Open-source Suite Research Articles

On-the-Fly Unsteady Adjoint Aerodynamic and Aeroacoustic Optimization Method

An on-the-fly unsteady adjoint-based aerodynamic and aeroacoustic optimization methodology is presented, aiming to achieve practical engineering applications to explore high-efficiency and low-noise design for aerodynamic shapes. Firstly, a novel on-the-fly hybrid CFD-CAA approach is developed with a close integration of unsteady Reynolds-averaged Navier–Stokes equations and a fully viscous time-domain FW-H formulation. Subsequently, an adjoint-based sensitivity analysis method is proposed for unsteady aerodynamic and aeroacoustic problems with either stationary or moving boundaries, wherein a unified architecture for discrete-adjoint sensitivity analysis of both aerodynamics and aeroacoustics is achieved by integrating the on-the-fly hybrid CFD-CAA approach. The on-the-fly approach facilitates direct evaluation of partial derivatives required for solving adjoint equations, eliminating the need for explicitly preprocessing flow and adjoint variables at all time levels in a standalone adjoint CAA solver and consequently substantially reducing memory consumption. The proposed optimization methodology is implemented within an open-source suite SU2. Results show that the proposed on-the-fly adjoint methodology is capable of achieving highly accurate sensitivity derivatives while significantly reducing memory requirements by an order of magnitude, and further demonstrations of single-objective and coupled aerodynamic and aeroacoustic optimizations highlight the potential of the proposed method in exploring high-efficiency and low-noise design for aerodynamic shapes.

ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications

BackgroundProcessing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another, in a disjointed stepwise fashion, increases the difficulty and sets forth higher error rates because of fragmented job executions in alignment, variant calling, and/or build conversion complications. As sequencing data availability grows, the ability for biologists to process it using stable, automated, and reproducible workflows is paramount as it significantly reduces the time to generate clean and reliable data.ResultsThe Iliad suite of genomic data workflows was developed to provide users with seamless file transitions from raw genomic data to a quality-controlled variant call format (VCF) file for downstream applications. Iliad benefits from the efficiency of the Snakemake best practices framework coupled with Singularity and Docker containers for repeatability, portability, and ease of installation. This feat is accomplished from the onset with download acquisitions of any raw data type (FASTQ, CRAM, IDAT) straight through to the generation of a clean merged data file that can combine any user-preferred datasets using robust programs such as BWA, Samtools, and BCFtools. Users can customize and direct their workflow with one straightforward configuration file. Iliad is compatible with Linux, MacOS, and Windows platforms and scalable from a local machine to a high-performance computing cluster.ConclusionIliad offers automated workflows with optimized time and resource management that are comparable to other workflows available but generates analysis-ready VCF files from the most common datatypes using a single command. The storage footprint challenge of genomic data is overcome by utilizing temporary intermediate files before the final VCF is generated. This file is ready for use in imputation, genome-wide association study (GWAS) pipelines, high-throughput population genetics studies, select gene candidate studies, and more. Iliad was developed to be portable, compatible, scalable, robust, and repeatable with a simplistic setup, so biologists that are less familiar with programming can manage their own big data with this open-source suite of workflows.

Multi-scale simulations of two dimensional material based devices: the NanoTCAD ViDES suite

NanoTCAD ViDES (Versatile DEvice Simulator) is an open-source suite of computing codes aimed at assessing the operation and the performance of nanoelectronic devices. It has served the computational nanoelectronic community for almost two decades and it is freely available to researchers around the world in its website (http://vides.nanotcad.com), being employed in hundreds of works by many electronic device simulation groups worldwide. We revise the code structure and its main modules and we present the new features directed towards (i) multi-scale approaches exploiting ab-initio electron-structure calculations, aiming at the exploitation of new physics in electronic devices, (ii) the inclusion of arbitrary heterostructures of layered materials to devise original device architectures and operation, and (iii) the exploration of novel low-cost, green technologies in the mesoscopic scale, as, e.g. printed electronics.

