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Molecular Diagnos/cs
• Development of new diagnos2c assays and epidemiological surveillance of viral pathogens of livestock and crops in East and Central Africa using LAMP assays
• East Coast fever (ECF) recombinant vaccine development • The plant virome ecology in African farming systems
Mobilizing biosciences for Africa’s development
BecA-‐ILRI Hub Genomics and Bioinforma/cs Pla=orms
This document is licensed for use under a Crea/ve Commons ACribu/on-‐Noncommercial-‐Share Alike 3.0 Unported License May 2013
Mark Wamalwa, Francesca Stomeo, Joyce Njuguna, Appolinaire Djikeng. BecA-‐ILRI Hub, Nairobi, PO Box 30709, 00100, Kenya ([email protected])
Highlights from projects using the BecA-‐ILRI Genomics and Bioinforma/cs Pla=orms
The BecA-‐ILRI Hub genomics plaIorm is equipped with both capillary (ABI 3130xl, ABI 3730xl and ABI 3500xl) and second-‐genera2on sequencing (the Roche 454 GSFLX™ Titanium pyrosequencer and Illumina MiSeq) plaIorms integrated with high performance compu2ng systems. The Bioinforma2cs plaIorm leverages on the current Genomics plaIorm to provide advanced computa2onal services, access to high performance compu2ng, data storage, bioinforma2cs support and consultancy services to African scien2sts and external users. Bioinforma2cs offers tremendous opportuni2es and has great poten2al to underpin biotechnological solu2ons to agricultural development constraints. In a nutshell, bioinforma2cs is the key to understanding the molecule of life, DNA. Using these plaIorms, the Hub has embarked on research ac2vi2es including various genome (par2al and complete) sequencing projects (cassava re-‐sequencing, viral genomics and metagenomics). Metagenomics projects have been par2cularly informa2ve, as they have provided the tools to quickly scan the bacterial and viral communi2es (pathogenic and non-‐pathogenic) in specific ecosystems with the poten2al of applica2ons to various food value chains. Hence experimental data output has considerably grown in size and complexity. These robust plaIorms will significantly increase our ability to address major issues related to pathogens discovery, crops improvement and food security and will con2nue to support capacity building and services demands in the BecA Hub region and beyond.
Capacity Building
• Training workshops: a) Introduc2on to Molecular Biology and Bioinforma2cs Workshop b) Advanced Genomics and Bioinforma2cs Workshop
• MSc and PhD student projects
hub.africabiosciences.org
Food security: Crop and livestock improvement
• Bacterial disease resistance in banana and enset • Late blight resistance in potato • Weevil resistance in sweet potato • Mosaic virus resistance in cassava. • Maize-‐sorghum hybrid/molecular marker • Climate-‐smart Brachiaria grasses for improving livestock produc2on Key partners include IITA, CIP, MARI (Tanzania), EIAR (Ethiopia)
ILRI Kenya
HPC Cluster (88 Nodes)
1.
2.
3.
4.
Quality Control
Assembly (De novo/Reference)
Feature predic2on
Data Visualiza2on
Bioinforma/cs Core Ac/vi/es
Sta/s/cal Support • Experimental design
Primary Data Analysis • NGS QC, spa2al defect removal • 454 GA Pipleline
Secondary/Downstream analysis • Differen2al Expression • Structural varia2on, geonomic rearrangements • SNP and CN analysis • microRNA profiling • GO enrichment
Training/Capacity Building • Mo2f Finding • Func2onal/Network Analysis
Data Management • NGS data storage and manipula2on • Data warehouse facili2es: databases
Soaware development • Bioconductor packages: NGS annota2on packages
• Automated NGS analysis packages Bioinforma/cs tools • Ensembl, Galaxy, Cytoscape
