This is the report (slides) of the working group "Some open problems in molecular biology from a graph drawing perspective". Biological data generated and analyzed in the life sciences can be often interpreted and represented by graphs. Although several general and special-purpose tools and libraries are available for drawing biological networks, there is a great demand for better approaches as existing tools are either not adequate for handling large graphs or do not adhere to the special drawing conventions and recognized layouts of biological networks. In this discussion group, we tried to identify some representative use cases that demonstrate the need for advanced algorithms for presenting, exploring, evaluating, and comparing biological network data. The result of the discussion has been submitted as paper to the International Symposium on Graph Drawing 2008.