Minerva
Minerva: a light-weight, narrative image browser for multiplexed tissue images - Published in JOSS (2020)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README and JOSS metadata -
○Academic publication links
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✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Repository
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.
Basic Info
- Host: GitHub
- Owner: labsyspharm
- License: mit
- Language: HTML
- Default Branch: master
- Homepage: https://minerva.im
- Size: 269 MB
Statistics
- Stars: 54
- Watchers: 11
- Forks: 14
- Open Issues: 19
- Releases: 0
Topics
Metadata Files
README.md
Minerva
Check out the Minerva website for tutorials, example Minerva Stories and frequently asked questions about Minerva.
We also published a paper describing Minerva Story and Author: Hoffer et al., (2020). Minerva: a light-weight, narrative image browser for multiplexed tissue images. Journal of Open Source Software, 5(54), 2579, https://doi.org/10.21105/joss.02579 .
Minerva Repository Structure
Minerva Story
The GitHub Pages site build is stored at minerva-story. The source code for the minified bundle is stored at minerva-browser.
Minerva Author
The Python Flask server along with automated testing is stored at minerva-author. The React UI is stored at minerva-author-ui
Running Minerva Story
Clone repository
bash
git clone git@github.com:labsyspharm/minerva-story.git
cd minerva-story
Install npm
Download and install Node.js for your platform.
Install npx to run the http-server:
bash
npm install -g npx
Run local server
In the project folder, run command:
bash
npx http-server -p 8000
Open browser to localhost:8000
Rebuilding minerva-browser
If you update the version of Minerva Browser in package.json, you will need to rebuild with webpack as shown below:
npm i
npm run build
Then you can run the local server with npx http-server -p 8000 as normal.
Owner
- Name: Laboratory of Systems Pharmacology @ Harvard
- Login: labsyspharm
- Kind: organization
- Email: hits@harvard.edu
- Location: Boston, MA
- Website: https://labsyspharm.org/
- Repositories: 150
- Profile: https://github.com/labsyspharm
Reinventing the fundamental science underlying the development of new medicines and their use in individual patients.
JOSS Publication
Minerva: a light-weight, narrative image browser for multiplexed tissue images
Authors
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
Mathworks, Natick, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, Department of Systems Biology, Harvard Medical School, Boston, MA
Editor
Juan Nunez-Iglesias
Tags
visualization image data cancer tissue storytellingGitHub Events
Total
- Watch event: 4
Last Year
- Watch event: 4
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| John Hoffer | j****n@h****n | 177 |
| dependabot[bot] | 4****] | 1 |
| Rumana (Ru) Rashid | 3****e | 1 |
| Juha Ruokonen | 5****n | 1 |
| Jeremy Muhlich | j****h@b****g | 1 |
| Han Xu | 8****s | 1 |
| Daniel S. Katz | d****z@i****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 70
- Total pull requests: 4
- Average time to close issues: 4 months
- Average time to close pull requests: 4 days
- Total issue authors: 18
- Total pull request authors: 4
- Average comments per issue: 0.6
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 1
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
- Ru-bixcube (17)
- tuuliavallius (11)
- madisonatyler (9)
- DanaeA (6)
- gjbaker (4)
- ghost (4)
- edn314 (3)
- sofroniewn (3)
- Juha-Ruokonen (2)
- jmuhlich (2)
- rjp21 (2)
- CReihsmann (1)
- ArtemSokolov (1)
- zhqjQill (1)
- shohpfizer (1)
Pull Request Authors
- hxu-hms (2)
- canopybiosciences (1)
- dependabot[bot] (1)
- danielskatz (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- beautifulsoup4 >=4.8.2
- boto3 >=1.12.14
- markdown >=3.2.1
- pyaml >=19.12.0