will be able to make that code fast using Python.
Despite a late night, due to the fourteen hour time difference between Austin and Tokyo, Travis spoke for over an hour. He later stated, “…it was nice to see that SciPy and NumPy have a user community in Japan.”