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427 results for “modularity”
Data from: A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics
<p>Data and results from the Imageomics Workflow. These include data files from the Fish-AIR repository (https://fishair.org/) for purposes of reproducibility and outputs from the application-specific imageomics workflow contained in the Minnow_Segmented_Traits repository (https://github.com/hdr-bgnn/Minnow_Segmented_Traits).</p> <p>Fish-AIR:<br> This is the dataset downloaded from Fish-AIR, filtering for Cyprinidae and the Great Lakes Invasive Network (GLIN) from the Illinois Natural History Survey (INHS) dataset. These files contain information about fish images, fish image quality, and path for downloading the images. The data download ARK ID is dtspz368c00q. (2023-04-05). The following files are unaltered from the Fish-AIR download. We use the following files:</p> <p>extendedImageMetadata.csv: A CSV file containing information about each image file. It has the following columns: ARKID, fileNameAsDelivered, format, createDate, metadataDate, size, width, height, license, publisher, ownerInstitutionCode. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.</p> <p>imageQualityMetadata.csv: A CSV file containing information about the quality of each image. It has the following columns: ARKID, license, publisher, ownerInstitutionCode, createDate, metadataDate, specimenQuantity, containsScaleBar, containsLabel, accessionNumberValidity, containsBarcode, containsColorBar, nonSpecimenObjects, partsOverlapping, specimenAngle, specimenView, specimenCurved, partsMissing, allPartsVisible, partsFolded, brightness, <br> uniformBackground, onFocus, colorIssue, quality, resourceCreationTechnique. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.</p> <p>multimedia.csv: A CSV file containing information about image downloads. It has the following columns: ARKID, parentARKID, accessURI, createDate, modifyDate, fileNameAsDelivered, format, scientificName, genus, family, batchARKID, batchName, license, source, ownerInstitutionCode. Column definitions are defined https://fishair.org/vocabulary.html and the persistent column identifiers are in the meta.xml file.</p> <p>meta.xml: A XML file with the metadata about the column indices and URIs for each file contained in the original downloaded zip file. This file is used in the fish-air.R script to extract the indices for column headers.</p> <p>The outputs from the Minnow_Segmented_Traits workflow are:</p> <p>sampling.df.seg.csv: Table with tallies of the sampling of image data per species during the data cleaning and data analysis. This is used in Table S1 in Balk et al. </p> <p>presence.absence.matrix.csv: The Presence-Absence matrix from segmentation, not cleaned. This is the result of the combined outputs from the presence.json files created by the rule “create_morphological_analysis”. The cleaned version of this matrix is shown as Table S3 in Balk et al.</p> <p>heatmap.avg.blob.png and heatmap.sd.blob.png: Heatmaps of average area of biggest blob per trait (heatmap.avg.blob.png) and standard deviation of area of biggest blob per trait (heatmap.sd.blob.png). These images are also in Figure S3 of Balk et al.</p> <p>minnow.filtered.from.iqm.csv: Filtered fish image data set after filtering (see methods in Balk et al. for filter categories).</p> <p>burress.minnow.sp.filtered.from.iqm.csv: Fish image data set after filtering and selecting species from Burress et al. 2017.</p>
NMRduino: A modular, open-source, low-field magnetic resonance platform
<p>The NMRduino is a compact, cost-effective, sub-MHz NMR spectrometer that utilizes readily available open-source hardware and software components. One of its aims is to simplify the processes of instrument setup and data acquisition control to make experimental NMR spectroscopy accessible to a broader audience. In this introductory paper, the key features and potential applications of NMRduino are described to highlight its versatility both for research and education.</p>
Test dataset for "Steam condensation scaled experiment in the presence of non-condensable gases for small modular reactor containment passive safety"
<p>This study presents scaled experiments using steam condensation with non-condensable gas (NCG)—helium (He), simulating hydrogen, and nitrogen (N<sub>2</sub>)—as these experiments are pivotal for water-cooled reactor passive containment cooling system (PCCS) design and analysis. Research into PCCSs for small modular reactors (SMRs) is especially important in light of SMR system design; however, studies in the literature reflect limitations due to test geometry and operational condition variations, without considering SMR prototypic design. To address these challenges, a scaled test facility was developed to accurately replicate SMR PCCSs. This facility includes vertical down-flow condensing test sections with 1-, 2-, and 4-in.-diameter condensing tubes, accompanied by annular water cooling. Experiments were conducted using both superheated and saturated steam, with steam mass flow rates in the presence of NCG varying from: (a) 55 to 66 kg/hr. of steam, and 1.8 to 22 kg/hr. of He (as the NCG); (b) 58 to 63 kg/hr. of steam, and 4.4 to 13.3 kg/hr. of N<sub>2</sub> (as the NCG). Test data were collected on (a) the axial temperatures of the annular cooling water; (b) the outer wall temperature of the condensers; and (c) the mass flow rate, temperature, and pressure at the test section inlets and outlets. These primary test data were used in conjunction with a standard data reduction methodology to estimate essential thermal parameters such as heat fluxes, heat transfer coefficients, and condensation rates. The effects of NCGs on steam condensation within the geometry of the scaled test sections were then presented in regard to various testing conditions.</p>
Raw data corresponding to the scientific paper: "A modular telerehabilitation architecture for upper limb robotic therapy" (Advances in Mechanical Engineering 2017, Vol. 9(1) 1-13)
<p>Acquired raw data necessary to implement the adaptive control strategy grounded on multimodal information.<br> In addition, raw data for the computation of the communication parameters needed for the assessment of the implemented telerehabilitation architecture are provided.</p> <p>a) End-effector positions and velocities (x, y, vx, vy) in three conditions: healthy (Fig 9) and constraint simulated stroke behaviour (Fig 10) without robotic assistance and simulated stroke behavior with robotic assistance (Fig 11)</p> <p>b) Performance indicators and control parameters for all the recruited subjects in both conditions healthy behaviour and simulated stroke behaviour (Fig 12a and Fig 12b)</p> <p>c) Computational values for evaluating telerehabilitation performance (Table 1)</p> <p> </p> <p> </p>
An updated modular set of synthetic spectral energy distributions for young stellar objects
<p>These are the models released with the following publication:</p> <p><strong><em>An updated modular set of synthetic spectral energy distributions for young stellar objects</em></strong> (<a href="https://ui.adsabs.harvard.edu/abs/2024ApJ...961..188R/abstract" target="_blank" rel="noopener">Richardson et al. 2024</a>).</p> <p>This is a set of young stellar object (YSO) models with associated spectral energy distributions (SEDs) calculated through radiative transfer. It is a significant update to the data published alongside Robitaille (2017, R17). It contains the parameters shaping each model and adds the newly calculated parameters of envelope mass, average dust temperature, disk stability, and line-of-sight extinction. It also makes explicit quantities, such as source luminosity, that were left implicit in the previous release. This set also convolves the SEDs with several new filters, primarily those on the James Webb Space Telescope, and adds a script to facilitate convolution of these models with additional filters as desired by users. All data included in Version 1.1 of the R17 set (the most recent) are included here.</p> <p>Like their predecessors, these models are versioned. Updates will be released as more models are completed or other changes are made.</p> <p>Files unzip to r+24_models-{version}/{geometry}. "files.tar.gz" contains scripts for SED convolution and main sequence comparison, the opacity to absorption of dust used in the radiative transfer calculations, main sequence T/L values used for results in the accompanying work, and reference material for the contents of the dataset and latest version.</p> <p>The primary use of these models is as templates for SED fitting. The R17 models were structured for use with the <a href="https://sedfitter.readthedocs.io/en/stable/" target="_blank" rel="noopener">sedfitter</a> python package, which enables fitting and analysis of the fit results. For a version of sedfitter which accommodates the new additions, use <a href="https://github.com/richardson-t/sedfitter/tree/dev" target="_blank" rel="noopener">this fork</a>.</p>
Dataset underlying the manuscript: MAViS: Modular Autonomous Virtualization System for Two-Dimensional Semiconductor Quantum Dot Arrays
<p>Datasets underlying the manuscript. Information on how to run the scripts is detailed in the README file.</p>
Supplemental Data from the article "The SmARTR pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data"
<h1><strong>Please, refer to <a href="https://github.com/MeVisLab/SmARTR-Networks">this GitHub repository</a> for additional info, updates, issue reports, and discussion<br></strong></h1> <p><strong>A collection of configuration files (SmARTR networks) published in "<a href="https://doi.org/10.1016/j.isci.2024.111475">The SmARTR Pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data</a>", enabling the creation of cinematic (photorealistic) renderings of 3D data in the FREE software <a href="https://www.mevislab.de/download">MeVisLab</a><br></strong></p> <ul> <li>Each folder in the archive contains one or more SmARTR network files, the scan and mask files required for the practical examples detailed in the <a href="https://www.cell.com/cms/10.1016/j.isci.2024.111475/attachment/8d79036b-acb6-4cda-a5ff-f56317691ebc/mmc1.pdf">Supplemental Data</a> of the article, and an additional folder with LUT presets.</li> </ul>
Supplementary codes and datasets for "Modular-topology optimization of structures and mechanisms with free material design and clustering"
