SB.OS / Systems Biology Operational Software

bootable_dvd

Anonymous (anonymous@undisclosed.example.com) — 2011-09-16T21:24:30+00:00

Creating a Bootable DVD / USB Stick You can run SB.OS on your computer without having to install anything. To create a bootable DVD just burn the disk image with your favourite burning software to a DVD. To create a bootable USB stick use UNetbootin together with our disk image. All you have to do now is to change the boot device of your computer to first boot from your DVD drive (this is the default on most computers) or to USB. Insert the DVD/USB stick and boot your computer.

changelog_german

Anonymous (anonymous@undisclosed.example.com) — 2011-10-26T10:57:04+00:00

0.6 in Arbeit * Basis ist Xubuntu natty * (erstmal) nur 64bit * Umstieg auf xfce4 als Desktop Environment, da unity kein ordentliches Menü hat, sich schlecht bedienen läßt, viele Bugs hat und für große Bildschirme ungeeignet ist. * Image liegt

installation_instructions

Anonymous (anonymous@undisclosed.example.com) — 2018-11-26T13:34:14+00:00

Installing SB.OS on your computer You can install SB.OS permanently on your computer: to do so, follow the instructions while SB.OS is booting. If you are going to install SB.OS beside an existing operating system, we recommend to prepare security backups of all critical data, even though the installer can resize partitions. You'll need at least 18,5

link_collection

Anonymous (anonymous@undisclosed.example.com) — 2010-05-07T08:18:07+00:00

Link collection The collected links will be included as browser bookmarks in future versions of SB.OS. General Systems Biology Graphical Notation (SBGN) Templates (use this to standardize your graphical network models) Wikipedia Social Network: myExperiment makes it easy to find, use and share scientific workflows and other Research Objects

logo

Anonymous (anonymous@undisclosed.example.com) — 2009-06-03T11:39:05+00:00

svg sb.os.svg png large png small

menu1

Anonymous (anonymous@undisclosed.example.com) — 2021-09-17T14:42:25+00:00

home news download contribute internal

menu2

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T11:24:49+00:00

* Software * Included on DVD (v1.0) * Available in repo (v1.0) * About SB.OS * Documentation (v 0.5) * SB.OS Team * Logo * Links * SBML * BioLinux * Klipp group TBP * Link collection

news

Anonymous (anonymous@undisclosed.example.com) — 2021-09-17T14:48:50+00:00

17.09.2021 Fixed the download link in the menu. Currently based on (x)ubuntu 20.04 LTS (SB.OS 1.4.2). 02.03.2018 Just updated this site and added separate software lists for Python 2, Python 3 and R packages, for better overview 05.05.2016 The base of SB.

sbos_team

Anonymous (anonymous@undisclosed.example.com) — 2011-10-04T13:57:55+00:00

SB.OS is compiled and maintained by Ivo Maintz, Wolfram Liebermeister, Falko Krause, Marvin Schulz at Theoretical Biophysics, Humboldt University Berlin and Institute of Biochemistry, Charite - Universitätsmedizin Berlin. The picture also shows Jannis Uhlendorf (now at INRIA Paris-Rocquencourt).

screenshots

Anonymous (anonymous@undisclosed.example.com) — 2010-03-18T10:32:03+00:00

software_exclude

Anonymous (anonymous@undisclosed.example.com) — 2009-09-10T09:06:45+00:00

Exclude Software We will not and can not include commercial software. To make it clear we will not include * Matlab, or any Matlab packages (???, uses xppaut) cannot be compiled anymore

software_full1.0

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T11:08:57+00:00

Python 2 packages Python 3 packages R packages antimony 2.9.4-1 ash 0.5.9.1-1 behaviorsearch 6.0.2-1 bfg 1.12.14-1 binom 2.5-1 bioformats-java 1.3.2-1 biomodels 31-1 biomodels-non-curated 31-1 bionetgen 2.2.6-1 bower 1.7.9-1 budgie-core 10.2.9-2 budgie-desktop 10.2.9-2 cain 1.10+dfsg-2

software_included

Anonymous (anonymous@undisclosed.example.com) — 2018-02-21T14:22:29+00:00

Systems Biology Software * CellDesigner 4.4 (including plugin SBMLsqueezer 1.1) * COPASI 4.22.171 * semanticSBML 1.1.0 * Xppaut 8.0.0 * Cytoscape 2.8.4 (including plugin BiNoM) * Cytoscape 3.6.0 * SBMLeditor * SBML2LaTeX * libSBML 5.16.0

software_included0.3.3

Anonymous (anonymous@undisclosed.example.com) — 2009-07-09T07:54:42+00:00

Systems Biology Software * CellDesigner 4.0.1 * COPASI 4.4.29 * semanticSBML 1.0.7 * Xppaut 5.98 * TiDE * libSBML 3.3.2 Systems Biology Models * BioModels Database Convenience Tools * gtk-recordMyDesktop * XML Copy Editor 1.2.0.2

