scholarly journals The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Lucian P. Smith ◽  
Frank T. Bergmann ◽  
Alan Garny ◽  
Tomáš Helikar ◽  
Jonathan Karr ◽  
...  
Keyword(s):  
Simulation Experiment ◽  
Computational Simulation ◽  
Spatial Models ◽  
Software Tools ◽  
Stochastic Simulations ◽  
Biological Research ◽  
Simulation Experiments ◽  
Additional Information ◽  
Parameter Estimations ◽  
Level 1

Abstract Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.

scholarly journals Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Frank T. Bergmann ◽  
Jonathan Cooper ◽  
Matthias König ◽  
Ion Moraru ◽  
David Nickerson ◽  
...  
Keyword(s):  
Time Course ◽  
Computational Models ◽  
Simulation Experiment ◽  
Computational Simulation ◽  
Biological Research ◽  
Markup Language ◽  
Formal Representation ◽  
Post Process ◽  
Experiment Description ◽  
Level 1

AbstractThe creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

scholarly journals SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

2016 ◽  
Author(s):  
Frank T Bergmann ◽  
David Nickerson ◽  
Dagmar Waltemath ◽  
Martin Scharm
Keyword(s):  
Simulation Experiment ◽  
Software Tools ◽  
Markup Language ◽  
Simulation Studies ◽  
Online Application ◽  
Web Tools ◽  
Experiment Description ◽  
Level 1

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.

scholarly journals SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

2016 ◽  
Author(s):  
Frank T Bergmann ◽  
David Nickerson ◽  
Dagmar Waltemath ◽  
Martin Scharm
Keyword(s):  
Simulation Experiment ◽  
Software Tools ◽  
Markup Language ◽  
Simulation Studies ◽  
Online Application ◽  
Web Tools ◽  
Experiment Description ◽  
Level 1

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.

scholarly journals Fetal surgery for spina bifida

2019 ◽  
Vol 24 (2) ◽  
pp. 105-114 ◽  
Author(s):  
Michael C. Dewan ◽  
John C. Wellons
Keyword(s):  
Maternal Morbidity ◽  
Morphological Changes ◽  
Fetal Surgery ◽  
Maternal Factors ◽  
Beneficial Effects ◽  
Additional Information ◽  
Fetal Repair ◽  
Technical Innovations ◽  
Level 1

The two-hit hypothesis of neural injury in the wake of open neural tube defects suggests an opportunity for preservation of function and potential reversibility of early morphological changes in the fetus diagnosed with myelomeningocele. The Management of Myelomeningocele Study (MOMS) demonstrated reduced need for shunting and improved neurological function in patients treated in utero relative to postnatally, thereby offering level 1 evidence supporting fetal repair. Subsequent studies have offered additional information about urological, orthopedic, radiological, and maternal factors surrounding fetal repair. The quest for robust long-term neurocognitive and motor function data is underway and poised to shape the future of fetal repair. In addition, technical innovations such as fetoscopic surgery aim to minimize maternal morbidity while conferring the beneficial effects observed with open intrauterine intervention.

scholarly journals Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

2015 ◽  
Vol 12 (2) ◽  
pp. 119-212 ◽  
Author(s):  
Frank T. Bergmann ◽  
Jonathan Cooper ◽  
Nicolas Le Novère ◽  
David Nickerson ◽  
Dagmar Waltemath
Keyword(s):  
Computational Models ◽  
Simulation Experiment ◽  
Extensible Markup Language ◽  
Markup Language ◽  
Minimum Information ◽  
Extensible Markup ◽  
Experiment Description ◽  
Simulation Results ◽  
Level 1 ◽  
Readable Format

Summary The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines.This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

scholarly journals Application of MOOC and Virtual Simulation Experiment in Experimental Teaching of Mechanical Design

2021 ◽  
pp. 318-329
Author(s):  
Shaoyong Han, Jingchun Zhan, Zhen Wang
Keyword(s):  
Simulation Experiment ◽  
Teaching Method ◽  
Mechanical Design ◽  
Virtual Simulation ◽  
Basic Knowledge ◽  
Engineering Practice ◽  
Simulation Experiments ◽  
Teaching System ◽  
Experimental Teaching ◽  
New Situation

The mechanical design experiment is a comprehensive experimental course that can cultivate the preliminary engineering practice ability of machinery students. Due to the high requirements for students' basic knowledge and ability of comprehensive application of knowledge, teaching is difficult and the teaching effect is general. This paper uses the MOOC teaching method, a new network-based teaching model, to study the experimental teaching of mechanical design and the construction of virtual simulation experiment teaching system under the new situation. Firstly, analyze the advantages in experimental teaching of mechanical design under virtual simulation experiment. Secondly, it puts forward suggestions for constructing the virtual simulation experiment teaching system of mechanical design, and discusses the advantages of the combination of MOOC and virtual simulation experiment technology, opportunities and reforms under the new situation. Lastly, it can be concluded that by using MOOC and virtual simulation experiments can break through the limitations of traditional teaching and improve teaching. This paper applies the MOOC and virtual simulation experiment to the experimental teaching of mechanical design, can not only improve the teaching of teachers, but also cultivate the practical ability and thinking innovation ability of machinery students. With the advantages of MOOC and virtual simulation experiments, it provides better opportunities and challenges for the teaching of mechanical design.

