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Code and data for publication "Assessing carbon cycle projections from complex and simple models under SSP scenarios" published in "Climatic Change"

Data and scripts for the article "Assessing carbon cycle projections from complex and simple models under SSP scenarios" by I. Melnikova, P. Ciais, O. Boucher and K. Tanaka was accepted for publication in Climatic Change (https://doi.org/10.1007/s10584-023-03639-5) We use bash, CDO, and python.SSP2.xlsx contains preprocessed annual estimates of climate and carbon cycle variables from ESMs and SCMs used in the paper.Two bash scripts contain preprocessing cdo commands for ESM output.s SCMs were preprocessed directly in python.Jupyter notebook (python) contains preprocessing of data and plotting of all figures of the manuscript. The folder "additional" contains some more Excel files needed to run Jupyter-Notebook. Please adapt the folder names.If you have any questions, please contact the corresponding author Irina MELNIKOVA at melnikova . irina@nies.go.jp

openmit-licenseNov 2023View details →

Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex

When using the data or code from this manuscript, please cite it as:Leiva FP, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.

Data for the publication "Developing a climatological simplification of aerosols to enter the cloud microphysics of a global climate model" - part 1

The data is split into two datasets, for each to be smaller than 50 GB.

Kinematic data and mathematical modeling of sea star locomotion

It is unclear how animals with radial symmetry control locomotion without a brain. Using a combination of experiments, mathematical modeling, and robotics, we tested the extent to which this control emerges in sea stars from the local control of their hundreds of feet and their mechanical interactions with the body. We discovered that these animals (Protoreaster nodosus) compensate for an experimental increase in their submerged weight by recruiting more feet that synchronize in the power stroke of the locomotor cycle. Mathematical modeling replicated this response to loading in the absence of nervous communication and demonstrated how the body weight serves as a regulator of recruitment. We built a robotic sea star with an array of independently-controlled actuators that were also recruited in greater numbers under higher loads due to their collective mechanics. These findings demonstrate that an array of actuators in biological and robotic systems are capable of cooperative transport with dynamic adjustments to loading. This form of distributed control contrasts the conventional view of animal locomotion as governed by the central nervous system and offers inspiration for the design of engineered devices with arrays of actuators.

Code and data for Bayesian joint species distribution model selection for community-level prediction

Code and data for reproducing the analysis in the manuscript "Bayesian joint species distribution model selection for community-level prediction." Provided data include percent cover observations for 39 modeled vascular plant species within boreal forest understory communities and environmental model covariates. R code is provided to generate model inputs, apply alternative models, generate out-of-sample predictions, and calculate associated community and species log scores and alternative model evaluation metrics. Further, R source code is provided to implement the multinomial joint species distribution model defined in the manuscript. Details on the data, its processing, and the alternative model definitions and structure can be found in the main text of the manuscript. Provided data are currently being used in ongoing analyses and coordination with authors may be warranted to avoid duplicate publication. Potential users are encouraged to consider collaboration with authors when useful and appropriate. Misinterpretation of data may occur if used outside the context of the original analysis. All data are made available in their current state. While significant efforts have been made to ensure data accuracy, complete accuracy cannot be guaranteed. Data may be updated periodically. It is the responsibility of the data user to check for updated versions of the data.

Data from: Integrated species distribution models to account for sampling biases and improve range wide occurrence predictions

Aim Species distribution models (SDMs) that integrate presence-only and presence-absence data offer a promising avenue to improve information on species' geographic distributions. The use of such 'integrated SDMs' on a species range-wide extent has been constrained by the often-limited presence-absence data and by the heterogeneous sampling of the presence-only data. Here, we evaluate integrated SDMs for studying species ranges with a novel expert range map-based evaluation. We build a new understanding about how integrated SDMs address issues of estimation accuracy and data deficiency and thereby offer advantages over traditional SDMs. Location South and Central America. Time period 1979-2017. Major taxa studied Hummingbirds. Methods We build integrated SDMs by linking two observation models – one for each data type – to the same underlying spatial process. We validate SDMs with two schemes: i) cross-validation with presence-absence data and ii) comparison with respect to the species' whole range as defined with IUCN range maps. We also compare models relative to the estimated response curves and compute the association between the benefit of the data integration and the number of presence records in each data set. Results The integrated SDM accounting for the spatially varying sampling intensity of the presence-only data was one of the top-performing models in both model validation schemes. Presence-only data alleviated overly large niche estimates, and data integration was beneficial compared to modelling solely presence-only data for species that had few presence points when predicting the species' whole range. On the community level, integrated models improved the species richness prediction. Main conclusions Integrated SDMs combining presence-only and presence-absence data are successfully able to borrow strengths from both data types and offer improved predictions of species' ranges. Integrated SDMs can potentially alleviate the impacts of taxonomically and geographically uneven sampling and to leverage the detailed sampling information in presence-absence data.

