The cancer translational research informatics platform

<p>Abstract</p> <p>Background</p> <p>Despite the pressing need for the creation of applications that facilitate the aggregation of clinical and molecular data, most current applications are proprietary and lack the necessary compliance with standards that would allow for cross-institutional data exchange. In line with its mission of accelerating research discoveries and improving patient outcomes by linking networks of researchers, physicians, and patients focused on cancer research, caBIG (cancer Biomedical Informatics Grid™) has sponsored the creation of the caTRIP (Cancer Translational Research Informatics Platform) tool, with the purpose of aggregating clinical and molecular data in a repository that is user-friendly, easily accessible, as well as compliant with regulatory requirements of privacy and security.</p> <p>Results</p> <p>caTRIP has been developed as an N-tier architecture, with three primary tiers: domain services, the distributed query engine, and the graphical user interface, primarily making use of the caGrid infrastructure to ensure compatibility with other tools currently developed by caBIG. The application interface was designed so that users can construct queries using either the Simple Interface via drop-down menus or the Advanced Interface for more sophisticated searching strategies to using drag-and-drop. Furthermore, the application addresses the security concerns of authentication, authorization, and delegation, as well as an automated honest broker service for deidentifying data.</p> <p>Conclusion</p> <p>Currently being deployed at Duke University and a few other centers, we expect that caTRIP will make a significant contribution to further the development of translational research through the facilitation of its data exchange and storage processes.</p

INVESTIGATION OF MAIN-CHAMBER AND DIVERTOR RECYCING IN DIII-D USING TANGENTIALLY VIEWING CID CAMERAS

OAK-B135 Measurements of the D{sub {alpha}} emission profiles from the divertor and main chamber region in DIII-D, performed in low-density L-mode, and low and high-density ELMy H-mode plasmas imply that core plasma fueling occurs through the divertor channel. Emission profiles of carbon, combined with UEDGE modeling of the L-mode plasmas, also suggests that chemical sputtering of carbon from the flux surface adjacent to the inner divertor walls, and temperature gradient forces in the scrape-off layer, determine the carbon content of the inner scrape-off layer

Measured signatures of low energy, physical sputtering in the line shape of neutral carbon emission

The most important mechanisms for introducing carbon into the DIII-D divertors [J.L. Luxon, Nucl. Fusion 42 (2002) 614] are physical and chemical sputtering. Previous investigations have indicated that operating conditions where one or the other of these is dominant can be distinguished by using CD and C2 emissions to infer C I influxes from dissociation of hydrocarbons and comparing to measured C I influxes. The present work extends these results through detailed analysis of the C I spectral line shapes. In general, it is found that the profiles are actually asymmetric and have shifted peaks. These features are interpreted as originating from a combination of an anisotropic velocity distribution from physical sputtering (the Thompson model) and an isotropic distribution from molecular dissociation. The present study utilitzes pure helium plasmas to benchmark C I spectral profiles arising from physical sputtering alone. © 2004 Elsevier B.V. All rights reserved

Measured signatures of low energy, physical sputtering in the line shape of neutral carbon emission

The most important mechanisms for introducing carbon into the DIII-D divertors [J.L. Luxon, Nucl. Fusion 42 (2002) 614] are physical and chemical sputtering. Previous investigations have indicated that operating conditions where one or the other of these is dominant can be distinguished by using CD and C2 emissions to infer C I influxes from dissociation of hydrocarbons and comparing to measured C I influxes. The present work extends these results through detailed analysis of the C I spectral line shapes. In general, it is found that the profiles are actually asymmetric and have shifted peaks. These features are interpreted as originating from a combination of an anisotropic velocity distribution from physical sputtering (the Thompson model) and an isotropic distribution from molecular dissociation. The present study utilitzes pure helium plasmas to benchmark C I spectral profiles arising from physical sputtering alone. © 2004 Elsevier B.V. All rights reserved

Non-linear MHD modelling of ELM triggering by pellet injection in DIII-D and implications for ITER

Edge localized mode (ELM) triggering by pellet injection in the DIII-D tokamak has been simulated with the non-linear MHD code JOREK with a view to validating its physics models. JOREK has been subsequently applied to evaluate the requirements for ELM control by pellet injection in ITER. JOREK modelling results for DIII-D show that the key parameter for the triggering of ELMs by pellets is the value of the localized pressure perturbation caused by pellet injection which leads to a threshold minimum pellet size for a given injection velocity, injection geometry and H-mode plasma characteristics. The minimum pellet size for ELM triggering is found to depend on injection geometry with the largest value being required for injection at the outer midplane, intermediate for injection near the X-point and the smallest one for injection at the high-field side. The first results of studies for ELM triggering by pellet injection in ITER 15 MA Q = 10 plasmas with the foreseen injection geometry in ITER are presented

Initial development of the DIII-D snowflake divertor control

Simultaneous control of two proximate magnetic field nulls in the divertor region is demonstrated on DIII-D to enable plasma operations in an advanced magnetic configuration known as the snowflake divertor (SFD). The SFD is characterized by a second-order poloidal field null, created by merging two first-order nulls of the standard divertor configuration. The snowflake configuration has many magnetic properties, such as high poloidal flux expansion, large plasma-wetted area, and additional strike points, that are advantageous for divertor heat flux management in future fusion reactors. However, the magnetic configuration of the SFD is highly-sensitive to changes in currents within the plasma and external coils and therefore requires complex magnetic control. The first real-time snowflake detection and control system on DIII-D has been implemented in order to stabilize the configuration. The control algorithm calculates the position of the two nulls in real-time by locally-expanding the Grad-Shafranov equation in the divertor region. A linear relation between variations in the poloidal field coil currents and changes in the null locations is then analytically derived. This formulation allows for simultaneous control of multiple coils to achieve a desired SFD configuration. It is shown that the control enabled various snowflake configurations on DIII-D in scenarios such as the double-null advanced tokamak. The SFD resulted in a 2.5× reduction in the peak heat flux for many energy confinement times (2-3 s) without any adverse effects on core plasma performance