Thanks Chris! I'd be happy to help out creating some notebooks... would be good for my own learning PDL! With teaching and researching, time is tight, but I'll try, and probably email the list for pointers.
here is the latest for the notebook I'm currently working on that uses HackaMol, PDL, PDL::LinearAlgebra, and PDL::Stats (awesome!!!). http://nbviewer.ipython.org/github/demianriccardi/HackaMol/blob/master/examples/Notebooks/HackaMol-GNM.ipynb I wish I could inline graphics! ... from plot.ly!!! Demian On Thu, Feb 5, 2015 at 6:56 AM, Chris Marshall <[email protected]> wrote: > Hi Demian- > > PDL::LinearAlgebra is bindings to existing "gold standard" > BLAS and LAPACK linear algebra routines. I think you'll be > ok with numerics from there. > > Regarding linear algebra for PDL, that is one of the areas > we've long desired improvement. I've adopted PDL::LinearAlgebra > for maintenance and in the hopes of improving the library > detection and build. However, the GNU Scientific Library has > a large number of computational routines including linear > algebra that could use PDL bindings. > > Cool to hear about your iperl notebook work. Would you be > interested in making an intro PDL tutorial for it? PDL-2.008 > is planned for this month. It would be nice to have some > flash and coolness with the announcement. :-) > > --Chris > > On 2/4/2015 22:03, Demian Riccardi wrote: > > Hello everyone, > > I’m working on a few iperl notebooks for a publication that I’m trying > to push through. I want to show an analysis of protein fluctuations and > correlated motion using a gaussian network model (GNM). GNM is easy to > implement, you just need to calculate a Kirchoff matrix and then compute > the pseudo inverse (first eigenvalue is zero). See the following: > > > https://github.com/demianriccardi/HackaMol/blob/master/examples/Notebooks/HackaMol-GNM.ipynb > > I use PDL::LinearAlgebra to calculate the pseudo inverse, but I felt a > little squeamish when I downloaded it and looked around at the test suite. > Is PDL::LinearAlgebra my best option, or are there other recommended ways > of going. > > Thanks! > > Demian > > p.s. Zaki’s iperl notebook has changed my life almost as much as moose > has. > >
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