Ten simple rules for creating reusable pathway models for computational analysis and visualization

Kristina Hanspers; Martina Kutmon; Susan L Coort; Daniela Digles; Lauren J Dupuis; Friederike Ehrhart; Finterly Hu; Elisson N Lopes; Marvin Martens; Nhung Pham; Woosub Shin; Denise N Slenter; Andra Waagmeester; Egon L Willighagen; Laurent A Winckers; Chris T Evelo; Alexander R Pico

doi:10.1371/journal.pcbi.1009226

Ten simple rules for creating reusable pathway models for computational analysis and visualization

PLoS Comput Biol. 2021 Aug 19;17(8):e1009226. doi: 10.1371/journal.pcbi.1009226. eCollection 2021 Aug.

Authors

Kristina Hanspers¹, Martina Kutmon^{2

3}, Susan L Coort², Daniela Digles⁴, Lauren J Dupuis², Friederike Ehrhart², Finterly Hu^{2

3}, Elisson N Lopes⁵, Marvin Martens², Nhung Pham^{2

3}, Woosub Shin², Denise N Slenter², Andra Waagmeester⁶, Egon L Willighagen², Laurent A Winckers², Chris T Evelo^{2

3}, Alexander R Pico¹

Affiliations

¹ Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America.
² Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands.
³ Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands.
⁴ Department of Pharmaceutical Sciences, Division of Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
⁵ Instituto de Ciencias Biologicas, Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
⁶ Micelio, Antwerp, Belgium.

No abstract available

Publication types

Editorial
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods*
Computer Graphics
Databases, Factual
Humans
Metabolic Networks and Pathways*
Models, Biological*
Terminology as Topic

Grants and funding

This work was funded by the European Union’s Horizon 2020 Research and Innovation Programme [OpenRiskNet: 731075 to MM, CTE; EJP-RD: 825575 to FE, WS, CTE; FNS-Cloud: 863059 to SLC, CTE; EU-ToxRisk: 681002 to MM, CTE; NanoCommons: 731032 to ELW, LAW], ZonMw [10430012010015 to MK, SLC, LJD, FE, FH, NP, ELW, CTE] and the National Institute of General Medical Sciences [R01 GM100039 to KH, ARP; R01 GM089820 to AW]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.