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OneStop:JWS Online's access point to SBML,SBGN and MIRIAM compliant annotation

Franco Du Preez, Jacky Snoep, Franco Du Preez, Stuart Owen, Katherine Wolstencroft, Olga Krebs, Wolfgang Müller, Carole Goble
2011 Nature Precedings  
JWS Online • Among the first online model repositories and simulators Repository 2.) DataFuse Goal • Link models to -Construction data -Validation data 3.)  ...  modeling workflows for users Generates data for model construction • SysMO is developing a software platform: -the SEEK • Uses JWS Online as model simulator • Review tool for some journals • 112 curated  ...  Acknowledgements • Funding: This work was funded by the BBSRC and the BMBF. SysMODB: Supporting Data Access and Integration (BBG0102181).  ... 
doi:10.1038/npre.2011.6349.1 fatcat:bzvqq67mdfbx5pmsmq2m37667e

OneStop:JWS Online's access point to SBML,SBGN and MIRIAM compliant annotation

Franco Du Preez, Jacky Snoep, Franco Du Preez, Stuart Owen, Katherine Wolstencroft, Olga Krebs, Wolfgang Müller, Carole Goble
2011 Nature Precedings  
Acknowledgements • SysMODB team • Funding: This work was funded by the BBSRC and the BMBF. SysMODB: Supporting Data Access and Integration (BBG0102181).  ...  SEEK integrated tool to: • construct, modify, save models in SBML format • SBGN schema generation • annotate model (MIRIAM), using semanticSBML webservices. • Uses JWS Online as model simulator the SEEK  ...  JWS Online • Among the first online model repositories and simulators Repository • Review tool for some journals • 112 curated models • SysMO is developing a software platform: the SEEK 3.)  ... 
doi:10.1038/npre.2011.6349 fatcat:53hg4epj45akpdq2wj5wahzbe4

The JWS online simulation database

Martin Peters, Johann J. Eicher, David D. van Niekerk, Dagmar Waltemath, Jacky L. Snoep
2017 Bioinformatics  
JWS Online is a web-based platform for construction, simulation and exchange of models in standard formats.  ...  Availability and Implementation: The Simulation Database is available on line at https://jjj.bio.vu. nl/models/experiments/. Contact: jls@sun.ac.za.  ...  This work was furthermore funded by the German Federal Ministry of Education and Research (BMBF) as part of the e:Bio SEMS project (FKZ 031 6194) and by the Biotechnology and Biological Sciences Research  ... 
doi:10.1093/bioinformatics/btw831 pmid:28130238 fatcat:hpv5cllhtbfrhcqxpkty3bpyc4

Toward Open and Reproducible Environmental Modeling by Integrating Online Data Repositories, Computational Environments, and Model Application Programming Interfaces

Young-Don Choi, Jonathan L. Goodall, Jeffrey M. Sadler, Anthony M. Castronova, Andrew Bennett, Zhiyu Li, Bart Nijssen, Shaowen Wang, Martyn P. Clark, Daniel P. Ames, Jeffery S. Horsburgh, Hong Yi (+4 others)
2020 Environmental Modelling & Software  
Recent efforts toward this goal have focused on advancing online repositories for data and model sharing, online computational environments along with containerization technology and notebooks for capturing  ...  We then present one possible implementation that integrates HydroShare (an online repository), CUAHSI JupyterHub and CyberGIS-Jupyter for Water (computational environments), and pySUMMA (a model API) to  ...  Acknowledgment This work was supported by the National Science Foundation under collaborative grants OAC-1664061, OAC-1664018, OAC-1664119, ICER-1928369, and ICER-1928315.  ... 
doi:10.1016/j.envsoft.2020.104888 fatcat:qkatdewc2zbftffckss6gsvp2e

Web-based applications for building, managing and analysing kinetic models of biological systems

D.-Y. Lee, R. Saha, F. N. K. Yusufi, W. Park, I. A. Karimi
2008 Briefings in Bioinformatics  
This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis.  ...  The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions.  ...  However, models and data are represented in different formats, which need to be integrated under a common framework.  ... 
doi:10.1093/bib/bbn039 pmid:18805901 pmcid:PMC2638623 fatcat:hf6nu6opujdnjlt6ti3r7z3ny4

WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results

Vineet K Joshi, Johannes M Freudenberg, Zhen Hu, Mario Medvedovic
2011 Source Code for Biology and Medicine  
The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers.  ...  Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results  ...  Acknowledgements This research was supported by grants from the National Human Genome Research Institute (R01 HG003749), National Library of Medicine (R21 LM009662) and NIEHS Center for Environmental Genetics  ... 
doi:10.1186/1751-0473-6-3 pmid:21241501 pmcid:PMC3033799 fatcat:agy4w46kwzgjjg3fomnvwqe5ya