<p>This repository supports Tyburec, M., Doškář, M., Zeman, J., & Kružík, M. (2022). Modular-topology optimization of structures and mechanisms with free material design and clustering. <em>Computer Methods in Applied Mechanics and Engineering</em>, <em>395</em>, 114977. <a href="https://doi.org/10.1016/j.cma.2022.114977">https://doi.org/10.1016/j.cma.2022.114977</a> (first published as preprint <a href="http://arxiv.org/abs/2111.10439">2111.10439</a> at arXiv.org).</p> <p>This repository contains:</p> <ol> <li>MATLAB source codes for <em>(modular) free material optimisation</em> and <em>hierarchical stiffness clustering</em> (folder <code>./mFMO/</code>)</li> <li>C++ source codes for <em>modular topology optimization</em> (folder <code>./MTO/</code>)</li> <li>Input/output data of the test suite (folder <code>./data/</code>)</li> </ol> <p><strong>1. Data flow</strong></p> <p>The test suite considered in the manuscript covers 4 problems:</p> <ol> <li>Messerschmitt-Bölkow-Blohm beam (labelled as <code>mbb</code>)</li> <li>Inverter compliant mechanism (labelled as <code>inv</code>)</li> <li>Gripper compliant mechanism (labelled as <code>grip</code>)</li> <li>Reusable design of both compliant mechanisms (labelled as <code>invgrip</code>)</li> </ol> <p>Each problem in the dataset is stored within a separate subfolder named according to the labels mentioned above. The final level of subdirectories <code>{X}color</code> comprises of the results for problems with <code>X</code> denoting the number of edge codes considered for each edge direction during the clustering (<code>0color</code> stands for a non-modular design and <code>1color</code> represents the design based on Periodic Unit Cell).</p> <p>Each of the folders contains outputs of the modular free material optimisation in the following form:</p> <ul> <li><code>{label}{X}.mat</code></li> <li><code>{label}{X}.til</code></li> <li><code>{label}{X}.tset</code></li> <li><code>{label}{X}guess.mat</code></li> </ul> <p>Files <code>*.til</code>, <code>*.tset</code>, and <code>*guess.mat</code> are then converted into a JSON input file for the modular topology optimization code with generator scripts which can be found in <code>./MTO/scripts</code> folder. Note that each of the problems in the test suite has its own generator script <code>generate_modular_problem_{MBB,inverter,gripper,inverterAndGripper}.mat</code>. The generator scripts make a directory named according to the key <code>MTO_{n}_kernelSensitivity</code>, where <code>n</code> denotes the resolution of each module (i.e. the number of nodes along one direction). The directory also contains the outputs of the modular topology optimisation in the form of the initial and the final state of the optimization in <code>VTK</code> files and visualisation of the final state in <code>SVG</code> files. The log file <code>log.txt</code> stores the optimized objective and progress of the value along with stopping criteria quantities during iterations.</p> <p><strong>2. Running codes</strong></p> <p><strong>2.1 Modular free material optimisation</strong></p> <p>MATLAB scripts and functions for (modular) Free Material Optimization (FMO) are contained in the <code>mFMO</code> data folder. The codes have been tested with MATLAB R2019b. To run the codes the user is required to install the <a href="http://www.penopt.com">PENNON optimizer</a>. A free academic license is provided by its authors on request.</p> <p>Input files for individual problems are defined in the <code>mFMO/problems</code> folder and are launched with the <code>runproblem(problemName, numClusters)</code>, where <code>problemName</code> refers to the file in the <code>mFMO/problems</code> folder without the file extension and <code>numClusters</code> denotes the maximum number of color codes in Wang tiling formalism.</p> <p>If successful, the optimization produces output files in <code>mFMO/fmo_fig/{label}/{X}colors/{T}/</code>:</p> <ul> <li><code>{label}{X}.mat</code> (contains clustering and tiling information)</li> <li><code>{label}{X}_tmp.mat</code> (contains results of non-modular FMO)</li> <li><code>{label}{X}.til</code> (the assembly plan)</li> <li><code>{label}{X}.tset</code> (Wang tile set)</li> <li><code>{label}{X}guess.mat</code> (guess for TO)</li> </ul> <p>where <code>T</code> is the optimization time stamp.</p> <p><strong>2.2 Modular topology optimisation</strong></p> <p>All results were obtained with version <code>v1.1.2</code>, which is also provided in the folder <code>MTO</code>, and linked Intel® oneAPI Math Kernel Library and the incorporated PARDISO sparse solver. For the recent development of the code see the open git repository at <a href="https://gitlab.com/MartinDoskar/modular-topology-optimization">https://gitlab.com/MartinDoskar/modular-topology-optimization</a>. The repository also contains a detailed description of input parameters and code design.</p> <p>Modular topology optimisation code uses CMake for the cross-platform build automation. For instance, under Linux, the whole code can be compiled in the standard five steps:</p> <pre><code>cd ./MTO mkdir build cd ./build cmake -DCMAKE_BUILD_TYPE=Release .. make </code></pre> <p>All executables are automatically stored in <code>./MTO/bin/</code> folder. Individual problems can be optimized by parsing the JSON files obtained from the generator scripts as an argument to the MTO.Application binary, e.g.,</p> <pre><code>./MTO/bin/MTO.Application.exe path_to_data/mbb/2color/MTO_100_kernelSensitivity/input_modular_mbb_2colours_100.json </code></pre> <p><strong>Acknowledgement</strong></p> <p>The related research and code development was supported by the <a href="https://gacr.cz/en/">Czech Science Foundation</a>, project No. 19-26143X.</p>
Modulares Erzählen: Annotierte Texte der Sieben weisen Meister
