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BioModels: expanding horizons to include more modelling approaches and formats

Mihai Glont, Tung V N Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M Wimalaratne, Varun B Kothamachu, Nicolas Rodriguez, Maciej J Swat, Jurgen Eils, Roland Eils (+5 others)
2017 Nucleic Acids Research  
To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk  ...  This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML.  ...  fruitful discussions and constructive suggestions that have resulted in JUMMP being significantly more user-friendly.  ... 
doi:10.1093/nar/gkx1023 pmid:29106614 pmcid:PMC5753244 fatcat:3e4bpcbu7bh2dklf7v4vxeduwu

Escalating model sizes and complexities call for standardized forms of representation

Michael Hucka, Andrew Finney
2005 Molecular Systems Biology  
Not only does this reduce errors due to human translation from one format to another, but it also permits models to be reused more effectively, built upon more directly, and published more precisely.  ...  apply new techniques and approaches-in short, to do better science.  ...  Not only does this reduce errors due to human translation from one format to another, but it also permits models to be reused more effectively, built upon more directly, and published more precisely.  ... 
doi:10.1038/msb4100015 pmid:16729046 pmcid:PMC1360139 fatcat:ohrcwootqrcarmlga3unikdt54

Infrastructure For Systems Biology Europe (Isbe) Business Case

Tracey Duncombe, Will Fitzmaurice, Richard Kitney, Angela Krueger, Martjin Mone, Gabriela Pastori, Adrian Pugh, Babette Regierer, Barbara Skene, Natalie Stanford, Roel Van Driel, Frans Van Nieuwpoort
2014 Zenodo  
It outlines the rationale for ISBE and how it can be achieved, as the project engages more widely in developing its strategy.  ...  The ISBE Business Case was first published in November 2014, following approval by the Steering Committee, funders and the Scientific Advisory Board.  ...  Further Information ACKNOWLEDGEMENTS ISBE would like to thank Bas Teusink and former director of the Kluyver Centre Jack Pronk for their assistance.  ... 
doi:10.5281/zenodo.14946 fatcat:tu2um6uh4raw7a63dgraadlpr4

Rapid Prototyping for Biomedical Engineering: Current Capabilities and Challenges

Andrés Díaz Lantada, Pilar Lafont Morgado
2012 Annual Review of Biomedical Engineering  
These new techniques and technologies are usually referred to as rapid prototyping and manufacturing technologies, and they allow prototypes to be produced in a wide range of materials with remarkable  ...  A new set of manufacturing technologies has emerged in the past decades to address market requirements in a customized way and to provide support for research tasks that require prototypes.  ...  The most notable research includes modeling the behavior of microorganisms (71) , modeling complex organisms and their systems (including human anatomy) (72) , and modeling the surfaces of organs and  ... 
doi:10.1146/annurev-bioeng-071811-150112 pmid:22524389 fatcat:xwa7tigqozdx7jpijkn6kzycza

Tissue engineering and regenerative medicine -where do we stand?

Raymund E. Horch, Ulrich Kneser, Elias Polykandriotis, Volker J. Schmidt, Jiaming Sun, Andreas Arkudas
2012 Journal of Cellular and Molecular Medicine  
The advent of either embryonic or mesenchymal adult stem-cell technology has fostered many of the efforts to combine this promising tool with TE approaches and has merged the field into the term Regenerative  ...  The synthesis of TE with innovative methods of molecular biology and stem-cell technology appears to be very promising.  ...  We thank the Xue Hong and Hanns Georg Geis Foundation for their continuous support of research in TE and RM. Parts of the work were supported by research grants from Baxter Healthcare Corporation.  ... 
doi:10.1111/j.1582-4934.2012.01564.x pmid:22436120 pmcid:PMC3823070 fatcat:wmigbija2rfppcrbi32w7ns6ru

Microbial Metabolomics

Jane Tang
2011 Current Genomics  
This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.  ...  provide a more accurate snap shot of the actual physiological state of the cell.  ...  Cell to Cell Signaling As microbial communities become more complex, a global systems approach is necessary to understand the formation of consortia, communication between members and functional interaction  ... 
doi:10.2174/138920211797248619 pmid:22379393 pmcid:PMC3178908 fatcat:s255k7dstvgz3ggftszg3svzwq

Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities

Nicholas Lewis, John Hedengren, Eric Haseltine
2015 Processes  
The second model is the ErbB model and shows the ability of the hybrid sequential and simultaneous method to solve large-scale biological models.  ...  Suggested methods are model reformulation to improve input-to-output model linearity, sensitivity ranking, and choice of solver.  ...  Acknowledgments The authors acknowledge the financial and technical support from Vertex Pharmaceuticals. Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.3390/pr3030701 fatcat:dptmkf5syvawxijcbt5v557f4e

