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BioModels-15 years of sharing computational models in life science

2019 Nucleic Acids Research  
Computational modelling has become increasingly common in life science research.  ...  With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature.  ...  ACKNOWLEDGEMENTS We would like to acknowledge the COMBINE community for the support and numerous contributions over the years.  ... 
doi:10.1093/nar/gkz1055 pmid:31701150 pmcid:PMC7145643 fatcat:kbsg5oncwfan3aq4h5arm3bo5i

Exploring autonomy through computational biomodelling

N. Palfreyman
2009 Briefings in Bioinformatics  
In this article we review the role played by computational biomodels in shedding light on the ontological status of organisms.  ...  We conclude that computational biomodelling plays a fertile role in furnishing a proof of concept for conjectures in the philosophy of biology, and suggests the need for a process-based ontology of biological  ...  Consequently computational biomodelling has a significant role to play in operationalising thoughtexperiments in philosophy of biology.  ... 
doi:10.1093/bib/bbp003 pmid:19276201 fatcat:5nvnsr5o5nhgbemh6k6rc7cqku

BioModels: Content, Features, Functionality, and Use

N Juty, R Ali, M Glont, S Keating, N Rodriguez, MJ Swat, SM Wimalaratne, H Hermjakob, N Le Novère, C Laibe, V Chelliah
2015 CPT: Pharmacometrics & Systems Pharmacology  
BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales.  ...  The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources.  ...  This work received support from the Biotechnology and Biological Sciences Research Council (BioModels, BB/J019305/  ... 
doi:10.1002/psp4.3 pmid:26225232 pmcid:PMC4360671 fatcat:4ki3pd2zdze5pdvtqo4qhjbi3a

Teaching facial fracture repair: A novel method of surgical skills training using three-dimensional biomodels

Neil D'souza, James Mainprize, Glenn Edwards, Paul Binhammer, Oleh Antonyshyn
2015 Plastic Surgery  
Based on the preoperative computed tomography (CT) image data, computer image processing and 3D modelling was used to generate a virtual 3D model of the patient's facial fractures.  ...  The level of previous clinical experience was variable. The study group comprised 15 third-year residents (R3), 11 fourth-year residents (R4), and three fifth-year residents (R5).  ... 
doi:10.1177/229255031502300214 pmid:26090347 pmcid:PMC4459413 fatcat:qnnylwgpajetpapar33ykp3pqa

Structural Heart Valve Disease in the Era of Change and Innovation: The Crosstalk between Medical Sciences and Engineering

Francesco Nappi, Antonio Nenna, Massimo Chello
2022 Bioengineering  
In recent years, both cardiology and cardiovascular surgery have witnessed an era of consistently evolving changes which have dramatically transformed the course and management of cardiovascular disease  ...  In this context, the use of FEA biomodeling allows the development of predictive models, for short-and long-term follow-up by means of computed biomodeling applied to TVT.  ...  Current Scenario and Future Openings The use of computational biomodeling with FEA in the field of cardiovascular science has emerged as an essential method to obtain valuable data about complicated real-world  ... 
doi:10.3390/bioengineering9060230 pmid:35735473 pmcid:PMC9220173 fatcat:r63hnbluprfczlfgrvdtvujg3e

Reproducibility in systems biology modelling

Krishna Tiwari, Sarubini Kananathan, Matthew G Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V N Nguyen, Mihai Glont (+2 others)
2021 Molecular Systems Biology  
In this piece, we assess mathematical model reproducibility and propose a scorecard for improving reproducibility in this field.  ...  Reproducibility of scientific results is a key element of science and credibility. The lack of reproducibility across many scientific fields has emerged as an important concern.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.15252/msb.20209982 pmid:33620773 fatcat:7rd6ltkcavbnjdjrlwxzc5mzsu

MAGPIE: Simplifying access and execution of computational models in the life sciences

Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche, Timothée Poisot
2017 PLoS Computational Biology  
We also outline the potential of MAGPIE to improve transparency and reproducibility of computational models in life sciences. A demo server is available at magpie.imb.medizin.tu-dresden.de.  ...  OPEN ACCESS Citation: Baldow C, Salentin S, Schroeder M, Roeder I, Glauche I (2017) MAGPIE: Simplifying access and execution of computational models in the life sciences.  ...  Availability and future directions Perspective The importance of computational models in application oriented science, such as biomedicine, has rapidly increased over the last years.  ... 
doi:10.1371/journal.pcbi.1005898 pmid:29244826 pmcid:PMC5747461 fatcat:kiskljruonghxleer6h7zefmna

Reproducibility in systems biology modelling [article]

