Integrating Hydrologic Modeling Web Services With Online Data Sharing to Prepare, Store, and Execute Hydrologic Models

Web based applications, web services, and online data and model sharing technology are becoming increasingly available to support hydrologic research. This promises benefits in terms of collaboration, computer platform independence, and reproducibility of modeling workflows and results. In this research, we designed an approach that integrates hydrologic modeling web services with an online data sharing system to support web-based simulation for hydrologic models. We used this approach to integrate example systems as a case study to support reproducible snowmelt modeling for a test watershed in the Colorado River Basin, USA. We demonstrated that this approach enabled users to work within an online environment to create, describe, share, discover, repeat, modify, and analyze the modeling work. This approach encourages collaboration and improves research reproducibility. It can also be adopted or adapted to integrate other hydrologic modeling web services with data sharing systems for different hydrologic models

Reproducible research using biomodels

Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research could easily be achieved by making use of existing resources, such as supplying models in standard formats and depositing code, models, and results in public repositories

Minimum Information About a Simulation Experiment (MIASE)

Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes

rSHUD v2.0: advancing the Simulator for Hydrologic Unstructured Domains and unstructured hydrological modeling in the R environment

Hydrological modeling is a crucial component in hydrology research, particularly for projecting future scenarios. However, achieving reproducibility and automation in distributed hydrological modeling research for modeling, simulation, and analysis is challenging. This paper introduces rSHUD v2.0, an innovative, open-source toolkit developed in the R environment to enhance the deployment and analysis of the Simulator for Hydrologic Unstructured Domains (SHUD). The SHUD is an integrated surface–subsurface hydrological model that employs a finite-volume method to simulate hydrological processes at various scales. The rSHUD toolkit includes pre- and post-processing tools, facilitating reproducibility and automation in hydrological modeling. The utility of rSHUD is demonstrated through case studies of the Shale Hills Critical Zone Observatory in the USA and the Waerma watershed in China. The rSHUD toolkit's ability to quickly and automatically deploy models while ensuring reproducibility has facilitated the implementation of the Global Hydrological Data Cloud (https://ghdc.ac.cn, last access: 1 September 2023), a platform for automatic data processing and model deployment. This work represents a significant advancement in hydrological modeling, with implications for future scenario projections and spatial analysis.</p

Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail

Replicability and reproducibility of computational models has been somewhat understudied by “the replication movement.” In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and model reproductions in computational neuroscience. We contend that model replicability, or independent researchers' ability to obtain the same output using original code and data, and model reproducibility, or independent researchers' ability to recreate a model without original code, serve different functions and fail for different reasons. This means that measures designed to improve model replicability may not enhance (and, in some cases, may actually damage) model reproducibility. We claim that although both are undesirable, low model reproducibility poses more of a threat to long-term scientific progress than low model replicability. In our opinion, low model reproducibility stems mostly from authors' omitting to provide crucial information in scientific papers and we stress that sharing all computer code and data is not a solution. Reports of computational studies should remain selective and include all and only relevant bits of code

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments