中文

ISB (in silico breeding) for the Prediction by Simulation in Plant Breeding

Introduction to Breeding Tools

Computer simulation has been widely used in many scientific fields and disciplines. Simulation in plant breeding can generate a large amount of data that is impossible or difficult to obtain from the empirical experiments or theoretical considerations. With the accumulation of our knowledge and understanding of the inheritance of breeding traits, it is anticipated that the simulation, prediction and decision-supported tools would be in high demand. Simulation can help to investigate many what-if crossing and selection scenarios in plant breeding, allow many scenarios to be tested and compared in silico in a short period of time, and finally let the breeders make important decisions before conducting resource-demanding field experiments. To conduct simulation experiments in genetic studies and breeding applications, suitable software packages, platforms and/or modules are fundamental. Blib is a multi-module platform which can handle complex genetic effects and models, such as mutation, cytoplasm effect, cyto-nucleus interaction, and epistasis networks. Two derived data types were first defined in Blib, one to hold the required information on genetic models, and the other one to represent the genetics and breeding populations. Subroutines common to diploid species were then developed to perform fundamental tasks, such as asexual and sexual propagation, mutation during propagation, and generation of female and male gametes from meiosis. Blib can be treated as a computing and programming library for the purpose of simulation studies in genetics and breeding. By using the library as fundamental components, various application modules can be developed to complete specific tasks. Cultivars applied in plant production can be classified into three major categories by the method of propagation and genetic constitution, i.e. clonal lines, pure (or fixed) lines, and hybrids. Breeding techniques for the three categories of cultivars are quite different. However, they share many common attributes from the genetics point of view. ISB (abbreviated from in silico breeding) is one major and unified application module of Blib that simulates the three categories of breeding programs for developing clonal, pure-line and hybrid cultivars in plants.

Payable license to access and use the ISB simulation tool

We have spent a large amount of efforts and resources developing Blib together with ISB and other Blib application modules. For better service and further improvement and optimization, we wish each user could contribute an amount of USD 5,000 for one license to access and use ISB in one personal computer.

Tool Download

ISB can simultaneously carry out simulation, optimization and prediction research on breeding process or breeding methods of three varieties, including pure line varieties, hybrid varieties and clone varieties
Language: English         Authorization method: Permanent authorization          Operating System: Win10，Win11        Download

Benefits as the licensed users of ISB

The licensed users have the right to access the executable code, interface of ISB (the MS Windows version), users’ manuals together with illustration examples. The users may design special genetic models, parental populations, and breeding methods, and then run relevant simulation experiments in ISB. Users have the right to freely access any updated versions of ISB, and acquire the services provided by the development team. However, we are not responsible for the suitability and scientific meaning of input information prepared by users. Neither do we have any guarantee that the simulation experiments conducted by users in ISB could be publishable.

Special services and developments

Blib was developed from our decades of research experience and advances in genetic analysis, breeding modeling and simulation, and computer tool and software development. Blib provides a library of programming for developing simulation modules in genetics and breeding. Separation of application modules from the library can save a great deal of time and effort when other researchers wish to develop new simulation tools or modify the existing modules. We do not expect that just one or a few modules could meet most purposes. On the contrary, we expect different modules be designed and developed for different purposes. For those who may have the requests to develop new simulation modules based on Blib, please contact the development team for making agreements.

Previous simulation studies on breeding applications

These publications demonstrate what breeding questions or issues could be investigated by simulation experiments in ISB or other application modules.

Previous simulation studies on genetic studies

These publications demonstrate what genetic questions or issues could be investigated by simulation experiments in ISB or other application modules.
Development team of the Blib platform and Blib-based modules
Professor LI Huihui, PhD（lihuihui@caas.cn）
Associate professor ZHANG Luyan, PhD（zhangluyan@caas.cn）
Assistant professor GAO Shang, PhD（gaoshang@caas.cn）
Professor WANG Jiankang, PhD（wangjiankang@caas.cn）
Associate Professor PAN Shouhui, PhD（pansh@nercita.org.cn）
Research Group on Algorithm and Modelling in Crop Intelligent Design (Originally called Quantitative Genetics Group)
CAAS Innovative Team on Crop Bioinformatics and Applications
CAAS Innovative Team on Big Data and Intelligent Design

Chinese Academy of Agricultural Sciences (CAAS)

Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences