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36 results for “Software Simulation”
Simulation results of adaptive multicast streaming for videoconferences in software-defined networks
<p>Real-time applications, such as video conferences, have strong Quality of Service requirements for ensuring a decent Quality of Experience. Nowadays, most of these conferences are performed over wireless devices. Thus, an appropriate management of both heterogeneous mobile devices and network dynamics is necessary. Software Defined Networking enables the use of multicasting and stream layering inside the network nodes, two techniques able to enhance the quality of live video streams. In this paper, we propose two algorithms for building and maintaining multicast sessions in a software-defined network. The first algorithm sets up the initial multicast trees for a given call. It optimally places the stream layer adaptation function inside the core network in order to minimize the bandwidth consumption. This algorithm has two versions: the first one, based on shortest path trees is minimizing the latency, while the second one, based on spanning trees is minimizing the bandwidth consumption. The second algorithm adapts the multicast trees according to the network changes occurring during a call. It does not recompute the trees, but only relocates the stream layer adaptation functions. It requires very low computation at the controller, thus making our proposal fast and highly reactive. Extensive simulation results confirm the efficiency of our solution in terms of processing time and bandwidth savings compared to existing solutions such as multiple unicast connections, Multipoint Control Unit solutions and application layer multicast.</p>
MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples
<p>These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with <a href="https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm">ART-bin-MountRainier-2016.06.05</a> using real abundance profiles (.abund files) available <a href="https://doi.org/10.5281/zenodo.2560288">elsewhere</a>, and <a href="http://progenomes1.embl.de/data/repGenomes/representatives.contigs.fasta.gz">proGenomes' representative contigs</a> as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples:</p> <pre><code>SAMEA2466916 SAMEA2466953 SAMEA2466965 SAMEA2621107 SAMEA2621229 SAMEA2621247</code></pre> <p>To convert them from the CRAM format back to fastq files:</p> <pre><code> ## 1. converting from cram to bam format: samtools view -b -T refgenome.fa -o file.bam file.cram ## 2. sorting the bam file: samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n) ## 3. converting from bam to fastq format: bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq </code></pre> <p> </p>
Testing 3D modelling software. Modelling charging pads for WPT of electric vehicles for EM emissions simulation.
<p>Even for the experienced 3D FEM modelers it may not be obvious which geometry discretization is the most appropriate and suitable for this type of problem. It may be a conservative approach to test the computation tool on a simplified geometry, on which the magnetic field distribution is known. As part of the “Metrology for inductive charging of electric vehicles” (MICEV) project (www.micev.eu), an axisymmetric geometry was used, with the results reported.</p>
Survey on the usage of Mathematical Modelling, Simulation and Optimization software
<p>This dataset contains the result of a survey we carried out in the context of the MSO4SC project in order to know which kinds of tools for simulation were using our stakeholders. The purpose was to prioritize functionalities depending on stakeholders' preferences. It was a survey with 41 questions grouped in 10 areas (impact of simulation software on their entities, usage of pre/post-processing, usage of visualization, etc...). The pdf file includes the list of questions for clarification. Such survey was answered by academia and industry from several European countries.</p>
A Modified Doyle-Fuller-Newman Model Enables the Macroscale Physical Simulation of Dual-ion Batteries - Dataset and Software
