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After retiring from the military in 2003, Lim served in the Ministry of Education as a Permanent Secretary until 2007 before assuming the position of Chairman of the Agency for Science, Technology and Research (A*STAR), a statutory board under the Ministry of Trade and Industry.
He also co-founded Singapore seed investment fund BAF Spectrum in 2006, which primarily invests in tech startups across Asia in a co-funding partnership with SPRING Singapore (a statutory board under the Ministry of Trade and Industry in Singapore).