Author: Justas

Compile .mod files with with (specify path after to compile specific mod files): nrnivmodl Check units with (nrnivmodl does not check unit consistency): modlunit file.mod Meaning of various NMODL keywords RANGE - varies with position (0-1) on a section. Read/set with section.var or section(0.5).var. If section.nseg > 1:section(0.5).var can have a different value than section(0 … Continue reading NEURON NMODL/MOD File Cheat Sheet

Often, I will quickly run a simulation test just using the NEURON GUI. However, once I'm ready to script the model and run from Python, it can be quite the hassle to figure the Python command(s) that are behind the actions I performed with the mouse. Luckily, there is a quick method do to that: … Continue reading How to find the command behind any NEURON GUI button

If you have unit tests or code coverage metrics enabled on your GitHub project that uses the NEURON simulator and you want Travis CI perform those automatically, then you'll need a Travis CI YAML file that will install NEURON before running the tests. The script below is essentially a pure script version of the manual … Continue reading Tutorial: Using NEURON simulator with Python and Travis CI

I have recently found myself having to pour over 100's of reconstructions of neurons from http://NeuroMorpho.org and make small changes before I can analyze them further. I needed a free tool that could: a) let me quickly preview the contents and b) make changes to the SWC files (e.g. move some branches around, set/change node … Continue reading Tools for editing SWC files (neuron morphology)

Spraying volcanic-like particles in the upper atmosphere would cost a fraction of today's wildfire and hurricane costs, and a fraction of fossil fuel company profits Why band-aid-like, simulated volcano eruptions (a.k.a. Stratospheric Aerosol Injections) will probably be the most cost-effective way to lower global temperatures while our civilization phases out the use of fossil fuels … Continue reading We will probably simulate volcanic eruptions to offset global warming

Binding Bound Coupled Decoupled Decouple from Decouple from world Peal off Peal away from the world Watch the world Watch the world as it is Do more with less Work smarter, not harder How? A loop A tight loop I'm in it I'm bound Need to uncouple from loop Watch more Pay attention Observe Don't … Continue reading Poem: Not bound to the world

Question: At what point self-augmentation of humans becomes so severe that the person stops being a human? First I observe the similarity of this question to the Sorites Paradox, which asks when does a heap of sand become a pile if you start taking single grains of stand away from it? Then, analogously,  if a human … Continue reading On Human-Cyborg Continuum

I've noticed a tendency to view the the nervous system and what it does in a kind of black box that receives input from and responds with output to the environment. Input is generally the sensory systems like vision, hearing, smell, taste, and touch. While output is mostly movements expressed through the motor system (and … Continue reading On nervous systems and environments

Clear an array array.length = 0 linq.js example Enumerable    .from(some_array)    .where(i => i.prop == test_value)    .select(i => {"a":i.a_val, "b":i.b_val})    .distinct(s => s["a"])    .toArray(); jQuery create new element, attach an event, and add it to the list of elements of a parent element jQuery("<span id='test'>Some text</span>")    .on("click", function() { alert(this.id … Continue reading JavaScript Cheat Sheet

Here is a working example of running a NEURON simulation of a cell to steady state, saving that state, restoring it in a new simulation, and using the Vector.play method to stimulate the cell with an arbitrary waveform. All this while using the variable integration method CVODE. First, build the cell, and run it to … Continue reading Tutorial: Making NEURON Vector.play() + SaveState.restore() + CVODE work