SBMLLevel 3: an extensible format for the exchange and reuse of biological models

Molecular Systems Biology, Journal Year: 2020, Volume and Issue: 16(8)

Published: Aug. 1, 2020

Review26 August 2020Open Access SBML Level 3: an extensible format for the exchange and reuse of biological models Sarah M Keating orcid.org/0000-0002-3356-3542 Computing Mathematical Sciences, California Institute Technology, Pasadena, CA, USA European Bioinformatics Institute, Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK BioQuant/COS, Heidelberg University, Heidelberg, Germany Search more papers by this author Dagmar Waltemath orcid.org/0000-0002-5886-5563 Medical Informatics, Community Health, University Medicine Greifswald, Matthias König orcid.org/0000-0003-1725-179X Theoretical Biology, Humboldt-University Berlin, Fengkai Zhang orcid.org/0000-0001-7112-9328 Immune System National Allergy Infectious Diseases, Institutes Bethesda, MD, Andreas Dräger orcid.org/0000-0002-1240-5553 Computational Systems Infection Antimicrobial-Resistant Pathogens, Biomedical Informatics (IBMI), Tübingen, Department Computer Science, German Center Research (DZIF), Claudine Chaouiya orcid.org/0000-0003-2350-0756 Aix-Marseille Université, CNRS, Centrale Marseille, France Instituto Gulbenkian de Ciência, Oeiras, Portugal Frank T Bergmann orcid.org/0000-0001-5553-4702 Andrew Finney ANSYS Ltd, Milton Park, Oxfordshire, Colin S Gillespie orcid.org/0000-0003-1787-0275 School Mathematics, Statistics Physics, Newcastle upon Tyne, Tomáš Helikar orcid.org/0000-0003-3653-1906 Biochemistry, Nebraska–Lincoln, Lincoln, NE, Stefan Hoops orcid.org/0000-0001-8503-8371 Biocomplexity & Initiative, Virginia, Charlottesville, VA, Rahuman Malik-Sheriff orcid.org/0000-0003-0705-9809 Stuart L Moodie orcid.org/0000-0001-6191-5595 Eight Pillars Edinburgh, Ion I Moraru orcid.org/0000-0002-3746-9676 Cell Analysis Modeling, UConn Farmington, CT, Chris J Myers orcid.org/0000-0002-8762-8444 Electrical Engineering, Utah, Salt Lake City, UT, Aurélien Naldi orcid.org/0000-0002-6495-2655 Institut Biologie l'ENS (IBENS), Département Biologie, École Normale Supérieure, INSERM, Université PSL, Paris, Brett G Olivier orcid.org/0000-0002-5293-5321 SysBioLab, AIMMS, Vrije Universiteit Amsterdam, Netherlands Sven Sahle James C Schaff orcid.org/0000-0003-3286-7736 Applied BioMath, LLC, Concord, MA, Lucian P Smith orcid.org/0000-0001-7002-6386 Bioengineering, Washington, Seattle, WA, Maciej Swat Simcyp (a Certara company), Sheffield, South Yorkshire, Denis Thieffry orcid.org/0000-0003-0271-1757 Leandro Watanabe orcid.org/0000-0001-7030-8690 Darren Wilkinson orcid.org/0000-0003-0736-802X The Alan Turing British Library, London, Michael Blinov orcid.org/0000-0002-9363-9705 Kimberly Begley orcid.org/0000-0002-1642-7493 R Faeder orcid.org/0000-0001-8127-609X Pittsburgh, PA, Harold F Gómez Biosystems Science ETH Zürich, Basel, Switzerland Thomas Hamm orcid.org/0000-0001-9579-7267 Yuichiro Inagaki orcid.org/0000-0003-4011-8487 Management IT Consulting Division, Mizuho Information Inc., Tokyo, Japan Wolfram Liebermeister orcid.org/0000-0002-2568-2381 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, Allyson Lister orcid.org/0000-0002-7702-4495 Oxford e-Research Centre (OeRC), Engineering Oxford, Daniel Lucio orcid.org/0000-0002-8912-7213 College NC State Raleigh, NC, Eric Mjolsness orcid.org/0000-0002-9085-9171 California, Irvine, Carole Proctor orcid.org/0000-0002-1366-1399 Cellular Medicine, Karthik Raman orcid.org/0000-0002-9311-7093 Biotechnology, Bhupat Jyoti Mehta Biosciences, Indian Technology (IIT) Madras, Chennai, India Initiative Biological (IBSE), IIT Robert Bosch Data Artificial Intelligence (RBC-DSAI), Nicolas Rodriguez orcid.org/0000-0002-9290-7894 Babraham Cambridge, Clifford A Shaffer orcid.org/0000-0003-0001-0295 Virginia Tech, Blacksburg, Bruce E Shapiro Northridge, Joerg Stelling orcid.org/0000-0002-1145-891X SIB Swiss Bioinformatics, Neil Swainston orcid.org/0000-0001-7020-1236 Integrative Liverpool, Naoki Tanimura Solutions John Wagner IBM Australia, Melbourne, Vic., Australia Martin Meier-Schellersheim orcid.org/0000-0002-8754-6377 Herbert Sauro orcid.org/0000-0002-3659-6817 Bernhard Palsson orcid.org/0000-0003-2357-6785 San Diego, La Jolla, Hamid Bolouri Immunology, Benaroya at Mason, Hiroaki Kitano orcid.org/0000-0002-3589-1953 Okinawa Okinawa, Akira Funahashi orcid.org/0000-0003-0605-239X Biosciences Keio Yokohama, Kanagawa, Henning Hermjakob orcid.org/0000-0001-8479-0262 Doyle orcid.org/0000-0002-1828-2486 Hucka Corresponding Author [email protected] orcid.org/0000-0001-9105-5960 3 members membersA complete list affiliations appears in Appendix 1Search Keating1,2,3,‡, Waltemath4,‡, König5, Zhang6, Dräger7,8,9, Chaouiya10,11, Bergmann3, Finney12, Gillespie13, Helikar14, Hoops15, Malik-Sheriff2, Moodie16, Moraru17, Myers18, Naldi19, Olivier1,3,20, Sahle3, Schaff21, Smith1,22, Swat23, Thieffry19, Watanabe18, Wilkinson13,24, Blinov17, Begley25, Faeder26, Gómez27, Hamm7,8, Inagaki28, Liebermeister29, Lister30, Lucio31, Mjolsness32, Proctor33, Raman34,35,36, Rodriguez37, Shaffer38, Shapiro39, Stelling40, Swainston41, Tanimura42, Wagner43, Meier-Schellersheim6, Sauro22, Palsson44, Bolouri45, Kitano46,47, Funahashi48, Hermjakob2, Doyle1, *,1, , Richard Adams, Nicholas Allen, Bastian Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Cox, Piero Dalle Pezze, Emek Demir, William Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard Harris, Benjamin Heavner, Ron Henkel, Hlavacek, Bin Hu, Hyduke, Hidde Jong, Nick Juty, Peter Karp, Jonathan Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean-Baptiste Pettit, Pfau, Phair, Tomas Radivoyevitch, Johann Rohwer, Oliver Ruebenacker, Julio Saez-Rodriguez, Scharm, Schmidt, Falk Schreiber, Schubert, Roman Schulte, Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie Stefan, Devin Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Ioannis Xenarios, Anna Zhukova Jeremy Zucker 1Computing 2European 3BioQuant/COS, 4Medical 5Institute 6Laboratory 7Computational 8Department 9German 10Aix-Marseille 11Instituto 12ANSYS 13School 14Department 15Biocomplexity 16Eight 17Center 18Department 19Institut 20SysBioLab, 21Applied 22Department 23Simcyp 24The 25California 26Department 27Department 28Management 29Université 30Oxford 31College 32Department 33Institute 34Department 35Initiative 36Robert 37The 38Department 39Department 40Department 41Institute 42Science 43IBM 44Department 45Systems 46The 47Okinawa 48Department ‡These authors contributed equally to work *Corresponding author. Tel: +1 626 395 3418; E-mail: (2020)16:e9110https://doi.org/10.15252/msb.20199110 Correction added on 4 September 2020, after first online publication: symbol row Distributions, column Specification was corrected a checkmark PDFDownload PDF article text main figures. ToolsAdd favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures Info Abstract biology has experienced dramatic growth number, size, complexity computational models. To reproduce simulation results models, researchers must unambiguous model descriptions. We review latest edition Markup Language (SBML), designed purpose. community modelers software developed over past decade. Its modular form consists core suited representing reaction-based packages that extend with features other types including constraint-based reaction-diffusion logical network rule-based leverages two decades rich ecosystem transformed how systems biologists build interact More recently, rise multiscale whole cells organs, new data sources such as single-cell measurements live imaging, precipitated ways integrating provide our perspectives challenges presented these developments provides foundation needed support evolution. Introduction modeling numerical simulations can be traced mid-20th century. Though general theorizing about began earlier, application analysis biolo

