sbos logo Version 0. 4. 5

 

SB.OS is a Linux live DVD designed to meet the needs of systems biologists. It features an up-to-date collection of free software tools and Systems Biology models installed in a Linux environment; the focus is on tools that support SBML (Systems Biology Markup Language). SB.OS allows beginners to get an impression of Systems Biology software without having to install them permanently while providing experts with a collection of useful modeling tools for testing and demonstration. It is based on the popular Linux distribution Ubuntu 10.04 and ready to use for all non-commercial purposes.

At www.sbos.eu, you can find even more information on SB.OS as well as the most recent version for download. We try to permanently improve SB.OS; if you can suggest improvements or software tools yet to be included, please contact us.

Topics on this page

 

List of software

In addition to standard Linux software, this DVD (SB.OS version 0. 4. 5) contains the tools and libraries for Systems Biology listed below. Most of them are stand-alone applications and can be started from the taskbar menu "Applications", field "Systems Biology". Please find detailed information at the software description.

Systems Biology

     
docu
www
video
binom logo
  BiNoM
(Cytoscape Plug-in)
documentation
home page
 
biomodels logo
  BioModels Database
documentation
home page
BioNetGen logo
  BioNetGen
documentation
home page
  BooleanNet
documentation
home page
celldesigner logo
  CellDesigner
documentation
home page
video tutorial
copasi logo
  COPASI
documentation
home page
video tutorialvideo tutorial
cytoscape logo
  Cytoscape
documentation
home page
video tutorial
EdinburghPathwayEditor logo
  EdinburghPathwayEditor
documentation
home page
video tutorial video tutorial
generalEditorOperations parenting propertyOutlineView
validateMap exportToImage
Graphviz logo
  Graphviz
documentation
home page
ISAinfrastructure logo
  ISAinfrastructure
home page
sbml logo
  JSim
home page
sbml logo
  libSBML
documentation
home page
ModelMage logo
  ModelMage
documentation
home page
 
openalea logo
  OpenAlea
documentation
home page
Protege logo
  Protégé
home page
PySCeS logo
  PySCeS
documentation
home page
sbmleditor logo
  SBMLeditor  
home page
 
sbmlsqueezer logo
  SBMLsqueezer
(Cell Designer Plug-in)
 
home page
 
sbml2latex logo
  SBML2LaTeX
documentation
home page
 
SBW logo
  SBW  
logo
  semanticSBML
documentation
home page
SQUAD logo
  SQUAD
documentation
home page
taverna logo
  Taverna
documentation
home page
video tutorialvideo tutorialvideo tutorial
sbml logo
  TIde
documentation
home page
 



→ Software Description




Other software

    gtk RecordMyDesktop
   
    PySces
   
python logo
  Python, IPython
documentation
    -R
   
    SciPy
   
    XML Copy Editor
   

Culture

star wars logo
  Star Wars: the classic movie in ASCII quality, online via telnet from towel.blinkenlights.nl (desktop menu "Games")

 

SBML

SBML is the most common exchange format for mathematical models in Systems Biology. It is based on XML and supported by a variety of software tools. Here is some advice for getting started:
  1. A variety of example models are contained in SB.OS. Models from the BioModels Database are stored in the directory /opt/Models/BioModels/curated. A large-scale model of yeast metabolism can be found in /opt/Models/YeastNet.
  2. A comprehensive list of tools supporting SBML is provided by the SBML software guide.
  3. The easiest way to check SBML files for syntactic correctness is to use the online SBML validator at www.sbml.org.
  4. Detailed documentation on SBML is available at www.sbml.org.
  5. The specification of SBML Level 2 Version 4 can be found here.

 

Introduction to kinetic modelling

systems biology a textbook systems biology in practice Test chapters of the book 'System Biology' can be found here and are available as pdf files. Beside the introduction to modelling, the chapter to 'kinetic modelling' offers a good possibility to get used with the subject.

Go to the example chapters page.

 

 

 

 

Video Tutorials

Axel Kowald prepared some video tutorials for the books "Systems Biology in Practice: Concepts, Implementation and Application" and "Systems Biology - A Textbook" of which he is coauthor. The video tutorials show the usage of COPASI and CellDesigner.

Go to the video tutorials page.

 

How to access files and directories on your hard disk


screenshot mount drive start menue

opening a mounted drive in semanticSBMLSB.OS (Version 0. 4. 5) creates a non-permanent user account (user name "ubuntu"), and all data that you write to the user's home directory (/home/ubuntu) will get lost after the end of the session.

If you want to store your results permanently, you need to write them to a hard drive or to a USB stick. To access your disk, click the "Places" menu in the top panel and select your hard disk (see screenshot on the right). This will mount your hard disk (i.e., create a link to it) in the directory /media/. You can now access your data in any application by navigating to your mounted disk (see the screenshot on the left).
In this way, you can access and modify all the data you have on your computer (hard drive or USB stick). Please be aware that by writing or deleting existing files, you may permanently damage your system. Ubuntu 9.10 can also read and write Windows formatted (NTFS, FAT32, FAT16) disks.

 

SB.OS Team

team

 

Theoretical Biophysics logo Humboldt-Universität zu Berlin logo SB.OS is compiled at Edda Klipp's Theoretical Biophysics Group, Humboldt University Berlin, by Ivo Maintz, Wolfram Liebermeister, Falko Krause, Marvin Schulz, and Jannis Uhlendorf.
We cordially thank the SBML community and all developers of the featured software tools, as well as Axel Kowald, the author of the video tutorials.