VSNi develops powerful data analytics to help researchers derive greater value from their vast datasets. Their products, GenStat, ASRelm and CycdesigN among others, are well established in breeding programs around the world. The IBP and VSNi are longstanding partners, having come together in 2011 to develop Breeding View, a statistical analysis module, designed on the solid basis of GenStat, to work exclusively with BMS Pro. This collaboration since flourished into a public-private partnership (PPP) leading to the creation of Biosci Thailand Co. Ltd in 2015 for the joint development of new apps, and to serve the APAC market. VSNi manages commercial assets in name of the IBP, where sales revenue from IBP products and services are fully reinvested into IBP product development and deployment activities.
Leafnode is an expert software engineering firm based in California, USA, with teams in Argentina, the Philippines and New Zealand. They build intuitive, functional, scalable and robust applications for clients across diverse industries. The IBP partnered with Leafnode early on to help bring disparate partner efforts in development under a same roof, and establish what would become the core code and architecture of BMS Pro. This core is mostly still powering BMS Pro today. Leafnode was key in transforming what could have remained an academic exercise into a professional software development operation, accompanying the IBP in the implementation of its own in-house development team and processes. Today, Leafnode helps the IBP by assigning and managing specialized technical experts to staff our international development team.
Biosci Thailand Co., Ltd.
Biosci (Thailand) Co., Ltd. was established in 2016 to represent VSN International Co., Ltd. and the Integrated Breeding Platform (IBP) in the APAC market. They provide support on data analysis software, data management solutions and training, including Genstat, ASreml, and BMS Pro. They also count with a development team, working on new apps to expand the possibilities of these products.
Wageningen Plant Research
Wageningen Plant Research combines knowledge and expertise in plant sciences to offer new perspectives for sustainable agriculture to their partners from industry, governments, research institutes and universities. With the IBP, they are developing an R package to work with BMS Pro as an open source option for statistical analysis.
Excellence in Breeding Platform (EiB)
The Excellence in Breeding Platform (EiB) is a project of CGIAR, created in 2016 as part of their new portfolio of research programs and platforms, and led by the International Maize and Wheat Improvement Center (CIMMYT). The IBP participates in the EiB's Advisory Group for Module 5 on bioinformatics, biometrics and data management. BMS Pro is available to their users as part of the EiB toolbox, and will be made to connect seamlessly to the EiB's Enterprise Breeding System (EBS) currently under development. As such, the EiB is a major funding contributor to the IBP, having allocated $3M for the continued development and maintenance of BMS Pro.
Though the IBP also originated from a CGIAR program, these are entirely independent but complementary initiatives. The IBP now operates under a non-profit corporation registered in the US.
The South Green platform is a local network of scientists based at the Agropolis campus in Montpellier, France, working together to develop bioinformatics applications and resources dedicated to genetics and genomics of tropical and Mediterranean plants. South Green relies on the computer technical platforms of its partner institutes, among which: CIRAD, IRD, INRA, SupAgro, Bioversity international as well as CGIAR. The IBP currently works with South Green to enable some interoperability between BMS Pro and their tools, such as GIGWA, a a web-based tool to manage and search genotyping data from NGS analyses.
The Breeding Application Programming Interface (BrAPI) brings together partners – including the IBP – for the definition of a standard Application Programming Interface (API) for plant breeding. It will serve to facilitate data exchange among different systems; expand the range of tools available; reduce unnecessary duplication of tasks, and to increase communication among programmers working on similar projects (CoP). BrAPI is a shared, community-developed and open API, that can be used by all data providers and data consumers who wish to participate. The IBP participates by developing and integrating BrAPI calls into BMS Pro to expand functionality by connecting to other applications, such as genotype visualization, data transfer, feld data collection and search functions.
Another important output of the Generation Challenge Programme (GCP), the Crop Ontology is a web-based set of controlled vocabularies and ontologies for the digital annotation of agricultural research data. The IBP plays a vital role in the ongoing efforts to maintain, extend, and enhance this invaluable resource.
The Genomic Open-source Breeding Informatics Initiative (GOBII) is a large-scale public-sector effort to systematically apply high-density genotypic information to the breeding of staple crops in the developing world. The project will develop and implement genomic data management systems, including databases, imputation systems, and decision support tools for plant breeders. The IBP works closely with GOBii, namely through the BrAPI initiative, to expand interoperability with BMS Pro.
For many years, the IBP website was hosted with Cyverse, (formerly iPlant Collaborative), a powerful and extensible platform for data storage, bioinformatics, image analyses, cloud services, APIs and more. This powerful computational infrastructure can handle huge datasets and complex analyses for data-driven science. We encourage you to register on the Cyverse platform to access their complete range of tools and services. In time, the IBP hopes to provide more integration with BMS Pro related services.