GMOD for Evolutionary Biology

The Generic Model Organism Database (GMOD, "http://gmod.org":http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data. GMOD is also a community of people addressing common challenges with biological data. Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.

This talk will focus on three areas of particular interest to iEvoBio participants. 
1) GBrowse_syn comparative genomics viewer
2) Natural Diversity Module of the Chado database schema
3) GMOD evolutionary biology hackathon 

The GBrowse_syn comparative genomics viewer displays synteny between a reference and any number of related species. It shows inversions, duplications, and indels, and can show synteny across non-contiguous regions. It is built on the widely used GBrowse genome viewer. The Natural Diversity Module is an extension to GMOD’s Chado database schema to enable Chado to support natural diversity, population genomics, individuals, breeding, phenotypes and geolocation information. This module is the first extension to Chado to be designed by the community, rather than at one institution. We will close by soliciting nominations and ideas for a GMOD Evolutionary Biology Hackathon. This hackathon will be held November 8-12, at NESCent, which is sponsoring the event. There will be an open call for participation in August.
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Spatially resolved observations of warm ionized gas and feedback in local ULIRGs

We present VLT/VIMOS-IFU emission-line spectroscopy of a volume limited sample of 18 southern ULIRGs selected with z<0.09 and dec<10. By covering a wide range of ULIRG types, this dataset provides an important set of templates for comparison with high-redshift galaxies. We employed an automated Gaussian line fitting program to decompose the emission line profiles of Halpha, [NII], [SII], and [OI] into individual components, and chart the Halpha kinematics, and the ionized gas excitations and densities. 11/18 of our galaxies show evidence for outflowing warm ionized gas with speeds between 500 and a few 1000 km/s, with the fastest outflows associated with systems that contain an AGN. Our spatially resolved spectroscopy has allowed us to map the outflows, and in some cases determine for the first time to which nucleus the wind is associated. In three of our targets we find line components with widths >2000 km/s over spatially extended regions in both the recombination and forbidden lines; in two of these three, they are associated with a known Sy2 nucleus. Eight galaxies have clear rotating gaseous disks, and for these we measure rotation velocities, virial masses, and calculate Toomre Q parameters. We find radial gradients in the emission line ratios in a significant number of systems in our study. We attribute these gradients to changes in ionizing radiation field strength, most likely due to an increasing contribution of shocks with radius. We conclude with a detailed discussion of the results for each individual system, with reference to the existing literature. Our observations demonstrate that the complexity of the kinematics and gas properties in ULIRGs can only be disentangled with high sensitivity, spatially resolved IFU observations. Many of our targets are ideal candidates for future high spatial resolution follow-up observations.Comment: 44 pages, 8 figures, 3 tables, accepted to MNRA

Timeline analysis and wavelet multiscale analysis of the AKARI All-Sky Survey at 90 micron

We present a careful analysis of the point source detection limit of the AKARI All-Sky Survey in the WIDE-S 90 $\mu$m band near the North Ecliptic Pole (NEP). Timeline Analysis is used to detect IRAS sources and then a conversion factor is derived to transform the peak timeline signal to the interpolated 90 $\mu$m flux of a source. Combined with a robust noise measurement, the point source flux detection limit at S/N $>5$ for a single detector row is $1.1\pm0.1$ Jy which corresponds to a point source detection limit of the survey of $\sim$0.4 Jy. Wavelet transform offers a multiscale representation of the Time Series Data (TSD). We calculate the continuous wavelet transform of the TSD and then search for significant wavelet coefficients considered as potential source detections. To discriminate real sources from spurious or moving objects, only sources with confirmation are selected. In our multiscale analysis, IRAS sources selected above $4\sigma$ can be identified as the only real sources at the Point Source Scales. We also investigate the correlation between the non-IRAS sources detected in Timeline Analysis and cirrus emission using wavelet transform and contour plots of wavelet power spectrum. It is shown that the non-IRAS sources are most likely to be caused by excessive noise over a large range of spatial scales rather than real extended structures such as cirrus clouds.Comment: 16 pages, 19 figures, 5 tables, accepted for publication in MNRA

Herschel SPIRE-FTS Observations of Excited CO and [CI] in the Antennae (NGC 4038/39): Warm and Cold Molecular Gas

