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The Systems Biology Markup Language (SBML) is a machine-readable language, based on XML, for representing models of biological processes. SBML can represent metabolic networks, cell-signaling pathways, regulatory networks, and many other kinds of systems.
SBML has three main purposes:
- enabling the use of multiple software tools without rewriting models for each tool;
- enabling models to be shared and published in a form other researchers can use even in a different software environment;
- ensuring the survival of models beyond the lifetime of the software used to create them.
SBML is not an attempt to define a universal language for quantitative models. SBML’s purpose is to serve as a lingua franca—an exchange format used by different present-day software tools to communicate the essential aspects of a computational model
Jmol is a molecule viewer. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The JmolApplet is a web browser applet that can be integrated into web pages, the Jmol application is a standalone Java application that runs on the desktop and the JmolViewer is a development tool kit that can be integrated into other Java applications.
- Free, open-source software licensed under the GNU Lesser General Public License
- Applet, Application, and Systems Integration Component
- Multi-language
- Cross-platform
- Supports all major web browsers…
- High-performance 3D rendering with no hardware requirements
- File formats (see also file formats section within Jmol Wiki):
- CIF/mmCIF – Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography
- CML – Chemical Markup Language
- CSF – Fujitsu CAChe chemical structure, now Fujitsu Sygress
- CTFile – Elsevier MDL chemical table
- GAMESS – General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University
- Gaussian 94/98/03 output – Gaussian, Inc.
- Ghemical
- HIN – HyperChem from Hypercube, Inc.
- Jaguar – Schrodinger, LLC
- MM1GP – Ghemical molecular mechanics
- MOL – Elsevier MDL structure
- MOLPRO – Molpro output
- MOPAC – MOPAC 93/97/2002 output (public domain)
- MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain)
- NWCHEM – NWChem output, Pacific Northwest National Laboratory
- odydata – Odyssey data, WaveFunction, Inc.
- PDB – Protein Data Bank, Research Collaboratory for Structural Bioinformatics
- QOUT – Q-Chem, Inc.
- SDF – Elsevier MDL structure
- SHELX – Structural Chemistry Department, University of Göttingen (Germany)
- SMOL – Spartan data, Wavefunction, Inc.
- spinput – Spartan data, Wavefunction, Inc.
- xodydata – Odyssey XML data, WaveFunction, Inc.
- XYZ – Minnesota Supercomputer Institute XMol file
- XYZ+vib – XYZ format files with added vibrational vector information
- XYZ-FAH – Folding@home XYZ file
- Animations
- Vibrations
- Basic support for unit cell and symmetry operations
- Schematic shapes for secondary structures in biomolecules
- Measurements
- Support for RasMol/Chime scripting language
- JavaScript support library
- Exports to .jpg, .png, .ppm, .pdf, and PovRay
- For more details, see the history of development.
  
Manual:
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