in silico Plants (isP) provides a single home for plant modeling research, publishing interdisciplinary, multidisciplinary and cross-disciplinary research at the interface between mathematics, computer science and plant biology. The journal publishes works that describe plant gene networks, protein synthesis, metabolic pathways, physiology, and growth using mathematical and conceptual modelling, systems analysis, computer simulations, and visualization.
Topics of the papers published by isP today include:
- the introduction of a new tool links models of different languages and scales to create entire plants, fields, or regions in silico;
- a review of how the development of high yielding crops can be expedited using phenomics, genomics and systems models in combination; and
- an evaluation of a generic biomass partitioning model’s ability to predict accurate temporal patterns of biomass and nitrogen partitioning.
The journal is managed by the Annals of Botany Company, a not-for-profit educational charity established to promote plant science worldwide.
You can also keep up to date on all aspects of plot modelling from isP and other sources by following the Botany One weblog produced by The Annals of Botany Company. You can also follow in silico Plants on its Twitter page.
Meet the Editors
Dr. Graeme Hammer is a Professor in Crop Science and Director of the Centre for Crop Science in the Queensland Alliance for Agriculture and Food Innovation (QAAFI), which is a research institute of The University of Queensland, Australia. He conducts research on the physiology and genetics of complex adaptive traits in field crops with a focus on water productivity in cereals. His research underpins the development of mathematical models of crop growth, development and yield that enable simulation of consequences of genetic and management manipulation of crops in specific target environments.
Dr. Stephen Long, FRS, is a Professor in the departments of Plant Biology and Crop Sciences at the University of Illinois and in Crop Sciences at Lancaster University. He has developed a range of mechanistic models at different scales relating environmental effect on photosynthesis to plant productivity. These have also been used to identify targets for breeding and bioengineering sustainable increases in crop productivity, successfully reduced to practice.
Dr. Amy Marshall-Colon is an Assistant Professor in the department of Plant Biology at the University of Illinois. Her research explores the regulatory mechanisms controlling nitrogen uptake and assimilation in plants using a systems biology approach. The overarching goal of her research is to use predictive network modeling to identify the most effective engineering strategies to improve crop productivity in response to environmental challenges imposed by global climate change.
Dr. Przemyslaw Prusinkiewicz, FRSC, is a Professor of the department of Computer Science at the University of Calgary. There, he leads the Biological Modeling and Visualization Laboratory. He is a pioneer in the computational modeling, simulation and visualization of plant development. His current research is focused on linking molecular-level processes to the macroscopic form of plants. He is the project lead of the Virtual Laboratory and L-studio plant modeling software, developed and distributed by his laboratory.
Dr. Xin-Guang Zhu is the Head of Plant Systems Biology Group at the Chinese Academy of Sciences – Max-Planck-Gesellschaft Partner Institute for Computational Biology. He develops multi-scale systems models, spanning from metabolic, leaf, canopy up to whole plant levels, and tools to support identification of new breeding or engineering targets to gain higher photosynthetic efficiency. Dr. Zhu’s lab also works on reconstruction of the evolutionary and developmental process of C4 photosynthesis from a C3 background.
How to submit your paper
in silico Plants uses the online system, ScholarOne Manuscripts, to manage manuscript submission and peer review.
in silico Plants publishes seven article types: Original Research, Technical Advances, Reviews, Opinions, Editorials, Letters to the Editor, and Commentaries. Read the Instructions for Authors for further information about how to prepare your manuscript for submission.
Brown, H. E., Huth, N. I., Holzworth, D. P., Teixeira, E. I., Wang, E., Zyskowski, R. F., & Zheng, B. (2019). A generic approach to modelling, allocation and redistribution of biomass to and from plant organs. In Silico Plants, 1(1). https://doi.org/10.1093/insilicoplants/diy004
Chang, T.-G., Chang, S., Song, Q.-F., Perveen, S., & Zhu, X.-G. (2019). Systems models, phenomics and genomics: three pillars for developing high-yielding photosynthetically efficient crops. In Silico Plants, 1(1). https://doi.org/10.1093/insilicoplants/diy003
Lang, M. (2019). yggdrasil: a Python package for integrating computational models across languages and scales. In Silico Plants, 1(1). https://doi.org/10.1093/insilicoplants/diz001
Long, S. P. (2019). Making our plant modelling community more than the sum of its parts: a personal perspective. In Silico Plants, 1(1). https://doi.org/10.1093/insilicoplants/diy002