Success story: „Visionary with a caterpillar“

VIENNA, Austria, November 2011 - Henrik Quintel is a German graduate computer scientist with a vision: he has spent years of his free time working on a model that improves the understanding of brain disorders. He is supported in his ambitious and difficult task by the simulation software AMUSE from Viennese software producer LieberLieber.

In a personal discussion, Quintel very quickly outs himself as a fan of Vienna: “I actually came upon the idea for my project through the works of Sigmund Freud. He wanted to learn more about the conscious mind using psychological methods. I also make use of technical resources to learn more about the complex processes in the brain!” The aim of his project is to use a robot to present movement disorders caused by brain disorders, having previously simulated them on the computer with AMUSE.
The graduate computer scientist, whose main job is in software quality assurance, maintains close contact in this regard with the Bernstein Network in Germany. This association promotes the new discipline of “Computational Neuroscience”, in which biologists, physicians, psychologists, physicists, mathematicians and computer scientists work together. The interdisciplinary approach combines experimentation, data analysis, theoretical modelling and computer simulation, facilitating the leap from basic research to purposeful application.

Best performance for the best price
As Quintel pursues his work solely in his free time, the price/performance ratio was also decisive when choosing the resources used. He started out 11 years ago with a piece of software that soon reached the limits of its capabilities, due to the complexity of the brain data. His attention was then drawn to the Australian company SparxSystems, and in 2005 he switched to their now widely distributed and more affordable UML software development tool, Enterprise Architect (EA). As the research work grew and grew, the amateur brain researcher soon started to search for simulation software. Here, too, he initially came across an expensive solution, before discovering AMUSE, an EA plug-in created by Viennese company LieberLieber, in 2009. “This solution is extremely affordable, offers excellent simulation possibilities and vastly simplifies my work. Since 2010, they have been friendly enough to provide me with an academic licence,” says a delighted Quintel. “We are proud that our AMUSE simulation solution is enabling progress to be made in the medical understanding of brain disorders, thanks to the untiring efforts of Henrik Quintel. We are naturally very keen to support this work by issuing him with an academic licence,” emphasises Daniel Siegl, CEO of LieberLieber.
The use of EA and AMUSE has proven particularly suitable for the presentation of neuroscientific data, as this solution also offers excellent possibilities for presenting the data in a visually attractive way. “The high integration quality of AMUSE and EA allows a fluid working method, starting from the modelling, through to the implementation of the model in code and its execution. It also enables outsiders to get a quick overview of a project,” says the graduate computer scientist.


Robot caterpillar from a kit
EA contains a database (name in project: “BrainUML”) which includes a data model that makes it possible to observe different brain disorders, which cause movement disorders, from a variety of perspectives. “This data model now comprises 95,000 elements with a data volume of 200 MB,” says Quintel, in reference to the constantly growing collection of data. The aim of the database is to support clinical and pharmaceutical research. It contains a partially hypothetical model for disorders of the central nervous system, such as stroke, Alzheimer’s, Parkinson’s, neurotrauma, spinal cord injuries and multiple sclerosis.
The data has an interface for exporting data related to movement disorders to a robot in the form of a butterfly caterpillar (name in project: “Evolving Possibilities”). This makes it possible to observe the effects of brain disorders in a model and at the same time simulate the neuronal process in a computer with AMUSE.
The amateur researcher was also economical in his search for a suitable robot: “I built the butterfly caterpillar out of an Arexx kit, available commercially for just over EUR 100.00. With its eight servomotors, it offers me maximum freedom in the presentation of the movement disorders triggered by brain disorders.” The complete system - database and robot - represents an integral approach to basic biological research and clinical research into disorders of the central nervous system with the aid of “Computational Neuroscience”.

