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<!DOCTYPE html>
<html lang="en">
<head>
<title>de.NBI-ModSim</title>
<meta charset="utf-8">
<meta name="author" content="Frank T. Bergmann">
<meta name="keywords" content="copasi,cna,cellnetanalyzer,de.NBI-ModSim,de.NBI-ModSim2,de.NBI">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<link href="https://fonts.googleapis.com/css?family=Montserrat" rel="stylesheet" type="text/css">
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<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<style>
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color: #fff !important;
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.navbar-nav li.active a {
color: #1CABDA !important;
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</style>
</head>
<body id="myPage" data-spy="scroll" data-target=".navbar" data-offset="60">
<nav class="navbar navbar-default navbar-fixed-top navbar-expand-lg navbar-light bg-light">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#myNavbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand hidden-sm" href="#myPage">de.NBI ModSim</a>
</div>
<div class="collapse navbar-collapse" id="myNavbar">
<ul class="nav navbar-nav">
<li class="hidden-sm hidden-md"><a href="#about">ABOUT</a></li>
<li><a href="#events">EVENTS</a></li>
<li><a href="#copasi">COPASI</a></li>
<li><a href="#cna">CellNetAnalyzer</a></li>
<li><a href="#screen">SCREEN SHOTS</a></li>
<li><a href="#contact">Contact</a></li>
</ul>
</div>
</div>
</nav>
<div class="jumbotron text-center">
<h1>de.NBI ModSim</h1>
<p>Resources, Services and Developments for Systems Biology Modeling</p>
<p>Partner project of the German Network for Bioinformatics Infrastructure (de.NBI)</p>
</div>
<!-- Container (About Section) -->
<div id="about" class="container-fluid">
<div class="row">
<div class="col-sm-8">
<h2>About de.NBI ModSim</h2><br>
<h4>Resources, Services and Developments for Systems Biology Modeling.</h4><br>
<p>de.NBI-ModSim is a partner project of de.NBI-SysBio node and has three major goals: </p>
<ol>
<li>Adding new resources to de.NBI: in particular, COPASI and CellNetAnalyzer, two complementary and
frequently used software packages for modeling biological networks and systems will be promoted by
de.NBI-ModSim.</li>
<li>Providing services: extended user support and organization of workshops and training courses on
mathematical modeling of biological systems including hands-on exercises with the software tools</li>
<li>de.NBI-relevant developments: for example, integration of COPASI and CellNetAnalyzer with existing
resources of de.NBI and make these tools compliant with model standardization and annotation schemes
propagated by the de.NBI-SysBio node. </li>
</ol>
<br><a href="http://www.denbi.de" target="_blank" class="btn btn-default btn-lg">More about de.NBI</a>
</div>
<div class="col-sm-4">
<div class="media">
<div class="media-right media-middle text-center img-responsive ">
<h2> </h2>
<img src="images/deNBI_logo.jpg" class="media-object center-block slideanim img-responsive" alt="de.NBI" />
</div>
</div>
</div>
</div>
</div>
<div id="events" class="container-fluid bg-grey">
<div class="row">
<div class="col-sm-4">
<span class="glyphicon glyphicon-globe logo slideanim"></span>
</div>
<div class="col-sm-8">
<h2>Events</h2><br>
<p> The following events are scheduled for 2024:</p>
<ul>
<li><span style="font-weight:bold;">5. - 6. Nov, 2024 (2p-6p CET / UTC +1):
</span> 2-day Virtual Workshop (1): CellNetAnalyzer / CNApy
<a href="http://denbi-modsim.de/workshop_2024/cna/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/e/1FAIpQLSexoWIrjLPNudaq9MXMHkc4NuxgwXDMmoiiiEj-9seX0Kw1DQ/viewform?vc=0&c=0&w=1&flr=0&usp=mail_form_link" target="_blank">registration</a>
</li>
<li><span style="font-weight:bold;">19. - 20. Nov, 2024 (9a-12p CET / UTC +1):
</span> 2-day Virtual Workshop (2): COPASI
