SIERRA: An Octree-based Spatial Data System for Neural Data

vi 1 Introduction 1 2 Earlier Work 6 2.1 Spatial data in bioinformatics . . . . . . . . . . . . . . . . . . . . 6 2.2 Spatial databases . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3 Methods 11 3.1 Spatial data structures . . . . . . . . . . . . . . . . . . . . . . . . 11 3.2 Linearization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.3 How spatial queries work . . . . . . . . . . . . . . . . . . . . . . 15 3.4 Implementation details . . . . . . . . . . . . . . . . . . . . . . . . 20 4 Conclusions 21 4.1 The role of SIERRA within NEUROSYS . . . . . . . . . . . . . . 21 4.2 Performance considerations . . . . . . . . . . . . . . . . . . . . . 23 4.3 Further work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 A SQL pseudocode 31 iv List of Figures 1.1 Cricket cercal system . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Microphotograph of cricket cercus . . . . . . . . . . . . . . . . . 3 3.1 Quadtree representation . . . . . . . ..

Computer Science Notes

protocols have to be implemented. Compare and contrast OSI vs TCP/IP styles of defining what it is the parts of a network should do. OSI The ISO 7-layer reference model of a network, defined by committee. 1. Physical Layer. Hardware that implements a commlink. 2. Data Link Layer. Framing mechanism, e.g. EtherNet. 3. Network Layer. Packet routing, e.g. IP. 4. Transport Layer. End-to-end messaging, e.g. TCP, UDP. 5. Session Layer. (Application datastream multiplexing?) 6. Presentation Layer. (Data Format, e.g. endianness, ASCII vs UTF8) 7. Application Layer. (The application proper) TCP/IP The IETF 4-layer model. This was never really formally defined: it just happened this way. 1. Network. Hardware + Data Link. e.g., NIC + 802.3 2. IP. routing for packet-switched data 3. TCP, UDP. transport for packet-switched data. 4. Application. End-user apps. In the TCP/IP model, applications may access any of the the lower layers, not just the transport layer of TCP and UDP. 7.2 Physically conne..

SIERRA: A Spatial Data System for Neuronal Data

Neuroinformatics requires the manipulation and querying of data in a spatial, visual, and relational milieu. SIERRA is a system for storing and querying neuronal data within a relational data framework, and hybridizes proven technologies (RDBMS, octrees) to meet stringent real-time visualization requirements in a simple yet elegant way. 1 Introduction We present SIERRA 1 , a spatial database system in which normalized spatial representations of objects can be efficiently stored, and the spatial relations of these objects graphically displayed, using a hybrid of octrees, RDBMS and 3-D visualization technology. SIERRA was developed in support of NEUROSYS 2 , a tool used to explore the functional relationships and connectivity patterns between small and large ensembles of neurons. In this paper, we will discuss how data are stored and queried in SIERRA, the role of SIERRA as a component of NEUROSYS, and future directions for research. The first test-version of SIERRA was implemented ..