epiphyte
Python toolkit for working with high-dimensional neural data recorded during naturalistic, continuous stimuli @a-darcher @rachrapp
Science Score: 54.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Keywords
Repository
Python toolkit for working with high-dimensional neural data recorded during naturalistic, continuous stimuli @a-darcher @rachrapp
Basic Info
Statistics
- Stars: 8
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
Epiphyte
What is Epiphyte?
Epiphyte is a worked data management solution that enables flexible analysis and parallel collaboration on complex datasets. This solution is applied specifically to data consisting of high-dimensional neural signals and a naturalistic, continuous stimulus, although it could be adapted to any paradigm.
Usage
Epiphyte is a worked example, and contains a series of tutorial notebooks meant to bring users through the process of configuring, designing, and deploying a database environment that enables remote collaboration across multiple cities on a complex dataset.
Going through the tutorials will yield a fully functional database, populated with generated mock neural activity and stimulus annotations. While users can in principle modify the import structure and table definitions, the goal of this project is: 1. to motivate a specific database structure for complex datasets, and 2. to provide a worked example for building and embedding such a database into an ecosystem that facilitates analysis and remote collaboration.
How to install Epiphyte?
Epiphyte can be configured and deployed for three main use cases, as found in the above flowchart.
Option A: Install a local instance of Epiphyte.
Use cases: * You want to test out the database infrastructure before deploying to a remote server. * You will be the only user and do not work with large data files.
Follow the installation instructions here:
and continue to Tutorial 4: Configure and connect to the database.
Option B: Install a remote instance of Epiphyte, without MinIO.
Use cases: * Multiple people, accessing from separate locations, will use the database. * You do not need to support large data files.
Complete Tutorial 1: Launch the MySQL Database
and skip to Tutorial 3: Install and set up Epiphyte.
Option C: Install a remote instance of Epiphyte, with MinIO.
Use cases: * Multiple people, accessing from separate locations, will use the database. * You use large data files (e.g., LFP, movie data, multi-hour calcium imaging).
Start at Tutorial 1: Launch the MySQL database and continue through the remaining tutorials.
Owner
- Name: mackelab
- Login: mackelab
- Kind: organization
- Website: www.mackelab.org
- Repositories: 29
- Profile: https://github.com/mackelab
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Epiphyte
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Alana
family-names: Darcher
email: alana.darcher@gmail.com
orcid: 'https://orcid.org/0000-0001-9048-9732'
- given-names: Rachel
family-names: Rapp
- given-names: Tamara
family-names: Mueller
repository-code: 'https://github.com/mackelab/epiphyte'
date-released: 2024-05-01
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 136
- Total Committers: 7
- Avg Commits per committer: 19.429
- Development Distribution Score (DDS): 0.507
Top Committers
| Name | Commits | |
|---|---|---|
| Alana Darcher | a****r@g****m | 67 |
| tamaramueller | 1****a@o****e | 32 |
| Alana Darcher | 3****r@u****m | 20 |
| tamaramueller | 3****r@u****m | 7 |
| tamara | g****t@t****e | 4 |
| dependabot[bot] | 4****]@u****m | 4 |
| augustes | s****e@g****m | 2 |
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 3
- Total pull requests: 19
- Average time to close issues: over 1 year
- Average time to close pull requests: 3 months
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.33
- Average comments per pull request: 0.21
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 17
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- a-darcher (2)
- Haydnspass (1)
Pull Request Authors
- dependabot[bot] (15)
- a-darcher (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 17 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 4
- Total maintainers: 1
pypi.org: epiphyte
a Python toolkit for high-dimensional neural data recorded during naturalistic, continuous stimuli
- Homepage: https://github.com/mackelab/epiphyte
- Documentation: https://epiphyte.readthedocs.io/
- License: GNU General Public License v3 (GPLv3)
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Latest release: 0.1.1
published over 5 years ago