<p>Die einzelnen XML-Dateien enthalten den Text verschiedener deutschsprachiger Versionen und Fassungen der spätmittelalterlichen Erzähltradition <em>Die sieben weisen Meister. </em>Sie bilden die Grundlage der textstatistischen Untersuchungen in Nico Kunkel: Modulares Erzählen. Serialität und Mouvance in der Erzähltradition der <em>Sieben weisen Meister</em>. Berlin/Boston (in Vorbereitung). Die Texte, die auf Editionen und Arbeitstranskriptionen zurückgehen, sind nach narratologischen Kriterien in einzelne Erzähleinheiten (= Erzählmodule) eingeteilt. Einige Dateien (<em>Allegatio</em>, Gießener/Brünner/Colmarer Fs.) liegen in Form von abgeleiteten Textformaten vor, da die Texte auf Editionen jüngeren Datums (1997/2001/2008/2008) zurückgehen. Sie enthalten jeweils nur das erste und letzte Wort eines Erzählmoduls, während alle anderen Wörter durch Platzhalter ("blank") ersetzt wurden. Auf diese Weise lassen sich statistische Abfragen (Modullänge/-sequenz) weiter umsetzen, während ein Genuss des literarischen Werks nicht mehr möglich ist. </p> <p> </p> <p> </p> <p><strong>Textgrundlagen:</strong></p> <ul> <li><em>Allegatio</em> = Text nach Steinmetz, Ralf-Henning (1997). „Der ‚Libellus muliebri nequitia plenus‘. Eine ungedruckte lateinische Version der 'Sieben weisen Meister' und ihre deutsche Übersetzung aus dem 15. Jahrhundert“. In: <em>Zeitschrift für deutsches Altertum und deutsche Literatur</em> 126. 297-446 (abgeleitetes Textformat).</li> <li>anV = Text nach „Von den sieben meistern“. In: <em>Altdeutsche Gedichte.</em> Hg. von Adalbert Keller Tübingen 1846, 15-241.</li> <li>Aventewr = Arbeitstranskription von Heidelberg, Universitätsbibl., cpg 101, 29r-39r.</li> <li>Brünner Fs = Text nach<em> Sieben weise Meister. Eine bairische und eine elsässische Fassung der „Historia septem sapientum“.</em> Hg. von Detlef Roth. Berlin 2008 (abgeleitetes Textformat).</li> <li>Bühnenfs = Arbeitstranskription von Wild Sebastian: <em>Schoener Comedien vnd Tragedien zwoelff: Auß heiliger goettlicher schrifft vnd auch auß etlichen historien gezogen […] Auffs new in Truck verfertigt durch Sebastian Wilden</em>. Augsburg 1566.</li> <li>Colmarer Fs = Text nach <em> Sieben weise Meister. Eine bairische und eine elsässische Fassung der „Historia septem sapientum“.</em> Hg. von Detlef Roth. Berlin 2008 (abgeleitetes Textformat).)</li> <li><em>DL</em> = Text nach Bühel, Hans von. <em>Dyocletianus Leben</em>. Hg. von Adalbert Keller. Quedlinburg/Leipzig 1846.</li> <li>Donaueschinger Fs = Arbeitstranskription von Karlsruhe, Landesbibl., Cod. Donaueschingen 145, 5ra-58ra.</li> <li>Gießener Fs = Text nach <em>Die Historia von den sieben weisen Meistern und dem Kaiser Diocletianus</em>. Hg. von Ralf-Henning Steinmetz. Tübingen 2001 (abgeleitetes Textformat).</li> <li>Heidelberger Fs = Arbeitstranskription von Universitätsbibl., Cpg 149, 1r-108r.</li> <li><em>Hystorij</em> = Transkription von <em>Die Hystorij von Diocleciano. In Abbildungen aus dem Codex 407 des Wiener Schottenstifts</em>. Hg. Ralf-Henning Steinmetz. Göppingen 1999.</li> <li>Vulgatfs = Arbeitstranskription von <em>Die Sieben weisen Meister</em>. Hg. von Günter Schmitz. Hildesheim 1974.</li> </ul>
Modular control of human movement during running: an open access data set
<p>The human body is an outstandingly complex machine including around 1000 muscles and joints acting synergistically. Yet, the coordination of the enormous amount of degrees of freedom needed for movement is mastered by our one brain and spinal cord. The idea that some synergistic neural components of movement exist was already suggested at the beginning of the XX century. Since then, it has been widely accepted that the central nervous system might simplify the production of movement by avoiding the control of each muscle individually. Instead, it might be controlling muscles in common patterns that have been called muscle synergies. Only with the advent of modern computational methods and hardware it has been possible to numerically extract synergies from electromyography (EMG) signals. However, typical experimental setups do not include a big number of individuals, with common sample sizes of five to 20 participants. With this study, we make publicly available a set of EMG activities recorded during treadmill running from the right lower limb of 135 healthy and young adults (78 males, 57 females). Moreover, we include in this open access data set the code used to extract synergies from EMG data using non-negative matrix factorization and the relative outcomes. Muscle synergies, containing the time-invariant muscle weightings (motor modules) and the time-dependent activation coefficients (motor primitives), were extracted from 13 ipsilateral EMG activities using non-negative matrix factorization. Four synergies were enough to describe as many gait cycle phases during running: weight acceptance, propulsion, early swing and late swing. We foresee many possible applications of our data, that we can summarize in three key points. First, it can be a prime source for broadening the representation of human motor control due to the big sample size. Second, it could serve as a benchmark for scientists from multiple disciplines such as musculoskeletal modelling, robotics, clinical neuroscience, sport science, etc. Third, the data set could be used both to train students or to support established scientists in the perfection of current muscle synergies extraction methods.