scholarly journals Bioinformatics: scope and challenges in aquaculture research of Bangladesh- a review

2021 ◽  
Vol 10 (2) ◽  
pp. 137-145
Author(s):  
KMS Rana ◽  
K Ahammad ◽  
MA Salam
Keyword(s):  
Health Management ◽  
National Level ◽  
Work Force ◽  
Disease Diagnosis ◽  
Software Tools ◽  
Biological Data ◽  
Biological Information ◽  
Biological Research ◽  
Future Research ◽  
Data Set

Bioinformatics is one of the ongoing trends of biological research integrating gene based information and computational technology to produce new knowledge. It works to synthesize complex biological information from multiomics data (results of high throughput technologies) by employing a number of bioinformatics tools (software). User convenience and availability are the determining factors of these tools being widely used in bioinformatics research. BLAST, FASTA (FAST-All), EMBOSS, ClustalW, RasMol and Protein Explorer, Cn3D, Swiss PDB viewer, Hex, Vega, Bioeditor etc. are commonly operated bioinformatics software tools in fisheries and aquaculture research. By default, these software tools mine and analyze a vast biological data set using the available databases. However, aquaculture scientists can use bioinformatics for genomic data manipulation, genome annotation and expression profiling, molecular folding, modeling, and design as well as generating biological network and system biology. Therefore, they can contribute in specified fields of aquaculture such as disease diagnosis and aquatic health management, fish nutritional aspects and culture-able strain development. Although having huge prospects, Bangladesh is still in infancy of applying bioinformatics in aquaculture research with limited resources. Research council at national level should be formed to bring all the enthusiastic scientists and skilled manpower under a single umbrella and facilitate to contribute in a collaborative platform. Besides, fully-fledged bioinformatics degree should be launched at University levels to produce knowledgeable and trained work force for future research. This review was attempted to shed light on bioinformatics, as young integrated field of bio-computational research, and its significance in aquaculture research of Bangladesh. Int. J. Agril. Res. Innov. Tech. 10(2): 137-145, December 2020

scholarly journals A Simulation Model of the Automotive Power System Based on the Finite State Machine

2014 ◽  
Vol 8 (1) ◽  
pp. 101-106
Author(s):  
Hongbin Li ◽  
Dong Li
Keyword(s):  
Control System ◽  
Power System ◽  
Simulation Model ◽  
Finite State Machine ◽  
Simulation Experiment ◽  
State Machine ◽  
Mechanical Transmission ◽  
Transmission Control ◽  
Simulation Experiments ◽  
Finite State

In order to validate the performance of the AMT (Automated Mechanical Transmission) control system by simulation experiment, a simulation model that can express the dynamic characteristic of the automotive power system during every phase of the vehicle driving process based on the finite state machine was proposed. Then a hard-in-loop half-real simulation system was established taking the simulation model as kernel. It was shown by the results of simulation experiments that the model could simulate the automotive power system effectively and could be used to evaluate the AMT control system.

Local temperature versus system temperature in a simulation experiment containing water molecules

2019 ◽  
Vol 21 (24) ◽  
pp. 12961-12967 ◽  
Author(s):  
Reza Jafari ◽  
Beheshteh Sohrabi
Keyword(s):  
Simulation Experiment ◽  
Local Temperature ◽  
Water Molecules ◽  
Simulation Experiments ◽  
Versus System ◽  
System Temperature ◽  
Water Models

Water models are commonly used in simulation experiments containing water molecules.

Forecast-Island and Bidding A*-Euclidean Selecting Boustrophedon Coordination Algorithm for Exploration

2021 ◽  
Author(s):  
Zhifeng Yao ◽  
Fengxia Xu ◽  
Chunsong Han
Keyword(s):  
Euclidean Distance ◽  
Simulation Experiment ◽  
Target Point ◽  
Current Position ◽  
A Algorithm ◽  
Simulation Experiments ◽  
Exploration Time ◽  
Long Time ◽  
The Cost ◽  
Walking Time

Exploration algorithms based on the Boustrophedon path seldom consider the impacts of a robot turning at corners on the exploration time. This paper proposes the Forecast-Island and Bidding A*-Euclidean Selecting Boustrophedon Coordination (FIBA*ESBC) algorithm to calculate the turning time at corners in the overall exploration time and introduces a method to estimate the walking time in the Boustrophedon paths in order to determine the directions for path execution. Typically, in bidding-based exploration tasks, the cost is the Euclidean distance between the current position of the robot and the target point. When there is an obstacle between two points, the cost is set to infinity. Therefore, the selected target point is sometimes not optimal. The FIBA*ESBC algorithm is based on the exploration cost of a combination of the Euclidean distance and A* algorithm walking path, which can effectively solve this problem. Because the bidding is based on a greedy algorithm, the robot has a small unexplored island in the later exploration stage; therefore, full exploration is not possible or requires a long time with several repeated paths. The FIBA*ESBC algorithm prioritizes the exploration and estimation of hidden and existing unexplored islands. It can realize complete exploration and decrease the exploration time. Through simulation experiments conducted using Gazebo and RViz, the feasibility of the FIBA*ESBC algorithm is verified. Moreover, a simulation experiment is conducted in MATLAB for comparison with other algorithms. The analysis of the experimental data shows that the proposed algorithm has a relatively short exploration time.

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