Workshop: Multi-Scale Modeling in Computational Neuroscience with GENESIS 3


3 - 8 September 2012, Universität zu Lübeck

Workshop Goals and Contents

As the field of computational neuroscience continues to mature, it is clear that understanding the nervous system from a computational point of view will require modeling at multiple levels of scale from sub-cellular to systems and behaviour.

This hands-on workshop will consider both issues and techniques involved in modeling nervous systems at single levels of scale as well as the opportunities for scientific discovery when models at different levels of scale are linked. With a strong emphasis on hands-on experience, the workshop will also include lectures focused on multi-scale modeling. It is designed for advanced graduate students, postdoctoral fellows or faculty interested in the practical application and development of multi-scale modeling techniques.

Although participants may choose another simulator for use in their modeling projects, this workshop will also introduce and provide an opportunity to explore the unique capabilities of GENESIS 3 (G3) for multi-scale modeling.






Model of a Purkinje cell from the cerebellum made with GENESIS by Erik de Schutter and James Bower

The international faculty include:

  • Dr. James M. Bower (University of Texas System) who has been involved in the development of software tools for multi-scale modeling for 30 years.
  • Dr. David Beeman (University of Colorado) who has supported multi-scale modeling both as an instructor in numerous international courses in computational biology as well as in his role as director of the GENESIS users group.
  • Dr. Avrama Blackwell (George Mason University) whose modeling and experimental expertise involves the investigation of molecular synaptic mechanisms.
  • Dr. Hugo Cornelis (University of Texas) who is a lead GENESIS developer with expertise both in the design and construction of multi-scale simulation systems as well as modeling at single cell and network levels.
  • Dr. Volker Steuber (University of Hertfordshire) with expertise in single cell, network and systems level analysis.
  • Dr. Mando Rodriguez (University of Texas San Antonio), an expert in interface design and interoperability in simulation systems.
The G-3 network viewer is typical of the Python visualization tools that will be used and developed during the workshop. Here it displays a frame from the animation of a layer 4 auditory cortex simulation, showing a propagating wave of excitation that follows a tone burst.


GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components.

Now it has been completely re-implemented as GENESIS 3 (G-3) in a modular framework, the CBI architecture. G-3 is particularly well suited for creating simulations that span multiple levels of scale and that interact with other simulators, databases, or visualization and analysis tools.


For further information please click the following links



Workshop Schedule

  • Monday, 3 September - Friday, 7 September, 9:00 - 18:00
  • Saturday, 8 September, 10:00-14:00
  • Wednesday, 5 September: conference dinner
  • Please click to view the detailed program!


Lübeck, close to the baltic sea and surrounded by rivers and waterways, is an attractive world heritage city with a small vibrant university focused on research and teaching at the interface of medicine and computing. The workshop will take place on campus.

How to get to Lübeck:

Lübeck is well connected to the railway system and has an airport providing connections to London, Budapest, Pisa, Bergamo, Palma, Barcelona, Gdansk, Stockholm and Kiev. Additionally there is a shuttle bus (Traveliner) departing 10 times a day to and from Hamburg airport. Further details on local transport will be sent in the confirmation email. 



Our workshop welcomes applications of PhD students and postdoctoral researchers. Please note that basic programming knowledge is required. To apply please 

  • submit a short abstract stating your motivation and research topic.
  • Furthermore please give your affiliation and your degree.
  • Please note: Space is limited and will be distributed on a first come-first served basis. 
  • Registration fee: 100€ for PhD students/ 200€ for PostDocs and faculty, covering lunches and conference dinner
  • For application, please send an email containing the required information (see above) to gen3(at)
  • Please wait for confirmation before booking your travel. A list of recommended accommodations will be sent with your confirmation email.
  • Application deadline is August 15th, 2012. Please contact us for last minute application. There are still few places left!


Christoph Metzner, Institute for Robotics and Cognitive Systems

Daphne Krioneriti, Institute for Neuro- and Bioinformatics

Katja Dau, GS CMLS Events/ Career Service

Further questions? Please contact us