</p> <p>The "RAW_DATA.RData" R list consists of elements of S3 class "EMG", each of which is a human locomotion trial containing cycle segmentation timings and raw electromyographic (EMG) data from 13 muscles of the right-side leg. Cycle times are structured as data frames containing two columns that correspond to touchdown (first column) and lift-off (second column). Raw EMG data sets are also structured as data frames with one row for each recorded data point and 14 columns. The first column contains the incremental time in seconds. The remaining 13 columns contain the raw EMG data, named with the following muscle abbreviations: ME = gluteus medius, MA = gluteus maximus, FL = tensor fasciæ latæ, RF = rectus femoris, VM = vastus medialis, VL = vastus lateralis, ST = semitendinosus, BF = biceps femoris, TA = tibialis anterior, PL = peroneus longus, GM = gastrocnemius medialis, GL = gastrocnemius lateralis, SO = soleus.</p> <p>The file "dataset.rar" contains data in older format, not compatible with the R package <a href="https://CRAN.R-project.org/package=musclesyneRgies">musclesyneRgies</a>.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Supplementary Tables
<p>This repository contains the Supplementary Tables for Suriyalaksh et al. Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes.</p> <p>The list of table files can be found in <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/Supplementary%20table%20guide.pdf">Supplementary Tables guide.pdf</a></p> <p>Tables S1, S2 and S3 corresponding to physical gene-gene interaction data are in a separate repository doi:10.5281/zenodo.4382337</p> <p>Details about some of the Supplementary tables:</p> <p>TableS4_inferred_networks.csv - list of inferred GRNs for specified input combinations (set of input regulators, length of the time sequence, NI tool and prior used).</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS5_consensus_network_member.xlsx">TableS5_consensus_network_member.xlsx</a> - list of groups of topologically similar GRNs (from Table S4)</p> <p>Table S6: edge lists (source,target) for each one of the three consensus networks selected according to the GS validation metrics: middle PFE/AUFE, max AUFE, max PFE.<br> TableS6a_max_AUFE_GRN.txt - max AUFE; largest network - this is the one we used in the main analysis and discussion<br> TableS6b_max_PFE_GRN.xt - max PFE<br> TableS6c_middle_AUFE_PFE_GRN.txt - middle PFE/AUFE</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS7_qRTPCR_ddCt_network_accuracy.csv">TableS7_qRTPCR_ddCt_network_accuracy.csv</a> - gene expression count differences for RNAi knockdown GRN validation experiments. </p> <p>Table S8: Group membership for each one of the nodes in each one of the selected networks according to the SBM that best describes the observed network topology. Each column shows the group membership for each level in a SBM block hierarchy. Our analysis is in the second most coarse-grained level (level 1).</p> <p>TableS8a_max_AUFE_SBM.csv<br> TableS8b_max_PFE_SBM.csv<br> TableS8c_middle_AUFE_PFE_SBM.csv</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS9_glp_gs_datasets.pdf">TableS9_glp_gs_datasets.pdf</a> - list of datasets used for defining functional clusters.</p> <p>TableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx - Day13 survival of fem-3(q20)ts vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx - Day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L4 vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS15a_glp1_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of glp-1(e2144)ts;rrf-3(pk1426)</p> <p>TableS15b_fem3_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of fem-3(q20)ts</p> <p>TableS17_input_regulators_annotated.csv - list input regulators used as input for Network Inference Tools annotated by source type (2nd column): GenAge, known transcription factors (TF) and gene with high variability in the gene expression time series (HV). The third column lists whether that regulator has an orthologue in human (y) according to WormBase (v 278).</p> <p>TableS20_epistasis_lifespan_data.xlsx - Epistasis lifespan data of glp-1(e2144)ts</p> <p>All the image (TIF) files represent representative images in the following genetic backgrounds (below) that have been treated </p> <p>with empty vector (EV) or RNAi against the gene highlighted in the title of the image. See methods section for details. </p> <p><strong>femliu1: </strong></p> <p><em>fem-3(q20)ts.; dhs-3p::dhs-3::gfp</em></p> <p><strong>femsod3:</strong></p> <p><em>fem-3(q20)ts.; sod-3p::gfp</em></p> <p><strong>glp1lgg1:</strong></p> <p><em>glp-1(e2144); lgg-1p:lgg-1:gfp</em></p>
JWST convolutions for a modular set of synthetic SEDs for young stellar objects (Robitaille, 2017)
<p>This is a companion to the models released alongside the publication:</p> <p><em>A modular set of synthetic spectral energy distributions for young stellar objects</em>, Robitaille (2017)</p> <p>The models are convolved with JWST filters taken from the SVO’s filter profile service. Some models with rotationally flattened envelopes (i.e. geometries with<strong> u</strong>)<strong> </strong>not present in the original model grid have since been completed; their convolved SEDs are included here.</p> <p>Files unzip to {geometry}/convolved/JWST/{SVO_filtername}.fits.</p> <p>This is a subset of the information included in https://doi.org/10.5281/zenodo.8114592.</p>
A Modular Quantum Compilation Framework for Distributed Quantum Computing
