The article presents information on PathwayStudio Central, a client-server software for visualization and analysis of biological pathways and gene regulation networks for biomedical research labs, biotechnology
although pathway analysis software provides detailed images of interactions among molecules, it does not exhibit how pathways interact with one another or with other biological processes under specific conditions. methods we propose a novel method to standardize descriptions of enriched pathways for a set...
varVAMP is open-source software for designing primers for tiled-amplicon sequencing and qPCR. It simplifies primer design for viral pathogens with high genomic variability by including sequence variations into primer sequences. Jonas Fuchs ,Johanna Kleine ...
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and pr
Our visualization framework to support pathway analysis, including (1) constructing a user-specified connectivity graph, (2) overlap-free rectangle placement, (3) maximizing screen space, (4) constructing orthogonal layout of each subgraph and (5) highlight relationships among different categories ...
The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is ...
One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally desc
PathMe is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data. References PathMe makes use of KEGG KGML files that are downloaded via the KEGG API for academic purposes (please make ...
functional analysis, and predication. However, there are few software packages available to deal with the sequence data in most biological laboratories and they are stored in file formats. File formats is another important issue for biological pathway data sources. XMl, SBML (systems biology markup ...
This paradigm is becoming increasingly popular [21, 23, 43, 44] and among others, “backward-causal” features have been introduced recently in Ingenuity Pathway Analysis software [43]. Using RNAi experimental data, Markowetz et al. showed that upstream pathway relationships between unobserved ...