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Welcome to the moose-development wiki!

What is MOOSE? Let's Make it Simple!

MOOSE is a computer program used by scientists to study how the brain and its parts work. It helps simulate, or "recreate," what happens in the brain using a computer.

Here’s how MOOSE works, explained in simple steps:

Many Sizes, One System

MOOSE can handle tiny LEGO pieces (like tiny parts of cells) all the way up to big buildings (like big groups of brain cells). It can handle all of these parts together.

It's Like Real Life, but in a Computer

MOOSE helps scientists study how the brain works in a computer. It can simulate how parts of the brain act and react. It can simulate both the electrical signals that pass between neurons, and the chemical reactions.

Building Blocks

MOOSE uses blocks like LEGO. Each block represents a piece of the brain, like a neuron or a chemical reaction. Scientists use these blocks to build their brain models.

The Math is Done For You

MOOSE is also really good at math. It has special tools that do all the hard calculations. This helps it simulate models very quickly.

More than Just Math

MOOSE isn't just about math; it can also show the results as pictures and graphs. It can also use many different ways to work with models and data.

Studying Small Parts of Cells:

MOOSE can focus on tiny parts inside a brain cell, like molecules and their chemical reactions. For example, it can help us see how certain chemicals inside the cell help it perform its job.

Understanding Single Brain Cells (Neurons):

A neuron is like a tiny messenger in the brain. It sends and receives signals to keep the brain working. MOOSE can create a computer version of a single neuron to study how it works in detail, like how it processes signals or reacts to chemicals.

Looking at Groups of Neurons:

Neurons don't work alone—they connect to form circuits or networks. MOOSE can simulate how a group of neurons communicates and works together to process information, like when you think or remember something.

Examining Large Brain Networks:

MOOSE can also simulate big networks of neurons, like how different parts of the brain interact when you're solving a problem, moving your hand, or feeling emotions.

Flexible Levels of Detail:

Scientists can choose how detailed the simulation should be. For example: At a very detailed level, MOOSE can show how individual molecules inside a neuron behave. At a simpler level, it can show how neurons send electrical signals to each other. It can also create larger, less detailed models to study overall patterns in a network of neurons.

MOOSE is Multiscale

MOOSE can calculate both chemical and electrical activities in the brain at the same time. For example:

It can simulate how neurons send electrical signals. It can also simulate how chemicals move and react inside or between neurons.

This makes MOOSE great for creating models that are realistic and detailed, just like the actual brain.

MOOSE is Object-Oriented

MOOSE organizes its work using "classes", which are like templates for different parts of the brain (e.g., neurons or molecules). Scientists can build brain models by creating these parts (called "instances") and connecting them, similar to assembling building blocks.

Special Helpers (Solvers):

MOOSE has solvers that quickly handle tough calculations, including:

Stochastic chemistry: Simulates random chemical reactions.
Deterministic chemistry: Simulates predictable chemical reactions.
Diffusion: Simulates how chemicals spread.
Multicompartment models: Simulates how neurons are divided into different compartments.

MOOSE is More Than a Calculator

MOOSE is a complete simulation environment, not just a math tool.

It provides tools to:
    Work with data.
    Solve problems.
    Create visual displays.

You can write scripts for MOOSE in Python to make it easier to use.

MOOSE supports graphical tools like:
    Matplotlib
    PyQt
    OpenGL

These tools help show results as charts or 3D images.

MOOSE Supports Many Formats

MOOSE can read and write data in many formats commonly used in brain research, including:

SBML
NeuroML
GENESIS
HDF5

This makes it easy to share or reuse models with other scientists.