VA_Tools
Tool |
Open Source? |
Type of Tool |
Brief Description |
Differentiating features |
Types of Data |
Size of Data |
Types of Analyses |
Strengths |
Limitations |
Contact Information |
Reviewed by |
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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 |
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 |
Bernice Rogowitz |
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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 |
Dynamic "brushing" between data representations at interactive speeds. |
Tabular data; also supports scatterplots of image thumbnails |
Over a million data values at interactive speed on a laptop |
Parallel coordinates , |
Powerful analysis tool. |
GUI for workbench version is not intuitive |
bernice.e.rogowitz@gmail.com |
Bernice Rogowitz |
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; |
http://bioinfo.bti.cornell.edu/cgi-bin/MetGenMAP/contact.cgi |
Lecong Zhou and Ruth Grene, 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; |
Find altered Bins (biological items and displays them in a heatmap) Pathway displays are usually very big (meaning a display of many items) |
Displays are Plant centric (currently), no sequenced based information like promoters (trivial to add though, if somebody convinces me of the usefulness) |
Björn Usadel (subjective view) |
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