Netzschleuder issueshttps://git.skewed.de/count0/netzschleuder/-/issues2020-10-02T19:23:52Zhttps://git.skewed.de/count0/netzschleuder/-/issues/2ValueError: unsupported pickle protocol: 52020-10-02T19:23:52ZFelipe VacaValueError: unsupported pickle protocol: 5Hi. I am trying to load 'london_transport' and 'eu_airlines' networks with graph-tool 2.35 and Python 3.6.9. Both loading the uncompressed file and using gt.collection.ns throw 'ValueError: unsupported pickle protocol: 5'; as shown below...Hi. I am trying to load 'london_transport' and 'eu_airlines' networks with graph-tool 2.35 and Python 3.6.9. Both loading the uncompressed file and using gt.collection.ns throw 'ValueError: unsupported pickle protocol: 5'; as shown below:
```
from graph_tool.all import *
g = collection.ns['london_transport']
Traceback (most recent call last):
File "<ipython-input-6-e0b0e8c60494>", line 1, in <module>
g = load_graph(out_dir+'/london_transport.gt')
File "/usr/lib/python3/dist-packages/graph_tool/__init__.py", line 3346, in load_graph
g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp)
File "/usr/lib/python3/dist-packages/graph_tool/__init__.py", line 2889, in load
ignore_ep, ignore_gp)
File "/usr/lib/python3/dist-packages/graph_tool/gt_io.py", line 71, in unpickler
return pickle.load(sstream, encoding="bytes")
ValueError: unsupported pickle protocol: 5
```https://git.skewed.de/count0/netzschleuder/-/issues/3Feature request2020-11-30T13:57:20ZFelipe VacaFeature requestHi. Could you please include the network tags
in **/api/nets** or **graph_tool.collection.ns_info**? Thank you.Hi. Could you please include the network tags
in **/api/nets** or **graph_tool.collection.ns_info**? Thank you.https://git.skewed.de/count0/netzschleuder/-/issues/4Upstream is unavailable on several data sets2021-03-24T22:27:49ZJean-Gabriel YoungUpstream is unavailable on several data setshttp://moreno.ss.uci.edu/ is MIA. All the Add Health entries are affected by this problem: http://moreno.ss.uci.edu/data.htmlhttp://moreno.ss.uci.edu/ is MIA. All the Add Health entries are affected by this problem: http://moreno.ss.uci.edu/data.htmlhttps://git.skewed.de/count0/netzschleuder/-/issues/5C. intestinalis (new dataset)2021-06-22T15:12:41ZAntoine AllardC. intestinalis (new dataset)# New dataset request
Please fill out the information below to request the addition of a new
dataset to the Netzschleuder repository.
## Necessary information
### Dataset title
C. intestinalis larva connectome
### Dataset descriptio...# New dataset request
Please fill out the information below to request the addition of a new
dataset to the Netzschleuder repository.
## Necessary information
### Dataset title
C. intestinalis larva connectome
### Dataset description
Entire connectivity matrix for the complete brain of a larva of Ciona intestinalis. Each directed edge represents a synaptic connection from pre-synaptic cell i to post-synaptic cell j (may not be a neuron). Edge weights represent the cumulative depth of presynaptic contacts in µm.
### Dataset tags
directed, weighted, biological, connectome
### Upstream URL
https://elifesciences.org/articles/16962#SD6-data (see caption of Fig 16 for further details)
If you wish to **host** the original dataset files in Netzschleuder,
i.e. have it act as the main upstream source, please upload the dataset
file(s) as attachments (or give a temporary URL) and indicate below:
- [ ] I am the owner of this dataset, and I wish the primary upstream dataset files to be hosted by Netzschleuder.
(Please do **not** tick the box above if you plan to host the dataset
yourself in your own website. Whether or not the upstream hosting is
done in a different format is irrelevant.)
### Citation
Ryan, K., Lu, Z., & Meinertzhagen, I. A. (2016). The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling. ELife, 5, e16962. DOI: 10.7554/eLife.16962
### License
CC BY 4.0
## Observations
- The preferred file formats are [gt](https://graph-tool.skewed.de/static/doc/gt_format.html), [GraphML](https://en.wikipedia.org/wiki/GraphML), and [GML](https://en.wikipedia.org/wiki/Graph_Modelling_Language), but any other upstream format is also accepted. For any non-standard format, including a Python parsing script would be helpful.
- [x] Please verify if the dataset entry can be found in [ICON](https://icon.colorado.edu). If so, please check this box.https://git.skewed.de/count0/netzschleuder/-/issues/6unweighted graph with Weighted tag2021-07-13T08:49:14ZAntoine Allardunweighted graph with Weighted tagHi! The networks "ambassador" have the tag "Weighted" but none of the 15 subnetworks have an edge property that could be used as weights. Thanks!Hi! The networks "ambassador" have the tag "Weighted" but none of the 15 subnetworks have an edge property that could be used as weights. Thanks!https://git.skewed.de/count0/netzschleuder/-/issues/7PSI network2023-02-19T14:49:24ZDaniele MontepietraPSI network# New dataset request
Please fill out the information below to request the addition of a new
dataset to the Netzschleuder repository.
## Necessary information
### Dataset title
Plant Photosystem I excitation energy transfer network.
...# New dataset request
Please fill out the information below to request the addition of a new
dataset to the Netzschleuder repository.
## Necessary information
### Dataset title
Plant Photosystem I excitation energy transfer network.
### Dataset description
Weighted directed network of the light-harvesting Photosystem Ι (PSI) of the plant _Pisum sativum_. The nodes represent chromophores with different identities (i.e. chlorophyll a, chlorophyll b, β-carotene and derivates, lutein, violaxanthin), while edges represent FRET transfer between chromophores. The link directionality connecting nodes in the PSI network depends on the energy levels of the connected chromophores. The weights correspond to the FRET Efficiency between connected chromophores.
### Dataset tags
Biological, Directed, Weighted
### Upstream URL
[PSI_graph.csv](/uploads/74f452351a6eb0e418d9bd0a78895f93/PSI_graph.csv)
If you wish to **host** the original dataset files in Netzschleuder,
i.e. have it act as the main upstream source, please upload the dataset
file(s) as attachments (or give a temporary URL) and indicate below:
- [X] I am the owner of this dataset, and I wish the primary upstream dataset files to be hosted by Netzschleuder.
(Please do **not** tick the box above if you plan to host the dataset
yourself in your own website. Whether or not the upstream hosting is
done in a different format is irrelevant.)
### Citation
Montepietra D., Bellingeri M., Ross A.M., Scotognella F. and Cassi D. 2020 "Modelling photosystem I as a complex interacting network" J. R. Soc. Interface
https://doi.org/10.1098/rsif.2020.0813
### License
N/A
## Observations
- The preferred file formats are [gt](https://graph-tool.skewed.de/static/doc/gt_format.html), [GraphML](https://en.wikipedia.org/wiki/GraphML), and [GML](https://en.wikipedia.org/wiki/Graph_Modelling_Language), but any other upstream format is also accepted. For any non-standard format, including a Python parsing script would be helpful.
- [ ] Please verify if the dataset entry can be found in [ICON](https://icon.colorado.edu). If so, please check this box.