John McCaskill founded the first Department for Molecular Information Processing at the Institute for Molecular Biotechnology (IMB) in Jena in 1992, after receiving a call to a full professorship in Theoretical Biochemistry at the University of Jena that year. Previously, McCaskill had for 5 years led a research group in Evolutionary Self-organization affiliated with nobel prize winner Manfred Eigen's department at the Max Planck Institute for Biophysical Chemistry in Göttingen. McCaskill was one of the first to focus research on the dynamic processing of molecular information, which is ubiquitous in biological systems, and in which lies a vast potential for future technology. His group's approach in Jena was synthetic, both theoretical and experimental, building novel spatially resolved molecular information systems to test core system behavior using simulation, biochemistry, microfluidics, fluorescence imaging and reconfigurable electronics.
In 1999, McCaskill accepted a call to move his group to form the research group Biomolecular Information Processing (BioMIP) at the German National Research Center in Information Technology (GMD) in Sankt Augustin near Bonn, taking leave of absence from his professorship in Jena, for five years (1999-2004). Following the political merger of the GMD Helmholtz Institutes with the Fraunhofer Gesellschaft (applied research) in 2001-2, basic research was no longer a priority at the Sankt Augustin campus. On the strength of the pioneering research by BioMIP in reconfigurable microfluidics, DNA computing and evolutionary self-organization, McCaskill won a competitive call as coordinator for an innovative integrated project in the EU FP6 FET proactive initiative in Complex Systems - PACE.
Since this large project did not match the Fraunhofer applied research profile it could not be pursued there. With the support of Prof. von Kiedrowski, McCaskill forged an agreement with the Ruhr Universität Bochum in 2004 to host the BioMIP group, to strengthen innovation in this area, with the Fraunhofer Gesellschaft offering an 18 month transition period for the group to find new labs. A return to Jena was not possible without the agreement of Fraunhofer to transfer the research equipment (some old, some new) back to Jena and was complicated by the fact that the Leibnitz Institute for Molecular Biotechnology, had in the meantime been transformed into a new institute for research in ageing. The University of Jena lacked resources to reequip the BioMIP group independently in Jena and so was not willing to accept the role of coordinator in PACE.
In 2005, McCaskill negotiated with a leading technology centre for microsystems research in Dortmund near Bochum to host both the RUB-BioMIP group and the startup firm Protostream. Cleanroom access was available in Dortmund and a limited reequipment was possible as part of the technology transfer program, so the majority of the group moved to Dortmund. From 2004-2008, the BioMIP group successfully coordinated the PACE project at the Ruhr University with labs in Dortmund, and evaluated the potential of chemical microprocessors for a startup business Protostream. In 2009, with an ongoing core interest in basic research, BioMIP moved to labs on campus at the Ruhr University Bochum, where it operated until 2017 as an external grant funded research group in the Chemistry and Biochemistry Faculty. McCaskill has been a guest professor there, and has also been active in master and PhD level teaching and supervising bachelor, master and PhD thesis work. Major recent research projects coordinated by BioMIP include PACE, ECCell & MICREAgents.