<p>This repository contains the data used for the plots in "<em>A Modular Quantum Compilation Framework for Distributed Quantum Computing</em>" by D. Ferrari, S. Carretta and M. Amoretti.</p> <p>Data is located in the <em>'data'</em> directory in <em>.csv</em> format, a python script to generate the plots can be found in the main directory. The script was tested with <strong>python3.10</strong> and needs <strong>matplotlib</strong>, <strong>pandas</strong> and <strong>seaborn</strong> packages. Plots are saved as <em>.pdf</em> files in the <em>'figures'</em> directory.</p>
Supplementary codes and datasets for "Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials"
<p>This repository provides data and codes for manuscript “Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials” by M. Doškář, M. Somr, R. Hlůžek, J. Havelka, J. Novák, and J. Zeman, published first as a preprint <a href="https://arxiv.org/abs/2305.09280">arXiv:2305.09280</a> at arXiv.org; see the actual description of the Zenodo entry for the latest reference.</p> <p>This repository contains:</p> <ol> <li>MATLAB and C++ source codes for combinatorial design and numerical analyses (folder <code>./numerics/</code>),</li> <li>experimental data (folder <code>./experiments/</code>),</li> <li>3D models of parts used in robotic-assembly (folder <code>./models/</code>),</li> <li>a control script for robotic assembly (folder <code>./robotics/</code>).</li> </ol> <p><strong>Numerics</strong></p> <p>All simulations were performed with an in-house MATLAB code, which extends the finite element toolbox for finite strain calculations accompanying the work of <a href="https://doi.org/10.1016/j.cma.2020.113333">van Bree, S. E. H. M., Rokoš, O., Peerlings, R. H. J., Doškář, M., & Geers, M. G. D. (2020). A Newton solver for micromorphic computational homogenization enabling multiscale buckling analysis of pattern-transforming metamaterials. Computer Methods in Applied Mechanics and Engineering, 372, 113333</a>. In particular, this snapshot corresponds to a cleaned-up version (excluding files unrelated to the publications) of commit <code>21cfc2e9</code>.</p> <p>The MATLAB codebase contains MEX files written in C++ to accelerate selected procedures. In order to run any code, these MEX files must be compiled first. We use CMake build automation, with the main <code>CMakeLists.txt</code> located in <code>./numerics/mex</code>.</p> <p>Combinatorial search was performed by the <code>RUN_modular_exploration.m</code> script; see definition of problems with the script. The results of the enumerations, stored in <code>./dat/exploration</code>, were analysed with <code>POST_modular_S_v3.m</code>, identifying layouts leading to the extreme (min/max) tilt angles.</p> <p>Comparison against experimental measurements was facilitated by a series of scripts <code>POST_DIC_{...}.m</code>. First, run <code>POST_DIC_step1_extract_points_in_mesh.m</code> to identify locations.mat. Next, post-process extensometer data with <code>POST_DIC_step2_merge_extensometer_data.m</code>, and use <code>POST_DIC_step3_impose_extracted_BC.m</code> to parse DIC results in a format suitable for imposing BC later in this script. Finally, comparison between experimental and computed displacements is provided by <code>POST_DIC_step4_modular_comparison_experiments.m</code>. (Note that the particular files need to be manually provided in the “Compute deformation process” part of <code>POST_DIC_step4_modular_comparison_experiments.m</code>.)</p> <p><strong>Experimental data</strong></p> <p>This folder contains data from (i) an unixaial tension test of a dogbone specimen (both from a MTS loading machine and DIC data) and (ii) two measurement sessions extracting the L-shape domain responses using DIC (<code>20_11_30 - Hluzek_Elka_newassemblyplan</code> and <code>21_04_12 - Hluzek_ Elka_quarters</code> with lower loading threshold). For post-processing, see the above-mentioned <code>POST_DIC_{...}.m</code> scripts. <code>*.mat</code> files present directly in <code>./experiments/</code> folder were obtained and are need by those scripts.</p> <p><strong>3D models</strong></p> <p>The folder contains geometrical models for individual parts needed for robot-assisted assembly of module molds for casting. This includes:</p> <ol> <li>a silo extension to store more tiles (file <code>silo_extension.stl</code>),</li> <li>formwork modules around the main structure for the purpose of casting silicone (file <code>tile_formwork.stl</code>),</li> <li>all types of tiles for the inside structure (file <code>tile_inside_types.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_1.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_2.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_3.stl</code>),</li> <li>connection for spacers (file <code>yumi_base_4.stl</code>),</li> <li>spacer holding a silo and the build plate (file <code>yumi_base_5.stl</code>),</li> <li>YuMi grippers with extensions to hold the tiles (file <code>grippers_extend.st</code>).</li> </ol> <p><strong>Robotics</strong></p> <p>The folder contains a single file with a script created in RobotStudio (RobotWare Version: 6.08.01.00, SmartGripper Version: 3.55.0000.00) to assemble the plan with YuMi IRB 14000-0.5/0.5 left hand.</p> <p><strong>Acknowledgement</strong></p> <p>The related research, experiments, and code development were supported by the <a href="https://gacr.cz/en/">Czech Science Foundation</a>, project No. 19-26143X.</p>
Benne: A Modular Data Stream Clustering Algorithm with Flexible Design Choices
<p>All of the source dataset with preprocessed format [id features class] that have been used for evaluation in the paper.</p>
Modular organization of the murine locomotor pattern in the presence and absence of sensory feedback from muscle spindles
<p>In this study, we made use of non-negative matrix factorization (NMF) to extract muscle synergies from electromyographic (EMG) data. We implemented the NMF algorithm in R version 3.5.1 (R Foundation for Statistical Computing, R Core Team, Vienna, Austria), a programming language available in a free software environment. However, even if the software does not require a paid license, often researchers are either not confident with or prefer not to spend time writing the code required to perform NMF. We make available, as we recently did with human data (Santuz <em>et al.</em>, 2018), an example open access data set of EMG and muscle synergy data for murine walking and swimming. The data presented in this supplementary information part is available in three formats: 1) the raw EMG of two example trials (one recorded during walking and the other during swimming in a wild type animal, six muscles), unprocessed together with the touchdown and lift-off timings of the recorded limb for walking and the cycle timings for swimming; 2) the filtered and time-normalized EMG and 3) the muscle synergies extracted via NMF. Moreover, we provide the R code for obtaining the results described in the previous three points. We do not report any metadata, since trials are relative to a single representative animal. The R code is profusely commented.</p>
Experimental Results for the study "A Modular Hybridization of Particle Swarm Optimization and Differential Evolution"
<p>This repository contains the experiment results and R scripts to analyze the data for the study "A Modular Hybridization of Particle Swarm Optimization andDifferential Evolution", which is accepted in <em>The Genetic and Evolutionary Computation Conference</em> (GECCO) '20 conference: </p> <p>Rick Boks, Hao Wang, and Thomas Bäck. 2020. A Modular Hybridization of Particle Swarm Optimization and Differential Evolution. In <em>Genetic and Evolutionary Computation Conference Companion (GECCO ’20 Companion), July 8–12, 2020, Cancún, Mexico. </em>ACM, New York, NY, USA, 8 pages. <a href="http://https: //doi.org/10.1145/3377929.3398123">https: //doi.org/10.1145/3377929.3398123</a></p> <p>Bibtex:</p> <pre><code class="language-markdown">@inproceedings{BoksWB20, author = {Rick Boks and Hao Wang and Thomas B\"ack}, title = {{A Modular Hybridization of Particle Swarm Optimization and Differential Evolution}}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference, {GECCO} 2020, Canc\'un, Mexico, July 8-12, 2020}, publisher = {{ACM}}, year = {2020}, url = {https://doi.org/10.1145/3321707.3321816}, doi = {doi.org/10.1145/3377929.3398123, }</code></pre> <p><strong>Data description:</strong> we benchmarked <strong>800 </strong>different<strong> </strong>hybridizations of the Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms on a well-known continuous black-box problem set called <a href="https://coco.gforge.inria.fr/">COCO/BBOB</a>, which consists of 24 test functions. 30 independent runs are conducted for each algorithm on each problem.</p> <ul> <li>'ERT.csv': a data frame with columns DIM (5D or 20D), funcId (F1-24), algId (algorithm names), target (<span class="math-tex">\(10^{\{-8,-7, \ldots, 1\}}\)</span>), ERT (expected running time), and sd (standard deviation).</li> <li>'raw-data.csv': the running time recorded in each independent run. </li> <li>'analysis.R': the R script that generates ERT tables in the paper.</li> <li>'ecdf.R': the R script that renders the ECDF (empirical cumulative distribution function) plots in the paper.</li> </ul>
Architectural Feature Re-Modularization for Software Product Line Evolution
<p>Extensive maintenance leads to the Software Product Line Architecture<br> (PLA) degradation over time. When there is the need of<br> evolving the Software Product Line (SPL) to include new features,<br> or move to a new platform, a degraded PLA requires considerable<br> effort to understand and modify, demanding expensive refactoring<br> activity. In the state of the art, search-based algorithms are used to<br> improve PLA at package level. However, recent studies have shown<br> that the most variability and implementation details of an SPL are<br> described in the level of classes. There is a gap between existing<br> approaches and existing practical needs. In this work, we extend<br> the current state of the art to deal with feature modularization in<br> the level of classes by introducing a new search operator and a set<br> of objective functions to deal with feature modularization in a finer<br> granularity of the architectural elements, namely at class level. We<br> evaluated the proposal in an exploratory study with a PLA widely<br> investigated and a real-world PLA. The results of quantitative and<br> qualitative analysis point out that our proposal provides solutions<br> to properly re-modularize features in a PLA, being preferred by<br> practitioners, in order to support the evolution of SPLs.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Database of Physical gene-gene Interactions in young adult C.elegans.
