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Average Rating: 5.0/5.0Number of Ratings: 2Number of Reviews: 1
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Most Helpful Reviews
The GenoViz project originated from the commercial codebase of Neomorphic, Inc. when it was known as the NGSDK (Neomorphic Genome Software Development Kit). The NGSDK was toolkit for visualizing numerous types of bioinformatics data sets and was used as the basis for several commercial projects. A few years after Neomorphic was acquired by Affymetrix in November 2000, the code was eventually open sourced as the GenoViz SourceForge project.
GenoViz is quite a mature codebase, having gone through several implementation cycles since the early days of the NGSDK. It is actively maintained principally by developers at Affymetrix, Inc. though anyone is welcome to join. IGB, the Integrated Genome Browser, is used as a data visualization tool by Affymetrix customers and perhaps a handful of other groups (there aren't any stats on the use of IGB/Genoviz, besides the download stats on the SourceForge site). Discussion forums for GenoViz and IGB can be found at http://sourceforge.net/forum/?group_id=129420 .
The chief strength of IGB is its scalability to large, whole-genome data sets. It also makes use of the semantic zooming concept, enabling a user to dynamically adjust their view of the data from bird's eye overview to a zoomed-in, basepair level of detail.
Some other IGB strengths include:
* Flexible preference configurations.
* Bookmark any given view of a data set for easy reference as well as sharing with collaborators.
* Optimized binary formats for rapid data transfer and rendering.
* Support for the Distributed Annotation System protocols (v1 and v2, see http://biodas.org ).
IGB is primarily a read-only viewer of genome annotations. Support for editing of annotations is in an experimental phase, made possible by the writeback aspect of the DAS/2 protocol. Support for protein annotations is something that is being explored as well.
The code was developed primarily by Gregg Helt with work from many others whose contributions will not show up within this Ohloh project because their work occurred in the Neomorphic days when this project was closed source. These hall of famers include: Cyrus Harmon, Eric Blossom, Joe Morris, Shaw Sun, and others.
Most Recent Reviews
The GenoViz project originated from the commercial codebase of Neomorphic, Inc. when it was known as the NGSDK (Neomorphic Genome Software Development Kit). The NGSDK was toolkit for visualizing numerous types of bioinformatics data sets and was used as the basis for several commercial projects. A few years after Neomorphic was acquired by Affymetrix in November 2000, the code was eventually open sourced as the GenoViz SourceForge project.
GenoViz is quite a mature codebase, having gone through several implementation cycles since the early days of the NGSDK. It is actively maintained principally by developers at Affymetrix, Inc. though anyone is welcome to join. IGB, the Integrated Genome Browser, is used as a data visualization tool by Affymetrix customers and perhaps a handful of other groups (there aren't any stats on the use of IGB/Genoviz, besides the download stats on the SourceForge site). Discussion forums for GenoViz and IGB can be found at http://sourceforge.net/forum/?group_id=129420 .
The chief strength of IGB is its scalability to large, whole-genome data sets. It also makes use of the semantic zooming concept, enabling a user to dynamically adjust their view of the data from bird's eye overview to a zoomed-in, basepair level of detail.
Some other IGB strengths include:
* Flexible preference configurations.
* Bookmark any given view of a data set for easy reference as well as sharing with collaborators.
* Optimized binary formats for rapid data transfer and rendering.
* Support for the Distributed Annotation System protocols (v1 and v2, see http://biodas.org ).
IGB is primarily a read-only viewer of genome annotations. Support for editing of annotations is in an experimental phase, made possible by the writeback aspect of the DAS/2 protocol. Support for protein annotations is something that is being explored as well.
The code was developed primarily by Gregg Helt with work from many others whose contributions will not show up within this Ohloh project because their work occurred in the Neomorphic days when this project was closed source. These hall of famers include: Cyrus Harmon, Eric Blossom, Joe Morris, Shaw Sun, and others.