In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Most studies of the dynamics of fluids with weak density gradients use the Boussinesq approximation, which neglects density variations in the inertial terms of the equation of motion. The significance of this approximation is investigated here. As a general matter, it appears that care is called for in the use of the approximation if quantities other than the non-dimensional density difference are small. Also, the existence of certain phenomena of interest and importance may depend on the small terms neglected by the Boussinesq approximation. This is shown by an investigation of solitary waves in a stratified fluid system. , I + y*, pu, u.] + gb& = 0, , , , , (8;. -1) yr*yu' 8, . + 6t. -0.

Most studies of the dynamics of fluids with weak density gradients use the Boussinesq approximation, which neglects density variations in the inertial terms of the equation of motion. The significance of this approximation is investigated here. As a general matter, it appears that care is called for in the use of the approximation if quantities other than the non-dimensional density difference are small. Also, the existence of certain phenomena of interest and importance may depend on the small terms neglected by the Boussinesq approximation. This is shown by an investigation of solitary waves in a stratified fluid system. (8;. -1) yr*yu' 8, . + 6t. -0. This research was supported by the Office of Naval Research under Project NR 082-104, Contract N-onr-4010(01), and by the U.S. Weather Bureau under Grant WBG-2 1. * More involved arguments have been given by SPIEGEL & VERONIS (1960).* From now on we use primed symbols for dimensional quantities and unprimed symbols for nondimensional quantities.Tellus XVII (1985), 1

A n experim e ntal inv es ti ga tion of e lec tro n imp ac t exc it a tion of th e 2p stat e of atomic hydrogen is desc ribed. A bea m o f e lec tron s wa s passed thruu g h a c hopp ed bea m of hydrogeil atoms in a high vacuum apparatus. Th e modulated flux of Lyman -a photons e mitted in the radiative decay of the . 2p s tatc wa s ta ke n as a meas ure me nt of th e excita tion probabilit y res ulting from d irect exc itation plus indirec t exc itation rcs ultin g from cascad in g. The region s urrounding th e inte rsec tion of the two beams was e lec tri ca ll y and mag ne ti ca ll y s hi e lded to p re ve nt qu e n c hing of me tastabl e 25 atoms a nd th ere b y to e ns ure that th e ob se rv ed Lyman-a flu x res ult ed from d ecay of th e s hort-live d 2p s tate.Th e experim e nt a l res ult s are consist e nt with th ose ob tained by F ite , S te bbin gs, and Brac kmann '[19591 , and co nfirm th e ex is te nce of a large di sc repa ncy be twee n th co re ti ca l a nd ex per im enta l res ult s in th c e lec tron e nergy range below 50 c V.,." .< Key Words: Atomic h ydroge n; beams; e lectron impa ct exc itation ; e xperimen ta l; hi gh vacuum;Lyman-a.

Figure 6 shows the measured electron densities vs 2 S~density (a quantitative measure of the intensity of the discharge) for He sample pressures of 0. 1 and 0. 22 torr. Under sample conditions closely approximating those employed and analyzed by McCusker et al. (8% absorption of He pumping light on He sample and pressure of 0. 1 torr) in extracting an optimum polarized electron beam, the electron density is approximately 7 &&10cm . However, the error could be as large as a factor of 2, primarily because of uncertainty in the proportionality constant k in Eq. (14), taken here to be 230 cm sec ' appropriate to a uniform electron distribution.fBased on a Master of Arts thesis by J. C. Hill (Rice University, 1969). Phys. Rev. 132, 2561.R. C. Greenhow, Phys. Bev. 136, A660 (1964). 4This relation holds only for P«1, a condition satisfied in the present experiment.The process of photoionization of polarized alkali atoms in an atomic beam has been studied for potassium and lithium. Depolarization processes associated with photoionization of alkali molecules and optically excited atoms were discovered. After eliminating these depolarization mechanisms, the measured photoelectron polarization agreed within an accuracy of 3% with the predicted polarization based on the current theory for this electric dipole process. Using a polarized Li' atomic beam and a pulsed uv light source, we have produced an intense and highly polarized electron beam with 2 x10 electrons in l.5 psec and with a polarization of 0.78, which is a suitable prototype injector source for a high-energy electron accelerator.