NAMIC Wiki - User contributions [en]

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-06T07:36:35Z

Kskinner:

[[SDIWG:NCBC_Software_Classification|Back to the Main NCBC Software Ontology and Classification Page]]

== NCIBI Software Classification & Metadata Examples ==

=== Edgewarp ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://vhp.med.umich.edu/edgewarpss.html

=== MiMi:Michigan Molecular Interactions ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Biotool --> Data Management -->Information retrieval, traversal and querying </nowiki>
* Description: MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize
* Data Input: MQuery
* Data Output: XML using MiMI's internal schema, PSI-MI format (version 2.5) and plain text
* Implementation Language: Timber native XML database
* Platforms tested: Web and Cytoscape Browsers
* Authors: Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish
* URL: http://mimi.ncibi.org/MiMI/home.jsp
* Keywords: data integration, protein interactions

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-06T07:34:56Z

Kskinner:

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-05T21:57:35Z

Kskinner:

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-05T21:53:07Z

Kskinner:

[[SDIWG:NCBC_Software_Classification|Back to the Main NCBC Software Ontology and Classification Page]]

== NCIBI Software Classification & Metadata Examples ==

=== Edgewarp ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://vhp.med.umich.edu/edgewarpss.html

=== MiMi Michigan Molecular Interactions(MiMI)===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Biotool --> Data Management -->Information retrieval, traversal and querying </nowiki>
* Description: MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize
* Data Input: MQuery
* Data Output: XML using MiMI's internal schema, PSI-MI format (version 2.5) and plain text
* Implementation Language: Timber native XML database
* Platforms tested: Web and Cytoscape Browsers
* Authors: Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish
* URL: http://mimi.ncibi.org/MiMI/home.jsp

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-05T21:44:21Z

Kskinner:

[[SDIWG:NCBC_Software_Classification|Back to the Main NCBC Software Ontology and Classification Page]]

== NCIBI Software Classification & Metadata Examples ==

=== Edgewarp ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://vhp.med.umich.edu/edgewarpss.html

=== Michigan Molecular Interactions(MiMI)===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Biotool --> Data Management -->Information retrieval, traversal and querying </nowiki>
* Description: MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize
* Data Input: MQuery
* Data Output: XML using MiMI's internal schema, PSI-MI format (version 2.5) and plain text
* Implementation Language: Timber native XML database
* Platforms tested: Web and Cytoscape Browsers
* Authors: Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish
* URL: http://mimi.ncibi.org/MiMI/home.jsp

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-05T21:36:03Z

Kskinner:

[[SDIWG:NCBC_Software_Classification|Back to the Main NCBC Software Ontology and Classification Page]]

== NCIBI Software Classification & Metadata Examples ==

=== Edgewarp ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://vhp.med.umich.edu/edgewarpss.html

=== Michigan Molecular Interactions(MiMI)===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Biotool --> Data Management -->Information retrieval, traversal and querying </nowiki>
* Description: MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize
* Data Input: MQuery
* Data Output: XML using MiMI's internal schema, PSI-MI format (version 2.5) and plain text
* Implementation Language: Timber native XML database
* Platforms tested: Web and Cytoscape Browsers
* Authors: Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish

SDIWG:NCBC Software Classification NCIBI Examples

2007-03-05T21:24:13Z

Kskinner:

[[SDIWG:NCBC_Software_Classification|Back to the Main NCBC Software Ontology and Classification Page]]

== NCIBI Software Classification & Metadata Examples ==

=== Edgewarp ===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://vhp.med.umich.edu/edgewarpss.html

=== Michigan Molecular Interactions(MiMI)===

* NCBC [http://bioontology.org/ontologies/SoftwareOntology/ Ontology Classification]<nowiki>: Modeling --> Algorithms --> Image Processing --> Registration </nowiki>
* Description: Edgewarp 3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging.
* Data Input: TBD
* Data Output: TBD
* Implementation Language: C and C++ code and makes extensive use of SGI's OpenGL graphics interface. Communication with the user is by textual and graphical interfaces managed using TCL/TK.
* Platforms tested: SGI/IRIX
* Version, Date, Stage: 3.2.7
* Authors: Fred Bookstein
* URL: http://mimi.ncibi.org/MiMI/home.jsp