Optimal synaptic assignment for locomotory behavior in C. elegans (Rakowski & Karbowski 2017)


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Accession:238985
"The detailed knowledge of C. elegans connectome for 3 decades has not contributed dramatically to our understanding of worm’s behavior. One of main reasons for this situation has been the lack of data on the type of synaptic signaling between particular neurons in the worm’s connectome. The aim of this study was to determine synaptic polarities for each connection in a small pre-motor circuit controlling locomotion. Even in this compact network of just 7 neurons the space of all possible patterns of connection types (excitation vs. inhibition) is huge. To deal effectively with this combinatorial problem we devised a novel and relatively fast technique based on genetic algorithms and large-scale parallel computations, which we combined with detailed neurophysiological modeling of interneuron dynamics and compared the theory to the available behavioral data. As a result of these massive computations, we found that the optimal connectivity pattern that matches the best locomotory data is the one in which all interneuron connections are inhibitory, even those terminating on motor neurons. ..."
Reference:
1 . Rakowski F, Karbowski J (2017) Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost. PLoS Comput Biol 13:e1005834 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Acetylcholine;
Simulation Environment: Java (web link to model); Mathematica (web link to model);
Model Concept(s): Invertebrate;
Implementer(s): Rakowski, Franciszek ;
Search NeuronDB for information about:  Acetylcholine;
(located via links below)
#!/bin/sh
#
# An example hook script to block unannotated tags from entering.
# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
#
# To enable this hook, rename this file to "update".
#
# Config
# ------
# hooks.allowunannotated
#   This boolean sets whether unannotated tags will be allowed into the
#   repository.  By default they won't be.
# hooks.allowdeletetag
#   This boolean sets whether deleting tags will be allowed in the
#   repository.  By default they won't be.
# hooks.allowmodifytag
#   This boolean sets whether a tag may be modified after creation. By default
#   it won't be.
# hooks.allowdeletebranch
#   This boolean sets whether deleting branches will be allowed in the
#   repository.  By default they won't be.
# hooks.denycreatebranch
#   This boolean sets whether remotely creating branches will be denied
#   in the repository.  By default this is allowed.
#

# --- Command line
refname="$1"
oldrev="$2"
newrev="$3"

# --- Safety check
if [ -z "$GIT_DIR" ]; then
	echo "Don't run this script from the command line." >&2
	echo " (if you want, you could supply GIT_DIR then run" >&2
	echo "  $0 <ref> <oldrev> <newrev>)" >&2
	exit 1
fi

if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
	echo "usage: $0 <ref> <oldrev> <newrev>" >&2
	exit 1
fi

# --- Config
allowunannotated=$(git config --bool hooks.allowunannotated)
allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
denycreatebranch=$(git config --bool hooks.denycreatebranch)
allowdeletetag=$(git config --bool hooks.allowdeletetag)
allowmodifytag=$(git config --bool hooks.allowmodifytag)

# check for no description
projectdesc=$(sed -e '1q' "$GIT_DIR/description")
case "$projectdesc" in
"Unnamed repository"* | "")
	echo "*** Project description file hasn't been set" >&2
	exit 1
	;;
esac

# --- Check types
# if $newrev is 0000...0000, it's a commit to delete a ref.
zero="0000000000000000000000000000000000000000"
if [ "$newrev" = "$zero" ]; then
	newrev_type=delete
else
	newrev_type=$(git cat-file -t $newrev)
fi

case "$refname","$newrev_type" in
	refs/tags/*,commit)
		# un-annotated tag
		short_refname=${refname##refs/tags/}
		if [ "$allowunannotated" != "true" ]; then
			echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
			echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
			exit 1
		fi
		;;
	refs/tags/*,delete)
		# delete tag
		if [ "$allowdeletetag" != "true" ]; then
			echo "*** Deleting a tag is not allowed in this repository" >&2
			exit 1
		fi
		;;
	refs/tags/*,tag)
		# annotated tag
		if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
		then
			echo "*** Tag '$refname' already exists." >&2
			echo "*** Modifying a tag is not allowed in this repository." >&2
			exit 1
		fi
		;;
	refs/heads/*,commit)
		# branch
		if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
			echo "*** Creating a branch is not allowed in this repository" >&2
			exit 1
		fi
		;;
	refs/heads/*,delete)
		# delete branch
		if [ "$allowdeletebranch" != "true" ]; then
			echo "*** Deleting a branch is not allowed in this repository" >&2
			exit 1
		fi
		;;
	refs/remotes/*,commit)
		# tracking branch
		;;
	refs/remotes/*,delete)
		# delete tracking branch
		if [ "$allowdeletebranch" != "true" ]; then
			echo "*** Deleting a tracking branch is not allowed in this repository" >&2
			exit 1
		fi
		;;
	*)
		# Anything else (is there anything else?)
		echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
		exit 1
		;;
esac

# --- Finished
exit 0