Krishna Tiwari, Sarubini Kananathan, Matthew G Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V N Nguyen, Mihai Glont (+2 others)
2020 bioRxiv   pre-print
Our analysis revealed that models published in journals across several fields of life science failed to reproduce, revealing a common problem in the peer-review process.  ...  The reproducibility crisis has emerged as an important concern across many fields of science including life science, since many published results failed to reproduce.  ...  Our collection covered models of a wide range of biological processes, originating from articles published in 152 life science journals.  ... 
doi:10.1101/2020.08.07.239855 fatcat:tos7joxearcobbb44ydahadvky

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail.  ...  Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes.  ...  Our BioModels team helped launch PharmML, a flexible format for exchanging computational models in pharmaceutical R&D, in 2016 (15) .  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

An online model composition tool for system biology models

Sarp A Coskun, A Ercument Cicek, Nicola Lai, Ranjan K Dash, Z Meral Ozsoyoglu, Gultekin Ozsoyoglu
2013 BMC Systems Biology  
SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers.  ...  a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway.  ...  Acknowledgements This research has been supported by the National Science Foundation grants DBI 0743705, DBI 0849956, CRI 0551603 and by the National Institute of Health grant GM088823.  ... 
doi:10.1186/1752-0509-7-88 pmid:24006914 pmcid:PMC3846440 fatcat:qn6h5d46praznpxvgwhz65dhvu

Combining computational models, semantic annotations and simulation experiments in a graph database

Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath
2015 Database: The Journal of Biological Databases and Curation  
Abstract Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems.  ...  The introduced concept notably improves the access of computational models and associated simulations in a model repository.  ...  Acknowledgements The authors thank Rebekka Alm for implementing part of the SED-ML storage and Markus Wolfien for creating and encoding the SED-ML files used in this article.  ... 
doi:10.1093/database/bau130 pmid:25754863 pmcid:PMC4352687 fatcat:mkeroo4ot5fhrhxoxokbydyauq

Quantifying the impact of public omics data

Yasset Perez-Riverol, Andrey Zorin, Gaurhari Dass, Manh-Tu Vu, Pan Xu, Mihai Glont, Juan Antonio Vizcaíno, Andrew F. Jarnuczak, Robert Petryszak, Peipei Ping, Henning Hermjakob
2019 Nature Communications  
The amount of omics data in the public domain is increasing every year. Modern science has become a data-intensive discipline.  ...  OmicsDI aggregates genomics, transcriptomics, proteomics, metabolomics and multiomics datasets, as well as computational models of biological processes.  ...  6000 models available in BioModels.  ... 
doi:10.1038/s41467-019-11461-w pmid:31383865 pmcid:PMC6683138 fatcat:gbh7v4yiwnahpfznf2xljmyuka

Ten top reasons for systems biology to get into model-driven engineering

Magali Roux-Rouquié, Debora Schuch da Rosa
2006 Proceedings of the 2006 international workshop on Global integrated model management - GaMMa '06  
Recent progresses in post-genomic biology allow addressing issues at the system level through the coupling of experimental and modeling approaches that constitute the core of Systems Biology (SB).  ...  Current models in SB are reviewed and the main requirements to conduct models integration are identified.  ...  By doing this, we should learn from each other's communities, hoping that sharing our efforts in the context of systems biology will inspire new ideas in computer sciences.  ... 
doi:10.1145/1138304.1138316 fatcat:bixas24amvexjovuapuw5z6swu

COMODI: an ontology to characterise differences in versions of computational models in biology

Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer
2016 Journal of Biomedical Semantics  
Methods: We manually studied changes in selected models from BioModels and the Physiome Model Repository.  ...  To improve this situation, we developed an ontology of terms describing changes in computational biology models.  ...  This work was conducted using the Protégé resource, which is supported by grant GM10331601 from the National Institute of General Medical Sciences of the United States National Institutes of Health.  ... 
doi:10.1186/s13326-016-0080-2 pmid:27401413 pmcid:PMC4940905 fatcat:a2dvawekzfhw5oa76qdi7feiz4

Semantic Web technologies for the big data in life sciences

Hongyan Wu, Atsuko Yamaguchi
2014 BioScience Trends  
The life sciences field is entering an era of big data with the breakthroughs of science and technology. More and more big data-related projects and activities are being performed in the world.  ...  The paper presents a survey of big data in life sciences, big data related projects and Semantic Web technologies.  ...  Acknowledgements This work has been supported by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).  ... 
doi:10.5582/bst.2014.01048 fatcat:x2rlpyjel5cybarma34ji6sq3y
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