Software Tools and Resources

The tools generated within the Center provide support for both graph theory-based and dynamical model development. The tools allow researchers to put their data in the context of current knowledge and develop a systems level view. All tools are freely available and the source code for software is deposited in Google Code or SourceForge. In addition, the Center publishes its software resources in the National Centers for Biomedical Computing's (NCBC) Biositemaps system. For a description of each of the software tools/systems, please visit the Software Tools and Compartmental Modeling Environment sections of this of the website. Researchers at the Center generate databases/datasets which are available for download as well as source code for a collection of dynamical models.

Gene Expression Data Analysis
Enrichr Integrative web-based and mobile gene-list enrichment analysis tool developed that includes over 30 gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library Data Driven Documents (D3). PMID: 23586463
Expression2Kinases Software used to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. PMID: 22080467
GATE (Grid Analysis of Time-series Expression) System used to analyze time-series expression data. GATE creates cluster files from time-series data for visualization as movies. PMID: 19892805
Gene-list Enrichment Analysis
Network2Canvas Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. PMID: 23749960
ChEA (ChIP-X Enrichment Analysis) Database of manually extracted datasets of transcription-factor/target-gene interactions experiments such as ChIP-chip, ChIP-seq, ChIP-PET applied to mammalian cells. PMID: 20709693
Genes2Networks System that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. PMID: 17916244
KEA (Kinase Enrichment Analysis) Web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. PMID: 19176546
Lists2Networks Web-based system that allows users to upload and analyze lists of mammalian gene-sets in a client-server software application. PMID: 20152038
Interoperability
Sig2BioPAX Java program that can be used to convert structured text files describing molecular interactions into the BioPAX Level 3 standard format. PMID: 21418653
Excel2BiositemapsAndHTML Tool that is used to convert an Excel file containing details about biomedical resources (tools, data, software) into a Biositemaps .rdf file.
Network Analysis/Visualization
Genes2FANs (G2F) A web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect input lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user's PubMed query. PMID: 22748121
Sets2Networks (S2N) A general method for network inference from repeated observations of sets of related entities. Given experimental observations of sets of related entities, S2N infers the underlying network of binary interactions between these entities by generating an ensemble of networks consistent with the data; the frequency of occurrence of a given interaction throughout this ensemble is interpreted as the probability that the interaction is present in the underlying real network. PMID: 22824380
Genes2WordCloud Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. PMID: 21995939
FNV (Flash-based Network Viewer) Flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. FNV can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials. PMID: 21349871
SNAVI (Signaling Network Analysis and Visualization) Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. PMID: 19154595
PathwayGenerator Automatically generated pathways from receptors to effectors created using the neuronal signalome. PMID: 16099987
AVIS: AJAX Viewer Visualization tool for viewing and sharing intracellular signaling, gene regulation and protein interaction networks. AVIS is implemented as an AJAX enabled syndicated Google gadget. PMID: 17855420
Compartmental Modeling Environment
MOOSE (Multiscale Objectoriented Simulation Environment) Designed to handle large complex simulations especially in biology. Spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. PMID: 19129924
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