BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

The genetic architecture of human reproductive behavior-age at first birth (AFB) and number of children ever born (NEB)-has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

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... überrechet Ihro Excellentz Unterthanig-verbundene Diener M. Joh. Friedrich Ruopp/ P. L. Argentin. des ältern Herrn Sohns Hoffmeister. Joh. Michael Bergmann, SS. Theol. Stud. der beeden jüngsten Hrn. Söhne HofmeisterErscheinungsjahr der Datierung im Titel entnomme

Messtechnische und energetische Validierung des BMVBS-Effizienzhaus Plus in Berlin - Messperiode März 2012 bis Februar 2013

In Berlin, the German Federal Ministry of Transport, Building and Urban Development (BMVBS) had a model building erected to pilot the new funding initiative 'Efficiency House Plus'. This model is also intended to test and prove the performance of various components of the concept and to provide experience for a wider application. During a 2-year monitoring programme conducted by Fraunhofer IBP, data of the occupied building will be measured and analysed with regard to its energy performance. This report presents the first preliminary results obtained from a 12-month survey period. Measurements found that - despite unfavourable meteorological boundary conditions - the power yields from façade-integrated PV systems still exceeded the energy needs of building services and building users during the survey period. The resultant surplus energy was used to cover about 25 % of the energy demand for electro-mobility. Under 'regular' weather conditions the House would have been able to completely cover the energy demand of the electric vehicles, and still there would have been energy left to be fed into the public grid. The meteorological boundary conditions that were prevailing in the measurement period from March 2012 through February 2013 caused a 20 % drop (3,320 kWh) in the solar power yield due to an actual reduction of the sunshine hours, which were about 40 % less than the annual average of the last ten years. In the survey period, the energy consumption in the building was about 75 % higher than predicted. This discrepancy was mainly due to the inefficient performance of the heating system (caused by substantially higher system temperatures than assumed). It was further due to the uncontrolled amount of outdoor air in the mechanical ventilation system and last but not least it was also due to the fact that the electricity consumption of household appliances was higher than expected. The results of the first year of operation suggest that in the case of high-performance buildings it is absolutely required to include a planned monitoring and regulation/control phase, to be capable of realising the design parameters in practice

Felici Auxilio! Programma De Bello Justo : Quo ad Illustrissimi & Celsissimi Comitis ac Domini, Dn. Friderici Antonii, S. R. I. Quatuor-Viri, Comitis Schwartzburgi & Hohnsteini ... Natalium Solennitates, Quales in Schola nostra Provinciali institui possunt & debent, ... unà cum ... Domino Rectore, invitat

FELICI AUXILIO! PROGRAMMA DE BELLO JUSTO : QUO AD ILLUSTRISSIMI & CELSISSIMI COMITIS AC DOMINI, DN. FRIDERICI ANTONII, S. R. I. QUATUOR-VIRI, COMITIS SCHWARTZBURGI & HOHNSTEINI ... NATALIUM SOLENNITATES, QUALES IN SCHOLA NOSTRA PROVINCIALI INSTITUI POSSUNT & DEBENT, ... UNÀ CUM ... DOMINO RECTORE, INVITAT Felici Auxilio! Programma De Bello Justo : Quo ad Illustrissimi & Celsissimi Comitis ac Domini, Dn. Friderici Antonii, S. R. I. Quatuor-Viri, Comitis Schwartzburgi & Hohnsteini ... Natalium Solennitates, Quales in Schola nostra Provinciali institui possunt & debent, ... unà cum ... Domino Rectore, invitat (1) Titelseite (1) In bello belli nihil est, sed bellat idipsum... (2

A comparative study on manual and automatic slice-to-volume registration of CT images

In order to assess the clinical relevance of a slice-to-volume registration algorithm, this technique was compared to manual registration. Reformatted images obtained from a diagnostic CT examination of the lower abdomen were reviewed and manually registered by 41 individuals. The results were refined by the algorithm. Furthermore, a fully automatic registration of the single slices to the whole CT examination, without manual initialization, was also performed. The manual registration error for rotation and translation was found to be 2.7+/-2.8 degrees and 4.0+/-2.5 mm. The automated registration algorithm significantly reduced the registration error to 1.6+/-2.6 degrees and 1.3+/-1.6 mm (p = 0.01). In 3 of 41 (7.3%) registration cases, the automated registration algorithm failed completely. On average, the time required for manual registration was 213+/-197 s; automatic registration took 82+/-15 s. Registration was also performed without any human interaction. The resulting registration error of the algorithm without manual pre-registration was found to be 2.9+/-2.9 degrees and 1.1+/-0.2 mm. Here, a registration took 91+/-6 s, on average. Overall, the automated registration algorithm improved the accuracy of manual registration by 59% in rotation and 325% in translation. The absolute values are well within a clinically relevant range

Programma De Linguis Pentecostalibus

PROGRAMMA DE LINGUIS PENTECOSTALIBUS Programma De Linguis Pentecostalibus ([1]) Title page ([1]) Text (2) Oda (11