Experiences with and interpretation of standard test methods of building energy analysis tools

The authors separately apply ANSI/ASHRAE Standard 140-2001 to the simulation program TRNSYS, comparing not only their results but the differences in their simulation assumptions and in their interpretations of the Standard's test cases. Results of the application are presented for all three authors, showing that there is a significant amount of leeway within a complex simulation tool such asTRNSYS for users of different backgrounds to apply their own common simulating practices and still fall comfortably within the range of acceptability specified by such Standards. Included in the application results are results of sensitivity tests that demonstrate the relative importance of assumption differences

Converging on a recommended set of interpretations and assumptions in applying standard tests to energy analysis tools

The authors, having individually applied ANSI/ASHRAE Standard 140-2001 to the simulation program TRNSYS in a previous project, compare their results, simulation assumptions, and interpretations of the Standard's test cases to arrive at a conformed set of recommended practices. Sensitivities to individual assumptions are investigated and results of applying the conformed set of assumptions are presented

Combining different validation techniques for continuous software improvement - Implications in the development of TRNSYS 16

Validation using published, high quality test suites can serve to identify different problems in simulation software: modeling and coding errors, missing features, frequent sources of user confusion. This paper discusses the application of different published validation procedures during the development of a new TRNSYS version: BESTEST/ASHRAE 140 (Building envelope), HVAC BESTEST (mechanical systems) and IEA ECBCS Annex 21 / SHC Task 12 empirical validation (performance of a test cell with a very simple mechanical system). It is shown that each validation suite has allowed to identify different types of problems. Those validation tools were also used to diagnose and fix some of the identified problems, and to assess the influence of code modifications. The paper also discusses some limitations of the selected validation tools

Simulation synergy : expanding TRNSYS capabilities and usability

Developers of simulation packages are now able to take advantage of the increase in available desktop computing power to expand the capabilities and usability of their programs. This paper will illustrate these opportunities by discussing the different techniques the developers of the TRNSYS software package have used to try and create a synergy between TRNSYS and external programs and between the developers and users of the program

Comet Dust: The Diversity of Primitive Particles and Implications

Comet dust is primitive and shows significant diversity. Our knowledge of the properties of primitive particles has expanded significantly through microscale investigations of cosmic dust samples (IDPs and AMMs) and of comet dust samples (Stardust and Rosetta's COSIMA), as well as through remote sensing (spectroscopy and imaging) via Spitzer and via spacecraft encounters with 103P/Hartley 2 and 67P/Churyumov-Gerasimenko. Microscale investigations show that comet dust and cosmic dust are particles of unequilibrated materials, including aggregates of materials unequilibrated at submicron scales. We call unequilibrated materials "primitive" and we deduce they were incorporated into ice-rich (H2O-, CO2-, and CO-ice) parent bodies that remained cold, i.e., into comets, because of the lack of aqueous or thermal alteration since particle aggregation; yet some Stardust olivines suggest mild thermal metamorphism. Primitive particles exhibit a diverse range of: structure and typology; size and size distribution of constituents; concentration and form of carbonaceous and organic matter; D-, N-, and O- isotopic enhancements over solar; Mg-, Fe-contentsof thesilicate minerals; the compositions and concentrations of sulfides, and of less abundant mineral species such as chondrules, CAIs and carbonates. The unifomity within a group of samples points to: aerodynamic sorting of particles and/or particle constituents; the inclusion of a limited range of oxygen fugacities; the inclusion or exclusion of chondrules; a selection of organics. The properites of primitive particles imply there were disk processes that resulted in different comets having particular selections of primitive materials. The diversity of primitive particles has implications for the diversity of materials in the protoplanetary disk present at the time and in the region where the comets formed

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

BACKGROUND: Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs). Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting because they may represent recent adaptive events, or potential future adaptive opportunities within the human lineage. Sequence analysis tools are needed, however, to decide whether these interpretations are likely, whether a particular set of LCRs represents nearly neutral drift creating junk DNA, or whether the appearance of LCRs reflects assembly error. Here we investigate an LCR family containing the sulfotransferase (SULT) 1A genes involved in drug metabolism, cancer, hormone regulation, and neurotransmitter biology as a first step for defining the problems that those tools must manage. RESULTS: Sequence analysis here identified a fourth sulfotransferase gene, which may be transcriptionally active, located on human chromosome 16. Four regions of genomic sequence containing the four human SULT1A paralogs defined a new LCR family. The stem hominoid SULT1A progenitor locus was identified by comparative genomics involving complete human and rodent genomes, and a draft chimpanzee genome. SULT1A expansion in hominoid genomes was followed by positive selection acting on specific protein sites. This episode of adaptive evolution appears to be responsible for the dopamine sulfonation function of some SULT enzymes. Each of the conclusions that this bioinformatic analysis generated using data that has uncertain reliability (such as that from the chimpanzee genome sequencing project) has been confirmed experimentally or by a "finished" chromosome 16 assembly, both of which were published after the submission of this manuscript. CONCLUSION: SULT1A genes expanded from one to four copies in hominoids during intra-chromosomal LCR duplications, including (apparently) one after the divergence of chimpanzees and humans. Thus, LCRs may provide a means for amplifying genes (and other genetic elements) that are adaptively useful. Being located on and among LCRs, however, could make the human SULT1A genes susceptible to further duplications or deletions resulting in 'genomic diseases' for some individuals. Pharmacogenomic studies of SULT1Asingle nucleotide polymorphisms, therefore, should also consider examining SULT1A copy number variability when searching for genotype-phenotype associations. The latest duplication is, however, only a substantiated hypothesis; an alternative explanation, disfavored by the majority of evidence, is that the duplication is an artifact of incorrect genome assembly

Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

BACKGROUND: When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. RESULTS: The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1) multiple sequence alignments, 2) mapping of alignment sites to crystal structure sites, 3) phylogenetic trees, 4) inferred ancestral sequences at internal tree nodes, and 5) amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. CONCLUSION: We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural bioinformatics resources that are useful for identifying experimentally testable hypotheses about the molecular basis of protein behaviors and functions, as illustrated with the examples from the cellular retinoid binding proteins