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PATIKA specifications


Unique identifier OMICS_02760
Alternative name Pathway Analysis Tools for Integration and Knowledge Acquisition
Restrictions to use None
Maintained No


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Publication for Pathway Analysis Tools for Integration and Knowledge Acquisition

PATIKA citations


What google maps can do for biomedical data dissemination: examples and a design study

BMC Res Notes
PMCID: 3658873
PMID: 23642009
DOI: 10.1186/1756-0500-6-179

[…] eting microarray expression such as Clusterview [], Hierarchical Clustering Explorer (HCE) [], and Spotfire [], systems for pathway and network analysis like Cytoscape [], VisANT [], Ingenuity [] and Patika [], or genome viewers such as Cinteny [] and Mizbee []. Most such systems are aimed at complex data exploration and analysis and have associated overhead costs such as deploying, learning and o […]


A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

BioData Min
PMCID: 3342218
PMID: 22448851
DOI: 10.1186/1756-0381-5-2

[…] network analysis software come with sophisticated methods for laying out networks. Such software packages, each providing a specific range of visualization options, include, e.g., VisANT, NAViGaTOR, PATIKA, PINA, MATISSE, GraphViz, Osprey, Graphle, CellDesigner, Biolayout, ProViz and Pajek; see [,,] and references therein. Among others, Cytoscape software platform for network analysis and visuali […]


An efficient biological pathway layout algorithm combining grid layout and spring embedder for complicated cellular location information

BMC Bioinformatics
PMCID: 2904761
PMID: 20565884
DOI: 10.1186/1471-2105-11-335

[…] , several types of drawing algorithms have been designed for biological pathways and they have been integrated in biological modeling and/or simulation software, e.g., Cell Illustrator [,], Pajek [], PATIKA [,], and CADLIVE [,].Karp and Paley extracted biological topologies such as linear, cyclic, and branching pathways and used them as the backbone of the layout []. For chemical reaction networks […]


LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB

BMC Bioinformatics
PMCID: 2825225
PMID: 20074382
DOI: 10.1186/1471-2105-11-31

[…] her demand for automatic visualization as an auxiliary analysis tool. Available drawing tools for biochemical networks are designed to work in certain network modeling platforms such as Cytoscape [], PATIKA [], VisANT [], Cell Illustrator [,], and CADLIVE [,]. Because these modeling platforms are designed for specific purposes, most network analysis related numerical utilities are not provided. In […]


An efficient grid layout algorithm for biological networks utilizing various biological attributes

BMC Bioinformatics
PMCID: 1821340
PMID: 17338825
DOI: 10.1186/1471-2105-8-76

[…] Modeling and simulations of large scale biological pathways are some of the most important tasks in Bioinformatics. Many applications, e.g., Cell Illustrator [,], Cytoscape [], Pajek [], PATIKA [,], and CADLIVE [,] have been developed in this area. Related to these topics, the visualization of biopathways is considered to play a key role in understanding biological systems. However, m […]


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PATIKA institution(s)
Department of Molecular Biology and Genetics Computer Engineering Department Center for Bioinformatics, Bilkent University, Ankara, Turkey

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