History of celegansneural
The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.
[entries] Add the date when each entry was added, and remove icon_hash beff7c9
The dates are those of the commits that first added the entries' files (2020-08-11 for the entries of the initial commit); renamed entries keep the date of their first name. Changed: none
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index bf5231d..afed299 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -29,7 +29,7 @@ tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://www-personal.umich.edu/~mejn/netdata'
citation = [('J. G. White, E. Southgate, J. N. Thomson, and S. Brenner, "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
('D.J. Watts and S.H. Strogatz, "Collective dynamics of \'small-world\' networks." Nature 393, 440-442 (1998).', 'https://doi.org/10.1038/30918')]
-icon_hash = '56a85c8e26855e083a2f78a3'
+date_added = '2020-08-11'
upstream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
files = [('celegansneural.zip:celegansneural.gml', None, 'gml')]
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) bc3dbbd
The lists of properties at the end of the descriptions marked edge properties with "Edge" but left node properties unmarked, or grouped them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property was often unclear. Every item now starts with (Node), (Edge) or (Graph), followed by the property names, a colon and the explanation, one item per property or group of properties; qualifications (kinds of nodes, networks) follow the names in parentheses. Properties that were only named got a short explanation, and a few items that named the wrong kind of property were corrected.
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 1cdd92e..bf5231d 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -23,8 +23,8 @@ description = """The neural network of the nematode *Caenorhabditis elegans*, co
The network has the following properties:
-- Nodes: `label`, the node number in Watts' original data file (the neuron names are not included).
-- Edges: `value`, the edge weight given by Watts (an integer from 1 to 70), which reflects the number of connections between the two neurons; its precise definition is not documented in the source."""
+- (Node) `label`: the node number in Watts' original data file (the neuron names are not included).
+- (Edge) `value`: the edge weight given by Watts (an integer from 1 to 70), which reflects the number of connections between the two neurons; its precise definition is not documented in the source."""
tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://www-personal.umich.edu/~mejn/netdata'
citation = [('J. G. White, E. Southgate, J. N. Thomson, and S. Brenner, "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
[entries] Remove unneeded code from the entries 2c69f19
Unneeded "global files" statements, unused imports and variables, f-strings without placeholders, duplicate keys in foodweb_little_rock (keeping the order and the values used), and the second definition of get_lines() in twitter_higgs. Nothing changes in the networks or descriptions. Changed: none
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 8bf47b7..1cdd92e 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -42,7 +42,6 @@ def fetch_upstream(force=False):
@coerce_props()
@annotate()
def parse(alts=None):
- global files
name = __name__.split(".")[-1]
for fnames, alt, fmt in files:
if alts is not None and alt not in alts:
[entries] Fix parse bugs and improve descriptions and metadata 6bb6851
- parse fixes from the review of the descriptions, e.g. us_patents (directed), celegans_2019 (synapse direction), ecoli_transcription and yeast_transcription (regulator to target), bitcoin (direction, phantom node), ego_social (Google+ features and circles), scotus_majority, arxiv_authors and social_location (as in SNAP), caida_as, dnc, dom, mist, reuters and bibsonomy (names on the right nodes), uci_zoo - every description now states explicitly what the nodes and edges represent; corrected titles, years, tags, citations and licences - the "Hypergraph" tag is removed; very large entries are marked `huge = True` (see --skip-huge) - ICON ids of partial duplicates added (hiv_transmission, congress_bills, openflights, dutch_school)
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 3e39652..8bf47b7 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -19,14 +19,18 @@
from .. import *
title = "C. elegans neurons (1986)"
-description = """A network representing the neural connections of the Caenorhabditis elegans nematode[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """The neural network of the nematode *Caenorhabditis elegans*, compiled by D. J. Watts and S. H. Strogatz from the original reconstruction of its nervous system from serial-section electron micrographs by J. G. White, E. Southgate, J. N. Thomson and S. Brenner (1986), and used in their study of small-world networks. Nodes are 297 neurons, and a directed edge represents a synaptic connection or gap junction between two neurons; the meaning of the edge direction is not documented in the source. The data were obtained from the website of D. J. Watts and redistributed by M. E. J. Newman, who renumbered the nodes consecutively.