Numerical Study of Flow Control on Simplified High-Lift Configurations

Enhancement in the aerodynamic performance of wings and airfoils is very notable when Active Flow Control (AFC) is applied to Short Take-off and Landing aircraft (STOL). The present numerical study shows the application of steady, pulsed and synthetic tangential jets applied to the plain flap shoulder of a modified NASA Trapezoidal Wing. Pulsed jets are modeled by sinusoidal and square waveforms while synthetic jets are modeled only by pure sine waveform. The freestream airflow conditions are Mach number equal to 0.2 and Reynolds number equal to 4.3 million based on the mean aerodynamic chord. The presented simulations are two-dimensional and based on RANS for steady jet cases and URANS for pulsed and synthetic cases, compiled with the open-source suite SU2 and adapted for time varying boundary conditions. Numerical results for modified configurations based on the same baseline wing profile considering different leading edges, jet slot height, flap position, blowing mass flow, type and frequency of the jets are presented. Curves of pressure coefficient distribution revealed a substantial influence upstream of the AFC, around the slat and main element. The jet slot height analysis showed that the lift gain is also influenced by the slot size due to the change of the local flow velocity considering the same blowing momentum coefficient. Regarding the jet frequency, no significant differences on the lift coefficients were found between the reduced frequencies F+ equal to 1 and 2. Results of aerodynamic loads showed an improved lift coefficient in relation to the baseline airfoil when pulsed and steady jets are employed. Pulsed jets under square waveform were effective even at high deflected flap condition at 50°, with a significant gain in the lift coefficient of 36%, in relation to the uncontrolled case, combined with a drag reduction of 20%, and a decrease in mass flow up to 49% in relation to the steady jet for the same lift gain. Although sine and square waveform results presented similar improvements for lift, the drag is around 15% higher for the former. When compared with the steady jet case, the mass flow reduction is 36% for the sinewave. Synthetic jets with zero-net-mass-flux proved superior to the baseline conventional multi-element airfoil only with deployed flap at 50°, where a modest lift improvement of 5% was observed.

Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline.

Cellular cryo-electron tomography (cryo-ET) enables three-dimensional reconstructions of organelles in their native cellular environment at subnanometer resolution. However, quantifying ultrastructural features of pleomorphic organelles in three dimensions is challenging, as is defining the significance of observed changes induced by specific cellular perturbations. To address this challenge, we established a semiautomated workflow to segment organellar membranes and reconstruct their underlying surface geometry in cryo-ET. To complement this workflow, we developed an open-source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics pipeline. This pipeline enables rapid modeling of complex membrane structures and allows detailed mapping of inter- and intramembrane spacing, curvedness, and orientation onto reconstructed membrane meshes, highlighting subtle organellar features that are challenging to detect in three dimensions and allowing for statistical comparison across many organelles. To demonstrate the advantages of this approach, we combine cryo-ET with cryo-fluorescence microscopy to correlate bulk mitochondrial network morphology (i.e., elongated versus fragmented) with membrane ultrastructure of individual mitochondria in the presence and absence of endoplasmic reticulum (ER) stress. Using our pipeline, we demonstrate ER stress promotes adaptive remodeling of ultrastructural features of mitochondria including spacing between the inner and outer membranes, local curvedness of the inner membrane, and spacing between mitochondrial cristae. We show that differences in membrane ultrastructure correlate to mitochondrial network morphologies, suggesting that these two remodeling events are coupled. Our pipeline offers opportunities for quantifying changes in membrane ultrastructure on a single-cell level using cryo-ET, opening new opportunities to define changes in ultrastructural features induced by diverse types of cellular perturbations.

The new GeoModel suite, a lightweight detector description and visualization toolkit for HEP

The GeoModel toolkit is an open-source suite of standalone tools that provides the user with lightweight tools to describe, visualize, test, and debug detector descriptions and geometries for HEP standalone studies and experiments. GeoModel has been designed with independence and responsiveness in mind and offers a development environment free of other large HEP tools and frameworks, and with a very quick development cycle. With very few and lightweight dependencies, GeoModel is easy to install on all systems, in a modular way; and pre-compiled binaries are provided for the major platforms, for a quick and easy installation. Coded entirely in C++, GeoModel offers the user tools to describe geometries inside C++ code or in external XML files, create persistent representation with a low disk footprint and interactively visualize and inspect the geometry in a 3D view. It also offers a plugin mechanism and an optional Geant4 application to simulate the described geometry in a standalone environment. GeoModel has been developed as part of the software for the ATLAS experiment at the LHC, and evolved towards an experiment-independent toolkit. In this contribution, we describe all the available tools, with a focus on the latest additions, which provide users with more visualization, debug, and simulation tools.

