Pre-war

At the start of 1928, Allen moved to the Federated Malay States, then a protected state of the British Empire, to become a bacteriologist in Kuala Lumpur's Institute for Medical Research.^[13] He acted as the institute's director^[14] for nearly a year across 1928 and 1929 while Allen Neave Kingsbury, the permanent director, was absent on leave.^[15][16]

Tan Teck Guan Building in Singapore, location of the office of the medical college's principal

College of Medicine Building in Singapore

In June 1929, Allen was appointed acting principal of King Edward VII College of Medicine in Singapore,^[17][18] then a part of the Straits Settlements crown colony. He was to deputise in the absence of Hugh Macalister, who had returned to Scotland on leave for ill health.^[19] Macalister in fact never returned to Singapore, retiring on account of his declining health^[20] shortly before his death on 2 November 1930 at the age of 51.^[21] Allen was confirmed as the permanent principal of the College with effect from 14 March 1930.^[22] While principal, Allen was also Professor of Clinical Medicine.^[23]

In addition to being principal of the medical college, from April 1932 Allen additionally served as president of Raffles College.^[11] In the few years since the college began admitting students in 1928, the colonial government's Director of Education had served concurrently as its president.^[24] This practice was criticised as creating a conflict of interest for the director,^[25] and resulting in a part-time president for the college.^[26] The appointment of Allen was welcomed as the potential first step towards a merger of Raffles College and the College of Medicine,^[27] but criticised as another part-time appointment.^[26] Allen served as concurrent head of both colleges until 1934,^[28][24] but by March 1935 the Director of Education was once again serving as president of Raffles College,^[29] while Allen continued as principal of the medical college only.

Allen served as the founding editor of the Journal of the Malayan Branch of the British Medical Association. The journal was published quarterly; the British Medical Journal reported receiving the first issue in August 1939.^[30]

World War II

As Singapore came under bombardment from the Japanese military in January 1942, Allen lead the College to serve as the island centre for blood transfusion.^[31] He also began to encourage people to grow more food in case supplies to the island were cut off.^[5] On 15 February, the British surrendered Singapore to the Japanese and the island fell under military occupation. From 17 February, Allen and his colleagues were initially imprisoned in a temporary civilian internment camp comprising a police station, a school and nearby houses.^[32] The College of Medicine ceased to function during the occupation, with the Imperial Japanese Army's Medical Corp using the college's buildings instead.^[31]

On 6 March, Allen and the many other internees were transferred to Changi Prison, now co-opted to serve as an internment camp.^[32][33] The camp officers permitted the inmates to organise their own internal affairs.^[34] Allen chaired a committee of inmates seeking to improve the quality of food available to prisoners. The group managed to improvise a balanced diet "from inadequate and unlikely sources which must have saved a good many lives",^[3] and were "instrumental in saving much serious illness".^[33] The committee continued to work after the civilian internees were transferred to Sime Road camp on 1 May 1944.^[32]

Allied prisoners after the liberation of the Singapore camps, c. 1945

Following Japan's formal surrender to the Allies on 2 September 1945, the Japanese forces occupying Singapore surrendered to the British on 12 September. In the 1946 New Year Honours, Allen was awarded a CBE for "services during internment".^[35] For the rest of his life he would periodically be incapacitated by a leg ailment caused by his time in internment.^[36] The Medical College re-opened on 20 June 1946, with Allen resuming his position as principal.^[37]

Post-war

Formerly Raffles College, now the Bukit Timah campus of the National University of Singapore

In 1947, Allen was appointed principal-designate of the envisioned new university college to be created by amalgamating King Edward VII College and Raffles College.^[38] Allen thereupon relinquished his position as principal of the College of Medicine, and was replaced by Desmond William G. Faris.^[39][40]

A commission chaired by Sir Alexander Carr-Saunders was tasked with determining the specifics of the new university college. The commissioners had toured the two crown colonies of Singapore and the Malayan Union, as they had become in the aftermath of the war, between March and April 1947.^[41] In the commission's report of April 1948, it recommended that instead of a precursory university college affiliated to the University of London, a full Malayan university with the power to confer its own degrees should be established as soon as possible.^[42][43] The commission's conclusions were influenced by the political situation in the region: among other grievances, the proposed availability of Malayan citizenship to all residents was deeply unpopular with ethnic Malays, who felt their interests had been betrayed.^[44] Carr-Saunders believed that establishing a Malayan university "could serve a valuable political purpose, firstly by becoming an object of pride and loyalty which would knit together the diverse races of the country and secondly, by enhancing the prestige of Malaya in Southeast Asia as a whole."^[45]

Upon its official foundation on 8 October 1949,^[46] Allen became the first Vice-Chancellor of the new University of Malaya.^[47] Since 1949 Allen had once again been serving as principal of Raffles College^[48][49] and was therefore the college's final principal.

The new university had three faculties: King Edward VII College became the faculty of medicine,^[50] Raffles College became the faculties of arts and science.^[51] The geologist and physicist Elizabeth Alexander served as temporary registrar during the setting up of the university.^[52] The first dean of the science faculty was Alexander's husband, Norman,^[53] professor of physics at Raffles College,^[54] and another fellow internee with Allen in Changi Prison and Sime Road Camp.^[52] Alexander Oppenheim, deputy principal^[55] and professor of mathematics at Raffles College, and dean of the informal "POW University" established in the Changi prisoner-of-war camp,^[56] became the first dean of the arts faculty.^[57] Faris, Allen's successor as principal of the medical college, became the first dean of the medicine faculty.

Allen was knighted in the 1952 New Year Honours,^[58] and in March of the same year was awarded an honorary Doctorate of Laws (LLD) by the University Malaya.^[59] He had planned to retire as vice-chancellor in June that year, but in fact left Singapore for England in April to be with his seriously-ill wife in London.^[60] He did not return to his university office, and was succeeded as Vice-Chancellor by Sir Sydney Caine.^[45][61]