TIER2 ReproHack Collaborative Hackpad
===

###### tags: `Reprohack` `hackpad`

:::info
- :earth_africa: **Location**: Vienna, Austria
- :calendar: **Date**: 30th June 2024
- :watch: **09:45 - 17:15 CEST**
- :arrow_forward: **Slides:** [Slides on HackMD](https://hackmd.io/@5qnA2_8tQ6i5tWuiy9xbAg/S1ns-QuLR)
- :scroll: **Participant Guidelines:** https://reprohack.org/participant_guidelines
- :purple_heart: **Code of Conduct:** https://reprohack.org/code-of-conduct
- :left_speech_bubble: **Chat on Zulip**:
https://tier2-reprohack.zulipchat.com/
- **New to HackMD? Check out the features:** https://hackmd.io/s/features

***

## Participants:
> **Please sign in below:**
- ***full name*** (pronouns/ Affiliation / social media handle)

- ***Friederike Kohrs*** (she/her, BIH QUEST Center for Responsible Research, https://www.linkedin.com/in/friederike-kohrs-490b191a5/)
- ***NGUYEN THI TRA MY*** (she/her/ELTE/https://www.linkedin.com/in/mynguyeneltehu/)
- ***Jan Kadlec*** (Weizmann Institute of science)
- ***Emma Wilson*** (She/her, University of Edinburgh, https://uk.linkedin.com/in/emma-wilson-68646011b?trk=public_post_follow-view-profile)
- Alex Bannach-Brown (she/her, Berlin Institute of Health @ Charité, https://www.linkedin.com/in/abannachbrown/)

---

# Team Names
>Group yourselves into teams based on the paper you are trying to reproduce.
*Please note*: Each team should create a new channel for communication on Zulip.
- Team 1:
**'FreakAzo1d'**
- **Team 2:** Pizzabrains
- **Team 3:**
- **Team 4:**
- **Team 5:**
- **Team 6:**

:::

# Papers for Selection

>Find a paper on the ReproHack webpage: https://www.reprohack.org/paper/
>
>Or have a look at the publications below which represent a selection of papers suggested by participants and us. Data and code has already been downloaded for these and you can find it here on OSF: https://osf.io/u5gjh/
>
::: success
**Berrío-Martinez et al., 2019**, The role of past experience in
development of feeding behavior in
common vampire bats, https://doi.org/10.7717/peerj.7448
**Comments:**
**Tags:**

**Millidge, 2019**, Combining Active Inference and Hierarchical Predictive Coding: A Tutorial Introduction and Case Study, https://doi.org/10.31234/osf.io/kf6wc
**Comments:**
**Tags:**

**Sullivan et al., 2023**, The influence of emotion regulation strategies and sleep quality on depression and anxiety , https://doi.org/10.1016/j.cortex.2023.06.001
**Comments:**
**Tags:**
:::

# Paper Registration

>Use the following template and register your reproducibility efforts below:

**Paper:** Title of the paper reproduced
**Team members:** Reviewer 1, Reviewer 2 etc.

- Team 1:**'FreakAzo1d'**
//
Paper: https://www.semanticscholar.org/paper/Combining-Active-Inference-and-Hierarchical-Coding%3A-Millidge/2ca7ec363579670846596172e2e65744dcb5611b
// GitHub:
https://github.com/BerenMillidge/Combining-Active-Inference-Paper-Code
//ReproHack Colab:
https://colab.research.google.com/drive/18LP52rt9s_Eod010YAaJB9KbMGojmEUr?usp=sharing
//Team-Members:
Aral, Simon, Fox

- **Paper**: NeuroDesk: https://www.reprohack.org/paper/96/
-**Team members**: Alex, Jan, Friederike, Emma, My

</br>

***

# Regrouping and 1st round of feedback
>Please add any notes here for discussion.

- PizzaBrains - Notes being collated here: https://docs.google.com/document/d/12ghVC6sx_VYi9oMsf0VfGKp9prdlnLM5BAFxrfqQC48/edit?usp=sharing

