Literature DB >> 32598315

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

Dagmar Waltemath1, Martin Golebiewski2, Michael L Blinov3, Padraig Gleeson4, Henning Hermjakob5, Michael Hucka6, Esther Thea Inau1, Sarah M Keating7, Matthias König8, Olga Krebs2, Rahuman S Malik-Sheriff5, David Nickerson9, Ernst Oberortner10, Herbert M Sauro11, Falk Schreiber12,13, Lucian Smith11, Melanie I Stefan14,15,16, Ulrike Wittig2, Chris J Myers14.   

Abstract

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Entities:  

Keywords:  COMBINE; community building; meeting report; standardization

Mesh:

Year:  2020        PMID: 32598315      PMCID: PMC7756615          DOI: 10.1515/jib-2020-0005

Source DB:  PubMed          Journal:  J Integr Bioinform        ISSN: 1613-4516


  73 in total

1.  Annotation and merging of SBML models with semanticSBML.

Authors:  Falko Krause; Jannis Uhlendorf; Timo Lubitz; Marvin Schulz; Edda Klipp; Wolfram Liebermeister
Journal:  Bioinformatics       Date:  2009-11-17       Impact factor: 6.937

2.  SourceData: a semantic platform for curating and searching figures.

Authors:  Robin Liechti; Nancy George; Lou Götz; Sara El-Gebali; Anastasia Chasapi; Isaac Crespo; Ioannis Xenarios; Thomas Lemberger
Journal:  Nat Methods       Date:  2017-10-31       Impact factor: 28.547

3.  Multiple ontologies in action: composite annotations for biosimulation models.

Authors:  John H Gennari; Maxwell L Neal; Michal Galdzicki; Daniel L Cook
Journal:  J Biomed Inform       Date:  2010-06-30       Impact factor: 6.317

4.  The JWS online simulation database.

Authors:  Martin Peters; Johann J Eicher; David D van Niekerk; Dagmar Waltemath; Jacky L Snoep
Journal:  Bioinformatics       Date:  2017-05-15       Impact factor: 6.937

5.  ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli.

Authors:  Tanvir Sajed; Ana Marcu; Miguel Ramirez; Allison Pon; An Chi Guo; Craig Knox; Michael Wilson; Jason R Grant; Yannick Djoumbou; David S Wishart
Journal:  Nucleic Acids Res       Date:  2015-10-19       Impact factor: 16.971

6.  ChEBI in 2016: Improved services and an expanding collection of metabolites.

Authors:  Janna Hastings; Gareth Owen; Adriano Dekker; Marcus Ennis; Namrata Kale; Venkatesh Muthukrishnan; Steve Turner; Neil Swainston; Pedro Mendes; Christoph Steinbeck
Journal:  Nucleic Acids Res       Date:  2015-10-13       Impact factor: 16.971

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

Authors:  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; Alan R Williams; Lars Malmström; Bernd Rinn; Wolfgang Müller; Carole Goble
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

8.  SBML Level 3 Package: Flux Balance Constraints version 2.

Authors:  Brett G Olivier; Frank T Bergmann
Journal:  J Integr Bioinform       Date:  2018-03-09

9.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

10.  Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

Authors:  N Del-Toro; M Duesbury; M Koch; L Perfetto; A Shrivastava; D Ochoa; O Wagih; J Piñero; M Kotlyar; C Pastrello; P Beltrao; L I Furlong; I Jurisica; H Hermjakob; S Orchard; P Porras
Journal:  Nat Commun       Date:  2019-01-02       Impact factor: 14.919

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  6 in total

1.  Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.

Authors:  Christopher Schölzel; Valeria Blesius; Gernot Ernst; Andreas Dominik
Journal:  NPJ Syst Biol Appl       Date:  2021-06-03

2.  Specifications of standards in systems and synthetic biology: status and developments in 2021.

Authors:  Falk Schreiber; Padraig Gleeson; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris J Myers; David P Nickerson; Björn Sommer; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2021-10-22

3.  Design considerations for representing systems biology information with the Systems Biology Graphical Notation.

Authors:  Falk Schreiber; Tobias Czauderna
Journal:  J Integr Bioinform       Date:  2022-07-04

Review 4.  Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.

Authors:  Richard Fitzpatrick; Melanie I Stefan
Journal:  Neuroinformatics       Date:  2022-05-11

5.  Simulation of the crosstalk between glucose and acetaminophen metabolism in a liver zonation model.

Authors:  Kazuhiro Maeda; Shuta Hagimori; Masahiro Sugimoto; Yasuyuki Sakai; Masaki Nishikawa
Journal:  Front Pharmacol       Date:  2022-09-23       Impact factor: 5.988

6.  Specifications of standards in systems and synthetic biology: status and developments in 2020.

Authors:  Falk Schreiber; Björn Sommer; Tobias Czauderna; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris Myers; David Nickerson; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2020-06-29
  6 in total

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