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lessdrf

https://github.com/compomics/lessdrf

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
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: CompOmics
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 54.1 MB
Statistics
  • Stars: 6
  • Watchers: 10
  • Forks: 8
  • Open Issues: 6
  • Releases: 1
Created about 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

lesSDRF

This github repository contains the code used to create the lesSDRF application which is available via https://lessdrf.streamlit.app/ A manual on the tool in pdf format is available here: https://github.com/compomics/lesSDRF/blob/main/lesSDRF_manual.pdf

The parsed ontologies used in the streamlit app are in the data folder. Every topic contains three types of data: - allelements: a list of every term in the ontology subset. Is used to check for ontology compatibility of local metadata. - dict: a nested dictionary that follows the ontology tree structure - nodes: a node like version of the nested dictionary according to the format required for the tree-select module: https://github.com/Schluca/streamlittree_select

To start the app locally you run: ** streamlit run Home.py ** This will then open the Home screen of the app. The following steps can be found in the pages folder and are numbered accordingly.

Alternatively, during development, you can use docker compose to build and run the app using the watch feature locally:

bash docker compose watch

This will automatically sync file changes from your local machine to the docker container. Streamlit will automatically pick up file changes and will offer to reload the application.

Open your browser and go to http://localhost:8501 to see the app running.

lesSDRF v0.1.0 has the following ontologies incorporated:

Streamlit version 1.19.0 and Python version 3.9.13<br>

PRIDE CV (version 2022-11-17)<br>

PSI-MS (version 2022-09-26) and NCBITaxon (version 2022-08-18) in obo format<br>

CL (version 2022-12-25) and HANCESTRO (version 2.6) in OWL format<br>

and EFO (version 3.49.0) in JSON format. <br>

Owner

  • Name: Computational Omics and Systems Biology Group
  • Login: CompOmics
  • Kind: organization
  • Email: compomics.list@gmail.com

The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Claeys
    given-names: Tine
    orcid: https://orcid.org/0000-0001-9408-488X
title: compomics/lesSDRF: lesSDRF v0.1.0
version: v0.1.0
doi:10.5281/zenodo.8406626 
date-released: 2023-10-04
article:

GitHub Events

Total
  • Issues event: 1
  • Member event: 1
  • Push event: 5
  • Create event: 1
Last Year
  • Issues event: 1
  • Member event: 1
  • Push event: 5
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 4
  • Total pull requests: 2
  • Average time to close issues: 7 months
  • Average time to close pull requests: 7 months
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 2
  • Average time to close issues: 7 months
  • Average time to close pull requests: 7 months
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 1.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • prvst (1)
  • jonasscheid (1)
  • levitsky (1)
  • fi7855ar (1)
  • enryH (1)
Pull Request Authors
  • levitsky (2)
  • nilshoffmann (1)
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Dependencies

requirements.txt pypi
  • jsonschema ==4.17.0
  • openpyxl ==3.1.1
  • pronto ==2.5.3
  • streamlit ==1.19.0
  • streamlit-aggrid ==0.3.4.post3
  • streamlit-tree-select ==0.0.5
  • zipp ==3.10.0
Dockerfile docker
  • python 3.9-slim build
docker-compose.yml docker
  • lessdrf latest