Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.

The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.

Millisecond pulsed radio frequency glow discharge time of flight mass spectrometry: temporal and spatial variations in molecular energetics.

The internal energy distributions, P(epsilon), of a millisecond pulsed radio frequency glow discharge plasma were investigated using tungsten hexcarbonyl W(CO)(6) as a "thermometer molecule". Vapor of the probe molecule, W(CO)(6), was introduced into the plasma and subjected to various ionization and excitation processes therein. The resultant molecular and fragment ions were monitored using a Time-of-Flight mass spectrometer. Ion abundance data were utilized in combination with the known energetics of W(CO)(6) to construct the P(epsilon) plots. The P(epsilon) of W(CO)(6) exhibited strong temporal dependence over the pulse cycle: Distinct internal energy distributions were found at the discharge breakdown period (prepeak), the steady state period (plateau), and the post-pulse period (afterpeak). Spatial variation in P(epsilon) was also observed, especially during the plateau regime. The observations suggest that this pulsed glow discharge affords excellent energy tunability that can be used to perform selective ionization and fragmentation for molecular, structural, and elemental information. Parametric studies were performed to evaluate the effects of discharge pressure and operating power on P(epsilon). These studies also provided insight into the correlation of the observed P(epsilon)s with the fundamental ionization and excitation mechanisms in the plasma. The temporal and spatial variations in P(epsilon) were hence attributed to changes in the dominant energy transfer processes at specific times in specific regions of the plasma. These data will be useful in future efforts to optimize the analytical performance of this source for chemical speciation.