<p>This dataset contains:</p> <p>- all the raw cycling data of the three-electrode cell used to gather the experimental data for the model validation (VMP data, exported with EC-LAB);<br>- the specific, processed data used in the model validation step (0.2C discharge, 5C discharge, EIS data);<br>- the COMSOL dual-ion battery model (version 6.0). IMPORTANT: activate the "Electric potential at the positive electrode current collector (only for EIS)" boundary condition when simulating impedance spectroscopy, and deactivate it when simulating charge/discharge curves; the charge-discharge profile can be modified by changing the duration of the test, the C-rate, and the conditions set in the "Events" section.</p> <p>Update: Fixed the model to work also in the 6.2 version of COMSOL (Substituted Dleff with Dleffxx in the modified weak expression of the cathode mass conservation equation). Download the new version!</p>
Simulation data and software scripts used in calculus of ∆36 signature from EMAC clumped O2 isotope-inclusive model
<p>This publication contains simulation data and software scripts for calculating quantities related to clumped oxygen isotope signature (∆<sub>36</sub>) derivation, as described in the "static" framework of Yeung‍ et‍ al. (2016), hereinafter "Y16") and subsequently used in Yeung‍ et‍ al.‍ (2019) analysis. We provide the output of the 1950–2011 transient simulation with EMAC model with explicit "dynamic" simulation of ∆<sub>36</sub> (i.e. <sup>18</sup>O<sup>18</sup>O isotopologues undergoing transport, mixing and O(<sup>3</sup>P)-mediated isotope equilibration) to demonstrate the importance of several assumptions/simplifications involved in the static calculus.</p> <p> </p> <p>Please refer to .README.pdf for details.</p>
Simulated benchmark metagenome used to demonstrate and evaluate MGLEX software
<p>This is a mock dataset of 120 000 artificial contigs of 1 kb length derived by simulating reads from 295 unique genomes and 44 species with each two or three strain genomes using the ART read simulator (Huang et al., 2012) and a lognormal abundance distribution. Genomes were chosen according to the CAMI2015 (www.cami-challenge.org) medium complexity toy dataset. The dataset contains four replicate samples with varied abundances and corresponding sequence feature files in MGLEX v0.1.1 format to use for genome reconstruction. Our aim was to create a benchmark dataset under controlled settings, minimizing potential biases introduced by specific software. This package also includes MGLEX benchmark scripts.</p>
Simulation data for benchmarking de novo long read transcriptome assembly software
<p>Method of simulation of differentially expressed biological replicates</p> <p>We first obtained a subset of transcripts that are widely expressed in the GTEx v9 dataset (92 samples) using Gencode comprehensive annotation (v44). We kept transcripts with more than 5 reads in at least 15 samples after Salmon quantification (18145 genes, 40509 transcripts), and stored their mean count per million (CPM) values as the control group’s baseline expression. We then generated a perturbed set of CPM values where transcript expression was changed by: (1) randomly selecting 1000 genes and changing all transcripts belonging to that gene concordantly (500 genes 2 fold up and 500 genes 2 fold down), (2) selected another 1000 genes randomly, and then select 2 random transcripts from the gene and swap their expression, (3) selected another 1000 genes randomly, and then select 1 random transcript to change its expression (500 transcripts 2 fold up and 500 transcripts 2 fold down). The updated CPM were stored as the perturbed group baseline expression. We then generated a count matrix and CPM matrix for 3 control replicates and 3 perturbed replicates with gamma distribution, followed by a Poisson distribution <a href="https://www.zotero.org/google-docs/?cUP4ui">(Baldoni et al., 2024)</a>. Both long-read and short-read FASTQ files were simulated using SQANTI-SIM with default settings and ONT R9.4 cDNA error profile (v 0.2.1) <a href="https://www.zotero.org/google-docs/?Qyopst">(Mestre-Tomás et al., 2023)</a>. The long read data contained 6 million reads in total, and an average read length of 1085 bp, and short read data was 100 bp paired-end. We then subsampled the short-read data to match the total number of base pairs in the long read data (6.5 billion bases). The simulated data was non-stranded, and contains 2000 DE genes, 2000 genes with DTU, 5927 transcripts with DTU and 6933 DE transcripts.</p> <p> </p>
Dataset and software to analyze and simulate neuronal morphogenesis in Drosophila class IV da neurons