Nonlinear dynamic verification of the boron injection lances for the Atucha-I Nuclear Power Plant

This work deals with the nonlinear transient dynamic verification of the boron injection lances for the Atucha-1 Pressurized Heavy Water Reactor backup shutdown system. The lances inside the moderator tank constitute the end part of the fast boron injection piping. The current dynamic verification of the lances is performed in the context of modifications in the piping and valve configuration for Atucha-I Long Term Operation (LTO). It is intended to ensure the structural integrity of the lances in the event of Loss of Coolant Accidents (LOCA) and spurious opening of level control valves (Spurious) scenarios. All boundary conditions have been provided by Nucleoeléctrica Argentina S.A. (NA-SA), and a 3-D numerical model of the lances was built and analyzed with the open-source suite Salome-Meca v2019 using the Code_Aster finite element solver. Results indicate that the displacement of the lances does not produce collisions with other reactor internals and that stresses on the lances and their fastening bolts are low enough to ensure the correct function of the system during LTO period.

Application-Oriented Performance Benchmarks for Quantum Computing

In this work we introduce an open source suite of quantum application-oriented performance benchmarks that is designed to measure the effectiveness of quantum computing hardware at executing quantum applications. These benchmarks probe a quantum computer's performance on various algorithms and small applications as the problem size is varied, by mapping out the fidelity of the results as a function of circuit width and depth using the framework of volumetric benchmarking. In addition to estimating the fidelity of results generated by quantum execution, the suite is designed to benchmark certain aspects of the execution pipeline in order to provide end-users with a practical measure of both the quality of and the time to solution. Our methodology is constructed to anticipate advances in quantum computing hardware that are likely to emerge in the next five years. This benchmarking suite is designed to be readily accessible to a broad audience of users and provides benchmarks that correspond to many well-known quantum computing algorithms.

Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores.

This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible data analysis in transcriptomic and epitranscriptomic studies. We introduce the key concepts of MoP2 and provide a step-by-step fully reproducible and complete example of how to use the workflow for the analysis of S. cerevisiae total RNA samples sequenced using MinION flowcells. The workflow starts with the pre-processing of raw FAST5 files, which includes basecalling, read quality control, demultiplexing, filtering, mapping, estimation of per-gene/transcript abundances, and transcriptome assembly, with support of the GPU computing for the basecalling and read demultiplexing steps. The secondary analyses of the workflow focus on the estimation of RNA poly(A) tail lengths and the identification of RNA modifications. The MoP2 code is available at https://github.com/biocorecrg/MOP2 and is distributed under the MIT license.

Assessment of a Point-Cloud Volume-of-Fluid method with sharp interface advection

Multiphase flows are ubiquitous in nature and industry. In order to fully describe multiphase systems, simulation approaches must be able to handle the interfaces separating the different phases properly. The Volume of Fluid (VOF) approach is widely used by researchers and engineers due to its intrinsic ability to conserve volume and handle large interface topology changes. A common problem that occurs in VOF Methods relates to the calculation of interfacial tension forces in the momentum equations while resolving a sharp interface. Common methods based on the gradients of the volume fraction field may lack accuracy due to the curvature and normal vector estimates through an abrupt transition. To address these points, the present work introduces a new proposal, where the VOF method based on a cloud of points for interface curvatures computation (PC-VOF) is extended by the coupling with the sharp-interface advection algorithm isoAdvector, implemented in the open source suite OpenFOAM®. The coupled method performs better than the ones implemented in the original solvers in a number of benchmark cases from the literature. It is shown to significantly reduce the spurious currents and also presents more stable and accurate results, especially for irregular triangular meshes.

Pressurized turbulent premixed CH4/H2/air flame validation using OpenFOAM

In this study, we use the Algebraic Flame Surface Wrinkling (AFSW) model to conduct numerical simulations of the PSI (Paul Scherrer Institute) high pressure, turbulent premixed Bunsen flame experiments. The AFSW model was implemented in the open-source computational fluid dynamics solver OpenFOAM, and the numerical simulations were performed using a two-dimensional axial-symmetric model with the standard k–ɛ turbulence model with wall functions. The numerical simulations were performed for two different fuel/air mixtures, namely, 100% CH4 volumetric ratio and 60% CH4 + 40% H2 volumetric ratio. The thermophysical and transport properties of the mixture were calculated as a function of temperature using the library Cantera (an open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes), together with the GRI-Mech 3.0 chemical mechanism. It was found that the outcome of the AFSW model implemented in OpenFOAM was in good agreement with the experimental results, quantitatively and qualitatively. Further assessment of the results showed that, as much as the chemistry, the turbulence model and turbulent boundary/initial conditions significantly impact the flame shape and height.

