docs.openworm.org
Modelling - OpenWorm
http://docs.openworm.org/en/latest/modeling
Closing the loop with neuromechanical modeling. Muscle / Neuron / Channel. Our main goal is to build the world's first virtual organism- an. In order to achieve these goals, we first began with an informal cartoon representation of a breakdown of cell types and various biological processes that the worm has. Here is a representation of a small subset of those processes, where arrows show the causal relationship between processes and cell types:. Crawling behavior of worms is relatively easy to measure.
docs.openworm.org
Resources - OpenWorm
http://docs.openworm.org/en/latest/Resources/resources
Muscle / Neuron / Channel. This page describes content that has been created by the project for use by the public. Currently we make simulation engines, visualization environments, and data sets available. Sibernetic is the code base that currently implements the crawling model. Sibernetic is a C / Python code base by Palyanov, Khayrulin and Vella that has been created expressly for the purpose of doing research and building the model quickly. More information on running Sibernetic is available online.
docs.openworm.org
FAQ - OpenWorm
http://docs.openworm.org/en/latest/faq
Muscle / Neuron / Channel. OpenWorm simulation and modeling. OpenWorm links and resources. Three different Nobel prizes have been awarded for work on this worm, and it is increasingly being used as a model for better understanding disease and health relevant to all organisms, including humans. When making a complex computer model, it is important to start where the data are the most complete. What does the real worm do? It has all sorts of behaviors! It finds food and mates. It avoids toxins and predators.
openworm.org
OpenWorm
http://www.openworm.org/index.html
Building the first digital life form. Open source. Worms are soft and squishy. So our model has to be too. We are building in the physics of muscles, soft tissues and fluids. Because it matters. Play with your own worm! Thanks to our kickstarter backers we have developed WormSim, a new interactive way to play with the worm in your browser and be up to date with our modeling progress! Every neuron the worm has, and how they connect. Everything in its right place. Now we are bringing it to life. All the co...
docs.openworm.org
Releases - OpenWorm
http://docs.openworm.org/en/latest/releases
Release 5,6,7 (2nd Half of 2013, 1st half of 2014, 2nd half of 2014). Release 4 (1st Half of 2013) January - July 2013. Release 3 (completed) May 2012 - November 2012. Release 2 (completed) October 2011 to April 2012. Release 1 (completed) May 2011 - September 2011. Muscle / Neuron / Channel. Release 5,6,7 (2nd Half of 2013, 1st half of 2014, 2nd half of 2014). Some key milestones that were reached:. First OpenWorm Paper published. Donation of Brown Lab worm movement data. Movement validation team formed.
fietkiewicz.wordpress.com
The Computational Neuroscientist | Thoughts along my journey in modeling the nervous system. | Page 2
https://fietkiewicz.wordpress.com/page/2
Thoughts along my journey in modeling the nervous system. May 27, 2015. Scientific brutality: animals or humans? There is a new editorial in Nature Neuroscience titled Inhumane treatment of nonhuman primate researchers. Logothetis’s declaration letter seems to not be public yet, but he did make available a letter that responded to recent accusations about animal cruelty. (The letter is available here. And an article that links to it is available here. The primary issue that concerns me about the letter i...
artificialbrains.com
OpenWorm - Whole brain emulation
http://www.artificialbrains.com/openworm
Last updated: Aug 14, 2012. A 3D rendering of the C. elegans nervous system. Is an attempt to build a complete cellular-level simulation of the nematode. Of the 959 cells in the hermaphrodite. 302 are neurons and 95 are muscle cells. The simulation will model electrical activity in all the muscles and neurons. An integrated soft-body physics. Simulation will also model body movement and physical forces within the worm and from its environment. Latest news / current status. Biology of C. elegans. The simu...
docs.openworm.org
Representation - OpenWorm
http://docs.openworm.org/en/latest/Projects/datarep
Data Collection and Representation. Muscle / Neuron / Channel. Data Collection and Representation. There is not a single data source for our simulation; in fact one of our unique challenges is coming up with new ways to work out how to integrate multiple data sets together. On this page you can read about how different dataset are used in the model. Consider the connectomics data. There are different useful ways to mine this data set. For example, a NetworkX. Here is a list of some of the data sets that ...
openworm.org
Getting Started
http://www.openworm.org/getting_started.html
Overview of the project, its contents, and how to get started. OpenWorm aims to build the first comprehensive computational model of the. A microscopic roundworm. With only a thousand cells. It solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. A brief introduction to. We are using a bottom-up. Approach, aimed at observing the worm behaviour emerge. While m...
fietkiewicz.wordpress.com
A Marr-ed view of connectomes | The Computational Neuroscientist
https://fietkiewicz.wordpress.com/2013/01/21/a-marr-ed-view-of-connectomes
Thoughts along my journey in modeling the nervous system. A Marr-ed view of connectomes. January 21, 2013. I saw an interesting post by Kresimir Josic on whole-brain simulations. And it included a link to a video of a debate between Sebastian Seung and Anthony Movshon. About the importance of connectomes. I highly recommend it simply for the amazing animations. I’m not sure what to suggest for an accessible coverage of the anti-connectome side except for this article by Ferris Jabr. 8221; and the separab...
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