<p>The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. Yet, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and discovered that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into a novel, agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell-types, as well as to branching at the subcellular and tissue levels.</p>
Figure 9. Experimental Page Rank dependency on Markov Chain length with balanced distribution-Study of a Random Navigation on the Web Using Software Simulation
<p>This paper explored different implementation choices for analyzing the most important<br> parameters about a web. Many researchers explored the use of new search engines for studying the<br> evolution of the web (Ntoulas, Cho and Olston, 2004). Another important research is realized about<br> the Link Structure Graph (LSG). The LSG captures a complete hyperlink structure from the web<br> and models link associations reflected in the page layout (Rodrigues, Milic-Frayling and Fortuna,<br> 2007). For further works ideas like extrapolation methods for accelerating page rank calculation can<br> be developed (Kamvar et al., 2003).</p>
Figure 7. Experimental Page Rank dependency on Markov Chain length-Study of a Random Navigation on the Web Using Software Simulation
<p>The next diagram proves that the values for Experimental Page Rank depend on the length<br> of the Markov Chain, while Algorithmic Page Rank remains constant.</p>
Figure 6. Outlinks degree distribution for all web sites-Study of a Random Navigation on the Web Using Software Simulation
<p>Some of the most important aspects of the analysis is obtaining the parameters which can<br> give the main information about a web. In the simulation implementation information as: page,<br> number of inlinks, number of outlinks, value for Algorithmic Page Rank and Experimental Page<br> Rank will be processed for obtaining the results of the analysis. For the first part it was necessary to<br> use experimental values as: inlinks, outlinks and in and out frequencies.</p>
Figure 1. Markov Chain Model&Figure 2. Transition matrix-Study of a Random Navigation on the Web Using Software Simulation
<p>For a good simulation it is very important to find methods for<br> navigating through the web (Levene and Wheeldon, 2004). John Kemeny and Laurie Snell have<br> proposed the use of Markov models for web simulations (Kemeny and Snell, 1960). Cadez et al. (2000)<br> used Markov models for classifying the sessions into different categories for browsers. Some other<br> proposed techniques choose to combine different order Markov models for obtaining low state<br> complexity and improving accuracy, as Deshpande and Karypis (2004). Dongshan and Junyi (2002)<br> used for predicting the access providing good scalability and high coverage a hybrid-order tree-like<br> Markov model. As an alternative to the Markov model Pitkow proposed a longest subsequence model<br> (Pitkow and Pirolli, 1999), also for predicting the next page accessed by the user Sarukkai chose<br> Markov models (Sarukkai, 2000).<br> Transitions are simulated using the Markov Chain nodes, Google matrix and an arbitrary initial<br> probability distribution. Examples can be seen in Figure 1 and Figure 2.</p>
Fig. 8. Algorithmic Page Rank-Study of a Random Navigation on the Web Using Software Simulation
<p>Another diagram shows that for each site there is only one constant value independent of the<br> length of Markov Chain. Algorithmic Page Rank only depends on the number of inlinks and<br> outlinks.Table 4 contains the values for Experimental Page Rank with balanced distribution. In the<br> following figure it is shown the diagram for the values obtained for Experimental Page Rank.<br> The Experimental Page Rank values oscillate between the same limits independently of the<br> change of Markov Chain length (N).</p>
Dataset and software to analyze and simulate neuronal morphogenesis in Drosophila class IV da neurons
Open the record for dataset details and reuse information.
Lulu - a software simulator for P colonies. Use case scenarios and demonstration videos
