Biodiesel is an important alternative to fossil fuels. A main challenge in the commercialization and public acceptance of biodiesel is its quality. Here IR spectroscopy is used to measure the quality of biodiesel through (1) the blending level of biodiesel in fuel mixtures, (2) the fatty acid content of biodiesel fuels derived from various oils, and (3) the concentration of impurities present in biodiesel. Methyl esters of four different oils—palm oil, sunflower oil, waste cooking oil, and coconut oil were tested. The predicted concentration and specific gravity of the biodiesel-diesel blends were compared with the actual values. Also to understand the combustion phenomenon of bio-diesel, a detailed combustion simulation of the same is required which is quite a difficult task to carry out. To determine the influence of various parameters on the combustion characteristics of bio-diesel, Methyl Formate, a surrogate molecule, having a chemical structure similar to the actual bio-diesel has been used. This is carried out in a diesel engine environment. An object oriented software tool, Cantera, usually used for reacting flows, including chemical kinetics, thermodynamics and transport process is used here. It is interfaced with MATLAB and python, and program for the analysis of ignition delay is done. The variation of ignition delay time with change in the equivalence ratio and compression ratio and also plots of various species concentration profiles are also presented.