Repositories list

• df-parallel

  Public
  Comparison of Dataframe libraries for parallel processing of large tabular files on CPU and GPU.

  gpu-computingdaskdataframes+ 6cuda-toolkitparallel-processingrapidsaidask-dataframesdask-cudfpyspark-dataframes

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •3•6•0•0•Updated Jun 27, 2024Jun 27, 2024

• kg-import

  Public
  kg-import automates the ingestion of heterogeneous datasets into a Knowledge Graph.

  knowledge-graphdata-integrationproperty-graph+ 3data-ingestiondatasets-preparationneo4j

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •4•5•4•0•Updated Apr 30, 2024Apr 30, 2024

• neo4j-ipycytoscape

  Public
  Demo of Neo4j graph visualization with the ipycytoscape Jupyter Lab extension

  knowledge-graphcytoscapegraph-visualization+ 3property-graphipycytoscapeneo4j

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •5•3•0•1•Updated Sep 29, 2023Sep 29, 2023

• mmtf-pyspark

  Public
  Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

  machine-learningbig-databinder+ 10apache-sparkjupyterprotein-data-bankprotein-structurejupyter-notebookpysparkscientific-computing+ 3

  Python

  •

  Apache License 2.0

  •27•68•8•0•Updated Mar 27, 2023Mar 27, 2023

• mmtf-benchmark

  Public
  Benchmark mmtf compression/decompression

  Java

  •1•0•0•0•Updated Feb 6, 2023Feb 6, 2023

• mmtf-genomics

  Public
  Methods for mapping genomic data onto 3D protein structure.

  genomicspysparkmutations+ 9protein-protein-interactionprotein-ligand-interactionscyverseprotein-drug-interactionsmmtf-pysparkbinderprotein-data-bank+ 2

  Jupyter Notebook

  •

  Apache License 2.0

  •10•28•0•0•Updated May 17, 2022May 17, 2022

• mmtf-workshop-2018

  Public
  Structural Bioinformatics Training Workshop & Hackathon 2018

  machine-learningbig-dataapache-spark+ 10jupyterhackathonprotein-data-bankjupyter-notebookpysparkworkshop-materials3d-visualization+ 3

  Jupyter Notebook

  •

  Apache License 2.0

  •34•58•3•0•Updated May 17, 2022May 17, 2022

• kg-bio

  Public
  Download and processes Biological Repositories for ingestion into Knowledge Graphs

  Jupyter Notebook

  •2•1•0•0•Updated May 16, 2022May 16, 2022

• kg-onto

  Public
  Create Node and Relationship files from BioPortal ontologies for import into Property Graphs

  neo4jontologyknowledge-graph+ 3data-integrationproperty-graphdata-ingestion

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•1•0•Updated Apr 9, 2022Apr 9, 2022

• sars-cov-2-variants

  Public
  SARS-CoV-2 Variant metadata

  Jupyter Notebook

  •0•0•0•0•Updated Aug 2, 2021Aug 2, 2021

• mexico-boundaries

  Public
  GeoPandas GeoDataFrames for Mexican States and Municipalities

  Jupyter Notebook

  •0•1•0•0•Updated Jul 13, 2021Jul 13, 2021

• coronavirus-knowledge-graph

  Public
  OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (see NEW VERSION: https://github.com/covid-19-net/covid-19-community)

  jupyter-notebookcoronaviruscoronavirus-analysis+ 2covid-19binder

  Jupyter Notebook

  •

  MIT License

  •13•18•0•0•Updated Nov 25, 2020Nov 25, 2020

• mmtf-proteomics

  Public
  Methods for mapping proteomics data on 3D protein structure.

  binderprotein-data-bankjupyter-notebook+ 2pysparkproteomics

  Jupyter Notebook

  •

  Apache License 2.0

  •1•15•0•0•Updated Jan 18, 2020Jan 18, 2020

• sifts-columnar

  Public
  Benchmark and demo of representing SIFTS UniProt to PDB mappings in columnar data formats.

  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•0•0•Updated Dec 14, 2019Dec 14, 2019

• mmtf-pyspark-benchmarks

  Public
  Benchmarks for mmtf-pyspark project

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Feb 11, 2019Feb 11, 2019

• mmtf-spark

  Public
  Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

  machine-learningbig-dataapache-spark+ 6protein-data-bankprotein-structurescientific-computingprotein-sequencesprotein-protein-interactionprotein-ligand-interactions

  Java

  •

  Apache License 2.0

  •32•21•9•0•Updated Feb 1, 2019Feb 1, 2019

• biojava-notebooks

  Public
  BioJava examples in Jupyter Notebooks

  bioinformaticspdbprotein-data-bank+ 5protein-structurejupyter-notebookbiojavajupyter-labbeakerx

  Jupyter Notebook

  •

  MIT License

  •1•6•1•0•Updated Dec 20, 2018Dec 20, 2018

• mmtf-hackathon-2018

  Public
  Hackathon projects repository for MMTF Workshop 2018

  Jupyter Notebook

  •

  Apache License 2.0

  •17•11•0•0•Updated Aug 30, 2018Aug 30, 2018

• mmtf-data

  Public
  Data files for mmtf projects

  MIT License

  •0•0•0•0•Updated Aug 14, 2018Aug 14, 2018

• metal-binding-prediction

  Public
  Methods to predict metal binding sites in a protein by its amino acid sequence

  Jupyter Notebook

  •2•9•0•0•Updated Jun 15, 2018Jun 15, 2018

• mm-dev

  Public
  Repository for the development of new methods for the mmtf-spark project

  Java

  •1•2•0•0•Updated Mar 31, 2018Mar 31, 2018

• mmtf-workshop-2017

  Public
  Structural Bioinformatics Training Workshop & Hackathon 2017

  HTML

  •

  Apache License 2.0

  •35•17•0•0•Updated Jan 23, 2018Jan 23, 2018

• QuickStructureSearch

  Public archive
  Obsolete student projects: Methods for fast structural database searches and clustering

  Java

  •

  GNU Lesser General Public License v2.1

  •6•2•0•0•Updated Feb 14, 2017Feb 14, 2017

• structurecodec

  Public archive
  Obsolete project: Provides high-density compression and decompression of biomolecular structures.

  Java

  •

  GNU Lesser General Public License v2.1

  •3•2•0•0•Updated Nov 16, 2015Nov 16, 2015