A framework for the simulation of structural software evolution

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2008 ACM.As functionality is added to an aging piece of software, its original design and structure will tend to erode. This can lead to high coupling, low cohesion and other undesirable effects associated with spaghetti architectures. The underlying forces that cause such degradation have been the subject of much research. However, progress in this field is slow, as its complexity makes it difficult to isolate the causal flows leading to these effects. This is further complicated by the difficulty of generating enough empirical data, in sufficient quantity, and attributing such data to specific points in the causal chain. This article describes a framework for simulating the structural evolution of software. A complete simulation model is built by incrementally adding modules to the framework, each of which contributes an individual evolutionary effect. These effects are then combined to form a multifaceted simulation that evolves a fictitious code base in a manner approximating real-world behavior. We describe the underlying principles and structures of our framework from a theoretical and user perspective; a validation of a simple set of evolutionary parameters is then provided and three empirical software studies generated from open-source software (OSS) are used to support claims and generated results. The research illustrates how simulation can be used to investigate a complex and under-researched area of the development cycle. It also shows the value of incorporating certain human traits into a simulation—factors that, in real-world system development, can significantly influence evolutionary structures

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

New methodology for calculating damage variables evolution in Plastic Damage Model for RC structures

The behavior of reinforced concrete (RC) structures under severe demands, as strong ground motions, is highly complex; this is mainly due to joint operation of concrete and steel, with several coupled failure modes. Furthermore, given the increasing awareness and concern for the important seismic worldwide risk, new developments have arisen in earthquake engineering. Nonetheless, simplified numerical models are widely used (given their moderate computational cost), and many developments rely mainly on them. The authors have started a long-term research whose final objective is to provide, by using advanced numerical models, solid basis for these developments. Those models are based on continuum mechanics, and consider Plastic Damage Model to simulate concrete behavior. Within this context, this paper presents a new methodology to calculate damage variables evolution; the proposed approach is based in the Lubliner/Lee/Fenves formulation and provides closed-form expressions of the compressive and tensile damage variables in terms of the corresponding strains. This methodology does not require calibration with experimental results and incorporates a strategy to avoid mesh-sensitivity. A particular algorithm, suitable for implementation in Abaqus, is described. Mesh-insensitivity is validated in a simple tension example. Accuracy and reliability are verified by simulating a cyclic experiment on a plain concrete specimen. Two laboratory experiments consisting in pushing until failure two 2-D RC frames are simulated with the proposed approach to investigate its ability to reproduce actual monotonic behavior of RC structures; the obtained results are also compared with the aforementioned simplified models that are commonly employed in earthquake engineering.Postprint (published version

Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material

Modeling structural change in spatial system dynamics: A Daisyworld example

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed

A modern vision of simulation modelling in mining and near mining activity

The paper represents the creation of the software simulation system, which reproduce the basic processes of mining and near production. It presents the consideration of such systems for both traditional and non-traditional mineral extraction systems. The principles of using computer recognition of processes are also presented in other processes of carbon-containing raw materials transition, as well as power production and waste utilization of mining production. These systems considerably expand the manageability of a rather complicated mining enterprise. The main purpose of such research is the simulation reproduction of all technological processors associated with the activity of mining enterprises on the display of the dispatch center. For this purpose, is used so-called UML-diagrams, which allows to simulate mining and near mining processes. Results of this investigation were included to the Roman Dychkovskyi thesis of the scientific degree of the Doctor of the Technique Sciences “Scientific Principles of Technologies Combination for Coal Mining in Weakly Metamorphoses Rockmass”

SimpactCyan 1.0 : an open-source simulator for individual-based models in HIV epidemiology with R and Python interfaces

SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework