Computational and Systems Biology |


Forging The Future of Scientific Discovery

Continuing the exponential increase in scientific and medical breakthroughs directly depends on our commitment to teaching the next generation of independent researchers. Our department is dedicated to providing cutting-edge research experiences and first-rate didactic training to students at the high school, undergraduate, and graduate levels, through both internal, intra- and inter-institutional programs to train our students in the rapidly evolving and highly interdisciplinary field of computational biology. Our department has implemented a Tiered Mentoring and Training (TMT) framework, which provides students with numerous opportunities to learn from multiple faculty, postdoctoral fellows, graduate students, and other summer undergraduates from a variety of areas and perspectives. These interactions also provide important professional development opportunities for these early-stage and nascent investigators, who will be future teachers and mentors

Joint Carnegie Mellon – University of Pittsburgh Computational Biology (CPCB) Graduate Program

Carnegie Mellon University and the University of Pittsburgh have joined forces to establish an exciting new interdisciplinary program leading to a Ph.D. in Computational Biology. The goal of this Ph.D. program is to provide intensive interdisciplinary education to enable outstanding students to become leaders in identifying and solving tomorrow’s biological problems using computational methods.

Training and Experimentation in Computational Biology (TECBio) Research Experiences for Undergraduates (REU) Summer Program

The TECBio REU @ Pitt is an NSF-funded Research Experiences for Undergraduates Program that provides a challenging graduate-level research experience in computational biology with a focus on “Simulation and Visualization of Biological Systems at Multiple Scales”. In addition to performing cutting-edge research, TECBio students will also participate in other academic and enrichment activities, such as classes, seminars, discussions, and professional development events, while experiencing the various social and cultural activities available in Pittsburgh – America’s most livable city

UPMC Hillman Cancer Center CompBio Academy Summer Research (formerly DiSCoBio)

The CompBio Academy on the Oakland Campus introduces rising high school juniors and seniors to the emerging fields of research that use both computational and experimental approaches to answer fundamental questions in Cancer Biology and related disciplines: Computational Structural Biology (studying how proteins move and interact with each other), Drug Discovery (theoretical and experimental designing and testing of candidate drug compounds), Genomics/Bioinformatics (analyzing large data sets of sequencing and other data), Image Analysis/Informatics (training a computer how to “see” and analyze biological image data), and Systems Biology (tackling biological questions using an integrated, holistic approach). In addition to having a primary research experience in one of these fields, scholars in the DiSCoBio Academy will learn about the fundamental concepts in each of these “New Biologies”, and will gain hands-on training in the tools and techniques central to these disciplines. Professional development activities will complement the research and didactic training to help prepare scholars for careers in science and/or medicine. Scholars should expect an immersive, challenging, and fulfilling research and training experience in a fast-growing area of cutting-edge, biomedical research.

Hands-on Workshop on Computational Biophysics

This workshop was presented by members of the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh and the members of the Theoretical and Computational Biophysics Group ( from the University of Illinois at Urbana-Champaign. It covered a wide range of physical models and computational approaches for the simulation of biological systems including ProDy,NAMD and VMD. The course was based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods were introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.

MMBioS Workshops

The annual MMBioS workshops provide hands-on and state-of-the-art training in topics related to our Technology Research & Development projects and other expertise present within MMBioS participants. These workshops are aimed at both experimental and computational scientists, and promote collaboration between the groups.

MCell Workshop

This workshop was organized by the Center for Multiscale Modeling of Biological Systems and covered theory and practice for the design and simulation of models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks. The lastest version of the MCell simulation environment ( were introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. During the workshop we they also introduced:

  1. Novel tools to incorporate rule-based modeling techniques into MCell simulations based on the BioNetGen Software (Faeder et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 113-167).
  2. Our new MCell model creation and visualization framework called CellBlender that builds on our previously developed model creation pipeline (Czech et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 237-287).

“We are proud of the incredible scientific talent at Pitt Health Sciences that is made up of career faculty & new recruits who are eager to solve the most difficult health issues facing society today."

  • Senior Vice Chancellor for the Health Sciences