Essential Open Source Software for Science (EOSS)

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https://chanzuckerberg.com/eoss/proposals/?cycle=1,2,3,4,5,6,d-i,

The Chan Zuckerberg Initiative (CZI) has funded numerous open source software projects through its Essential Open Source Software for Science (EOSS) program. Here is a list of some of the funded projects with brief descriptions:

Cycle 1

  • BioDynaMo: A platform for agent-based simulation of biological systems.
  • Bioconda: A distribution of bioinformatics software using conda.
  • CellProfiler: Software for quantitative analysis of biological images.
  • Cytoscape: An open-source platform for visualizing complex networks.
  • DeepLabCut: A toolbox for markerless pose estimation of animals.
  • Galaxy: An open, web-based platform for data-intensive biomedical research.
  • iSEE: Interactive visualization of single-cell data.
  • Jupyter Notebooks: A web-based interactive computing platform.
  • OpenMM: A high-performance toolkit for molecular simulations.
  • scikit-image: Image processing in Python.

Cycle 2

  • Bioconda: Continued support for the software distribution.
  • CellProfiler Analyst: Extension for machine learning-based image analysis.
  • Napari: Multi-dimensional image viewer for Python.
  • Pandas: Data structures for data analysis in Python.
  • Rao Lab’s HiGlass: Tool for exploring large genomic contact maps.
  • Scanpy: Scalable analysis of single-cell RNA sequencing data.

Cycle 3

  • CWL-Airflow: Workflow engine based on Apache Airflow.
  • Galaxy: Continued support for the platform.
  • Pangeo: Community platform for big data geoscience.
  • Project Jupyter: Further development of Jupyter Notebooks.
  • Sourmash: Scalable search of genomic data.

Cycle 4

  • GEMmaker: RNA-Seq pipeline tool.
  • Jupyter Book: Interactive, computational documents for data science.
  • NCBI BLAST+: Tool for comparing gene and protein sequences.
  • Scanpy: Continued support for single-cell RNA sequencing analysis.

Cycle 5

  • Community and Code: Promoting diversity in open source.
  • DeepLabCut: Continued support for animal pose estimation.
  • OpenMM: Further development for molecular simulations.
  • QHub: Managed JupyterHub deployments for collaborative research.
  • SciPy: Python-based ecosystem for mathematics, science, and engineering.

Cycle 6

  • BioSimSpace: Computational toolset for molecular simulations.
  • MetPy: Meteorological data analysis tools in Python.
  • Open Data Cube: Platform for analyzing large-scale Earth observation data.
  • TOPMed DCC: Data coordination for Trans-Omics for Precision Medicine.

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