C. elegans is a tiny worm, about 1mm in length, which lives in the soil in many parts of the world..

C. elegans is a tiny worm, about 1mm in length, which lives
in the soil in many parts of the world. It is a non-hazardous, non-infectious,
non-pathogenic, non-parasitic organism and only has about 1000 cells and
exactly 302 neurons. Despite its small size (or perhaps because of it), it is
also one of the most studied creatures in nature. In fact, thousands of
scientists are working full time to try to understand it. Between October 1994
and January 1995, 73 scientific articles about C. elegans appeared in
international science journals. Three different Nobel prizes have been awarded
for

C. elegans is a tiny worm, about 1mm in length, which lives
in the soil in many parts of the world. It is a non-hazardous, non-infectious,
non-pathogenic, non-parasitic organism and only has about 1000 cells and
exactly 302 neurons. Despite its small size (or perhaps because of it), it is
also one of the most studied creatures in nature. In fact, thousands of
scientists are working full time to try to understand it. Between October 1994
and January 1995, 73 scientific articles about C. elegans appeared in
international science journals. Three different Nobel prizes have been awarded
for work on the worm, and it was the first multicellular organism to have its
whole genome sequenced and the wiring between its neurons (its ‘connectome’)
completely mapped out. Right now, an international consortium of laboratories
is collaborating on a project to sequence the entire 100 000 000 bases of its
DNA. As the worm is so well understood and described in the scientific
literature, it was a good candidate for a project seeking to build a computer
model of a real organism. In 2007, two software engineers, Giovanni Idili and
Matteo Cantarelli, started to discuss how they might simulate C. elegans, but
they were unable to progress their idea as they lacked any knowledge about
neuroscience. This changed in 2010 when they came in contact with biology PhD
student Stephen Larson, who joined them to found OpenWorm, an open science,
open source software project. Their goal is to build the world’s first virtual
organism for the purpose of understanding the events and mechanisms of living
cells. What the team is doing is implementing each of the worm’s 1000 cells and
302 neurons as software elements and having them interact with each other as
they do in the real worm, to study the behaviour that emerges. For example, if
the worm needs to find food, the appropriate neurons send signals to the
appropriate muscle cells to get it to move. The team recreates this and they
know which of their artificial neurons are the correct ones to fire from the
existing scientific literature. The team have even built a robot using the Lego
Mindstorms kit to illustrate this movement outside of a computer. The goal of
creating a virtual living organism is no easy task and the team still has some
way to go (and they are always on the lookout for more contributors). However,
they have achieved several major milestones. They have finished a software
engine called Geppetto. Written in Java, Geppetto is an open source modular
platform which enables interactive simulation of biological systems. It
incorporates algorithms which describe how neuron/cell signals behave and
features a visualizer that can be run through a normal web browser. Again,
these algorithms come from the existing scientific literature. For example, the
algorithm that decides whether a neuron ‘fires’ (sends a signal to a cell)
comes from work done in the 1950s. The team is open for anyone to join, and
they have roles available for all levels of experience and technical expertise.
These include roles in programming (particularly in Java and C++ if you want to
give it a go), neuroscience, technical writing and web development, and they
are even looking for artists to create visuals that will ‘inspire people’. The
team uses social media to share information and each month has a virtual
meeting using Google Hangouts.

Questions

1 What could a virtual worm be used for?

2 What other software could an open science team use to
co-ordinate their work?

3 How could ‘visuals’ inspire people to get involved in
OpenWorm?

4 Why would a neuroscientist get involved in an open source
software project?

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