Data for Tekran Model 3425 performance evaluation report for elemental mercury

During the SI-Hg performance evaluation of elemental mercury gas generators on the market three generators were tested, e.g., PSA 10.536 elemental Hg generator, bell-jar and Tekran Model 3425. Key characteristics were determined e.g.; the stabilisation period, short-term drift, precision, i.e., reproducibility and repeatability of the concentration generated, linearity, bias, sensitivity to sample gas pressure, sensitivity to surrounding temperature and sensitivity to electrical voltage. All three generators could be tested according to the calibration protocol developed within the project. The results obtained with the different gas generator clearly shows the importance of a metrological calibration. All three candidate generators show a different bias for the setpoint compared to the calibrated output. The data obtained during the performance evaluation of the Tekran Model 3425 is published in this repository. The files of the following experiments can be found here:<ul><li>m1<ul><li>Calibration Tekran mercury gas generator m1 20230612</li><li>Calibration_Tekran_m1</li></ul></li><li>m2<ul><li>Calibration Tekran mercury gas generator m2 20230619</li><li>Calibration_Tekran_m2</li></ul></li><li>m3<ul><li>Calibration Tekran mercury gas generator m3 20230626</li><li>Calibration_Tekran_m3</li></ul></li><li>m4<ul><li>Calibration Tekran mercury gas generator m4 20230629</li><li>Calibration_Tekran_m4</li></ul></li><li>short-term drift<ul><li>m2<ul><li>Calibration Tekran mercury gas generator short term drift m2</li><li>Tekran_Short_Term_M2</li></ul></li><li>m3<ul><li>Calibration Tekran mercury gas generator short term drift m3</li><li>Tekran_Short_Term_M3</li></ul></li><li>m4<ul><li>Calibration Tekran mercury gas generator short term drift m4</li><li>Tekran_Short_Term_M4</li></ul></li><li>m5<ul><li>Calibration Tekran mercury gas generator short term drift m5</li><li>Tekran_Short_Term_M5</li></ul></li></ul></li><li>stability<ul><li>Calibration Tekran mercury gas generator 20230609 stability</li></ul></li></ul>

Data from: A dynamical model of growth and maturation in Drosophila

The decision to stop growing and mature into an adult is a critical point in development that determines adult body size, impacting multiple aspects of an adult's biology. In many animals, growth-cessation is a consequence of hormone release that appears to be tied to attainment of particular body size or condition. Nevertheless, the size-sensing mechanism animals use to initiate hormone synthesis is poorly understood. Here we develop a simple mathematical model of growth cessation in Drosophila melanogaster, which is ostensibly triggered by attainment of a critical weight early in the last instar. Attainment of critical weight is correlated with synthesis of the steroid hormone ecdysone, which causes a larva to stop growing, pupate and metamorphose into the adult form. Our model suggests that, contrary to expectation, the size-sensing mechanism that initiates metamorphosis occurs before the larva reaches critical weight; that is, the critical-weight phenomenon is a downstream consequence of an earlier size-dependent developmental decision, not a decision point itself. Further, this size-sensing mechanism does not require a direct assessment of body size, but emerges from the interactions between body size, ecdysone and nutritional signaling. Because many aspects of our model are evolutionarily conserved among all animals, the model may provide a general framework for understanding how animals commit to maturing from their juvenile to adult form.

Training and test data, plus saved models for the upcoming paper `Top-down perceptual inference shaping the activity of early visual cortex'

Each .pkl file contains a training or test dataset in the form of a Python dictionary (generated with Python 3.8.5) with the following fields:<ul><li>'train_images': 640,000 float32 images used for model training. These are 40px images that contain 1600 pixel intensities each.</li><li>'train_labels': float32 labels for each image in 'train_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li><li>'test_images': 64,000 float32 images used for model testing. These are 40px images that contain 1600 pixel intensities each.</li><li>'test_labels': float32 labels for each image in 'test_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li></ul>The .zip file contains a saved model snapshot and various intermediate evaluative data. Details on these are coming soon.