software_included0.3.4

Anonymous (anonymous@undisclosed.example.com) — 2009-07-09T07:42:23+00:00

Systems Biology Software * CellDesigner 4.0.1 (including plugin SBMLsqueezer 1.1) * COPASI 4.4.29 * semanticSBML 1.0.8 * Xppaut 5.98 * TiDE * Cytoscape 2.6.2 (including plugin BiNoM) * SBMLeditor * SBML2LaTeX * OpenAlea * libSBML 3.3.2

software_included0.3.5

Anonymous (anonymous@undisclosed.example.com) — 2009-11-13T10:30:04+00:00

software_included0.4.3

Anonymous (anonymous@undisclosed.example.com) — 2010-06-22T13:12:33+00:00

Systems Biology Software * CellDesigner 4.0.1 (including plugin SBMLsqueezer 1.3) * COPASI 4.5.30 * Cytoscape 2.6.3 (including plugin BiNoM) * Edinburgh Pathway Editor 1.3.0 * ISATools 1.1 * libSBML 3.4.1 * modelMage 1.0beta * OpenAlea

software_included0.4.6

Anonymous (anonymous@undisclosed.example.com) — 2010-08-24T12:50:25+00:00

Systems Biology Software * BioNetGen 2.1.5 * CellDesigner 4.1beta (including plugin SBMLsqueezer 1.3) * COPASI 4.5.30 with java and python bindings * Cytoscape 2.6.3 (including plugin BiNoM 1) * Edinburgh Pathway Editor 1.3.0 * Ekee 2.0.2

software_included0.5

Anonymous (anonymous@undisclosed.example.com) — 2011-03-01T14:55:41+00:00

Systems Biology Software * BioNetGen 2.1.5 * Cain 1.5 * CellDesigner 4.1 (including plugin SBMLsqueezer 1.3) * COPASI 4.5.30 with java and python bindings * Cytoscape 2.8.1 (including plugin BiNoM 1) * Edinburgh Pathway Editor 3.0.0 * Ekee 2.0.2

software_included1.0

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T09:26:00+00:00

antimony 2.9.4 binom 2.5-1 biomodels 31 bionetgen 2.3.1 cain 1.10 celldesigner 4.4 cellid 1.4.6 cellprofiler 3.0.0rc7 cobra-toolbox 2.0.6.1 coot 0.8.7 copasi 4.21.166 cytoscape3 3.6.0 fenics3 1:2017.1.0.1 fiji 20180214 jupyter 1.0.0 jupyter-qtconsole 4.3.0

software_javascript

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T11:22:53+00:00

libjs-backbone 1.3.3~dfsg-1 libjs-d3-format 1.2.0-1 libjs-es6-promise 3.2.2+ds-1 libjs-html2canvas 0.5.0~beta4+ds1-2 libjs-jed 1.1.1-1 libjs-jquery-typeahead 2.10.1+dfsg1-1 libjs-jquery-ui 1.12.1+dfsg-3 libjs-moment 2.18.1+ds-1 libjs-preact 8.2.5-1

software_pending

Anonymous (anonymous@undisclosed.example.com) — 2011-09-28T21:44:08+00:00

Software higher priority FASIMU for flux balance analysis Software lower priority * SBRML lib (.NET based needs Mono) * SBGN: Arcadia (completly untested ) * Javasim () ??? * E-cell System * SBML ODE Solver (Christoph Flamm University of Vienna, Austria

software_python2

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T11:10:53+00:00

antimony 2.9.4-1 anytree 2.4.3-1 assimulo 2.9-1 autopep8 1.3.3-1 backports-abc 0.5-1 backports.functools-lru-cache 1.4-1 backports-shutil-get-terminal-size 1.0.0-1 backports.ssl-match-hostname 3.5.0.1-1 bioformats 1.3.2-1 biomart 0.9.0-1 bioservices 1.5.1-1

software_python3

Anonymous (anonymous@undisclosed.example.com) — 2018-03-02T11:13:18+00:00

antimony 2.9.4-1 anytree 2.4.3-1 assimulo 2.9-1 autopep8 1.3.3-1 bioformats 1.3.2-1 biomart 0.9.0-1 bioservices 1.5.1-1 bokeh 0.12.13-1 bottleneck 1.2.1-1 cachey 0.1.1-1 cellh5 1.3.0-1 certifi 2017.11.5-1 click-configfile 0.2.3-1 click-log 0.1.8-1

start

Anonymous (anonymous@undisclosed.example.com) — 2021-05-19T13:39:59+00:00

[SB.OS logo] Welcome to SB.OS - Systems Biology Operational Software SB.OS is a live DVD based on Ubuntu Linux that comes with a comprehensive selection of Systems Biology Software. Text and video documentation material, as well as an offline copy of BioModels Database, the largest repository of SBML models, are included.

stats

Anonymous (anonymous@undisclosed.example.com) — 2009-06-03T12:08:05+00:00

nb of pages: pagesize