AMUSE simplifies model verification
Neuronal models are highly complex. They possess a great nesting depth and are strongly connected to other models they interact with. The amount of time required to verify such models is thus correspondingly large. AMUSE supports the developer not only with the creation of complex models, but also with automatic generation of the documentation. A model’s consistency is ensured through intensive testing, its understanding, for example, through the diverse possibilities of single-step simulation (performing the simulation “step by step”).
Says Quintel, “Due to the high complexity of a model, it is easy to lose sight of the relationships. This gives rise to logical or functional errors, which would be recognised too late or not at all if simulation were not available. That would mean having to spend a lot of time and effort finding and eliminating these types of error!” AMUSE supports the modeller with finding and eliminating errors. This also benefits outsiders, who have to work with an unfamiliar model. In addition, AMUSE also helps to make a model comprehensible to non-experts on the basis of its visualisation features. “AMUSE brings a ‘complex’ model back down to earth. This makes it possible to maintain a model’s consistency. A high degree of consistency ensures that the results of the simulation on the computer with AMUSE are identical to the real results on the robot,” says the amateur researcher in conclusion.

(Box 1)
Henrik Quintel on his experiences with AMUSE from LieberLieber
“AMUSE is a professional tool that supports the two languages UML and SYSML in conformity with standards, and is used in professional software development. The high degree of interactivity stands out, especially when it comes to following the course of phase diagrams. Because AMUSE is a plug-in of EA, it is particularly easy to simulate existing and new UML diagrams and save time. The high integration quality of AMUSE and EA allows a fluid working method, starting from the model through to the implementation of the model in code and its execution. In addition, it allows outsiders to get a quick overview of a project, to understand a project, especially the flow of phase diagrams and their relationships both with one another and with other models. As an added bonus, you learn to better understand the two languages UML and SYSML, identify relationships or learn to apply them in a complementary way. The development of complex models is therefore quick and easy.”

(Box 2)
Julius Bernstein (1839–1917)
Back in 1902, when scarcely a house was connected to the power supply and electric light was a luxury, Julius Bernstein (1839–1917) postulated a mechanism, which explained how electrical excitations propagate over the membranes of nerve cells. Bernstein’s “membrane theory” is the first physical-chemical explanation of electrical events in biology, and the first quantitative theory of electrophysiology. Of course, Bernstein had no idea about the possibilities offered by today’s computers. Nevertheless, he used his mathematical description of neuronal processes to pave the way to simulating complex processes of the brain in the computer.



(Box 3)
Computational Neuroscience
Thinking, feeling, learning, remembering - the human brain is the seat of all mental functions. At the same time, it is one of the most complex structures created by biological evolution. Understanding the brain is a prerequisite for the prevention and treatment of disorders of the nervous system and the development of more efficient teaching and learning strategies, as well as for the development of new, “intelligent” technical resources, such as neuroprostheses and high-performance computer systems.
Research into the brain, the new discipline of “Computational Neuroscience”, on which biologists, physicians, psychologists, physicists, mathematicians and computer scientists collaborate, promises to be particularly successful. The interdisciplinary approach combines experimentation, data analysis, theoretical modelling and computer simulation, facilitating the leap from basic research to purposeful application.




A free version of the new release, AMUSE 2.0, is available to download:
http://www.lieberlieber.com/unser-angebot/amuse-uml-execution-fuer-enterprise-architect.html
In order to use the full range of features of AMUSE 2.0, we recommend the latest version of the Enterprise Architect in the Ultimate Edition. You can test this by visiting www.sparxsystems.de (download trial).

Visit LieberLieber at the OMG Technical Meeting Exhibition: December 12-16, 2011 – Hyatt Regency Santa Clara, 5101 Great America Parkway,  Santa Clara, CA 95054 – Our CEO Daniel Siegl would be pleased to explain all new features of AMUSE 2.0


About LieberLieber Software
LieberLieber Software GmbH is an internationally active company with maximum competence and headquarters in Vienna. The core competences of the Viennese software company are in the area of the extensions for SparxSystems Enterprise Architect (software development with UML) as well as modern user interfaces for web, Windows, embedded systems and multi-touch systems.
With a globally networked and synergetically acting partner network, LieberLieber develops creative and innovative solutions, and modern technologies for companies active in Austria and abroad. The team at LieberLieber is noted for its high level of technical competence and the use of multifunctional teams of experts.

All pictures: Quintel/LieberLieber