Simulations and Networks Analyzer (Snazer)

Category Cross-Omics>Pathway Analysis/Tools

Abstract The Simulations and Networks Analyzer (Snazer) is a modular software tool designed to aid in the processes of visualizing and manipulating reactive models, as well as to share and interpret time-course data produced by 'stochastic simulators' or by any other means.

Snazer upgrades the viewer of the Beta Workbench (BetaWB) product (see G6G Abstract Number 20383) and interfaces its output format.

It loads ‘biological networks’ encoded in Systems Biology Markup Language (SBML) as well, and stores graph layouts in standard GraphML files (GraphML is an XML-based file format for graphs).

Moreover, it loads time-course data exported in comma separated values (CSV), compresses and prepares them for remote sharing and statistical processing.

To enhance interoperability, Snazer has been equipped with a public, Extensible Markup Language (XML)-based, schema to allow other tools both to encapsulate and structure their time-course data and to package their 'interaction networks'.

Snazer features/capabilities include:

1) Import from: 'Beta Workbench' output, CSV, SBML and (proprietary) XML file formats.

2) Export to: CSV, GraphML and (proprietary) XML file formats.

3) An interacting view of 'chemical reactive networks'.

4) Color auto-tuning for 'color-blind' users.

5) Node importance highlighting (degree distribution).

6) Custom and minimum information requested in the annotation of biochemical models (MIRIAM)-compliant annotation support.

7) Statistical analysis of simulated multi-traces.

8) The statistical outcome export is in the Support Vector Graphics (SVG) format.

Snazer currently offers five (5) layout algorithms:

1) Spring is the simplest 'force directed' layout algorithm. Edges between nodes are represented as springs with natural lengths. The energy of the system is minimized by iteratively arranging the nodes.

2) Kamada-Kawai is a force directed layout algorithm (KKLayout). It moves the nodes and changes the forces among them until the energy of the system is minimized. Nodes looks like steel rings and edges act as springs among them.

3) ISOM layout is based on a 'competitive learning algorithm'. It builds a sort of ‘elastic net’ where nodes coordinates depend on their connections weights. Its main advantages are flexibility and adaptability to arbitrary visualization spaces.

4) Fruchterman-Reingold algorithm (FRLayout) works on unweighted, undirected graphs. It is a force-directed algorithm as well.

Attractive forces result only among adjacent vertices, and repulsions occur between every pair of vertices. Each iteration computes the sum of the forces on each vertex, and then moves the vertices to their new positions.

5) Circle is the most simple layout algorithm. Each vertex is evenly spaced on a circular trajectory. It does Not undergo sequential arrangement since it is a static layout.

Snazer performs analyses by means of analyzers --

Series - Series produces time series as output, one for each selected statistics for each selected species.

The available statistics are: mean, root mean square, variance, standard deviation, standard error, geometric mean, harmonic mean, skew and kurtosis (i.e., if an user ask for the mean value of molecule, the output will be a time series representing the mean value across all runs, for the duration of the simulation).

First hitting - This analyzer calculates the same statistics as Series, but the samples, instead of being extracted from each run at each timestamp, are taken from each run at the 'first instant' when the specified State Set is verified.

Pointwise - This analyzer is similar to Series, but the sampling is performed at regular user-specified intervals, rather than at each timestamp.

Steady state - This analyzer calculates the same statistics as Series, but the samples are chosen randomly for each run, in a time interval specified by the user (usually, between a 'depolarization time' and the end of the data source).

Cumulative - This analyzer measures the cumulative value of a species, in time intervals that are specified by a State Set.

Time - This analyzer allows you to inspect the time intervals duration.

Raw data - This analyzer simply copies and plot values from the data source to the chart (graph).

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G6G Abstract Number 20384

G6G Manufacturer Number 104021