We present Herschel SPIRE-FTS observations of the Antennae (NGC 4038/39), a well studied, nearby ($22$ Mpc) ongoing merger between two gas rich spiral galaxies. We detect 5 CO transitions ($J=4-3$ to $J=8-7$), both [CI] transitions and the [NII]$205\mu m$ transition across the entire system, which we supplement with ground based observations of the CO $J=1-0$, $J=2-1$ and $J=3-2$ transitions, and Herschel PACS observations of [CII] and [OI]$63\mu m$. Using the CO and [CI] transitions, we perform both a LTE analysis of [CI], and a non-LTE radiative transfer analysis of CO and [CI] using the radiative transfer code RADEX along with a Bayesian likelihood analysis. We find that there are two components to the molecular gas: a cold ($T_{kin}\sim 10-30$ K) and a warm ($T_{kin} \gtrsim 100$ K) component. By comparing the warm gas mass to previously observed values, we determine a CO abundance in the warm gas of $x_{CO} \sim 5\times 10^{-5}$. If the CO abundance is the same in the warm and cold gas phases, this abundance corresponds to a CO $J=1-0$ luminosity-to-mass conversion factor of $\alpha_{CO} \sim 7 \ M_{\odot}{pc^{-2} \ (K \ km \ s^{-1})^{-1}}$in the cold component, similar to the value for normal spiral galaxies. We estimate the cooling from H$_2$, [CII], CO and [OI]$63\mu m$to be$\sim 0.01 L_{\odot}/M_{\odot}$. We compare PDR models to the ratio of the flux of various CO transitions, along with the ratio of the CO flux to the far-infrared flux in NGC 4038, NGC 4039 and the overlap region. We find that the densities recovered from our non-LTE analysis are consistent with a background far-ultraviolet field of strength$G_0\sim 1000$. Finally, we find that a combination of turbulent heating, due to the ongoing merger, and supernova and stellar winds are sufficient to heat the molecular gas.Comment: 50 pages, 15 figures, 8 tables, Accepted for publication in The Astrophysical Journa

MAMBO 1.2mm observations of luminous starbursts at z~2 in the SWIRE fields

We report on--off pointed MAMBO observations at 1.2 mm of 61 Spitzer-selected star-forming galaxies from the SWIRE survey. The sources are selected on the basis of bright 24um fluxes (f_24um>0.4mJy) and of stellar dominated near-infrared spectral energy distributions in order to favor z~2 starburst galaxies. The average 1.2mm flux for the whole sample is 1.5+/-0.2 mJy. Our analysis focuses on 29 sources in the Lockman Hole field where the average 1.2mm flux (1.9+/-0.3 mJy) is higher than in other fields (1.1+/-0.2 mJy). The analysis of the sources multi-wavelength spectral energy distributions indicates that they are starburst galaxies with far-infrared luminosities ~10^12-10^13.3 Lsun, and stellar masses of ~0.2-6 x10^11 M_sun. Compared to sub-millimeter selected galaxies (SMGs), the SWIRE-MAMBO sources are among those with the largest 24um/millimeter flux ratios. The origin of such large ratios is investigated by comparing the average mid-infrared spectra and the stacked far-infrared spectral energy distributions of the SWIRE-MAMBO sources and of SMGs. The mid-infrared spectra exhibit strong PAH features, and a warm dust continuum. The warm dust continuum contributes to ~34% of the mid-infrared emission, and is likely associated with an AGN component. This constribution is consistent with what is found in SMGs. The large 24um/1.2mm flux ratios are thus not due to AGN emission, but rather to enhanced PAH emission compared to SMGs. The analysis of the stacked far-infrared fluxes yields warmer dust temperatures than typically observed in SMGs. Our selection favors warm ultra-luminous infrared sources at high-z, a class of objects that is rarely found in SMG samples. Our sample is the largest Spitzer-selected sample detected at millimeter wavelengths currently available.Comment: Accepted for publication in ApJ (51 pages; 16 figures). The quality of some figures has been degraded for arXiv purposes. Full resolution version available at this http://www.iasf-milano.inaf.it/~polletta/mambo_swire/lonsdale08_ApJ_accepted.pd

ALBACORE OBS recovery cruise report

The primary goal of the 2011 ALBACORE (Asthenosphere and Lithosphere Broadband Architecture from the California Offshore Region Experiment) cruise was to recover 34 ocean bottom seismometers (OBSs) in a 150 km (north-south) by 400 km (east-west) region off the coast of Southern California (Fig. 1). The cruise took place on R/V New Horizon, departing out of San Diego on Sept 7, 2011 and arriving back in San Diego on Sept 16, 2011 with no port stops in between