<p>The videos show three different examples of using the Lulu P colony simulator.</p> <p>The Lulu P colony simulator is available under an open-source MIT license at https://github.com/andrei91ro/lulu_pcol_sim. All of the secondary applications, including Lulu_Kilobot are available (also under open-source licenses) at https://github.com/andrei91ro.</p> <p>The first two videos present the simulator running addition (+1) and subtraction (-1). In these two examples, the simulator is ran in a step by step mode in order to clearly visualize the results of running each simulation step. For this reason the total simulation time reported at the end of the simulation is in the order of minutes.</p> <p>The average (of five runs) simulation time for a normal (non-interactive) simulation is 0.0021050 seconds for the addition and 0.0047492 seconds for the subtraction examples.</p> <p>The third example (lulu_kilobot_30_steps) presents the simulator running a more complex P colony that controls a Kilobot robot simulated in V-REP. This P colony is based on the subtraction P colony in the sense that each move the robot makes is marked by the removal of an f object from the environment.</p> <p>The input file used in the addition example (lulu_sim_ag_increment):</p> <p>pi = {<br /> A = {l_p};<br /> e = e;<br /> f = f;<br /> n = 2;<br /> env = {f, f, f, l_p};<br /> B = {AG_1};<br /> AG_1 = ({e, e}; < e->f, e<->l_p >, < l_p->e, f<->e >);<br /> }</p> <p>The input file used in the subtraction example (lulu_sim_ag_decrement):</p> <p>pi = {<br /> A = {l_m, l_p, l_z};<br /> e = e;<br /> f = f;<br /> n = 2;<br /> env = {f, f, f, l_m};<br /> B = {AG_1};<br /> AG_1 = ({e, e};<br /> < e->e, e<->l_m >,<br /> < l_m->l_p, e<->f/e<->e >,<br /> < f->e, l_p<->e >,<br /> < l_p->l_z, e<->e >,<br /> < e->e, l_z<->e > );<br /> }</p> <p>The input file used in the Kilobot example (lulu_kilobot_30_steps):</p> <p>pi = {<br /> A = {l_m, m_0, m_S, m_L, m_R, c_R, c_G, c_B};<br /> e = e;<br /> f = f;<br /> n = 2;<br /> env = {f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, f, l_m};<br /> B = {AG_command, AG_motion};<br /> AG_command = ({e, e};<br /> < e->e, e<->l_m >,<br /> < l_m->m_S, e<->f/e<->e >,<br /> < f->e, m_S<->e >,<br /> < m_S->m_0, e<->e >,<br /> < e->e, m_0<->e > );</p> <p> AG_motion = ({e, e};<br /> < e->l_m, e<->m_S >,<br /> < m_S->e, l_m<->e/e->e ><br /> < e->e, e<->m_0 >,<br /> < m_0->e, e<->m_0/e->e >);<br /> }</p> <p> </p>
Simulations of FLEXPART-WRF used for testing TRansport Of water VApor (TROVA) software (Part II)
<p>Necessary data for carrying out the tests using TRansport Of water VApor (TROVA) software for backward in time. The TROVA software, was developed in Python and Fortran for the study of moisture sources and sinks. <span><span><span>In addition, the Python code is provided for the representation of the results.</span></span></span></p>
Dataset for Cost-effective Simulation-based Test Selection in Self-driving Cars Software with SDC-Scissor
<p><strong>SDC-Scissor tool for Cost-effective Simulation-based Test Selection in Self-driving Cars Software</strong></p> <p>This dataset provides test cases for self-driving cars with the BeamNG simulator. Check out the repository and demo video to get started.</p> <p><strong>GitHub:</strong> <a href="https://github.com/ChristianBirchler/sdc-scissor">github.com/ChristianBirchler/sdc-scissor</a></p> <p>This project extends the tool competition platform from the <a href="https://github.com/se2p/tool-competition-av">Cyber-Phisical Systems Testing Competition</a> which was part of the <a href="https://sbst21.github.io/">SBST Workshop in 2021</a>.</p> <p><strong>Usage</strong></p> <p><strong>Demo</strong></p> <p> <a href="https://youtu.be/Cn8p648KnfQ">YouTube Link</a></p> <p><strong>Installation</strong></p> <p>The tool can either be run with <a href="https://docs.docker.com/get-docker/">Docker</a> or locally using <a href="https://python-poetry.org/docs/">Poetry</a>.</p> <p>When running the simulations a working installation of <a href="https://beamng.gmbh/research/">BeamNG.research</a> is required. Additionally, this simulation cannot be run in a Docker container but must run locally.</p> <p>To install the application use one of the following approaches:</p> <ul> <li>Docker: <code>docker build --tag sdc-scissor .</code></li> <li>Poetry: <code>poetry install</code></li> </ul> <p><strong>Using the Tool</strong></p> <p>The tool can be used with the following two commands:</p> <ul> <li>Docker: <code>docker run --volume "$(pwd)/results:/out" --rm sdc-scissor [COMMAND] [OPTIONS]</code> (this will write all files written to <code>/out</code> to the local folder <code>results</code>)</li> <li>Poetry: <code>poetry run python sdc-scissor.py [COMMAND] [OPTIONS]</code></li> </ul> <p>There are multiple commands to use. For simplifying the documentation only the command and their options are described.