PyCSP: A Python package for the analysis and simplification of chemically reacting systems based on Computational Singular Perturbation

PyCSP is a Python package for the analysis and simplification of chemically reacting systems, using algorithms based on the Computational Singular Perturbation (CSP) theory. It provides tools for the local characterization of the chemical dynamics, enabled by the recognition of a convenient projection basis which carries out a timescale-based uncoupling. The tools supplied within the package allow one to identify the rate-controlling chemical reactions, the intrinsic chemical timescales, the driving chemical timescale and indicators of the system's explosive or dissipative propensity. Possible applications are the analysis of numerical simulations of reacting flows, and the reduction of chemical kinetics models, based on the CSP information. This manuscript provides a brief overview of the foundations of CSP, a description of the libraries, and demonstrations of the features implemented in PyCSP with code examples, along with practical advices and guidelines for users. Program summaryProgram Title:PyCSPCPC Library link to program files:https://doi.org/10.17632/59pw7pvkkb.1Developer's repository link:https://github.com/rmalpica/PyCSPLicensing provisions: MITProgramming language: PythonSupplementary material: Code documentation and Python scripts employed to generate the figures.Nature of problem: The evermore increasing availability of high-performance computing resources, and the compelling need for more advanced and sustainable energy conversion devices, based on unconventional combustion regimes and alternative fuels, are driving towards an unprecedented massive production of data in numerical simulations of reacting flows. The research questions behind the production of such huge datasets are typically related to (i) the fundamental understanding of combustion phenomena, and (ii) the development of reduced order models and/or turbulence-chemistry interaction sub-grid scale (closure) models, both with the aim of accelerating large scale simulations of real combustion devices.Solution method: Both categories of research questions can widely benefit from the numerical tools available in PyCSP. The computational singular perturbation (CSP) framework allows one to extract concise information from chemically reacting systems, automatically and at reasonable cost. This is especially useful when the dataset is so massive and the number of degrees of freedom so large, i.e., hundreds of species/reactions per cell, that even a visual inspection becomes unmanageable. PyCSP offers a fast, user-friendly implementation of numerous analysis tools, enabling a more systematic data processing and, ultimately, providing the user with a deeper physical understanding of the problem under investigation. Moreover, the CSP theoretical framework can be exploited to generate reduced order models (ROMs), tailored to and to be employed in specific applications, in order to drastically reduce the computational cost of a numerical simulation, while retaining accuracy in global observables. The ROM is in the form of a skeletal kinetic mechanism of adjustable fidelity, or an adaptive chemistry integrator.Additional comments including restrictions and unusual features:PyCSP relies on Cantera, an open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes, to efficiently incorporate detailed chemical thermo-kinetics models into the CSP calculations.

Scalable and accessible personalized photodynamic therapy optimization with FullMonte and PDT-SPACE.

.Significance: Open-source software packages have been extensively used in the past three decades in medical imaging and diagnostics, aiming to study the feasibility of the application ex vivo. Unfortunately, most of the existing open-source tools require some software engineering background to install the prerequisite libraries, choose a suitable computational platform, and combine several software tools to address different applications.Aim: To facilitate the use of open-source software in medical applications, enabling computational studies of treatment outcomes prior to the complex in-vivo setting.Approach: FullMonteWeb, an open-source, user-friendly web-based software with a graphical user interface for interstitial photodynamic therapy (iPDT) modeling, visualization, and optimization, is introduced. The software can perform Monte Carlo simulations of light propagation in biological tissues, along with iPDT plan optimization. FullMonteWeb installs and runs the required software and libraries on Amazon Web Services (AWS), allowing scalable computing without complex set up.Results: FullMonteWeb allows simulation of large and small problems on the most appropriate compute hardware, enabling cost improvements of versus always running on a single platform. Case studies in optical property estimation and diffuser placement optimization highlight FullMonteWeb’s versatility.Conclusion: The FullMonte open source suite enables easier and more cost-effective in-silico studies for iPDT.