+
+The network has the following properties:
+
+- Nodes: `label`, the node number in Watts' original data file (the neuron names are not included).
+- Edges: `value`, the edge weight given by Watts (an integer from 1 to 70), which reflects the number of connections between the two neurons; its precise definition is not documented in the source."""
tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://www-personal.umich.edu/~mejn/netdata'
-citation = [('J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
+citation = [('J. G. White, E. Southgate, J. N. Thomson, and S. Brenner, "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
('D.J. Watts and S.H. Strogatz, "Collective dynamics of \'small-world\' networks." Nature 393, 440-442 (1998).', 'https://doi.org/10.1038/30918')]
icon_hash = '56a85c8e26855e083a2f78a3'
-ustream_license = None
+upstream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
files = [('celegansneural.zip:celegansneural.gml', None, 'gml')]
Update copyright information 73a4f0d
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index d583b09..3e39652 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2026 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 3d288ea
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index bbc197a..d583b09 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 8d005ae
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 49bf7e6..bbc197a 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright info db2efcc
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index c0711dc..49bf7e6 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update citations to use DOIs e878874
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 241f1db..c0711dc 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -23,8 +23,8 @@ description = """A network representing the neural connections of the Caenorhabd
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://www-personal.umich.edu/~mejn/netdata'
-citation = [('J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
- ('D.J. Watts and S.H. Strogatz, "Collective dynamics of \'small-world\' networks." Nature 393, 440-442 (1998).', 'research.yahoo.com/files/w_s_NATURE_0.pdf')]
+citation = [('J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, "The structure of the nervous system of the nematode Caenorhabditis elegans", Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
+ ('D.J. Watts and S.H. Strogatz, "Collective dynamics of \'small-world\' networks." Nature 393, 440-442 (1998).', 'https://doi.org/10.1038/30918')]
icon_hash = '56a85c8e26855e083a2f78a3'
ustream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index d358ed6..241f1db 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -3,18 +3,18 @@
#
# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Affero General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
from .. import *
Add explicit attribution to descriptions obtained from ICON 1645314
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
index 9193afa..d358ed6 100644
--- a/entries/celegansneural/__init__.py
+++ b/entries/celegansneural/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "C. elegans neurons (1986)"
-description = "A network representing the neural connections of the Caenorhabditis elegans nematode"
+description = """A network representing the neural connections of the Caenorhabditis elegans nematode[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://www-personal.umich.edu/~mejn/netdata'
citation = [('J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
Initial commit cc85872
diff --git a/entries/celegansneural/__init__.py b/entries/celegansneural/__init__.py
new file mode 100644
index 0000000..9193afa
--- /dev/null
+++ b/entries/celegansneural/__init__.py
@@ -0,0 +1,50 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+
+title = "C. elegans neurons (1986)"
+description = "A network representing the neural connections of the Caenorhabditis elegans nematode"
+tags = ['Biological', 'Connectome', 'Weighted']
+url = 'http://www-personal.umich.edu/~mejn/netdata'
+citation = [('J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, Phil. Trans. R. Soc. London 314, 1-340 (1986)', 'https://doi.org/10.1098/rstb.1986.0056'),
+ ('D.J. Watts and S.H. Strogatz, "Collective dynamics of \'small-world\' networks." Nature 393, 440-442 (1998).', 'research.yahoo.com/files/w_s_NATURE_0.pdf')]
+icon_hash = '56a85c8e26855e083a2f78a3'
+ustream_license = None
+upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
+files = [('celegansneural.zip:celegansneural.gml', None, 'gml')]
+
+def fetch_upstream(force=False):
+ return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+ force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+ global files
+ name = __name__.split(".")[-1]
+ for fnames, alt, fmt in files:
+ if alts is not None and alt not in alts:
+ continue
+ if isinstance(fnames, str):
+ fnames = [fnames]
+ with ExitStack() as stack:
+ fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
+ g = parse_graph(fs, fmt, directed=True)
+ yield alt, g