</p> <ul> <li>Generation of tests: <ul> <li><code>generate-tests --out-path /path/to/store/tests</code></li> </ul> </li> <li>Automated labeling of Tests: <ul> <li><code>label-tests --road-scenarios /path/to/tests --result-folder /path/to/store/labeled/tests</code></li> <li><em>Note:</em> This only works locally with BeamNG.research installed</li> </ul> </li> <li>Model evaluation: <ul> <li><code>evaluate-models --dataset /path/to/train/set --save</code></li> </ul> </li> <li>Split train and test data: <ul> <li><code>split-train-test-data --scenarios /path/to/scenarios --train-dir /path/for/train/data --test-dir /path/for/test/data --train-ratio 0.8</code></li> </ul> </li> <li>Test outcome prediction: <ul> <li><code>predict-tests --scenarios /path/to/scenarios --classifier /path/to/model.joblib</code></li> </ul> </li> <li>Evaluation based on random strategy: <ul> <li><code>evaluate --scenarios /path/to/test/scenarios --classifier /path/to/model.joblib</code></li> </ul> </li> </ul> <p>The possible parameters are always documented with <code>--help</code>.</p> <p><strong>Linting</strong></p> <p>The tool is verified the linters <a href="https://flake8.pycqa.org/en/latest/">flake8</a> and <a href="https://pylint.org/">pylint</a>. These are automatically enabled in <a href="https://code.visualstudio.com/">Visual Studio Code</a> and can be run manually with the following commands:</p> <pre>poetry run flake8 . poetry run pylint **/*.py</pre> <p><strong>License</strong></p> <p>The software we developed is distributed under GNU GPL license. See the <a href="https://github.com/ChristianBirchler/sdc-scissor/blob/main/LICENSE.md">LICENSE.md</a> file.</p> <p><strong>Contacts</strong></p> <p>Christian Birchler - Zurich University of Applied Science (ZHAW), Switzerland - <a href="mailto:birc@zhaw.ch">birc@zhaw.ch</a></p> <p>Nicolas Ganz - Zurich University of Applied Science (ZHAW), Switzerland - <a href="mailto:gann@zhaw.ch">gann@zhaw.ch</a></p> <p>Sajad Khatiri - Zurich University of Applied Science (ZHAW), Switzerland - <a href="mailto:mazr@zhaw.ch">mazr@zhaw.ch</a></p> <p>Dr. Alessio Gambi - Passau University, Germany - <a href="mailto:alessio.gambi@uni-passau.de">alessio.gambi@uni-passau.de</a></p> <p>Dr. Sebastiano Panichella - Zurich University of Applied Science (ZHAW), Switzerland - <a href="mailto:panc@zhaw.ch">panc@zhaw.ch</a></p> <p><strong>References</strong></p> <ul> <li>Christian Birchler, Nicolas Ganz, Sajad Khatiri, Alessio Gambi, and Sebastiano Panichella. 2022. Cost-effective Simulation-based Test Selection in Self-driving Cars Software with SDC-Scissor. In 2022 IEEE 29th International Conference on Software Analysis, Evolution and Reengineering (SANER), IEEE.</li> </ul> <p><strong>If you use this tool in your research, please cite the following papers:</strong></p> <pre><code>@INPROCEEDINGS{Birchler2022, author={Birchler, Christian and Ganz, Nicolas and Khatiri, Sajad and Gambi, Alessio, and Panichella, Sebastiano}, booktitle={2022 IEEE 29th International Conference on Software Analysis, Evolution and Reengineering (SANER), title={Cost-effective Simulationbased Test Selection in Self-driving Cars Software with SDC-Scissor}, year={2022}, }</code></pre>
Wastewater Treatment data simulated by WEST software
<p>This data was simulated by "WEST" software running for 30 days. This process is an oxidation wastewater treatment process. This data set includes all the necessary quality related variables, particularly, effluent qualities.</p>
Biases of STRUCTURE software when exploring introduction routes: Datasets, STRUCTURE outputs, simulation and analysis pipeline
<p>This archive is associated with the article “Biases of STRUCTURE software when exploring introduction routes of invasive species”. Authors: Eric Lombaert, Thomas Guillemaud & Emeline Deleury.</p> <p>The file contains the 22,500 simulated datasets, the corresponding 900,000 STRUCTURE outputs and the summary statistics files. It also contains SIM_STRUCT which is a home-made pipeline developed for the purpose of carrying out analyzes as described in the manuscript. It can be used to simulate and summarize datasets, and to perform STRUCTURE analyses in batch on those simulated datasets. It is currently based on several softwares such as DIYABC, ARLSUMSTAT and STRUCTURE, as well as on some home-made PERL scripts. A tutorial is included.<br> See the Readme file for details.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.