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

M. Swat, S. M. Kielbasa, S. Polak, B. Olivier, F. J. Bruggeman, M. Q. Tulloch, J. L. Snoep, A. J. Verhoeven, H. V. Westerhoff
2010 Interface Focus  
In order to facilitate a fruitful synergy between SB and PK -PD, and between PK and PD, we present a new platform that combines standard phenomenological models used in the PK/PD field with mechanism-based  ...  SB models and approaches.  ...  The Biomodels and JWS online groups work closely together and actively exchange models.  ... 
doi:10.1098/rsfs.2010.0011 pmid:22419971 pmcid:PMC3262244 fatcat:kgecaimpsrb4lh6tkskhxkfrui

MAMMOTh: A new database for curated mathematical models of biomolecular systems

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai
2018 Journal of Bioinformatics and Computational Biology  
Thus, to simulate the internal nature and dynamics of the whole biological system we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary  ...  systems, which are fit to the experimental data.  ...  For this purpose we have used either APIs of the corresponding services or the manual data extraction (JWS online).  ... 
doi:10.1142/s0219720017400108 pmid:29172865 fatcat:yt5zbiwkmferdb3ctxt3tmdtya

Smart Home Entertainment System with Personalized Recommendation and Speech Emotion Recognition Support

Zheng Wan
2016 International Journal of Smart Home  
In this paper a personalized recommendation and speech emotion recognition based smart home entertainment system, which integrates multiple entertainment resources including online movies/TV serial, TV  ...  programs and online music, is proposed.  ...  Only normal smart phone, PC and TV are needed. (2) Integrate multiple kinds of entertainment resources: online movies and TV serials, TV programs and online music.  ... 
doi:10.14257/ijsh.2016.10.8.14 fatcat:koigspknsjdlbhfsrbdvfdlrdq

Arabic web pages clustering and annotation using semantic class features

Hanan M. Alghamdi, Ali Selamat, Nor Shahriza Abdul Karim
2014 Journal of King Saud University: Computer and Information Sciences  
The quality of the clustering result has evaluated the use of the purity and the mean intra-cluster distance (MICD) evaluation measures.  ...  To reach semantic similarities, the approach extracts the semantic class features and integrates them into the similarity weighting schema.  ...  Acknowledgments The authors would like to extend their thanks to the Ministry of Education, Malaysia, Universiti Teknologi Malaysia (UTM) under Vot 03H02, Umm Al-Qura University (UQU) and the Ministry  ... 
doi:10.1016/j.jksuci.2014.06.002 fatcat:os6ei63opfghzomx5clyytonry

MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems [article]

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai
2016 bioRxiv   pre-print
Thus, to simulate the internal nature and dynamics of the whole biological system we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary  ...  systems, which are fit to the experimental data.  ...  For this purpose we have used either APIs of the corresponding services or the manual data extraction (JWS online).  ... 
doi:10.1101/053652 fatcat:33jw3gcyiff4dfuaoiolcru72u

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

2018 11-ая Международная конференция по биоинформатике регуляции и структуры геномов и системной биологии  
It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API  ...  The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https:// fairdomhub.org/) for the Systems Biology community.  ...  ACKNOWLEDGEMENTS The authors would like to thank Martin Scharm, Dagmar Waltemath, Andrew Millar, project ambassador 'PALS' and all others who have supported them in their efforts to develop and deploy  ... 
doi:10.18699/bgrssb-2018-111 fatcat:ap5rnoslqbdi7ankay3yhcbqr4

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk (+5 others)
2016 Nucleic Acids Research  
It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API  ...  The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https:// fairdomhub.org/) for the Systems Biology community.  ...  ACKNOWLEDGEMENTS The authors would like to thank Martin Scharm, Dagmar Waltemath, Andrew Millar, project ambassador 'PALS' and all others who have supported them in their efforts to develop and deploy  ... 
doi:10.1093/nar/gkw1032 pmid:27899646 pmcid:PMC5210530 fatcat:tuhlhnr2zrazfaqbxmegmk4aii

Online Bearing Fault Diagnosis Based on Packet Loss Influence-Inspired Retransmission Mechanism

Zhe Tong, Wei Li, Enrico Zio, Bo Zhang, Gongbo Zhou
2022 Mathematics  
We evaluate the retransmission scheme using a fault diagnosis model based on K-nearest neighbor (KNN) for timely online bearing fault diagnosis.  ...  discrepancies between a data stream and the historical datasets.  ...  Let us denote the data sent as x ds (n), and data received as x dr (n), where n = 0, • • • , MN − 1.  ... 
doi:10.3390/math10091422 fatcat:mwoxcufskja27irj55wazoyvzu

The Use of Wireless Network Combined with Artificial Intelligence Technology in the Reform of Music Online Teaching System

Fan Chen, Huan Meng, Narasimhan Venkateswaran
2022 Wireless Communications and Mobile Computing  
These models include music online composition teaching model, music online teaching scoring model, and music online lyric writing teaching model.  ...  combination model of AI technology and music online education system in 5th-generation (5G) wireless network environment is proposed.  ...  The system designed mainly includes three parts: music online composition teaching model, music online teaching scoring model, and music online lyric writing teaching model.  ... 
doi:10.1155/2022/5957708 fatcat:yznklf5xjba23b4xiorpj742ee
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