Tools

Active Schemas

Latest release of BDML and PDPML schemas can be found here. Some browsers will try to render the XSD files when you click on the link below. This can result in either a blank screen or a screen of unformatted text. Please choose to either download the file or view the source.

Please see BDML manual, OmicsBDML manual, and PDPML manual for more details.

• bdml.xsd - Version 3.0, updated on October 03, 2017. The main schema used to describe quantitative biological and dynamical data
• omicsbdml.xsd - Version 1.0, updated on October 03, 2017. The sub schema used to describe quantitative biological and dynamical data
• pdpml.xsd - Version 1.0, update on October 03, 2017. The PDPML schema used to describe data processing of the quantitative biological data

File Formats

• bdz, Zarr-based format for storing quantitative biosystems dynamics data
  • https://github.com/openssbd/bdz

• BD5_samples, Sample codes and tools for reading and writing BD5 file format
  • https://github.com/openssbd/BD5_samples

• BDML2BD5 - a software package for converting numerical data in the BDML format (ver. 0.18) into BD5 format. Please see sample codes on Github for details.
  • bdml2bd5v018.zip - It supports for BDML version 0.18, and released April 18, 2018.

Softwares

• QTBD5Viewer - A visualizer for BD5-format files.
  • https://github.com/openssbd/QTBD5Viewer

• BDML4Viewer - a plugin of ImageJ for visalizing BDML files. Please see BDML4DViewer manual
  • BDML4DViewer015_.jar - It supports for BDML version 0.15, and released June 18, 2014.
  • BDML4DViewer018_.jar - It supports for BDML version 0.18, and released June 18, 2014.
  • BDML4DViewer020_.jar - It supports for BDML version 0.20, and released August 28, 2014.

• phenochar - a software package for extracting phenotypic characters from BDML files. Please see phenochar manual for details.
  • phenochar1.0v3.zip: It supports for BDML version 0.15, and updated November 27, 2015.
  • phenochar2.0v2.zip: It supports for BDML version 0.18, and updated November 27, 2015.
  • phenochar3.0v1.zip: It supports for BDML version 0.20, and released August 28, 2014.

• SSBD-OMERO.insight - a plugin of ImageJ for reading to the images stored in SSBD. Please see SSBD-OMERO.insight manual for details.
  • SSBD-OMERO.insight-ij-5.0.4-ice34.zip: It supports for OMERO.web version 5.0.4, and released October 3, 2014.
  • SSBD-OMERO.insight-ij-5.4.4-ice36.zip: It supports for OMERO.web version 5.4.4, and released March 20, 2018.
  • SSBD-OMERO.insight-ij-5.4.10-ice36.zip: It supports for OMERO.web version 5.4.10, and released April 22, 2019.

• Example codes using SSBD-OMERO API
  • Python package on Github - Python example codes to access SSBD-OMERO API. It is released on October 03, 2017

• OpenSSBD - the open-source version of SSBD for managing quantitative biological dynamics data. Please see Github README page for more details.
  • OpenSSBD on GitHub- It is released on April 11, 2016.
  • OpenSSBD in a docker container- Please visit GitHub page for more details. It is released on April 11, 2016.

• Example codes using SSBD REST API
  • Python package on Github: Python reference implementation to access SSBD API and example codes. It is released on April 11, 2016.
  • Java package on Github: Java reference implementation to access SSBD API and example codes. It is released on April 11, 2016.