On Tue, Nov 26, 2013 at 10:03 PM, William Stein <wst...@gmail.com> wrote: > On Tue, Nov 26, 2013 at 11:43 AM, William Stein <wst...@gmail.com> wrote: >> On Tue, Nov 26, 2013 at 11:01 AM, Jose Guzman <sjm.guz...@gmail.com> wrote: >>> >>>>> >>>>> >>>>> http://pub.ist.ac.at/~jguzman/doc/neuron/tutorial/Tutorial0.html#to-build-the-neuron-shared-library-for-python >>>> >>>> >>>> Thanks -- so it's a library for "Computational Neuroscience"? Cool. >>>> Maybe I should just make it available systemwide for everybody, and >>>> update it regularly? >>>> >>> >>> Yes, it's a platform for simulations of the electrical properties of neurons >>> based on the cable equation. I use it a lot in combination with Sage. To >>> have it all together in the cloud would be awesome! >> >> OK, this is more challenging than I thought. [...] >> However, that link is broken... I wonder where you get the source >> install from? I tried the github repos, but they require one to run >> autoconf, etc., which of course doesn't work (for me). > > OK, I found the script build.sh, and with that I was able to build > neuron with little difficulty. This will be installed systemwide (iv > and nrn) in /usr/local/, and also the neuron python library is > installed into the Sage python. Again, this will be live when I next > reboot the VM's. > > salvus@salvus-base:~$ sage > ┌────────────────────────────────────────────────────────────────────┐ > │ Sage Version 5.12, Release Date: 2013-10-07 │ > │ Enhanced for the Sagemath Cloud │ > │ Type "help()" for help. │ > └────────────────────────────────────────────────────────────────────┘ > sage: import neuron > Warning: no DISPLAY environment variable. > --No graphics will be displayed. > NEURON -- Release 7.3 (980:01f9410e41bc) 2013-10-31 > Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
For the record, here's what I did to install this into sage and /usr/local: umask 022; sage -sh; cd /tmp hg clone http://www.neuron.yale.edu/hg/neuron/iv; hg clone http://www.neuron.yale.edu/hg/neuron/nrn cd iv; ./build.sh; ./configure --prefix=/usr/local/; make -j16; sudo make install cd ../nrn; ./build.sh; ./configure --prefix=/usr/local/ --with-iv=/usr/local/ --with-nrnpython make -j16; sudo make install # ignore python error (?) cd src/nrnpython/; python setup.py install -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