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

Fabian Fröhlich, Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan, Moritz Schütte, Ji-Hyun Lim, Matthias Heinig, Fabian J. Theis, Hans Lehrach (+3 others)
2018 Cell Systems  
We anticipate this to be the starting point for development of more comprehensive models allowing a deeper mechanistic insight. (2017).  ...  Here, we present a computational framework for the parameterization of large-scale mechanistic models and its application to the prediction of drug response of cancer cell lines from exome and transcriptome  ...  To quantify the scale and comprehensiveness of our model, we compared it to curated mechanistic pathway models available in the BioModels database (Li et al., 2010) and also-in more detail-to a set of  ... 
doi:10.1016/j.cels.2018.10.013 fatcat:on4fgrx5ofhs5cuzann4hufc6y

Systems analysis of salivary gland development and disease

Melinda Larsen, Kenneth M. Yamada, Kurt Musselmann
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Taking a more global approach, multiple groups are currently profiling the transcriptome, the proteome, and other "omes" in both developing mouse tissues and in human patient samples.  ...  The greatest challenge for the future will be to develop realistic models that integrate multiple types of data to both describe and predict embryonic development and human disease.  ...  This work was sponsored in part by the NIH/NIDCR by grants RO1DE019244, R21DE019197 and RC1DE020402 (to M.L.) and NIDCR Intramural support (to K.M.Y.).  ... 
doi:10.1002/wsbm.94 pmid:20890964 pmcid:PMC3398465 fatcat:xywcnmdeprcj5pglbcuox4komm

Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits [article]

Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Eugenio Piasini, Justas Birgiolas, Robert C Cannon, N Alex Cayco-Gajic, Sharon Crook, Andrew P Davison, Salvador Dura-Bernal (+13 others)
2018 biorxiv/medrxiv   pre-print
Open Source Brain makes neural models transparent and accessible and facilitates testing, critical evaluation and refinement, thereby helping to improve the accuracy and reproducibility of models, and  ...  However, biologically detailed neuronal and circuit models are complex and implemented in a range of specialized languages, making them inaccessible and opaque to many neuroscientists.  ...  To further lower the barriers to model creation on OSB, we are also expanding the functionality of the platform to include tighter integration with the experimental data used to build models and test their  ... 
doi:10.1101/229484 fatcat:cipxjeoofzfovf7kfg2vle7xuu

Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits

Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Sadra Sadeh, Eugenio Piasini, Justas Birgiolas, Robert C. Cannon, N. Alex Cayco-Gajic, Sharon Crook, Andrew P. Davison (+15 others)
2019 Neuron  
To address this, we have developed Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species.  ...  In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease.  ...  To further lower the barriers to model creation on OSB, we are also expanding the functionality of the platform to include tighter integration with the experimental data used to build models and test their  ... 
doi:10.1016/j.neuron.2019.05.019 pmid:31201122 pmcid:PMC6693896 fatcat:oextrgyvzzfw3akfwmdjim73ei

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
2017 Metabolic Engineering  
Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis.  ...  Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing  ...  This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement no 686070.  ... 
doi:10.1016/j.ymben.2016.12.002 pmid:27939572 pmcid:PMC5249239 fatcat:3py442kfwfhjnpsiwqwqrfcefm

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics [article]

Mahnoor Naseer Gondal, Safee Ullah Chaudhary
2021 bioRxiv   pre-print
Cancer systems biology models built on top of this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis  ...  Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multiscale biomolecular cancer data, (ii) systems biology models developed using this data,  ...  Over time, KEGG has significantly expanded to include high-throughput multi-omics data (124) .  ... 
doi:10.1101/2021.05.17.444410 fatcat:vbfvmtb5irdapglgkmh5na73je

Sociocultural dynamics and information civilization as one of the vectors of the evolution of 21st century culture

Rida Zekrist, Maxim Bakhtin, D. Rudoy, A. Olshevskaya, V. Kankhva
2020 E3S Web of Conferences  
New approaches used in the work are developed on the basis of a synergistic expansion of the research method.  ...  The article considers the problem of developing conceptual principles of philosophical and cultural studies of society that are adequate to its current metastable state, taking into account its transition  ...  However, global informatization of society, the development of computer networks leads to the formation of interdisciplinary approaches.  ... 
doi:10.1051/e3sconf/202021017033 fatcat:bckst2stjzhrnpncsbu4sd3yri

Chaos as an interpretable benchmark for forecasting and data-driven modelling [article]

William Gilpin
2021 arXiv   pre-print
model training, and benchmarking symbolic regression algorithms.  ...  Chaotic systems inherently challenge forecasting models, and across extensive benchmarks we correlate forecasting performance with the degree of chaos present.  ...  Author statement and hosting plan The authors bear all responsibility in case of rights violations. The data license has been included elsewhere in this appendix.  ... 
arXiv:2110.05266v1 fatcat:762cndr4a5bzzbfkablmkvbk7u
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