Stephen Larson slarson

We have been fortunate to have a series of good press from the online community. This page is an attempt to capture the links back to those articles, blog posts and links.

2011

Ghosh, S., Larson, S. D., Hefzi, H., Marnoy, Z., Cutforth, T., Dokka, K., et al. (2011). Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature, 472(7342), 217-220. Nature Publishing Group. doi: http://dx.doi.org/10.1038/nature09945.
Hawrylycz, M., Baldock, R. a, Burger, A., Hashikawa, T., Johnson, G. A., Martone, M., et al. (2011). Digital Atlasing and Standardization in the Mouse Brain. (L. J. Graham, Ed.)PLoS Computational Biology, 7(2), e1001065. doi: http://dx.doi.org/10.1371/journal.pcbi.1001065.
This is the brain the crowd built, Wired UK
Science Magazine NSF Visualization Challenge Honorable Mention
- http://www.nsf.gov/new

garbagehttp://www.nsf.gov/new

	# -- coding: utf-8 --
	# <nbformat>3.0</nbformat>

	# <markdowncell>

	# Full [Hodgkin Huxley Model](http://en.wikipedia.org/wiki/Hodgkin-Huxley_model)
	# ==========================
	#
	# By Stephen Larson ([email protected]) for [OpenWorm](http://openworm.org)
	#

	import scipy as sp
	import pylab as plt
	from scipy.integrate import odeint
	from scipy import stats
	import scipy.linalg as lin

	## Full Hodgkin-Huxley Model (copied from Computational Lab 2)

	# Constants
	C_m = 1.0 # membrane capacitance, in uF/cm^2

	unknown1040f3847b74:generatedNeuroML2 slarson$ ls -l CElegans.net.nml
	-rw-r--r-- 1 slarson staff 794999 Jan 13 16:43 CElegans.net.nml
	unknown1040f3847b74:generatedNeuroML2 slarson$ pip show libNeuroML
	---
	Name: libNeuroML
	Version: 0.1.9.1
	Location: /usr/local/lib/python2.7/site-packages
	Requires:
	unknown1040f3847b74:generatedNeuroML2 slarson$ python
	Python 2.7.6 (default, Jan 2 2014, 15:58:06)

	unknown1040f3847b74:CElegans slarson$ ls
	CElegans.ncx cellMechanisms generatedMorphML generatedNeuroML2 morphologies
	README.md dataSets generatedNeuroML images pythonScripts
	unknown1040f3847b74:CElegans slarson$ cd generatedNeuroML2/
	unknown1040f3847b74:generatedNeuroML2 slarson$ ls
	ADAL.nml BAGL.nml MuscleCellConnections.net.nml SABD.nml
	ADAR.nml BAGR.nml NSML.nml SABVL.nml
	ADEL.nml BDUL.nml NSMR.nml SABVR.nml
	ADER.nml BDUR.nml OLLL.nml SDQL.nml
	ADFL.nml CANL.nml OLLR.nml SDQR.nml

	unknown1040f3847b74:neuroConstruct slarson$ ./nC.sh
	Running neuroConstruct from: . with max Java heap size of 450M

	neuroConstruct v1.7.0 starting...
	To start application with extra memory, see nC.sh in the neuroConstruct home directory.

	12:49:11.057> UncaughtExceptionInfo : * ERROR* : Uncaught exception, no GUI warning...
	12:49:11.057> UncaughtExceptionInfo : * ERROR* : apple/awt/CGraphicsDevice
	12:49:11.065> UncaughtExceptionInfo : * ERROR* : java.lang.NoClassDefFoundError: apple/awt/CGraphicsDevice
	12:49:11.066> UncaughtExceptionInfo : * ERROR* : at javax.media.j3d.GraphicsConfigTemplate3D.<clinit>(GraphicsConfigTemplate3D.java:55)

	Stephens-MacBook-Air-3:geppetto slarson$ ./bin/startup.sh
	The JAVA_HOME environment variable is not defined. Using PATH instead.
	[2013-10-05 09:22:14.391] startup-tracker <KE0001I> Kernel starting.
	[2013-10-05 09:22:17.785] startup-tracker <KE0002I> Kernel started.
	[2013-10-05 09:22:18.112] system-artifacts <DE0000I> Installing plan 'org.eclipse.virgo.kernel.userregion.blueprint' version '3.6.0'.
	[2013-10-05 09:22:18.298] system-artifacts <DE0000I> Installing bundle 'org.eclipse.gemini.blueprint.core' version '1.0.2.RELEASE'.
	[2013-10-05 09:22:18.350] system-artifacts <DE0000I> Installing bundle 'org.eclipse.gemini.blueprint.extender' version '1.0.2.RELEASE'.
	[2013-10-05 09:22:18.363] system-artifacts <DE0000I> Installing bundle 'org.eclipse.gemini.blueprint.io' version '1.0.2.RELEASE'.
	[2013-10-05 09:22:18.374] system-artifacts <DE0000I> Installing bundle 'org.eclipse.virgo.kernel.agent.dm' version '3.6.0.RELEASE'.

	{
	"metadata": {
	"name": "BAMS-To-NeuroLex"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [
	{