ChromaX: a fast and scalable breeding program simulator.

SUMMARY: ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes. AVAILABILITY AND IMPLEMENTATION: The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.

The benefits and struggles of FAIR data: the case of reusing plant phenotyping data.

Plant phenotyping experiments are conducted under a variety of experimental parameters and settings for diverse purposes. The data they produce is heterogeneous, complicated, often poorly documented and, as a result, difficult to reuse. Meeting societal needs (nutrition, crop adaptation and stability) requires more efficient methods toward data integration and reuse. In this work, we examine what "making data FAIR" entails, and investigate the benefits and the struggles not only of reusing FAIR data, but also making data FAIR using genotype by environment and QTL by environment interactions for developmental traits in potato as a case study. We assume the role of a scientist discovering a phenotypic dataset on a FAIR data point, verifying the existence of related datasets with environmental data, acquiring both and integrating them. We report and discuss the challenges and the potential for reusability and reproducibility of FAIRifying existing datasets, using metadata standards such as MIAPPE, that were encountered in this process.

The current and future uses of machine learning in ecosystem service research.

Machine learning (ML) expands traditional data analysis and presents a range of opportunities in ecosystem service (ES) research, offering rapid processing of 'big data' and enabling significant advances in data description and predictive modelling. Descriptive ML techniques group data with little or no prior domain specific assumptions; they can generate hypotheses and automatically sort data prior to other analyses. Predictive ML techniques allow for the predictive modelling of highly non-linear systems where casual mechanisms are poorly understood, as is often the case for ES. We conducted a review to explore how ML is used in ES research and to identify and quantify trends in the different ML approaches that are used. We reviewed 308 peer-reviewed publications and identified that ES studies implemented machine learning techniques in data description (64%; n = 308) and predictive modelling (44%), with some papers containing both categories. Classification and Regression Trees were the most popular techniques (60%), but unsupervised learning techniques were also used for descriptive tasks such as clustering to group or split data without prior assumptions (19%). Whilst there are examples of ES publications that apply ML with rigour, many studies do not have robust or repeatable methods. Some studies fail to report model settings (43%) or software used (28%), and many studies do not report carrying out any form of model hyperparameter tuning (67%) or test model generalisability (59%). Whilst studies use ML to analyse very large and complex datasets, ES research is generally not taking full advantage of the capacity of ML to model big data (1138 medium number of data points; 13 median quantity of variables). There is great further opportunity to utilise ML in ES research, to make better use of big data and to develop detailed modelling of spatial-temporal dynamics that meet stakeholder demands.

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

Towards a new generation of agricultural system data, models and knowledge products: Information and communication technology.

Agricultural modeling has long suffered from fragmentation in model implementation. Many models are developed, there is much redundancy, models are often poorly coupled, model component re-use is rare, and it is frequently difficult to apply models to generate real solutions for the agricultural sector. To improve this situation, we argue that an open, self-sustained, and committed community is required to co-develop agricultural models and associated data and tools as a common resource. Such a community can benefit from recent developments in information and communications technology (ICT). We examine how such developments can be leveraged to design and implement the next generation of data, models, and decision support tools for agricultural production systems. Our objective is to assess relevant technologies for their maturity, expected development, and potential to benefit the agricultural modeling community. The technologies considered encompass methods for collaborative development and for involving stakeholders and users in development in a transdisciplinary manner. Our qualitative evaluation suggests that as an overall research challenge, the interoperability of data sources, modular granular open models, reference data sets for applications and specific user requirements analysis methodologies need to be addressed to allow agricultural modeling to enter in the big data era. This will enable much higher analytical capacities and the integrated use of new data sources. Overall agricultural systems modeling needs to rapidly adopt and absorb state-of-the-art data and ICT technologies with a focus on the needs of beneficiaries and on facilitating those who develop applications of their models. This adoption requires the widespread uptake of a set of best practices as standard operating procedures.