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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Class of {varphi}X174 Mutants Relatively Deficient in Synthesis of Viral RNA

Nonpermissive cells infected with {varphi}X174 gene D amber mutants synthesized some sixfold less viral RNA than permissive cells. The decrease was unaffected by increasing the multiplicity of infection and was a consequence of an overall decrease in all viral RNA species. It is suggested that the gene D product may function in replicative form DNA unwinding to expose the template for transcription

Preparing for War: The 25th Battalion in Halifax, 1914–15

The 25th Battalion was authorized in November 1914 and recruited men from throughout Nova Scotia before departing for England in May 1915. It spent the winter and early spring of 1914–15 in Halifax, where it was based at the Armoury and on the Common. Robert Clements, a native of Yarmouth, enlisted in the battalion in November 1914 and served in it throughout the war, rising to the rank of lieutenant. Many years later he wrote an informal history of the battalion, giving a colourful account based on his personal experiences and observations. These excerpts from his soon to be published manuscript, describe the battalion’s experiences in Halifax as the men trained, coped with inadequate equipment and inexperienced officers, and prepared to go overseas

Houston in 1900 Part 1. The rise of the regional city

Cities and towns

A Cholesky-MIDAS model for predicting stock portfolio volatility

This paper presents a simple forecasting technique for variance covariance matrices. It relies significantly on the contribution of Chiriac and Voev (2010) who propose to forecast elements of the Cholesky decomposition which recombine to form a positive definite forecast for the variance covariance matrix. The method proposed here combines this methodology with advances made in the MIDAS literature to produce a forecasting methodology that is flexible, scales easily with the size of the portfolio and produces superior forecasts in simulation experiments and an empirical application.Cholesky, Midas, volatility forecasts

A Kernel Technique for Forecasting the Variance-Covariance Matrix

The forecasting of variance-covariance matrices is an important issue. In recent years an increasing body of literature has focused on multivariate models to forecast this quantity. This paper develops a nonparametric technique for generating multivariate volatility forecasts from a weighted average of historical volatility and a broader set of macroeconomic variables. As opposed to traditional techniques where the weights solely decay as a function of time, this approach employs a kernel weighting scheme where historical periods exhibiting the most similar conditions to the time at which the forecast if formed attract the greatest weight. It is found that the proposed method leads to superior forecasts, with macroeconomic information playing an important role.Nonparametric, variance-covariance matrix, volatility forecasting, multivariate

Residual analysis methods for space--time point processes with applications to earthquake forecast models in California

Modern, powerful techniques for the residual analysis of spatial-temporal point process models are reviewed and compared. These methods are applied to California earthquake forecast models used in the Collaboratory for the Study of Earthquake Predictability (CSEP). Assessments of these earthquake forecasting models have previously been performed using simple, low-power means such as the L-test and N-test. We instead propose residual methods based on rescaling, thinning, superposition, weighted K-functions and deviance residuals. Rescaled residuals can be useful for assessing the overall fit of a model, but as with thinning and superposition, rescaling is generally impractical when the conditional intensity $\lambda$ is volatile. While residual thinning and superposition may be useful for identifying spatial locations where a model fits poorly, these methods have limited power when the modeled conditional intensity assumes extremely low or high values somewhere in the observation region, and this is commonly the case for earthquake forecasting models. A recently proposed hybrid method of thinning and superposition, called super-thinning, is a more powerful alternative.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS487 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Imaginary Invalid

The famous hypochondriac in this classic farce not only complains of a million imaginary ills, but also of his astronomical medical bills. If he marries his daughter to a doctor, he reasons, he will have free medical care. He chooses a double-Latin-talking numskull without consulting the daughter, who is already smitten by another. The inventive maid exposes the doctor and his father as charlatans and demonstrates to the master that his second wife loves his money, not him. Thus are truth and love triumphant and all troubles, real and imaginary, relieved by laughter.https://digitalcommons.cedarville.edu/theatre_productions/1018/thumbnail.jp

Evaluation of primary rumen epithelial cell culture techniques in sheep

Objectives of this study were to determine if the number of cells incubated in primary rumen epithelial cell cultures affects production rates of metabolites and to standardize reporting criteria by obtaining an optimum mode of data expression. Epithelial tissue was excised from five Suffolk x Dorset crossbred sheep and subjected to serial tryptic digestion to isolate cells. Isolated cells were incubated for 90-minutes in 25 mM propionate and 10 mM butyrate at concentrations of 0.5, 1, 5,10, 20 and 40-million cells per flask (total vol. = 3mL). Production of acetoacetate (AcAc), β-hydroxybutyrate (β-HBA), lactate (LAC) and pyruvate (PYR) were measured. Data were expressed as either cell number, cell dry matter or cell total protein alone or per epithelial wet tissue weight, body weight (BW) or metabolic BW to generate twelve different forms of data expression. Coefficients of variation were calculated for all 12 modes of expression. Expressing data per cell number resulted in the lowest variation (P \u3c .01) and data adjusted for metabolic BW had less variation than BW. Acetoacetate concentrations were largest at 0.5-million cells/flask (P \u3c .05) and there were no differences between 1, 5,10 and 20 and only 40 differed from 0.5 and 5-million cells/flask. β-HBA concentrations were largest at 1 and 5-million cells/flask. However, 1 and 5 only differed significantly (P \u3c .05) from 20 and 40-million cells/flask. Lactate and PYR concentrations were largest at 1-million cells/flask, but no significant differences were found. Ratios of β-HBA:AcAc were below one for the 0.5-million cells/flask indicating low mitochondrial redox potentials (P \u3c .05). A suggested range of rumen epithelial cells to include in incubations is 5 to 20-million/flask. This range will minimize the potential for altered metabolite production caused by incubating large cell quantities as well as the experimental error associated with using low cell numbers. When rumen tissue is taken from animals of the same species, size and stage of development, data adjusted by cell number is preferred. However, it is recommended that metabolic BW, cell protein and cell dry matter be included to facilitate future comparison between laboratories and species