<a href="http://denbi-modsim.de/workshop_2024/copasi/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/e/1FAIpQLSeEgdDiZVQsfwN05RBXxCqLgJWpCQDyVYdKxZp3v799wQV0dA/viewform?usp=sf_link" target="_blank">registration</a>
</li>
<li><span style="font-weight:bold;">25. - 26. Nov, 2024 (2p-6p CET / UTC +1):
</span> 2-day Virtual Workshop (3): SABIO-RK / SEEK
<a href="http://denbi-modsim.de/workshop_2024/hits/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/1vupBcgBWe02_OOYCDzKQfNuBDtl2_Rkz-qam8JMpqPM" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2023:</p>
<ul>
<li><span style="font-weight:bold;">28. - 30. Nov, 2023:
</span> 3-day virtual workshop (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_11-2023/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/e/1FAIpQLScBXS1LfcZhcO8l2zD0jK7shs-It2_JO8HCde6vyqJ070OaMQ/viewform?usp=sf_link" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2022:</p>
<ul>
<li><span style="font-weight:bold;">9. - 11. Aug, 2022:
</span> 3-day virtual workshop (with
COPASI, CellNetAnalyzer and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_08-2022/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/e/1FAIpQLSdSA314ZWw4F5wRyvXXcHc0euwx7OHODIaBj--lV-T_qRdTNA/viewform?usp=sf_link" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2021:</p>
<ul>
<li><span style="font-weight:bold;">20. - 22. Apr, 2021:
</span> 3-day virtual workshop (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_2021/" target="_blank">more information</a> |
<a href="https://docs.google.com/forms/d/e/1FAIpQLSc0sHUUqageFqAcbasSmDwmO3SvRKVEUskLJGHuUDzSHtNC_g/viewform" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2020:</p>
<ul>
<li><span style="font-weight:bold;">21. - 23. Sep, 2020:
</span> 3-day virtual workshop (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_09-2020/" target="_blank">more information</a> |
<a href="https://forms.gle/VRi97qKQ7gWWSCxb9" target="_blank">registration</a>
</li>
<li>CANCELLED <del> <span style="font-weight:bold;">27. - 29. April, 2020:
</span> 3-day workshop in Magdeburg (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_2020/" target="_blank">more information</a>
</del>
</li>
</ul>
<p> The following events are scheduled for 2019:</p>
<ul>
<li><span style="font-weight:bold;">31. Oct, 2019: </span> Advanced modeling with COPASI
<a href="http://denbi-modsim.de/icsb_copasi_2019/" target="_blank">more information</a> | <a
href="https://forms.gle/NepBmMjrXmTzuCpy9" target="_blank">registration</a>
</li>
<li><span style="font-weight:bold;">15. Okt, 2019: </span> Analyzing and redesigning metabolic networks with
CellNetAnalyzer - FOSBE <a
href="https://www.denbi.de/training/677-analyzing-and-redesigning-metabolic-networks-with-cellnetanalyzer"
target="_blank">more information</a> </li>
<li><span style="font-weight:bold;">12. Aug, 2019: </span> Analyzing metabolic networks with CellNetAnalyzer -
MPA <a href="https://www.denbi.de/training/630-analyzing-metabolic-networks-with-cellnetanalyzer-mpa"
target="_blank">more information</a> </li>
<li><span style="font-weight:bold;">18. - 20. Mar, 2019: </span> 3-day workshop in Heidelberg (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_2019/" target="_blank">more information</a> | <a
href="https://goo.gl/forms/6UNvjb7Amf0aZGmT2" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2018:</p>
<ul>
<li><span style="font-weight:bold;">27. Oct, 2018: </span> Advanced modeling with COPASI
<a href="http://denbi-modsim.de/icsb_copasi_2018/" target="_blank">more information</a> | <a
href="https://goo.gl/forms/BDLwkCyLwoHlj59P2" target="_blank">registration</a>
</li>
<li><span style="font-weight:bold;">27. Oct, 2018: </span> COMBINE & de.NBI Tutorial: Modelling and Simulation
Tools in Systems Biology
<a href="http://co.mbine.org/events/tutorial2018" target="_blank">more information</a>
</li>
<li><span style="font-weight:bold;">24. - 26. Apr, 2018: </span> 3-day workshop in Magdeburg (with
