GCP collaborators working on a rice project in The Philippines start to see the results of their hard work come to fruition as the outcomes of their research feature in journal articles and press releases.
Results from the GCP SP2 Commissioned project G4005.35 ‘Sequencing multiple and diverse rice varieties: connecting whole-genome variation with phenotype’, led by Ken McNally of IRRI, have been published online in the Proceedings of the National Academy of Sciences (PNAS), news which was also featured in two press releases.
To view these press releases, as well as media attention given to other GCP projects, please visit our Public Awareness page.
A workshop on next generation sequencing (NGS) technology data analysis was held at ICRISAT Headquarters in India from 21–23 July 2009. The workshop, part of SP4 Commissioned project G4009.04: ‘Data analysis support for existing projects in SP2 with emphasis on analysis of Next Generation Sequencing data’, led by Rajeev Varshney (ICRISAT/GCP), was attended by approximately by 30 collaborators.
The aim of the workshop, primarily designed for bioinformaticians and programmers, and coordinated by Rajeev Varshney and B Manjula (ICRISAT), was to plan and develop strategies and tools for analysing NGS data, in light of the limitations of current tools. The event, spread over three days, followed a tightly-packed schedule comprising a mix of formal sessions on topics such as genomic resources, assembly and visualisation, SNP discovery and gene expression, as well as more informal brainstorming sessions, where the exchange of ideas and new insights amongst the varied and expert participants was facilitated.
Presentations and other materials from the workshop will be made available in due course.
Contact: Rajeev Varshney
From 29th June to 3rd July 2009, 26 participants from around the globe came together for an essentially practical, hands-on course on Marker-Assisted Breeding. The course, supported by GCP’s Subprogramme 5 and led by instructors Joost van Heerwaarden (University of California–Riverside), Hans Jansen and Marcos Malosetti (Wageningen University and Research Centre), with coordination from GCP’s SP5 Leader Carmen de Vicente, primarily targeted collaborators of GCP’s Tropical Legumes project. Course content comprised a healthy balance of theoretical sessions (derived from lectures and presentations) and practical tasks (based on example data together with the option for participants to work with their own data sets). Some of the key topics covered during the course included genetic linkage maps, phenotypic data analysis, QTL and QTLxE mapping, genetic diversity analysis and LD mapping.
To view presentations and other materials from the workshop, please visit our Capacity-building Corner.
GCP's SP5 is delighted to announce the launch of its molecular marker 'Toolbox'. This new resource aims to provide easy and unlimited access to existing information on publicly available molecular markers ready for use for marker-assisted selection in 19 food security crops, and aims to serve of particular use to developing country biotechnologists and plant breeders who often face difficulties in accessing such current information. The tool, which contains a wealth of information gathered from internet sources, public databases and papers, is the result of an SP5 project led by consultant Veerle Van Damme. For several months, Veerle has worked in close collaboration with an array of experts working on the 19 respective crops in order to collate a current and comprehensive set of molecular marker information. To find out more, please visit the Capacity-building corner website.
The Generation Challenge Programme (GCP) is seeking an informatics specialist to coordinate all aspects of data and information management for the Molecular Breeding Platform – a one-stop-shop for breeding services, informatics applications, information and training to facilitate molecular breeding in developing countries. The Informatics Coordinator will be responsible for ensuring users have access to data management and analysis applications supported by the Platform, providing user support and coordinating training on informatics aspects of molecular breeding. The Informatics Coordinator will work with users to articulate requirements for informatics technology through a user committee and will liaise with researchers and developers to ensure those requirements are met.
She/He will be responsible for establishing quality standards and verifying their application through the use of templates for data generated through the platform and for publishing data for secondary use by the breeding community as appropriate. The Informatics Coordinator will report to the Platform Manger and will interact with several members of the GCP Management Team to ensure that data management and documentation as well as training material on information management and data curation for the platform match with the GCP overall practices and strategies. This international position, based at GCP headquarters in Mexico, is for an initial fixed-term contract of three years, with a high possibility for renewal subject to performance and funding.
We are seeking candidates with the following qualifications:
- Master Degree or desirable Ph.D. in statistics, biometrics or informatics
- At least 7 years of appropriate experience
- Experience with consulting, training and supporting users of informatics applications
- Knowledge of the principles of database architecture and information mangement.
- Experience in managing complex biological databases.
- Knowledge of bioinformatics and statistical procedures for biological data
- Experience with quality assurance for research data
- Affinity for international agricultural research and development.
- Ability to work well as part of a multidisciplinary and decentralised team.
- Excellent communications skills in written and spoken English.
Experience in the following areas would also be considered a major asset:
- Managing information for crop breeding programmes
- Analysis of data from genetics and molecular biology
Deadline for applications: 15th August 2009
The Generation Challenge Programme (GCP) is seeking a highly innovative and self-motivated senior scientist to manage the implementation and operation of the Molecular Breeding Platform – a one-stop-shop for genotyping and phenotyping services, informatics applications, information and training to facilitate molecular breeding in developing countries. For this five-year, 20 million dollar initiative we require an experienced manager who will supervise project staff members, and liaise with users, service providers and developers to ensure coordination of activities, achievement of milestones outlined in the proposal and good communication among those teams. Access to the Platform will be through an internet portal and helpdesk which the manager will commission and maintain. The manager will work with the GCP Management Team with specialist knowledge of different components, advised by a technical advisory committee, to meet user requirements articulated through a user committee. He/she will arrange meetings, organise training opportunities, maintain communication with different stakeholders, and promote and represent the platform and its respective user communities.
We are seeking candidates with the following qualifications:
- Ph.D. in plant breeding, plant genetics, statistics or bioinformatics, or 10 years’ equivalent experience in plant science.
- Experience in project management and monitoring of complex workflows.
- Experience in building productive strategic partnerships.
- Good understanding of modern plant breeding and related needs.
- Experience with data and information management and knowledge of the principles of database architecture.
- Affinity for international agricultural research and development.
- Ability to work well as part of a multidisciplinary and decentralised team.
- Excellent communications skills in written and spoken English.
Experience in the following areas would also be considered a major asset:
- Experience of marker technologies, marker-assisted selection pipelines, especially in the private sector.
- Experience in plant phenotyping and physiology under field conditions.
- Experience with economic analysis of process options, such as alternative breeding strategies.
- Ability to promote the Platform to different stakeholders and users.
Deadline for applications: 15th August, 2009
More information, including how to apply
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