Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation

2012 ◽  
Vol 7 (3) ◽  
pp. 579-593 ◽  
Author(s):  
Astrid Junker ◽  
Hendrik Rohn ◽  
Tobias Czauderna ◽  
Christian Klukas ◽  
Anja Hartmann ◽  
...  
Keyword(s):  
Systems Biology ◽  
Web Based ◽  
Graphical Notation

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

2018 ◽  
Vol 14 (2) ◽  
pp. e1005740 ◽  
Author(s):  
Vasundra Touré ◽  
Nicolas Le Novère ◽  
Dagmar Waltemath ◽  
Olaf Wolkenhauer
Keyword(s):  
Systems Biology ◽  
Biological Pathways ◽  
Graphical Notation

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language

2017 ◽  
Vol 24 (12) ◽  
pp. 1226-1229 ◽  
Author(s):  
Haitham Elmarakeby ◽  
Mostafa Arefiyan ◽  
Elijah Myers ◽  
Song Li ◽  
Ruth Grene ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Systems Biology ◽  
Signal Transduction Pathways ◽  
Graphical Notation

scholarly journals Systems Biology Graphical Notation: Process Description language Level 1

2010 ◽  
Author(s):  
Stuart Moodie ◽  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Falk Schreiber
Keyword(s):  
Systems Biology ◽  
Description Language ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1

E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria

2016 ◽  
pp. 316-322 ◽  
Author(s):  
Matej Troják ◽  
David Šafránek ◽  
Jakub Hrabec ◽  
Jakub Šalagovič ◽  
Františka Romanovská ◽  
...  
Keyword(s):  
Systems Biology ◽  
Web Based

scholarly journals MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 288
Author(s):  
Julia Koblitz ◽  
Dietmar Schomburg ◽  
Meina Neumann-Schaal
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Metabolic Pathways ◽  
Common Knowledge ◽  
Numerical Data ◽  
Omics Data ◽  
Web Based ◽  
Ongoing Research ◽  
Complex Interactions ◽  
Biology Research

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

scholarly journals Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)

2011 ◽  
Author(s):  
Nicolas Le Novere ◽  
Emek Demir ◽  
Huaiyu Mi ◽  
Stuart Moodie ◽  
Alice Villeger
Keyword(s):  
Systems Biology ◽  
Graphical Notation ◽  
Language Level ◽  
Level 1 ◽  
Entity Relationship

scholarly journals Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

2015 ◽  
Vol 12 (2) ◽  
pp. 340-381 ◽  
Author(s):  
Huaiyu Mi ◽  
Falk Schreiber ◽  
Stuart Moodie ◽  
Tobias Czauderna ◽  
Emek Demir ◽  
...  
Keyword(s):  
Systems Biology ◽  
Biological Activities ◽  
Negative Influence ◽  
Positive Influence ◽  
Binding Activity ◽  
Biological Knowledge ◽  
Protein Kinase Activity ◽  
Graphical Notation ◽  
Biochemical Systems ◽  
Entity Relationship

Summary The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

scholarly journals Systems Biology Graphical Notation: Process Diagram Level 1

2008 ◽  
Author(s):  
Nicolas Le Novere ◽  
Stuart Moodie ◽  
Anatoly Sorokin ◽  
Michael Hucka ◽  
Falk Schreiber ◽  
...  
Keyword(s):  
Systems Biology ◽  
Graphical Notation ◽  
Level 1
Sign in / Sign up

Export Citation Format

Share Document