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https://github.com/broadinstitute/beclust3d

https://github.com/broadinstitute/beclust3d

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 719 MB
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 8
  • Releases: 0
Created about 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

BEClust3D

Colab Notebook Example

Examples of how to use the BE method development pipeline is provided in the following colab notebook:

| Link | Description | |---------|-------------| Open In Colab | Example of how to use the BE pipeline for single screen input

🚀 Installation Guide

🐧 Linux (x86_64)

✅ Option 1: Using Conda Environment YAML

Create the environment directly from the pre-configured YAML file:

```bash conda env create -f requirements_linux64.yaml

```

Option 2: Manual Setup with requirements.txt

Create an anaconda environment bash conda create -n beclust3d python=3.10 conda activate beclust3d Install external dependencies bash conda install salilab::dssp conda install -c conda-forge boost=1.73 conda install bioconda::clustalo Install Python dependencies bash pip install -r requirements.txt

For Google Colab

Add the following line at the top of your notebook: ! apt-get update ! apt-get install dssp clustalo

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 2
  • Delete event: 10
  • Issue comment event: 1
  • Member event: 1
  • Push event: 153
  • Pull request event: 43
  • Create event: 22
Last Year
  • Issues event: 2
  • Delete event: 10
  • Issue comment event: 1
  • Member event: 1
  • Push event: 153
  • Pull request event: 43
  • Create event: 22

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 56
  • Average time to close issues: N/A
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 1
  • Total pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.04
  • Merged pull requests: 47
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 2
  • Pull requests: 47
  • Average time to close issues: N/A
  • Average time to close pull requests: about 4 hours
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.04
  • Merged pull requests: 45
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • YoochanMyung (2)
Pull Request Authors
  • xycalvin (36)
  • dependabot[bot] (15)
  • surya-money (12)
  • YoochanMyung (4)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
dependencies (15)

Dependencies

pyproject.toml pypi
  • DSSPparser *
  • biopandas *
  • biopython *
  • matplotlib *
  • numpy *
  • pandas *
  • scikit-learn *
  • scipy *
  • seaborn *
  • wget *
requirements.txt pypi
  • GitPython ==3.1.42
  • Jinja2 ==3.1.3
  • MarkupSafe ==2.1.5
  • Pillow ==10.1.0
  • PyPDF2 ==3.0.1
  • PyYAML ==6.0.1
  • Theano ==1.0.5
  • aiohttp ==3.9.3
  • aiosignal ==1.3.1
  • annotated-types ==0.6.0
  • anyio ==4.1.0
  • appdirs ==1.4.4
  • attrs ==23.2.0
  • certifi ==2023.7.22
  • charset-normalizer ==3.3.0
  • click ==8.1.7
  • colorama ==0.4.6
  • contourpy ==1.2.0
  • cycler ==0.12.1
  • datasets ==2.18.0
  • dill ==0.3.8
  • distro ==1.8.0
  • docker-pycreds ==0.4.0
  • filelock ==3.13.3
  • fonttools ==4.44.0
  • frozenlist ==1.4.1
  • fsspec ==2024.2.0
  • gitdb ==4.0.11
  • h11 ==0.14.0
  • httpcore ==1.0.2
  • httpx ==0.25.2
  • huggingface-hub ==0.22.1
  • idna ==3.4
  • joblib ==1.3.2
  • kiwisolver ==1.4.5
  • lxml ==5.1.0
  • matplotlib ==3.8.1
  • mpmath ==1.3.0
  • multidict ==6.0.5
  • multiprocess ==0.70.16
  • networkx ==3.2.1
  • npm ==0.1.1
  • numpy ==1.26.0
  • openai ==1.3.8
  • optional-django ==0.1.0
  • packaging ==23.2
  • pandas ==2.1.1
  • pandoc ==2.3
  • pdfmerger ==0.5.0
  • plumbum ==1.8.2
  • ply ==3.11
  • portalocker ==2.8.2
  • protobuf ==4.25.3
  • psutil ==5.9.8
  • pyarrow ==15.0.2
  • pyarrow-hotfix ==0.6
  • pydantic ==2.5.2
  • pydantic_core ==2.14.5
  • pyparsing ==3.1.1
  • python-dateutil ==2.8.2
  • pytz ==2023.3.post1
  • regex ==2023.12.25
  • requests ==2.31.0
  • sacrebleu ==2.4.1
  • safetensors ==0.4.2
  • scikit-learn ==1.3.1
  • scipy ==1.11.2
  • sentry-sdk ==1.44.0
  • setproctitle ==1.3.3
  • six ==1.16.0
  • smmap ==5.0.1
  • sniffio ==1.3.0
  • sympy ==1.12
  • tabulate ==0.9.0
  • threadpoolctl ==3.2.0
  • tokenizers ==0.15.2
  • torch ==2.2.2
  • tqdm ==4.66.1
  • transformers ==4.39.2
  • typing_extensions ==4.9.0
  • tzdata ==2023.3
  • ucimlrepo ==0.0.2
  • urllib3 ==2.0.6
  • wandb ==0.16.5
  • xxhash ==3.4.1
  • yarl ==1.9.4