Machine Boss: rapid prototyping of bioinformatic automata

Motivation Many software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone. Results We present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line ‘recipes’ for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage and nanopore sequence analysis. Availability and implementation Machine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/. Supplementary information Supplementary data are available at Bioinformatics online.

Machine Boss: Rapid Prototyping of Bioinformatic Automata

ABSTRACTMotivationMany C++ libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting, and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone.ResultsWe present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line “recipes” for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage, and nanopore sequence analysis.Availability and ImplementationMachine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/.ContactIan Holmes, [email protected]

Optimization of Design of Pitched Roofs According to Phase Shift of Thermal Oscillation

It is important to take into account some more parameters, e.g. heat transfer coefficient, hygienic criterion or globalised energetic criterion, nowadays. It is a time when there is a big emphasize on thermal protection of residential buildings. Therefore an important calculation parameter is spoken more often - temperature loss and phase shift of thermal oscillation. This two parameters are very important especially in case of building envelopes based on lightweight supporting and used insulation materials. A pitched roof in residential building or family house is a typical example. This problem is growing even more, if we are taking adverse ratio of outer surface to volume of the space into account. This paper is showing analysis of such building envelope construction, its designing and influence on optimal values of phase shift of thermal oscillation.

Research on Lane Departure Warning System

Lane departure warning system includes lane identification and lane departure determination. Lane identification is crucial for lane departure warning system. In this paper, A linear mode which can only bring out small distance error and angle error is used to detect lane boundaries. A region of interest (ROI) appropriate is set to reduce nonessential cost of computation. According to the characteristics of lane position, we improve the Hough transform, reduce the detection and tracking transform angle and raise the speed of calculation. Parameter angle form Hough transform is used to lane departure determination, this method does not calibrate the camera and can get the lane departure rate. Experiments show that the system is well to detect and track the lane line and give alarm correctly.

Determining Preconsolidation Pressure of the Lakeside New District Soft Clay of Hefei Based on Casagrande Method by Matlab

The preconsolidation pressure is an important index to determine the stress history of soil and also a major calculation parameter for the analysis of soil stratum’s deformation in the different stress history. Casagrade method is worldwide applied to determine the preconsolidation pressure. On the basis of research on consolidation test about the lakeside new district soft clay of Hefei by high pressure consolidation apparatus, and conformed to Casagrande method, the paper adopts quartic polynomial and least square method to fit the compression curve, and the preconsolidation pressure of the lakeside new distract soft clay of Hefei is determined by matlab software. The result provides reference for the calculation of foundation settlement considering stress history.

Seismic Analysis on Masonry Structures Strengthened with Reinforced Concrete Splint

Strengthening the brick walls with reinforced concrete splint is a conventional and effective method of strengthening masonry structures. To the method, the text process and analysis of 6 brick walls strengthened with reinforced concrete splint and the existing calculation analysis method about bearing capacity are introduced in this paper. Through the series of low-cycle repeated load experiments, we study the different performance between unreinforced brick wall and brick wall strengthened with reinforced concrete splint. Based on the analysis, we find the seismic capacity of the brick wall strengthened with reinforced concrete splint such as the bearing capacity and ductility is enhanced clearly. Meanwhile, the calculation parameter in technical specification for seismic strengthening of buildings has good accordance with the experiment results.

Influences of Ice-Snow on Capacity of Signalized Intersection and the Minimum Green Time

In order to evaluate traffic operation status of signalized intersection and improve pedestrian traffic safety under the condition of ice-snow, it was studied that the influence of ice-snow on capacity of signalized intersection and the minimum green time. Saturated headway data of nine signalized intersections were observed by video method. And the influence of ice-snow melting pavement, compacted partly snowy pavement, compacted snowy pavement and normal pavement on saturated flow rate of signalized intersection were analyzed respectively. Correction coefficients of capacity of signalized intersection on different ice-snow pavement were given. Pedestrian’s crossing speed at nine signalized intersection on snowy pavement, icy pavement and normal pavement were observed and compared. And then the suggestion values of minimum green time calculation parameter were put forward.

Von der Nachhaltigkeit als Beschränkung zur nachhaltigen Entwicklung als Programm | From Sustainability as a Limiting Factor to a Sustainable Development as a Policy

The development of sustainability is presented on the basis of quotations from German forestry literature published from the 17th century up until now. At the beginning of this time period, the demand for sustainability was limited to the exploitation of the increment. However, in the 19th century,the conservation of the site's production capacity was included and ‹sustainability› was backed up by arguments such as the forest’s role within the forest economy. In the 20th century,sustainability developed from a mere calculation parameter to a behavioural norm with regard to all interventions dealing with forest and ecosystems.