Tag: SVG

GenomeD3Plot – SVG based Genome Viewer written in Javascript using D3

GenomeD3Plot

:: DESCRIPTION

GenomeD3Plot (formerly Islandplot) is an SVG based genome viewer written in javascript using D3

::DEVELOPER

Brinkman lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • javascript

:: DOWNLOAD

GenomeD3Plot

:: MORE INFORMATION

Citation:

GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications.
Laird MR, Langille MG, Brinkman FS.
Bioinformatics. 2015 Jun 20. pii: btv376.

SVGenes 0.4.1 -SVG Format Genome Browser Style Pictures

SVGenes 0.4.1

:: DESCRIPTION

SVGenes (bio-svgenes) is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface.

::DEVELOPER

Team MacLean – Bioinformatics @ The Sainsbury Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Ruby
  • BioRuby

:: DOWNLOAD

 SVGenes

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1890-2. doi: 10.1093/bioinformatics/btt294. Epub 2013 Jun 6.
SVGenes: a library for rendering genomic features in scalable vector graphic format.
Etherington GJ1, MacLean D.

BioSVG 0.02 – Generate Scalable Vector Graphics (SVG) data for Biological objects

BioSVG 0.02

:: DESCRIPTION

 BioSVG is a Perl framework to generate Scalable Vector Graphics (SVG) data for biological objects.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

   BioSVG

:: MORE INFORMATION

 

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net