Computersandcomputationalmethodsplayanincreasinglyimportantroleinthelifesciences,andcurrentlyform an indispensable tool for a wide range of scientific applications. These range from classical bioinformatics, which concerns with the use of computer methods in molecular biology, to numerical models of complex physiological systems. To this date, these scientific fields have been fairly disconnected, but the situation is changing with the increasingavailabilityofhighperformancecomputingtools,whichallowssystemphysiologymodelstobedeveloped with more detail and realism. Existing computer models have already demonstrated direct links between gene data and organ function, and the current development will inevitably narrow the gap between classical bioinformatics and systems physiology modeling. The successful combination of these two fields holds a huge potential for scientific progress,asitmayrepresentamechanisticlinkfromknowledgeandexplorationonamolecularscale,tothefunction of biological tissues, organs and organ systems. However, this large potential is paired with substantial challenges, many of which are directly related to computer science. These include the management and integration of huge data banks, computational resources required for solving complex multiscale mathematical models, and software engineering issues related to development and validation of increasingly complicated software systems.