- Pizzabrains - Browser
- Opening Neurodesk Play for 1st time - received error message: Spawn failed: Server at http://10.42.0.23:8888/user/798689a5-6d74-48fe-8a44-8eca1d8a95b8/ didn't respond in 30 seconds
- `git clone https://github.com/iishiishii/neurodesk_paper.git` we wre trying to run this in the terminal and it gave the following error: `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` -- Googling this issue seems to suggest this might be a firewall issue (port 443). As most users will be using this code on Uni-managed computers, perhaps instructions on what to do to work around this world be worthwhile
- following code also gives error: `(base) jovyan@neurodesktop-:~$ git clone [e-mail]:iishiishii/neurodesk_paper.git Cloning into 'neurodesk_paper'...
[e-mail]: Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.`
- `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 ...` works
- This code `osf -p e6pw3 clone /home/jovyan/neurodesk_paper/data` gives the following error: `(base) jovyan@neurodesktop-:~$ osf -p e6pw3 clone /home/jovyan/neurodesk_paper/data 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 85, in create_connection raise err File "/opt/conda/lib/python3.11/site-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused. 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 218, in _new_conn raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7fc7a6e1bad0>: Failed to establish a new connection: [Errno 111] Connection refused 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 NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fc7a6e1bad0>: Failed to establish a new connection: [Errno 111] Connection refused')) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/bin/osf", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/__main__.py", line 120, in main
exit_code = args.func(args)
^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/cli.py", line 98, in wrapper
return_value = f(cli_args)
^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/cli.py", line 158, in clone
project = osf.project(args.project)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/api.py", line 33, in project
type_ = self.guid(project_id)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/api.py", line 41, in guid
return self._json(self._get(self._build_url('guids', guid)), 200)['data']['type']
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/models/core.py", line 23, in _get
return self.session.get(url, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/models/session.py", line 25, in wrapper
return func(self, url, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/osfclient/models/session.py", line 75, in get
response = super(OSFSession, self).get(url, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='api.osf.io', port=443): Max retries exceeded with url: /v2//guids/e6pw3/ (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fc7a6e1bad0>: Failed to establish a new connection: [Errno 111] Connection refused'))`
- In the tutorial about [mriqc](https://www.neurodesk.org/tutorials-examples/tutorials/functional_imaging/mriqc/), it's great but it'd be even nicer to show an example on a provided dataset. It's a bit unclear what and where the data are and how to work with the path within neurodesk.
- It's unclear where and what the data are at https://ida.loni.usc.edu/ as that opens only the general page. There is a supplementary file associated with the article that is not on OSF. Is it the same data?
- This link ([https://play-sydney.neurodesk.org/v2/gh/iishiishii/neurodesk_paper/main](https://play-sydney.neurodesk.org/v2/gh/iishiishii/neurodesk_paper/main)) from the OSF (https://osf.io/e6pw3/) folder to run the data in Neurodesk Play doesn't work (the site doesn't exist).

-
-

</br>

***
# Feedack to Authors

- Reproducibibility
- Operating System
- Documentation
- Reusability

If you reproduced a paper on ReproHack, submit your review here: https://www.reprohack.org/review/new

Or submit your review here: https://forms.office.com/e/12bbKr7whf

***

# Regrouping and final round of feedback at the end
>Please provide feedback below

### One thing you enjoyed:

- Fun and nice poeple, learning a lot
- Thanks to Ronny & Claus for the location
- Good experience - hackathons are always fun! Nice community.
- Casual event, not stressful. Group size small and casual.
- Structure with general introduction and the mindset and then straight into the coding, basic needs (food drinks) are taken care of.
- Happy that is was adjecent to FENS - in connection with the conf was useful
- Surprised that groups were formed quickly, some groups separated in the end.

### One thing that could be improved:

- Not operating on Sunday, no time to explore
- Hard time to find the location and closed
- Spread the word online, more people to get the word out.
- FENS dissemination feedback
- Would have been better to have more backgrounds/more people, skill share
- Which paper you choose has a massive impact.
- Good to have standard papers for different skill levels. Some tutorial papers would be useful.
- More information on FAIR principles, checklist on FAIR principles on how to assessing.

### Any other feedback?
-
-
-

</br>

# :+1: Thank you for joining us!!