Supplementary data and code to article "Single-Well Microseismic Focal Mechanism Inversions Using Different Source Models: A Case Study in the Ordos Basin, China"

Supplementary data and code to article "Single-Well Microseismic Focal Mechanism Inversions Using Different Source Models: A Case Study in the Ordos Basin, China".Transformations among the parameters of the moment tensor model refer to the code package from Tape and Tape (https://github.com/carltape/mtbeach/; https://github.com/carltape/surfacevel2strain; Tape and Tape, 2009, 2012, 2013, 2015).Tape, C., P. Muse, M. Simons, D. Dong, and F. Webb (2009). Multiscale estimation of GPS velocity fields, Geophys. J. Int. 179, no.2, 945-971, doi: 10.1111/j.1365-246X.2009.04337.x.Tape, W., and C. Tape (2012). A geometric setting for moment tensors, Geophys. J. Int. 190, no. 1, 476–498, doi: 10.1111/j.1365-246X.2012.05491.x.Tape, W., and C. Tape (2013). The classical model for moment tensors, Geophys. J. Int. 195, no. 3, 1701–1720, doi: 10.1093/gji/ggt302.Tape, W., and C. Tape (2015). A uniform parametrization of moment tensors, Geophys. J. Int. 202, no. 3, 2074–2081, doi: 10.1093/gji/ggv262.

opencc-by-4.0Dec 2023View details →

Supplementary material for "Exploring Conceptual Data Modeling Processes: Insights from Clustering and Visualizing Modeling Sequences"

This material supplements the following conference publication: Winkler, Rosenthal, Strecker (2024). "Exploring Conceptual Data Modeling Processes: Insights from Clustering and Visualizing Modeling Sequences". Modellierung 2024.

opencc-by-4.0Dec 2023View details →

Investigation of the post-2007 methane renewed growth with high-resolution 3-D variational inverse modelling and isotopic constraints - Input data

This dataset contains all the input data utilized to perform the inversions in Thanwerdas et al. (2023). First, we store here some data used in the paper but originally generated for other studies. Because these original datasets did not have any DOI, the authors have graciously agreed to store their dataset here. Note that the paper associated to each dataset must be properly referenced if utilized. <ul> <li>Cl Concentrations - Wang et al. (2021).zip: Original Cl concentrations field from Wang et al. (2021). </li> <li>CH4 Fluxes - Saunois et al. (2020).zip: Original CH4 fluxes used as prior data for the inversions performed as part of the Global Methane Budget 2000-2017 (Saunois et al., 2020).</li> </ul> Second, we store the processed input data generated for the purpose of our study. <ul> <li>CH4 Fluxes - LMDz9696.zip: Aggregated CH4 fluxes remapped on LMDz horizontal resolution for the five emission categories used in the paper.</li> <li>d13C Signatures - LMDz9696.zip: δ(13C, CH4) at LMDz horizontal resolution for the five emission categories used in the paper.</li> <li>dD Signatures - LMDz9696.zip: δ(D, CH4) at LMDz horizontal resolution for the five emission categories used in the paper.</li> <li>OH O1D Concentrations - LMDz9696-INCA.zip: OH and O1D monthly concentrations simulated with LMDz-INCA.</li> <li>Masks regions.zip: Masks for the regions used for the input data and the analysis.</li> </ul>

opencc-zeroDec 2023View details →

Matlab code to calibrate a structured-PDE model to data from in vitro experiments

Matlab code for the calibration of a PDE model of evolutionary dynamics of a well-mixed population of aggressive breast cancer cells from in vitro data on MCF7-sh-WISP2 cell line and bootstrapping for uncertainty quantification. For more details, see the associated publication: "Evolutionary dynamics of glucose-deprived cancer cells: insights from experimentally-informed mathematical modelling", by L. Almeida, J. Denis, N. Ferrand, T. Lorenzi, A. Prunet, M. Sabbah, C. Villa (corresponding author, author of code), 2023. In press in the journal of the Royal Society Interface.

opencc-by-nc-4.0Nov 2023View details →

CoUDlabs_WP8_T812_EAWAG_001. Sediment depth measurements for surrogate modeling of sediment build-up in gully pots using temperature data

This dataset contains the results of the experimental campaign and how data were collected on the the <a href="https://co-udlabs.eu/">Co-UDlabs</a> Work Package 8 (Joint Research Activity 3): Improving resilience and sustainability in urban drainage solutions; Task 8.1: Development of consensus on measurement of hydraulic and water quality performance of urban drainage technologies; Subtask 8.1.2: Development of scalable measurement protocols to assess the pollutant retention and release potential of urban drainage structures. Co-UDlabs is a project funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 101008626.This database was developed as part of the Master Thesis in Environmental Engineering at ETH Zurich (Switzerland). Fuchs, L. (2023). Automated surrogate model to estimate sediment accumulation from temperatures in urban drainage systems. MSc Thesis, ETH Zurich. https://polybox.ethz.ch/index.php/s/IyiM38rRy1vlHWD. Accessed on 10th of October of 2023.

Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models

Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used 8–23 selected CpG sites to build age estimation models with machine learning methods with about only $3–7 per sample, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples), and five Panthera species (96 samples). The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and Panthera spp., respectively. Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.

opencc-by-4.0Jan 2024View details →

Data for: Implementing detailed nucleation predictions in the Earth system model EC-Earth3.3.4: sulfuric acid-ammonia nucleation

Model dataset variables produced from the IFS and TM5 modules in EC-Earth3 version 3.3.4. which contains the control case and three experiments with the NPF lookup table. This paper is published at EGUshpere by journal: Geoscientific Model Development. The files contain: Compressed tar file of NetCDF data from IFS output for all four simulations. All IFS data have been averaged to monthly means from 6-hourly grib datasets. The post-process bash script which contains the function for the CDN and cloud effective radius weighted average towards cloud_time is found in the supplemented zendo link. NetCDF files from TM5 general output for each simulation.

Subject-specific knee models, data, and results for specimen S192803

This dataset is part of an ongoing manuscript to validate that sources of data from currently available in vivo methods are sufficient to create computational models of the knee compared with existing in vitro techniques. The data included in this repository is for the S192803 specimen of that dataset and includes experimental data, working models, code, and results obtained for that model and used in that manuscript.

Data from: In vivo functional phenotypes from a computational epistatic model of evolution

Computational models of evolution are valuable for understanding the dynamics of sequence variation, to infer phylogenetic relationships or potential evolutionary pathways, and for biomedical and industrial applications. Despite these benefits, few have validated their propensities to generate outputs with in vivo functionality, which would enhance their value as accurate and interpretable evolutionary algorithms. Utilizing the Hamiltonian of the joint probability of sequences in the family as fitness metric, we sampled and experimentally tested for in vivo beta-lactamase activity in E. coli TEM-1 variants. These variants retain family-like functionality while being more active than their WT predecessor. We found that depending on the inference method used to generate the epistatic constraints, different parameters simulate diverse selection strengths. Under weaker selection, local Hamiltonian fluctuations reliably predict relative changes to variant fitness, recapitulating neutral evolution. In this dataset, we include input datasets, simulation trajectories as well as experimental data to support the publication: "In vivo functional phenotypes from a computationa epistatic model of evolution".

opencc-by-4.0Dec 2023View details →

Software and data underlying the article 'A serious game approach for lake modeling and management: the EscapeBLOOM'

Here we share the player version of the EscapeBLOOM, a dummy version showcasing the techniques to create a similar digital escape room, and the anonymized data of the quantitative survey as presented in the publication 'A serious game approach for lake modeling and management: the EscapeBLOOM'. Anyone is free to play or adjust the game for their own educational purposes. The dummy and supplementary material of the publication 'A serious game approach for lake modeling and management: The EscapeBLOOM' <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.envsoft.2024.105941" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.envsoft.2024.105941</a> together provide guides on how to create a new game from the start and may help to adjust the existing game. The data of the survey was used for the analysis of perceived learning in the publication 'A serious game approach for lake modeling and management: the EscapeBLOOM'.

Data for: Reintroduced Oriental stork bayesian hierarchical model data

Long-lived territorial bird populations often consist of a few territorial breeding adults and many non-breeding individuals. Some populations are threatened by anthropogenic activities, because of human conflicts for high-quality breeding habitat. Therefore, habitat restoration projects have been widely implemented to improve avian population status. In conjunction with habitat restoration, conservation translocations have been increasingly implemented. Adequate non-breeder survival can be a key factor in the success of these attempts because non-breeding birds may represent reservoirs for the replacement of breeders. The maintenance of breeding pair numbers is also influenced by the transition rate of non-breeders to breeders. The reintroduction of Oriental stork (Ciconia boyciana), a long-lived, territorial, endangered species, was initiated in Japan in 2005 using captive birds in hopes of increasing the population's use of restored habitat. Our objective of this study was to elucidate the factors determining reintroduced stork survival and recruitment to the breeding populations. We estimated the survival rate and breeding participation rate by sex, age, generation, wild-born or not, haplotypes, and breeding status in storks reintroduced during 2005–2022 using Bayesian hierarchical models. There was no significant difference in survival rate between non-breeders and breeders. However, the survival rate was lower in wild-born birds than released birds, which may be related to the longer-distance natal dispersal of new generations. Accelerated habitat restoration around breeding areas and preventive measures for collision with human-built structures should be implemented for the sustained growth of reintroduced populations. A low survival rate was also detected for a specific mtDNA haplotype that accounts for the majority of the reintroduced population. This phenomenon might be explained by mtDNA-encoded mutations. Moreover, captive breeding and release history might contribute to an increase in the proportion of this haplotype in the wild.