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ESSENCE on Health Research initiative has created a good practice document on research costing. It includes a review of the funding practices related to the definition and funding of direct and indirect costs. 

Research costing has been highlighted as a major challenge for institutions in low- to medium-income countries (LMICs) that are seeking to develop and maintain sustainable research environments. The good practice document  was developed by members of ESSENCE on Health Research initiative (WHO/TDR hosts the secretariat) and the research institutions they support. It provides information that will:

• help all parties to better understand the challenges and requirements of research costing;
• develop appropriate mechanisms for costing future research accurately and sustainably; and
• act as a channel for further engagement between funders and institutions.

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Guidance Doc in English:

http://whqlibdoc.who.int/hq/2012/TDR_ESSENCE_1.12_eng.pdf

Guidance Doc in French:

http://apps.who.int/iris/bitstream/10665/75514/1/TDR_ESSENCE_1.12_2_fre.pdf