A novel approach to scientific investigations, besides analysis of individual phenomena, integrates different, interdisciplinary sources of knowledge about a complex system to obtain an understanding of the system as a whole. This innovative way of research called system-level science, requires advanced methods and tools for enabling collaboration of research groups. This paper presents a new approach to development and execution of collaborative applications. These applications are built as experiment plans with a notation based on the Ruby language. The virtual laboratory, which is an integrated system of dedicated tools and servers, provides a common space for planning, building, improving and performing in-silico experiments by a group of developers. The application is built with elements called gems which are available on the distributed Web- and Grid-based infrastructure. The process of application developments and the functionality of the virtual laboratory are demonstrated with a real-life example of the drug susceptibility ranking application from the HIV treatment domain.