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Biology Goes Digital An array of 5,700 Spartan FPGAs brings the BioWall to “life.” by Gianluca Tempesti, Ph.D. Assistant Professor Swiss Federal Institute of Technology gianluca.tempesti@epfl.ch Christof Teuscher Research Assistant Swiss Federal Institute of Technology christof@teuscher.ch 40 Xcell Journal Fall 2003
A unique, scientific research instrument and art piece, the BioWall models bio-inspired electronic tissues capable of evolution, selfrepair, self-replication – and learning. Much pure and applied scientific research has focused on replicating biological functions in digital hardware. Here, at the Logic Systems Laboratory of the Swiss Federal Institute of Technology in Lausanne (EPFL), we have utilized 5,700 Xilinx Spartan FPGAs, in multiple configurations, to build bio-inspired computing machines that exploit three essential biological models: • Phylogenesis – the history of the evolution of the species • Ontogenesis – the development of an individual as directed by his genetic code • Epigenesis – the development of an individual through learning processes (nervous system, immune system), influenced both by genetic code (the innate) and environment (the acquired). Although we have individually and jointly investigated all three models, we have concentrated on the ontogenetic model through the Embryonics (embryonic electronics) Project. This project studies the development of multi-cellular organisms for the purpose of obtaining in digital hardware some of the features of biological organisms, notably growth and fault tolerance. Our work has attracted a flattering amount of interest in the most varied and sometimes unexpected milieus. Among the most unexpected sources of funding and support came from Mrs. Jacqueline Reuge. Mrs. Reuge decided to fund the construction of the BioWall to display the principles of embryonics within a museum built to honor the memory of her late husband. Her generous support has allowed us to maintain our tradition of verifying our theoretical concepts in hardware. Without Mrs. Reuge’s support, we could not have constructed a computing machine of such magnificent proportions. We named this machine BioWall because of its biological inspiration, as well as its size Figure 1 – The BioWall reacts to touch. (5.3m x 0.6m x 0.5m = 3.68m 3 , or 130 cubic feet). The main purpose of creating the BioWall is to demonstrate the features of our embryonics systems to the public through a visual and tactile interaction (Figure 1). Interconnections with neighbor cells Transparent touch-sensitive element Two-color LED display Bio-Inspired Machines We implemented – for the first time in actual hardware – an organism endowed with all of the features of an embryonics machine, as it has often been defined in the literature. One of the functions of our organism is the BioWatch, which counts hours, minutes, and seconds. It demonstrates the growth and self-repair capabilities of our systems. The implementation of the BioWatch would have been sufficient to justify the effort that went into the construction of our embryonic BioWall. However, in developing our machine, we quickly realized that the capabilities of such a platform were not limited to a single application. In fact, it is an ideal platform to prototype many different kinds of twodimensional cellular systems, which are systems comprising arrays of small, locally connected elements. For example, “cellular automata” (CA) are very common environments in bioinspired research. The BioWall is ideally suited to the implementation of CAs, but it is by no means limited to it. We have only begun to explore the possibilities of the BioWall as a research tool. Xilinx Behind the Scenes We built the BioWall to demonstrate an embryonic machine. The structure of such machines is hierarchical: Organisms (application-specific systems) are created by the parallel operation of a number of cells (small processors). Each cell is implemented as an array of molecules (programmable logic elements). To implement this kind of machine, the BioWall is structured as a two-dimensional tissue comprising units (each unit corresponds to a molecule). As shown in Figure 2, each unit consists of: • An input element (a touch-sensitive membrane) • An output element (an array of 64 two-color LEDs) • A programmable computing element (a Xilinx Spartan XCS10XL FPGA). Fall 2003 Xcell Journal 41 FPGA Figure 2 – The BioWall’s basic building block
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Page 3 and 4: EDITOR IN CHIEF Carlis Collins edit
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