VA_Tools

Ondex

GNU on Source Forge http://www.ondex.org/verify.php

Data integration, visualization and analysis.  Generic graph-based representation and analysis of many types of biological data. 

General tool for ingesting  heterogenous data from multiple sources to analyze patterns across data types. 

Underlying data model.  Semantic ontologies to guide data mapping.  Generalized data structure to support linked metadata

Biological Network data
and data mapped onto networks, e.g.,microarray expression data, protein-protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks

100,000s of "concepts," e.g., genes, proteins

Visual and analytical methods for analyzing heterogeneous interactions, e.g., Protein-protein interaction networks fused with gene expression values.

Well-thought out fundamental approach to semantics of network data.

User-control of visual mapping can create confusing visualizations; defaults or guidance would help

http://www.ondex.org

Bernice Rogowitz
3/18/2010

Visualization and Visual Analysis (ViVA) Workbench and APIs

Open source permission granted from IBM; needs to be posted externally 

Interactive data visualization and analysis 

General tool for interactive visual analysis of numerical and categorical data
Workbench version plus underlying JAVA libraries (APIs) 

Dynamic "brushing" between data representations at interactive speeds. 
Rich math library (250 functions) integrated with the visualization. 

Tabular data; also supports scatterplots of image thumbnails 

Over a million data values at interactive speed on a laptop

Parallel coordinates ,
Scatterplots,
Histograms,
Dendograms,
Tree maps,
Descriptive statistics,
transforms,
Principal components analysis, etc.

Powerful analysis tool.
Interactive "what-if" visual and analytical experiments
Dynamic brushing
Well documented

GUI for workbench version is not intuitive

Presentation graphics could be more aesthetic

Some "rust"

bernice.e.rogowitz@gmail.com
Workbench version will be on the wiki soon.

Bernice Rogowitz
3/18/2010

Plant MetGenMAP

A web-based system (http://bioinfo.bti.cornell.edu/cgi-bin/MetGenMAP/home.cgi); registration and login required; open source or mirroring is possible.

An Integrative Analysis System for Plant Systems Biology

Integrate, analyze and visualize large-scale gene expression and metabolite profile data sets, and identify regulatory motifs in promoter regions; developed by Boyce Thompson Institute for Plant Research, Cornell University.

Display both gene expression and metabolite data, at pathway level.

Use analyzed gene expression and metabolite data, with fold changes and p-values as input.

At transcriptome and/or metabolome scale.

Identify significantly altered biochemical pathways and biological processes under given conditions;  identify candidate promoter motifs in responsive genes.

Can identify altered pathways,  overrepresented GO terms, and enriched regulatory motifs; Integrative display of pathways with qualitative changes in genes and metabolites; Targeted to plants, for both annotated genomes or less understood genomes.

0/1 type of visualization; currently ready for only 3 plant species; lack of support for output retrieving;
a bug found (inconsistent results in repeative runs of the same GO term analysis); graphic output needs further improvement to be of publishable or readable quality (eg., display of fold changes should be removed).

http://bioinfo.bti.cornell.edu/cgi-bin/MetGenMAP/contact.cgi

Lecong Zhou and Ruth Grene, 3/31/2010.
Also see Excel sheet in the attachechment by Björn Usadel (upper left corner)
3/31/2010

MapMan

Mostly standalone but some webbased components. Free for academia

Integrative Data Analysis and Visualisation

Integrate, viusualize and statistuically anaylze omics datasets of proteins, transcripts and metabolites

Display up to four different entities using squares, up- down triangles and transcripts

Log2 Fold change and p-values or other information (e.g. expressio n height) for filtering

Limited by user RAM only; easily long term courses of 10ths of time points by 10ks of genes on typical machines

Identify changed categories; Display Pathways; Cluster Data using Kmeans;
Generate Venn Diagrams (up to 4way)

Find altered Bins (biological items and displays them in a heatmap) Pathway displays are usually very big (meaning a display of many items)
Mapping onto Chromosomes.
Direct display of relevant Arabidopsis publications when online (biomobyed)
Data available via Biomoby
Output in glossy quality
Any (plant) species is supported by generating template files online based on sequence information

Displays are Plant centric  (currently), no sequenced based information like promoters (trivial to add though, if somebody convinces me of the usefulness)

http://mapman.gabipd.org

Björn Usadel (subjective view)
Also see Excel sheet for point ot point comparison with Plant Metgenmap
3/31/2010