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phylonext2

PhyloNext v2 GUI - https://phylonext.gbif.org/

https://github.com/vmikk/phylonext2

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

PhyloNext v2 GUI - https://phylonext.gbif.org/

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

PhyloTwin-GUI - GUI for GBIF occurrence data processing pipeline

The GUI is hosted at GBIF.org: https://phylonext.gbif.org/
(a GBIF.org user account is required: Create account)

User documentation: https://vmikk.github.io/PhyloNext2/

PhyloNext v2 is part of the BioDT prototype Digital Twins

Other components of the workflow:

  • https://github.com/vmikk/phylotwin-preprocessor
  • https://github.com/vmikk/phylotwin

Local development

Install Java using SDKMAN (required for Nextflow):

```bash

Install SDKMAN

curl -s https://get.sdkman.io | bash

.. Open a new terminal

and install Java

sdk install java 17.0.10-tem java -version ```

Install Nextflow and pull the core pipeline:

```bash

Install Nextflow

curl -s https://get.nextflow.io | bash

Pull the core pipeline

nextflow pull vmikk/phylotwin -r main ```

Pull pipeline dependencies:

bash docker pull vmikk/phylotwin:0.6.0 docker pull vmikk/biodiverse:1.6.0

Install Node.js and npm:

```bash

Download and install nvm

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.1/install.sh | bash

Download and install Node.js

nvm install 22

Verify the Node.js version

node -v # v22.12.0 nvm current # v22.12.0

Verify npm version

npm -v # 10.9.0 ```

Install project dependencies:

```bash

Install project dependencies for the client

cd client npm install --legacy-peer-deps

Install project dependencies for the server

cd ../server npm install --legacy-peer-deps ```

Start the development servers - need two terminal tabs

```bash

Terminal 1 (for the backend) - In the server directory

npm run dev

nodemon server.js # assuming server.js is your entry point

Terminal 2 (for the frontend) - In the client directory

npm start ```

Frontend is at http://localhost:3000
Backend API is at http://localhost:5000

Debugging

To set development mode and enable detailed logs: bash export NODE_ENV=development

Production mode logs only errors and warnings: bash export NODE_ENV=production

To see the logs in the browser: - Open developer tools - Go to the Console tab - You'll see all client-side logs when submitting the form

In the server terminal, one may find detailed logs about: - Job initialization - File contents - Nextflow command being executed - Process output and errors

Update instructions

```bash

Update the current repository

git pull

Update the core pipeline

nextflow pull vmikk/phylotwin ```

Previous version of the GUI

The first version of the GUI was developed by Thomas Stjernegaard Jeppesen at GBIF

React web app - frontend

https://github.com/gbif/phylonext-ui

Backend

https://github.com/gbif/phylonext-ws

Owner

  • Name: Vladimir Mikryukov
  • Login: vmikk
  • Kind: user
  • Location: Tartu, Estonia
  • Company: The University of Tartu

Citation (CITATION.cff) 

cff-version: 1.2.0
title: "PhyloNext v2 graphical user interface"
type: software
authors:
- family-names: "Mikryukov"
  given-names: "Vladimir"
  orcid: "https://orcid.org/0000-0003-2786-2690"
- family-names: "Ivanov"
  given-names: "Filipp"
- family-names: "Jeppesen Stjernegaard"
  given-names: "Thomas"
- family-names: "Guldberg Frøslev"
  given-names: "Tobias"
doi: 10.5281/zenodo.15716479
url: "https://github.com/vmikk/PhyloNext2"
repository-code: "https://github.com/vmikk/PhyloNext2"
license: MIT
version: 2.0.0
date-released: 2025-05-12

GitHub Events

Total
  • Push event: 14
Last Year
  • Push event: 14

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 271
  • Total Committers: 2
  • Avg Commits per committer: 135.5
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 271
  • Committers: 2
  • Avg Commits per committer: 135.5
  • Development Distribution Score (DDS): 0.011
Top Committers
Name Email Commits
Vladimir Mikryukov v****v@g****m 268
Thomas Stjernegaard Jeppesen t****n@g****g 3
Committer Domains (Top 20 + Academic)
gbif.org: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • thomasstjerne (3)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

docker-compose.yml docker
server/Dockerfile docker
  • node 23.5 build
client/package-lock.json npm
  • 1358 dependencies
client/package.json npm
  • @testing-library/jest-dom *
  • @testing-library/react *
  • @testing-library/user-event *
  • antd *
  • axios *
  • base-64 *
  • d3-graphviz *
  • graphviz-react *
  • history *
  • leaflet *
  • leaflet-draw *
  • lodash *
  • marked *
  • moment *
  • phylotree *
  • react *
  • react-dom *
  • react-iframe *
  • react-jss *
  • react-leaflet *
  • react-leaflet-draw *
  • react-router-dom *
  • react-scripts *
  • save-svg-as-png *
  • web-vitals *
client/Dockerfile docker
  • node 23.5 build
server/package-lock.json npm
  • 137 dependencies
server/package.json npm
  • async *
  • axios *
  • body-parser *
  • composable-middleware *
  • cors *
  • csv-parse *
  • express *
  • express-request-id *
  • form-data *
  • lodash *
  • lowdb *
  • multer *
  • nodemon *
  • request *
  • request-promise *
  • stream-transform *
.github/workflows/jekyll.yml actions
  • actions/checkout v4 composite
  • actions/configure-pages v5 composite
  • actions/deploy-pages v4 composite
  • actions/jekyll-build-pages v1 composite
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docs/Dockerfile docker
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docs/Gemfile rubygems
  • github-pages >= 0 development