CellNetAnalyzer, COPASI and SABIO RK hands-on exercises)
<a href="http://denbi-modsim.de/workshop_2018/" target="_blank">more information</a> | <a
href="https://goo.gl/forms/8iUxUnNZrpkoaDKE2" target="_blank">registration</a>
</li>
</ul>
<p> The following events are scheduled for 2017:</p>
<ul>
<li><span style="font-weight:bold;">12. / 13. September, 2017: </span> 2-days workshop (with COPASI and
CellNetAnalyzer hands-on exercises)
<a href="http://denbi-modsim.de/workshop_2017/" target="_blank">more information</a>
</li>
<li><span style="font-weight:bold;">August 6, 2017:</span>joint COMBINE Tutorial ICSB 2017 (Blacksburg, VA) <a
href="http://www.denbi.de/22-training-cat/training-courses/351-icsb2017" target="_blank">more
information</a></li>
<li><span style="font-weight:bold;">August 7, 2017:</span>Advanced COPASI Tutorial at ICSB 2017 (Blacksburg,
VA)</li>
</ul>
</div>
</div>
</div>
<!-- Container (COPASI Section) -->
<div id="copasi" class="container-fluid text-left">
<h2>COPASI</h2>
<h4>COPASI is a software tool for editing, simulating, and analyzing models of biochemical reaction networks. COPASI
is available
for all major platforms (Linux, Windows, OS X), easy to install COPASI is free and open source software.
</h4>
<p>
<a href="http://www.copasi.org" target="_blank" class="btn btn-default btn-lg">COPASI Website</a>
<a href="https://groups.google.com/forum/#!forum/copasi-user-forum" target="_blank"
class="btn btn-default btn-lg">User Forum</a>
</p>
<br />
<ul class="nav nav-tabs">
<li class="active"><a data-toggle="tab" href="#features">Features</a></li>
<li><a data-toggle="tab" href="#usage">Usage</a></li>
<li><a data-toggle="tab" href="#support">Support & Training</a></li>
</ul>
<div class="tab-content well">
<div id="features" class="tab-pane fade in active">
<h3>Features</h3>
<ul>
<li>ODE-based and stochastic formalisms</li>
<li>Sensitivity analyses</li>
<li>Optimization and parameter estimation</li>
<li>Computation of stable states and properties of nonlinear, dynamical systems, e.g. Lyapunov exponents</li>
<li>Hybrid simulation methods</li>
<li>Model reduction techniques</li>
<li>Further properties:</li>
<li>COPASI is SBML compatible</li>
<li>Standards, e.g. for model annotations are implemented</li>
</ul>
<p> A <a href="http://copasi.org/Support/Features/" target="_blank"> complete list of features </a> is available
on the COPASI website. </p>
</div>
<div id="usage" class="tab-pane fade">
<h3>Usage of COPASI - global view</h3>
<img alt="COPASI - global usage map" src="images/usage_copasi_global.jpg" class="img-responsive" />
<p>Note: only approx. 30% of the publications,
having used COPASI have been included so far.
For more information see <a href="http://copasi.org/Research/Map/" target="_blank"> the live page </a>.
</p>
</div>
<div id="support" class="tab-pane fade">
<h3>Support</h3>
<ul>
<li><a href="https://groups.google.com/forum/#!forum/copasi-user-forum" target="_blank"> COPASI User Forum
</a> for feedback from developers and the community. </li>
<li><a href="http://tracker.copasi.org" target="_blank"> COPASI Bug Tracker </a> to file feature requests.
</li>
</ul>
<h3>Training</h3>
<ul>
<li><a href="http://copasi.org/Support/Video_Tutorials/" target="_blank"> Online Video Tutorials </a> </li>
<li><a href="https://www.youtube.com/user/CopasiTutorials" target="_blank"> COPASI Youtube Channel </a> </li>
<li><a href="http://copasi.org/Events/" target="_blank"> COPASI Training Events </a> </li>
</ul>
</div>
</div>
<br>
</div>
<!-- Container (CellNetAnalyzer Section) -->
<div id="cna" class="container-fluid text-left bg-grey">
<h2>CellNetAnalyzer</h2>
<h4>CellNetAnalyzer (CNA) is a MATLAB toolbox providing a graphical user interface and various (partially unique)
computational methods and algorithms for exploring structural and functional properties of metabolic, signaling,
and regulatory networks.