<p>This repository contains Supplementary Information for manuscript Suriyalaksh et al Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes corresponding to the curation of physical gene-gene interactions for young adult C elegans worms </p> <p>We manually curated 239,001 regulatory interactions from 289 young adult wild-type (WT) C.elegans datasets, consisting of 126 genes and 495 unique transcription factors (see TableS1_datasets_for_prior.csv for references). </p> <p>This repository contains 3 different files:</p> <p>TableS1_datasets_for_prior.csv - contains datasets used as sources for physical gene-gene or TF-gene interactions</p> <p>TableS2_physical_priors.xlsx - contains three tabs:<br> ChIPATAC - contains physical TF-gene interactions from 115 L4 or young-adult ChIP-seq datasets from modERN (Kudron et al., 2018) + ChIP-seq datasets (GSE28350, GSE81521) from (Hochbaum et. al, 2011, Li et. al, 2016).</p> <p>eY1HATAC- contains 3,501 TF-gene interactions from eY1H assay by Fuxman Bass et al. (2016).</p> <p>motifATAC - contains 202 unique TF DNA recognition motifs using “direct evidence” option from CiS-BP motif database (Weirauch et al., 2014), obtained through RTFBSDB R package (Wang et al., 2016) - see TableS1</p> <p>TableS3_WT_functional_priors.csv - contains functional knockdown data that we use as gold standard to validate inferred networks in Suriyalaksh et al. (see TableS1_datasets_for_prior.csv for sources)</p> <p>---</p> <p>Description of methodology to obtain regulatory interactions in TableS2:</p> <p>Regulatory sequences for each gene were acquired from ENSEMBL (Aken et al., 2017), obtained using biomaRt R package (accessed on 31st Oct 2017). This study used WBcel235/ce11 version of the C. elegans genome, and WormBase WS260 genome annotations.</p> <p>For motifs, TFs whose motifs overlapped with an open ATAC-seq region by at least one base pair were kept. For ChIP-seq, TF binding sites that overlapped with an open ATAC-seq region by at least one base pair were kept using bedtools intersect and bedtools merge commands.</p> <p>An interaction from a TF to a gene was inferred by aligning transcription start sites (TSS) using bedtools window commands with 1000 bp window size to the TF-binding locations from ChIP-seq and motifs.</p> <p>For eY1H data, an interaction is included if the TSS site of the target gene overlaps with an open ATAC-seq region by at least one base pair.</p> <p>For gene-gene interactions, of the 298 studies compiled in WormExp v1.0 database (Yang et al, 2016, updated 27/07/16), 98 studies were included in the database spanning 126 different genes (see Table S1 in this repository).</p>
A modular set of synthetic spectral energy distributions for young stellar objects - Robitaille (2017) - v1.1 [Hyperion files]
<p>These are the input and output files for the radiative transfer code (Hyperion) for the model sets presented in</p> <p><em>A modular set of synthetic spectral energy distributions for young stellar objects</em>, Robitaille (2017)</p> <p>Each model set is provided as a single tar file. Each tar file expands to <strong>grids-1.1/<set name></strong>, so if you expand all tar files in the same folder, you will end up with a single <strong>grids-1.1</strong> folder with 18 sub-folders, one for each model set.</p> <p>For a given model set, the files are as follows:</p> <ul> <li>grids-1.1/<set name>/input - input Hyperion files</li> <li>grids-1.1/<set name>/log - log files from Hyperion</li> <li>grids-1.1/<set name>/output - output Hyperion files</li> <li>grids-1.1/<set name>/par - parameters for each model</li> <li>grids-1.1/<set name>/ranges.conf - ranges of parameters varied in the model set</li> <li>grids-1.1/<set name>/parameters.hdf5 - table of parameters for all models</li> <li>grids-1.1/<set name>/d03_5.5_3.0_A_sub.hdf5 - dust file used for the models</li> </ul> <p>Given the large number of models for some of the model sets, the models are not all stored directly inside the par, input, output or log directories - instead these directories contain folders formed from the first two characters (forced to lowercase) of the names of the models they contain. For example, a3 contains all models whose name starts with a3 or A3. This was done to avoid having too many files in a single folder which can cause issues on certain file systems.</p> <p>For the Hyperion input and output files, in some cases an _sed file is present. In these cases, the output SEDs (and polarization spectra) should be read from the _sed file, not the original output file. This is the case for all models that are in a set for which the ambient medium was present, as described in §4.2.3 of Robitaille (2017). Furthermore, in some cases the SED file is called _sed_noscat to indicate that scattering was not included, as described in §5.1 of Robitaille (2017).</p> <p>To avoid taking up too much disk space, the Hyperion HDF5 input/output files use external links to refer to each other and to the dust file. To make sure the links work, you should do all operations with the input/output files from the directory containing <strong>grids-1.1</strong>. For example, to open a Hyperion output file, you would need to do (in Python):</p> <p> In [1]: from hyperion.model import ModelOutput</p> <p> In [2]: mo = ModelOutput('grids-1.1/s---s-i/output/a3/A3kQmQtj.rtout')</p> <p>A notebook with examples of reading in the output files can be found here:</p> <p>https://github.com/hyperion-rt/paper-2017-sed-models/blob/master/notebook_raw/reading_raw_files.ipynb</p> <p>More information on using Hyperion, including reading input/output files, can also be found at http://docs.hyperion-rt.org</p> <p>For <strong>announcements</strong> of new versions of these models, you can subscribe to the following mailing list:</p> <p>https://groups.google.com/forum/#!forum/protostars</p> <p>For <strong>questions or issues</strong> using these models, you can open a GitHub issue in the companion repository:</p> <p>https://github.com/hyperion-rt/paper-2017-sed-models/issues/new</p>
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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
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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.