Integrative Toolkit to Analyze Cellular Signals: Forces, Motion, Morphology, and Fluorescence

Quantitative assessment of cellular forces and motion advanced considerably over the last four decades. These advancements provided the framework to examine insightful mechanical signaling processes in cell culture systems. However, the field currently faces three problems: lack of quality standardization of the acquired data, technical errors in data analysis and visualization, and perhaps most importantly, the technology remains largely out of reach for common cell biology laboratories. To overcome these limitations, we developed a new experimental platform - Integrative Toolkit to Analyze Cellular Signals (iTACS). iTACS consists of two components: Acquisition and Training Module (AcTrM) and Analysis and Visualization Module (AnViM). AcTrM is based on µManager - an NIH-ImageJ-based microscope control software - and facilitates user self-training and automation of common image acquisition protocols. AnViM is based on NIH-ImageJ and facilitates user-friendly automation of data analysis and insightful visualization of results. These experiments involve culturing adherent cells on hydrogels, imaging fiducial markers embedded in the hydrogel, and finally extracting from these images a comprehensive mechanical characterization of the cells. Currently, iTACS enables the user to analyze and track a wide array of properties, including morphology, motion, cytoskeletal forces, and fluorescence of individual cells and their neighboring region. The quality standardization issue was addressed in AcTrM with, a reference image-guided refocusing technique. The technical issues in data analysis were addressed in AnViM with a multi-pronged image segmentation procedure, a user-friendly approach to identify boundary conditions, and a novel cellular property-based data visualization. AcTrM is designed to facilitate the straightforward transformation of basic fluorescence microscopes into experimental cell mechanics rigs, and AnViM is equipped to enable users to measure cellular mechanical signals without requiring an engineering background. iTACS will be available to the research community as an open-source suite with community-driven development capabilities.

Integrative Toolkit to Analyze Cellular Signals: Forces, Motion, Morphology, and Fluorescence.

Quantitative assessment of cellular forces and motion advanced considerably over the last four decades. These advancements provided the framework to examine insightful mechanical signaling processes in cell culture systems. However, the field currently faces three problems: lack of quality standardization of the acquired data, technical errors in data analysis and visualization, and perhaps most importantly, the technology remains largely out of reach for common cell biology laboratories. To overcome these limitations, we developed a new experimental platform - Integrative Toolkit to Analyze Cellular Signals (iTACS). iTACS consists of two components: Acquisition and Training Module (AcTrM) and Analysis and Visualization Module (AnViM). AcTrM is based on µManager - an NIH-ImageJ-based microscope control software - and facilitates user self-training and automation of common image acquisition protocols. AnViM is based on NIH-ImageJ and facilitates user-friendly automation of data analysis and insightful visualization of results. These experiments involve culturing adherent cells on hydrogels, imaging fiducial markers embedded in the hydrogel, and finally extracting from these images a comprehensive mechanical characterization of the cells. Currently, iTACS enables the user to analyze and track a wide array of properties, including morphology, motion, cytoskeletal forces, and fluorescence of individual cells and their neighboring region. The quality standardization issue was addressed in AcTrM with, a reference image-guided refocusing technique. The technical issues in data analysis were addressed in AnViM with a multi-pronged image segmentation procedure, a user-friendly approach to identify boundary conditions, and a novel cellular property-based data visualization. AcTrM is designed to facilitate the straightforward transformation of basic fluorescence microscopes into experimental cell mechanics rigs, and AnViM is equipped to enable users to measure cellular mechanical signals without requiring an engineering background. iTACS will be available to the research community as an open-source suite with community-driven development capabilities.

Turbulent Premixed Flame Modeling Using the Algebraic Flame Surface Wrinkling Model: A Comparative Study between OpenFOAM and Ansys Fluent

Hereafter, we used the Algebraic Flame Surface Wrinkling (AFSW) model to conduct numerical simulations of the Paul Scherrer Institute (PSI) high-pressure, turbulent premixed Bunsen flame experiments. We implemented the AFSW model in OpenFOAM and in Ansys Fluent, and we compared the outcome of both solvers against the experimental results. We also highlight the differences between both solvers. All the simulations were performed using a two-dimensional axisymmetric model with the standard k−ϵ turbulence model with wall functions. Two different fuel/air mixtures were studied, namely, a 100%CH4 volumetric ratio and a 60%CH4+ 40%H2 volumetric ratio. The thermophysical and transport properties of the mixture were calculated as a function of temperature using the library Cantera (open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes), together with the GRI-Mech 3.0 chemical mechanism. It was found that the outcome of the AFSW model implemented in both solvers was in good agreement with the experimental results, quantitatively and qualitatively speaking. Further assessment of the results showed that, as much as the chemistry, the turbulence model and turbulent boundary/initial conditions significantly impact the flame shape and height.

An Updated Experimental Evaluation of Graph Bipartization Methods

We experimentally evaluate the practical state-of-the-art in graph bipartization (Odd Cycle Transversal (OCT)), motivated by the need for good algorithms for embedding problems into near-term quantum computing hardware. We assemble a preprocessing suite of fast input reduction routines from the OCT and Vertex Cover (VC) literature and compare algorithm implementations using Quadratic Unconstrained Binary Optimization problems from the quantum literature. We also generate a corpus of frustrated cluster loop graphs, which have previously been used to benchmark quantum annealing hardware. The diversity of these graphs leads to harder OCT instances than in existing benchmarks. In addition to combinatorial branching algorithms for solving OCT directly, we study various reformulations into other NP-hard problems such as VC and Integer Linear Programming (ILP), enabling the use of solvers such as CPLEX. We find that for heuristic solutions with time constraints under a second, iterative compression routines jump-started with a heuristic solution perform best, after which point using a highly tuned solver like CPLEX is worthwhile. Results on exact solvers are split between using ILP formulations on CPLEX and solving VC formulations with a branch-and-reduce solver. We extend our results with a large corpus of synthetic graphs, establishing robustness and potential to generalize to other domain data. In total, over 8,000 graph instances are evaluated, compared to the previous canonical corpus of 100 graphs. Finally, we provide all code and data in an open source suite, including a Python API for accessing reduction routines and branching algorithms, along with scripts for fully replicating our results.

Virtualization Costs: Benchmarking Containers and Virtual Machines Against Bare-Metal

DevOps advocates the usage of Virtualization Technologies (VT), such as Virtual Machines and Containers. However, it is complex to predict how the usage of a given VT will impact on the performance of an application. In this paper, we present a collection of reference benchmarks that developers can use to orient when looking for the best-performing VT w.r.t their application profile. To gather our benchmarks in a resource-wise comprehensive and comparable way, we introduce VTmark: a semi-automatic open-source suite that assembles off-the-shelf tools for benchmarking the different resources used by applications (CPU, RAM, etc.). After performing a survey of VTs in the market, we use VTmark to report the benchmarks of 6 of the most widely adopted and popular ones, namely Docker, KVM, Podman, VMWare Workstation, VirtualBox, and Xen. To validate the accuracy of our reference benchmarks, we show how they correlate with the profile performance of a production-grade application ported and deployed on the considered VTs. Beyond our immediate results, VTmark let us shed light on some contradicting findings in the related literature and, by releasing VTmark , we provide DevOps with an open-source, extendable tool to assess the (resource-wise) costs of VTs.

HeapCraft: Quantifying and Predicting Collaboration in Minecraft

We present Heapcraft: an open-source suite of tools for monitoring and improving collaboration in Minecraft. At the core of our system is a data collection and analysis framework for recording gameplay. We collected over 3451 player-hours of game behavior from 908 different players, and performed a general study of online collaboration. To make our game analytics easily accessible, we developed interactive information visualization tools and an analysis framework for players, administrators, and researchers to explore graphs, maps and timelines of live server activity. As part of our research, we introduce the collaboration index, a metric which allows server administrators and researchers to quantify, predict, and improve collaboration on Minecraft servers. Our analysis reveals several possible predictors of collaboration which can be used to improve collaboration on Minecraft servers. Heapcraft is designed to be general, and has the potential to be used for other shared online virtual worlds.

Implementation of the Marchenko multiple elimination algorithm

The Marchenko multiple elimination (MME) and transmission compensation schemes retrieve primary reflections in the two-way traveltime domain without model information or using adaptive subtraction. Both schemes are derived from projected Marchenko equations and are similar to each other, but they use different time-domain truncation operators. The MME scheme retrieves a new data set without internal multiple reflections. The transmission-compensated Marchenko multiple elimination scheme does the same and additionally compensates for transmission losses in the primary reflections. Both schemes can be solved with an iterative algorithm based on a Neumann series. At each iteration, a convolution or correlation between the projected focusing function and the measured reflection response is performed, and, after each convolution or correlation, a truncation in the time domain is applied. After convergence, the resulting projected focusing function is used for retrieving the transmission-compensated primary reflections and the projected Green’s function is used for the physical primary reflections. We have determined that internal multiples are removed by using time-windowed input data that only contain primary reflections. We evaluate both schemes in detail and develop an iterative implementation that reproduces the presented numerical examples. The software is part of our open-source suite of programs and fits into the Seismic Unix software suite of the Colorado School of Mines.