We attempted to access Neurodesk Play through the Jupyter Notebook. The instructions could be clearer and more detailed (e.g. open Neurodesk via the url, select location (Europe etc.), open terminal). Sometimes when trying to access (https://play.neurodesk.org/) the server times out: Spawn failed: Server at http://10.42.0.23:8888/user/798689a5-6d74-48fe-8a44-8eca1d8a95b8/ didn't respond in 30 seconds
BUILDING THE PAPER WITH NEURODESK:
PART 1: DOWNLOAD THE DATA We were able to download the data but this was not easily findable. The link to data in the OSF guide (https://ida.loni.usc.edu/) leads to a webpage that doesn’t seem to contain the data. The data availability section in the PDF version of the paper (linked to on ReproHack) only links to the lab group website, not the data. The online version of the paper (which is behind a paywall) contains a link to the data (NII files) in the paper supplement. Unfortunately, this link to the correct data does not appear in the PDF version nor on ReproHack / OSF. Ideally, the data should be stored in a permanent repository rather than a journal supplement.
PART 2: OPEN NEURODESK We had multiple problems running the terminal code provided in the OSF guide. We believe this had to do with connection issues possibly caused by firewall / proxy settings. As we use an institutional computer we were not able to change these settings.
The following code gave connection errors:
git clone https://github.com/iishiishii/neurodesk_paper.git This code gave an error, likely related to firewall / proxy of university managed computers? Cloning into 'neurodesk_paper'...
fatal: unable to access 'https://github.com/iishiishii/neurodesk_paper.git/': Failed to connect to github.com port 443 after 6 ms: Connection refused
The following code also gives error: (base) jovyan@neurodesktop-:~$ git clone git@github.com:iishiishii/neurodesk_paper.git´Cloning into 'neurodesk_paper'... git@github.com: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists.`
osf -p e6pw3 clone /home/jovyan/neurodesk_paper/data gives the following error: `Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/urllib3/connection.py", line 203, in _new_conn
sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/urllib3/util/connection.py", line 60, in create_connection
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/socket.py", line 962, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
socket.gaierror: [Errno -3] Temporary failure in name resolution
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/urllib3/connectionpool.py", line 791, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/urllib3/connectionpool.py", line 492, in _make_request
raise new_e
File "/opt/conda/lib/python3.11/site-packages/urllib3/connectionpool.py", line 468, in _make_request
self._validate_conn(conn)
File "/opt/conda/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1097, in _validate_conn
conn.connect()
File "/opt/conda/lib/python3.11/site-packages/urllib3/connection.py", line 611, in connect
self.sock = sock = self._new_conn()
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/urllib3/connection.py", line 210, in _new_conn
raise NameResolutionError(self.host, self, e) from e
urllib3.exceptions.NameResolutionError:
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/urllib3/connectionpool.py", line 845, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/urllib3/util/retry.py", line 515, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='api.osf.io', port=443): Max retries exceeded with url: /v2//guids/e6pw3/ (Caused by NameResolutionError("
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/bin/osf", line 8, in
The following code also gave an error: mkdir /home/jovyan/neurodesk_paper/data gives the following error: (base) jovyan@neurodesktop-:~$ mkdir /home/jovyan/neurodesk_paper/data mkdir: cannot create directory ‘/home/jovyan/neurodesk_paper/data’: No such file or directory -- using mkdir -p home/jovyan/neurodesk_paper/data works
Members of the reviewing team have used Jupyter Notebooks before. We understand Jupyter Notebooks are usually helpful to avoid dependancies and issues related to downloading materials on different computer systems, however in our case we were still unable to completely install and use the software. We are unfamiliar with NeuroDesk.
None
Web browser (Bing)
Findability of the data could be improved; experienced connection issues when trying to run terminal code (see first review comment).
We think the option to run Neurodesk through a web browser is a good idea, and potentially would be easier than installing software locally. The OSF page is nice and more details on installation and error handling would be useful.
Checking links go to correct place would be useful. Overall, more detail would be helpful. It would be great if the OSF page has a direct link to the data, to improve findability.
It offered direction, albeit without a lot of detail, on different ways of installing the software.
Due to problems with installation, we could not access the software itself to assess the code and methods.
Code is licensed via MIT license (shown in the paper and GitHub repo), but we cannot find a license for the data.
We like the idea behind this project and the authors' attempt to make this as open and accessible as possible. Unfortunately we had issues early in the process of trying to reproduce the code..
