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The analysis of iTRAQ data was assisted by the software program ProteinPilot (Applied Biosystems MDS Sciexx).
Organisation of data was assisted by use of the N-Vivo software given the large size of the data set.
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Data analysis was assisted by the computer package QSR NVivo 10, 40 which allowed the systematic treatment of data, keeping explicit track of all coding steps.
Data analysis was assisted by detrended correspondence analysis (DCA), similarity percentage analysis (SIMPER) and other statistical tests.
The EM data, acquired using a GEM-2 apparatus for frequency sounding and an EM-31 apparatus for geometrical sounding, has been handled using the prototype eGMS software tool, being developed by the eGMS international research consortium; the depth sounding data interpretation was assisted by 1D inversions obtained with the EM1DFM software developed by the University of British Columbia.
Data extraction was assisted by EPPI-Centre software, EPPI Reviewer.
Data entry was assisted by Monde Mwikisa and Grace Chewe.
Data management was assisted by the use of a computer program (NVivo 8).
Data collection was assisted by the fact that patients requiring hospital admission were cared for in the adjacent medical center.
Filtering and trimming of original data set was assisted by Galaxy Web Server [ 16- 18], filtering by quality using the sliding window method (window size 25 with a minimum quality in the window of 20), and sequences shorter than 200 bp were removed.
MTM facilitated each interview and to improve the depth of the data collected, she was assisted by a Kiswahili/English research assistant, who was acquainted with the norms and culture of the area.
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