Language: Английский

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Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(9), P. 4645 - 4645

Published: April 22, 2022

Big data in health care is a fast-growing field and new paradigm that transforming case-based studies to large-scale, data-driven research. As big dependent on the advancement of standards, technology, relevant research, future development applications holds foreseeable promise modern day revolution. Enormously large, rapidly growing collections biomedical omics-data (genomics, proteomics, transcriptomics, metabolomics, glycomics, etc.) clinical create major challenges opportunities for their analysis interpretation open computational gateways address these issues. The design robust algorithms are most suitable properly analyze this by taking into account individual variability genes has enabled creation precision (personalized) medicine. We reviewed highlighted significance analytics personalized medicine focusing mostly machine learning perspectives medicine, genomic models with respect application mining as well we facing right now analytics.

Language: Английский

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Building digital twins of the human immune system: toward a roadmap

npj Digital Medicine, Journal Year: 2022, Volume and Issue: 5(1)

Published: May 20, 2022

Abstract Digital twins, customized simulation models pioneered in industry, are beginning to be deployed medicine and healthcare, with some major successes, for instance cardiovascular diagnostics insulin pump control. Personalized computational also assisting applications ranging from drug development treatment optimization. More advanced medical digital twins will essential making precision a reality. Because the immune system plays an important role such wide range of diseases health conditions, fighting pathogens autoimmune disorders, have especially high impact. However, their presents challenges, stemming inherent complexity difficulty measuring many aspects patient’s state vivo. This perspective outlines roadmap meeting these challenges building prototype twin. It is structured as four-stage process that proceeds specification concrete use case model constructions, personalization, continued improvement.

Language: Английский

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Patient-specific Boolean models of signalling networks guide personalised treatments

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Feb. 15, 2022

Prostate cancer is the second most occurring in men worldwide. To better understand mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model prostate which considers major signalling pathways known to be deregulated. We personalised this Boolean molecular data reflect heterogeneity specific response perturbations patients. A total 488 samples were used build patient-specific models compared available clinical data. Additionally, eight cell line-specific built validate our approach with dose-response several drugs. The effects single combined drugs tested these under different growth conditions. identified 15 actionable points interventions one whose inactivation hinders tumorigenesis. results, nine small molecule inhibitors five those putative targets found dose-dependent effect on four them, notably targeting HSP90 PI3K. These results highlight predictive power illustrate how they can for precision oncology.

Language: Английский

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Erythrocyte metabolism

Acta Physiologica, Journal Year: 2024, Volume and Issue: 240(3)

Published: Jan. 25, 2024

Abstract Our aim is to present an updated overview of the erythrocyte metabolism highlighting its richness and complexity. We have manually collected connected available biochemical pathways integrated them into a functional metabolic map. The focus this map on main consisting glycolysis, pentose phosphate pathway, redox metabolism, oxygen purine/nucleoside membrane transport. Other recently emerging are also curated, like methionine salvage glyoxalase system, carnitine lands cycle, as well remnants carboxylic acid metabolism. An additional goal review dynamics providing key numbers used perform basic quantitative analyses. By synthesizing experimental computational data, we conclude that foundations Additionally, can sense levels oxidative stress adjusting mechanics, function. In conclusion, fine‐tuning controls one most important biological processes, is, loading, transport, delivery.

