Specifications of Standards in Systems and Synthetic Biology: Status, Developments, and Tools in 2024

Overview

Journal J Integr Bioinform

Specialty Biology

Date 2024 Jul 19

PMID 39026464

Authors

Martin Golebiewski

Gary Bader

Padraig Gleeson

Thomas E Gorochowski

Sarah M Keating

Matthias Konig

Chris J Myers

David P Nickerson

Bjorn Sommer

Dagmar Waltemath

Falk Schreiber

Affiliations

Soon will be listed here.

Citing Articles

Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma.

Voropaeva E, Orlov Y, Loginova A, Seregina O, Maksimov V, Pospelova T PeerJ. 2025; 13():e18661.

PMID: 39802185 PMC: 11720970. DOI: 10.7717/peerj.18661.

References

Olivier B, Bergmann F . SBML Level 3 Package: Flux Balance Constraints version 2. J Integr Bioinform. 2018; 15(1). PMC: 6167036. DOI: 10.1515/jib-2017-0082. View

Bergmann F, Rodriguez N, Le Novere N . COMBINE Archive Specification Version 1. J Integr Bioinform. 2015; 12(2):261. DOI: 10.2390/biecoll-jib-2015-261. View

Courtot M, Juty N, Knupfer C, Waltemath D, Zhukova A, Drager A . Controlled vocabularies and semantics in systems biology. Mol Syst Biol. 2011; 7:543. PMC: 3261705. DOI: 10.1038/msb.2011.77. View

Demir E, Cary M, Paley S, Fukuda K, Lemer C, Vastrik I . The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010; 28(9):935-42. PMC: 3001121. DOI: 10.1038/nbt.1666. View

Lang P, Jain A, Rackauckas C . SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem. J Integr Bioinform. 2024; 21(1). PMC: 11294517. DOI: 10.1515/jib-2024-0003. View

Neal M, Konig M, Nickerson D, Misirli G, Kalbasi R, Drager A . Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 2018; 20(2):540-550. PMC: 6433895. DOI: 10.1093/bib/bby087. View

Keating S, Waltemath D, Konig M, Zhang F, Drager A, Chaouiya C . SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol. 2020; 16(8):e9110. PMC: 8411907. DOI: 10.15252/msb.20199110. View

Babur O, Dogrusoz U, Demir E, Sander C . ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics. 2009; 26(3):429-31. PMC: 2815657. DOI: 10.1093/bioinformatics/btp665. View

Juty N, Le Novere N, Laibe C . Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 2011; 40(Database issue):D580-6. PMC: 3245029. DOI: 10.1093/nar/gkr1097. View

10.

Bergmann F, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M . COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014; 15:369. PMC: 4272562. DOI: 10.1186/s12859-014-0369-z. View

11.

Schreiber F, Gleeson P, Golebiewski M, Gorochowski T, Hucka M, Keating S . Specifications of standards in systems and synthetic biology: status and developments in 2021. J Integr Bioinform. 2021; 18(3). PMC: 8573232. DOI: 10.1515/jib-2021-0026. View

12.

Hucka M, Bergmann F, Chaouiya C, Drager A, Hoops S, Keating S . The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform. 2019; 16(2). PMC: 6798823. DOI: 10.1515/jib-2019-0021. View

13.

Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F . NetPyNE, a tool for data-driven multiscale modeling of brain circuits. Elife. 2019; 8. PMC: 6534378. DOI: 10.7554/eLife.44494. View

14.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N . COPASI--a COmplex PAthway SImulator. Bioinformatics. 2006; 22(24):3067-74. DOI: 10.1093/bioinformatics/btl485. View

15.

Clark C, Scott-Brown J, Gorochowski T . paraSBOLv: a foundation for standard-compliant genetic design visualization tools. Synth Biol (Oxf). 2021; 6(1):ysab022. PMC: 8546602. DOI: 10.1093/synbio/ysab022. View

16.

Goncalves E, van Iersel M, Saez-Rodriguez J . CySBGN: a Cytoscape plug-in to integrate SBGN maps. BMC Bioinformatics. 2013; 14:17. PMC: 3599859. DOI: 10.1186/1471-2105-14-17. View

17.

Bergmann F, Keating S, Gauges R, Sahle S, Wengler K . SBML Level 3 package: Render, Version 1, Release 1. J Integr Bioinform. 2018; 15(1). PMC: 6167038. DOI: 10.1515/jib-2017-0078. View

18.

Clerx M, Cooling M, Cooper J, Garny A, Moyle K, Nickerson D . CellML 2.0. J Integr Bioinform. 2020; 17(2-3). PMC: 7756617. DOI: 10.1515/jib-2020-0021. View

19.

Sorokin A, Le Novere N, Luna A, Czauderna T, Demir E, Haw R . Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J Integr Bioinform. 2015; 12(2):264. DOI: 10.2390/biecoll-jib-2015-264. View

20.

Buecherl L, Myers C . Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology. Curr Opin Microbiol. 2022; 68:102155. DOI: 10.1016/j.mib.2022.102155. View