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The ESSENCE on Health Research initiative has created a good practice document on Planning, Monitoring and Evaluation Framework for Capacity Strengthening in Health Research.
The framework consists of three parts, which aim to share the principles of 'how to' for capacity strengthening, ouline the key indications for planning, monitoring and evaluation, and document lessons learnt.
ESSENCE on Health Research is an initiative between funding agencies, which aims to coordinate and harmonise research investments and capacity building.
You can access the guidelines here: http://whqlibdoc.who.int/hq/2011/TDR_essence_11.1_eng.pdf?ua=1