Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/big-data-lab-team/reproducibility-bioinfo

A repo for reproducibility studies in bioinformatics

https://github.com/big-data-lab-team/reproducibility-bioinfo

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: plos.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.0%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

A repo for reproducibility studies in bioinformatics

Basic Info
  • Host: GitHub
  • Owner: big-data-lab-team
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 31.4 MB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 4
  • Open Issues: 5
  • Releases: 0
Created about 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

Membrane Protein Classification: a Reproducibility Study

In this project, we tried to reproduce the SVM-based model from the TrSSP paper, for "Prediction of Membrane Transport Proteins and Their Substrate Specificities" using python3, Scikit-Learn, Numpy, Pandas and Matplotlib (Version information is available in requirements.txt).

Run this Notebook for the pipeline details and results.

Reference

Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information Nitish K. Mishra,Junil Chang,Patrick X. Zhao(2014)

Owner

  • Name: /bin
  • Login: big-data-lab-team
  • Kind: organization
  • Location: Montreal, Quebec, Canada

/Big Data Infrastructures for Neuroinformatics. We like Linux, Git, containers and much more!

GitHub Events

Total
Last Year

Dependencies

requirements.txt pypi
  • certifi ==2019.6.16
  • chardet ==3.0.4
  • cycler ==0.10.0
  • idna ==2.8
  • joblib ==0.13.2
  • kiwisolver ==1.1.0
  • matplotlib ==3.0.2
  • numpy ==1.15.1
  • pandas ==0.23.4
  • pyparsing ==2.4.0
  • python-dateutil ==2.8.0
  • pytz ==2019.1
  • requests ==2.21.0
  • scikit-learn ==0.21.2
  • scipy ==1.3.0
  • six ==1.12.0
  • sklearn ==0.0
  • urllib3 ==1.24.3