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Best Practices for Making Reproducible Biochemical Models.

ABSTRACT: Like many scientific disciplines, dynamical biochemical modeling is hindered by irreproducible results. This limits the utility of biochemical models by making them difficult to understand, trust, or reuse. We comprehensively list the best practices that biochemical modelers should follow to build reproducible biochemical model artifacts-all data, model descriptions, and custom software used by the model-that can be understood and reused. The best practices provide advice for all steps of a typical biochemical modeling workflow in which a modeler collects data; constructs, trains, simulates, and validates the model; uses the predictions of a model to advance knowledge; and publicly shares the model artifacts. The best practices emphasize the benefits obtained by using standard tools and formats and provides guidance to modelers who do not or cannot use standards in some stages of their modeling workflow. Adoption of these best practices will enhance the ability of researchers to reproduce, understand, and reuse biochemical models.

SUBMITTER: Porubsky VL

PROVIDER: S-EPMC7480321 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The academia-industry interface is important, and, despite challenges that inevitably occur, bears the potential for positive synergies to emerge. Perceived barriers to wider collaboration in academia-industry oncology research in Europe need to be addressed, current academic cooperative group and industry models for collaboration need to be discussed, and a common terminology to facilitate understanding of both sectors' concerns needs to be established with an eye towards improving academia-industry partnerships on clinical trials for the benefit of patients with cancer. CAREFOR (Clinical Academic Cancer Research Forum), a multi-stakeholder platform formed to improve the direction for academic clinical trials in the field of oncology in Europe, formed the CAREFOR-Industry Working Group comprised of experienced professionals from European academic cooperative groups joined by industry representatives selected based on their activities in the area of medical oncology. They jointly discussed academic cooperative groups, clinical trials conducted between academic cooperative groups and industry, examples of successful collaborative models, common legal negotiation points in clinical trial contracts, data access, and principles of interaction. Four principles of interaction between the academia and industry are proposed: (1) clarify the roles and responsibilities of all partners involved in the study, (2) involve legal teams from an early stage; (3) acknowledge that data is an important output of the study, (4) agree on the intent of the trial prior to its start. The CAREFOR-Industry Working Group describes current models, challenges, and effective strategies for academia-industry research in Europe with an eye towards improving academia-industry partnerships on clinical trials for patients with cancer. Current perceived challenges are explained, and future opportunities/recommendations for improvement are described for the areas of most significant impact. Challenges are addressed from both the academic and industry perspectives, and principles of interaction for the optimal alignment between academia and industry in selected areas are proposed.

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Best Practices for Making Reproducible Biochemical Models.

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