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omegacommons

The OmegaCommons Application Programming Interface (API) facilitates the extraction of OMEGA libraries for custom plugin development and contains key data structures for storing data in OMEGA.

https://github.com/omegaproject/omegacommons

Science Score: 18.0%

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    Low similarity (9.7%) to scientific vocabulary
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Repository

The OmegaCommons Application Programming Interface (API) facilitates the extraction of OMEGA libraries for custom plugin development and contains key data structures for storing data in OMEGA.

Basic Info
  • Host: GitHub
  • Owner: OmegaProject
  • License: gpl-3.0
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 18.5 MB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created over 7 years ago · Last pushed over 4 years ago
Metadata Files
Readme License Citation

README.md

OmegaCommons API

Extraction of OMEGA libraries

OmegaCommons facilitates the extraction of OMEGA libraries for custom plugin development. For this purpose it contains the following : 1. Java classes used as building blocks for the construction of individual plugins. 2. Java interfaces necessary to mediate the communication between plugins and the core. 3. Components used for event-driven communication. 4. All foundational libraries necessary for trajectory analysis in OMEGA: Such libraries are composed of math-oriented static Java classes, are sub-divided in five categories based on the tracking measure they are responsible for (i.e. Intensity, Mobility, Velocity, Diffusivity and Diffusivity Measures Uncertainty Estimation), and are specifically designed to facilitate the generation of stand-alone Tracking Measures tools. 5. Generic GUI elements, as well as common constants and exceptions were included here to facilitate the application accessibility by third-party plugins.

Data Structures

In addition, Commons API contains three categories of data structures that are designed to store image data and metadata as well as the results produced at run time by the OMEGA application: 1. The first group includes structures designed to contain data and metadata originating from OME-XML specific elements, such as Project, Dataset, Image, Experimenter and Experimenter Group. 2. The second group of data structures was created on the basis of the OMEGA data model and MIAPTE specifications to store data produced as output by the analysis pipeline. Since most of OMEGA data-producing processes require parameter input, these data structures are constructed to allow the storage of both results and parameter settings associated with each analysis runs. 3. The third group contains generic data structures whose purpose is, for example, to store data necessary to establishing connections with remote data stores, such as server information (i.e. hostname and port) and user credentials (i.e. username, encrypted password). This arrangement allows developers to extend or implement each components thereby facilitating the development of third-party plugins for connecting OMEGA to servers other than OMERO and OMEGA.

Owner

  • Name: Open Microscopy Environment inteGrated Analysis
  • Login: OmegaProject
  • Kind: organization
  • Email: caterina.strambio@umassmed.edu
  • Location: UMass Medical School, Worcester, MA

Citation (CITATION) 

cff-version: 1.0.3
message: If you use OmegaCommons, please cite both the software and the papers as indicated in the scope of each reference.
authors:
  - family-names: Rigano
    given-names: Alessandro
    affiliation: University of Massachusetts Medical School
    email: alessandro.rigano@umassmed.edu
  - family-names: Strambio-De-Castillia
    given-names: Caterina
    affiliation: University of Massachusetts Medical School
    email: caterina.strambio@umassmed.edu
    orcid: https://orcid.org/0000-0002-1069-1816
title: OmegaCommons
version: v0.01.0-beta
doi: https://doi.org/10.5281/zenodo.2538197
date-released: 2019-01-11
repository: https://github.com/OmegaProject/OmegaCommons
description: The OmegaCommons Application Programming Interface (API) facilitates the extraction of OMEGA libraries for custom plugin development. In addition to general utility methods, it includes Java classes used as building blocks for the construction of individual plugins, interfaces necessary to mediate the communication between plugins and the core, and the system used for event-driven communication. Commons API also contains all foundational libraries necessary for trajectory analysis in OMEGA. In addition, Commons API contains data structures that are designed to store image data and metadata as well as the results produced at run time by the OMEGA application.
keywords:
  - java
  - particle-tracking
  - particle-localization
  - particle-detection
  - motion-analysis
  - error-propagation
  - data-provenance
  - data-management
  - classification
  - trajectory-segmentation
license: GNU General Public License v.3
references:
  - type: article
    scope: Cite this paper every time you use this software
    authors:
      - family-names: Rigano
        given-names: Alessandro
        affiliation: University of Massachusetts Medical School
        email: alessandro.rigano@umassmed.edu
      - family-names: Galli
        given-names: Vanni
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Clark
        given-names: Jasmine M
        affiliation: Nell Hodgson Woodruff School of Nursing, Emory University
      - family-names: Pereira
        given-names: Lara E
        affiliation: Division of Sexual Transmitted Diseases Prevention, Centers for Disease Control and Prevention
      - family-names: Grossi
        given-names: Loris
        affiliation:  Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Luban
        given-names: Jeremy
        affiliation: University of Massachusetts Medical School
        orcid: https://orcid.org/0000-0001-5650-4054
      - family-names: Giulietti
        given-names: Raffaello
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Leidi
        given-names: Tiziano
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Hunter
        given-names: Eric
        affiliation: Emory Vaccine Center at Yerkes National Primate Research Center
      - family-names: Valle
        given-names: Mario
        affiliation: Swiss National Supercomputing Centre
      - family-names: Sbalzarini
        given-names: Ivo F.
        affiliation: Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: University of Massachusetts Medical School
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    title: "OMEGA: a software tool for the management, analysis, and dissemination of 	intracellular trafficking data that incorporates motion type classification and quality control"
    year: 2018
    journal: bioRxiv.org
    doi: 10.1101/251850
    url: https://doi.org/10.1101/251850

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Dependencies

pom.xml maven
  • flanagan:flanagan 1
  • jcommon:jcommon 1.0.16
  • jfreechart:jfreechart 1.0.13
  • junit:junit 4.11 test