ITM Probe statistics
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ITM Probe specifications
Information
| Unique identifier | OMICS_24196 |
|---|---|
| Name | ITM Probe |
| Interface | Web user interface |
| Restrictions to use | None |
| Output data | A list of the top ranking nodes together with an image of the sub-network consisting of these nodes. |
| Computer skills | Basic |
| Stability | Stable |
| Maintained | Yes |
Maintainer
- person_outline Yi-Kuo Yu
Information
| Unique identifier | OMICS_24196 |
|---|---|
| Name | ITM Probe |
| Software type | Application/Script |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux |
| Programming languages | Python |
| Computer skills | Advanced |
| Version | 1.5.4 |
| Stability | Stable |
| Requirements |
qmbpmn
|
| Maintained | Yes |
Versioning
No version available
Maintainer
- person_outline Yi-Kuo Yu
Publications for ITM Probe
Information flow in interaction networks.
ITM Probe citations
(6)Identifying diseases related metabolites using random walk
[…] the similarity of diseases by gene functional network. Gene functional network can provide the information flow which can be used to calculate the disease similarity. To analyze the information flow, ITM Probe [] is employed which included three models: absorbing, emitting and channel. Each disease is a boundary node in the network, besides, each gene is a transient node.Each disease has several r […]
InfAcrOnt: calculating cross ontology term similarities using information flow by a random walk
[…] m walk ends at, emitting model assigns nodes the random walk starts from and channel model integrates both absorbing and emitting models for directed information flow.Information Transduction Module (ITM) Probe [] program has implemented all of these three models. It outputs the expected number of visits to each transient and sink node by random walker originated from every node. The ITM takes an […]
Measuring disease similarity and predicting disease related ncRNAs by a novel method
[…] In this study, we designed a novel method to compute disease similarity by modelling the information flow in the comprehensive GFN. In the previous study, a tool called ITM Probe [] was created for analyzing information flow in the network based on random walk with damping. Currently, three models involving absorbing, emitting, and channel were employed in ITM Probe. […]
Using biological networks to integrate, visualize and analyze genomics data
[…] rmation flow analysis, a computational biology method that uses random walk algorithms to model how signals flow through large networks. One example of software that performs this type of analysis is ITM Probe [], which is also available as a Cytoscape App []. In ITM Probe, the user can define source nodes (nodes that emit information, e.g., receptors) and sink nodes (target nodes that absorb info […]
Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
[…] rk studies , . A number of programs have been developed for the calculation of certain aspects of network dynamics, such as network simulation tools based on Boolean dynamics –, the random-walk based ITM-Probe , the law of mass action-based PerturbationAnalyzer , or the biological system modeling tool, BIOCHAM . However, to our knowledge, no stand-alone program exists, which can easily integrate a […]
CytoITMprobe: a network information flow plugin for Cytoscape
[…] Subnetwork nodes are selected through a ranking attribute, which assigns a numerical value from ITM Probe results to each node. The nodes are listed in descending order of the ranking attribute and top nodes are displayed as the ITM subnetwork. The number of top nodes is determined by specifying […]
Citations
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