Torc

Abstract: We present and describe Torc - (Tools for Open Reconfigurable Computing) - an open-source infrastructure and tool set, provided entirely as C++ source code and available at http://torc.isi.edu. Torc is suitable for custom research applications, for CAD tool development, and for architecture exploration.The Torc infrastructure can (1) read, write, and manipulate generic netlists - currently EDIF, (2) read, write, and manipulate physical netlists - currently XDL, and indirectly NCD, (3) provide exhaustive wiring and logic information for commercial devices, and (4) read, write, and manipulate bitstream packets (but not configuration frame contents). Torc furthermore provides routing and unpacking tools for full or partial designs, soon to be augmented with BLIF support, and with packing and placing tools.The architectural data for Xilinx devices is generated from non-proprietary XDLRC files, and currently supports 140 devices in 11 families: Virtex, Virtex-E, Virtex-II, Virtex-II Pro, Virtex4, Virtex5, Virtex6, Virtex6L, Spartan3E, Spartan6, and Spartan6L. We believe that Altera architectures and designs could be similarly supported if the necessary data were available, and we have successfully used Torc internally with custom architectures.

Abstract: The expression of the Escherichia coli torCAD operon, which encodes the anaerobically expressed trimethylamine N-oxide (TMAO) reductase respiratory system, requires the presence of TMAO in the medium. The response regulator, TorR, has recently been identified as the regulatory protein that controls the expression of the torCAD operon in response to TMAO. The torC regulatory region contains four direct repeats of a decameric consensus motif designated the tor boxes. Alteration by base substitutions of any of the four tor boxes in a plasmid containing a torC'-lacZ fusion dramatically reduces TorR-dependent torC expression. In addition, deletion of the distal tor box (box1) abolishes torC induction whereas the presence of a DNA fragment starting three bases upstream from box1 suffices for normal torC expression. Footprinting and gel-retardation experiments unambiguously demonstrated that TorR binds to the torC regulatory region. Three distinct regions are protected by TorR binding. One of approximately 24 nucleotides covers the first two tor boxes (box1 and box2); the second is located upstream from the -35 promoter sequence and includes the third tor box (box3); the last is found downstream from the -35 sequence and corresponds to the fourth tor box (box4). Binding to the upstream tor boxes (box1 and box2) appears to be stronger than binding to the downstream tor boxes (box3 and box4) since only the upstream region is protected at the lower concentration of TorR used in the footprinting experiments. We propose a model in which multiple binding sites (i.e. the tor boxes) contribute to the formation of a nucleoprotein complex, but only one particular proximal site positions TorR properly so that it interacts with RNA polymerase.