</h4>
<p>
<a href="https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html" target="_blank"
class="btn btn-default btn-lg">CNA Website</a>
<a href="https://groups.google.com/forum/#!forum/cellnetanalyzer-user-forum" target="_blank"
class="btn btn-default btn-lg">User Forum</a>
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<li class="active"><a data-toggle="tab" href="#features_cna">Features</a></li>
<li><a data-toggle="tab" href="#usage_cna">Usage</a></li>
<li><a data-toggle="tab" href="#support_cna">Support & Training</a></li>
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<div id="features_cna" class="tab-pane fade in active">
<h3>Features</h3>
<p>Numerous methods and algorithms from stoichiometric and constraint-based modeling:</p>
<ul>
<li>conservation relations</li>
<li>metabolic flux analysis</li>
<li>flux balance analysis (FBA) / flux optimization</li>
<li>flux variability analysis</li>
<li>elementary-modes and pathway analysis</li>
<li>minimal cut sets (design/redesign of metabolic networks)</li>
<li>SBML import / export</li>
</ul>
<p>Support for influence graphs / boolean networks including :</p>
<ul>
<li>logical steady-sate analysis (qualitative I/O behvaior)</li>
<li>minimal intervention sets</li>
<li>feedback loops and signaling paths</li>
<li>global interdependency of species</li>
<li>data-driven inference of signaling network toplogies</li>
<li>simulation of logic-based ODEs (ODEfy)</li>
<li>Support of the SBML Level 3 Qual extension</li>
</ul>
<p> for a <a href="http://www2.mpi-magdeburg.mpg.de/projects/cna/description.html" target="_blank"> detailed
description </a> of CellNetAnalyzer's
capabilities please see the CNA website. </p>
</div>
<div id="usage_cna" class="tab-pane fade">
<h3>Usage of CellNetAnalyzer - global view</h3>
<img alt="CellNetAnalyzer - global usage map" src="images/usage_cna_global.jpg" class="img-responsive" />
</div>
<div id="support_cna" class="tab-pane fade">
<h3>Support</h3>
<ul>
<li><a href="https://groups.google.com/forum/#!forum/cellnetanalyzer-user-forum" target="_blank"> CNA User
Forum </a> for feedback from developers and the community. </li>
</ul>
<h3>Training</h3>
<ul>
<li><a href="http://www2.mpi-magdeburg.mpg.de/projects/cna/description.html" target="_blank"> Detailed
Description </a> </li>
<li><a href="http://www2.mpi-magdeburg.mpg.de/projects/cna/manual_cellnetanalyzer.pdf" target="_blank"> Manual
</a> </li>
<li><a href="http://www2.mpi-magdeburg.mpg.de/projects/cna/CNA_tutorial.pdf" target="_blank"> Tutorial </a>
</li>
<li><a href="https://www.youtube.com/playlist?list=PLvcqZyZHMRRR7ZUg0_yyFKMK5VJLB4Cj1" target="_blank"> Videos
on Youtube</a> </li>
</ul>
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<h2>Screen Shots</h2><br>
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<p>Model overview / time course simulation in COPASI</p>
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<img alt="constraint-based modelling in CellNetAnalyzer" src="images/metnet.gif"
class="img-responsive center-block" />
<p>stoichiometric / constraint-based modelling in CellNetAnalyzer</p>
</div>
<div class="item">
<img alt="influence graphs / boolean networks in CellNetAnalyzer" src="images/signet_egf.gif"
class="img-responsive center-block" />
<p>influence graphs / boolean networks in CellNetAnalyzer</p>
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<h2>Contact</h2>
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<p><a href="http://www.cos.uni-heidelberg.de/index.php/u.kummer?l=_e" target="_blank">Prof Dr. Ursula Kummer</a>
</p>
<p>INF 267<br />69120 Heidelberg<br /><br /></p>
<p>ursula.kummer @ bioquant.uni-heidelberg.de</p>
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<p><a href="http://www.mpi-magdeburg.mpg.de/klamt" target="_blank">Steffen Klamt</a></p>
<p>Max Planck Institute for Dynamics of Complex Technical Systems<br />Sandtorstr. 1<br />D-39106 Magdeburg
Germany</p>
<p>klamt @ mpi-magdeburg.mpg.de
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