Language: Английский

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Reproducibility in systems biology modelling

Molecular Systems Biology, Journal Year: 2021, Volume and Issue: 17(2)

Published: Feb. 1, 2021

Reproducibility of scientific results is a key element science and credibility. The lack reproducibility across many fields has emerged as an important concern. In this piece, we assess mathematical model propose scorecard for improving in field.

Language: Английский

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The 27th annual Nucleic Acids Research database issue and molecular biology database collection

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 48(D1), P. D1 - D8

Published: Dec. 22, 2019

Abstract The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten are updates most recently elsewhere. This issue three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences their cognate antigens; SCOP returns with a schema breaks away from purely hierarchical structure; while Alliance of Genome Resources brings together number Model Organism pool knowledge tools. Major returning nucleic acid miRDB miRTarBase. Databases for protein sequence analysis CDD, DisProt ELM, alongside no fewer than four newcomers proteins involved liquid–liquid phase separation. In metabolism signaling, Pathway Commons, Reactome Metabolights all contribute papers. PATRIC MicroScope update microbial genomes human model organism genomics Ensembl, Ensembl UCSC Browser. Immune-related covered by IPD-IMGT/HLA AFND, as well VDJbase OGRDB. Drug design is catered IUPHAR/BPS Guide Pharmacology Therapeutic Target Database. entire freely available online website (https://academic.oup.com/nar). NAR Molecular Biology Collection has been revised, updating 305 entries, adding 65 eliminating 125 discontinued URLs; so bringing current total 1637 databases. It at http://www.oxfordjournals.org/nar/database/c/.

Language: Английский

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From integrative structural biology to cell biology

Journal of Biological Chemistry, Journal Year: 2021, Volume and Issue: 296, P. 100743 - 100743

Published: Jan. 1, 2021

Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, dynamic systems, such as the ∼52-MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, completeness. Key challenges improving integrative include expanding model representations, increasing variety input information, quantifying match between information Bayesian fashion, inventing more efficient sampling, well developing better validation, analysis, visualization. In addition, two community-level are being addressed under auspices Worldwide Protein Data Bank (wwPDB). First, impact maximized PDB-Development, prototype wwPDB repository for archiving, validating, visualizing, disseminating structures. Second, scope biology expanded linking resource archives that have not been generally used structure determination but computing structures, various types mass spectrometry, spectroscopy, optical microscopy, proteomics, genetics. To address largest problems, type called metamodeling developed; combines different models opposed to compute output model. Collectively, these developments will facilitate mindset cell underpin spatiotemporal mapping entire cell.

Language: Английский

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The European Bioinformatics Institute (EMBL-EBI) in 2021

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D11 - D19

Published: Nov. 23, 2021

Abstract The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major type in the life sciences. This year's service update for EMBL-EBI new PGS Catalog AlphaFold DB, updates on existing including COVID-19 Data Platform, trRosetta RoseTTAfold models introduced Pfam InterPro, launch Genome Integrations with Function Sequence by UniProt Ensembl. Furthermore, we highlight projects through has contributed to development community-driven standards guidelines, Recommended Metadata Biological Images (REMBI), BioModels Reproducibility Scorecard. Training is one EMBL-EBI’s core missions key component provision bioinformatics services users: this many improvements that have been developed online training offering.

Language: Английский

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Modelling microbial communities: Harnessing consortia for biotechnological applications

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 3892 - 3907

Published: Jan. 1, 2021

Microbes propagate and thrive in complex communities, there are many benefits to studying engineering microbial communities instead of single strains. Microbial being increasingly leveraged biotechnological applications, as they present significant advantages such the division labour improved substrate utilisation. Nevertheless, also some interesting challenges surmount for design efficient processes. In this review, we discuss key principles interactions, followed by a deep dive into genome-scale metabolic models, focussing on vast repertoire constraint-based modelling methods that enable us characterise understand capabilities communities. Complementary approaches model those based graph theory, briefly discussed. Taken together, these provide rich insights interactions between microbes how influence community productivity. We finally overview allow generate test numerous synthetic compositions, tools methodologies can predict effective genetic interventions further improve productivity With impending advancements high-throughput omics stage is set rapid expansion engineering, with impact

Language: Английский

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