November 2017 Conference


University of California, Riverside
Genomics Auditorium
November 15th &16th, 2017


Sponsored by:


Co-organizers: Mark Alber, University of California, Riverside, USA; Ronan MT Fleming, Université du Luxembourg, University of Leiden, The Netherlands; Feilim Mac Gabhann, Johns Hopkins University, USA


Participants of the Conference will present talks and discuss interactions of methods developed for addressing three main challenges to bridging scales from molecular to clinical by catalyzing collaborations with clinicians. Clinicians will lead discussions on establishing interdisciplinary collaborations on development of new patient specific treatment strategies. Researchers from pharmaceutical companies will be also invited to participate in discussions.

1. Multi-scale modeling of cell behavior and tissue growth in patients under stress conditions or with chronic or acute diseases including, among others, cancer, thrombosis and sepsis. For example, modeling blood clot formation in cancer patients or patients with diabetes. Data for patients with acute stage of a disease or with untreated chronic disease are often not available making calibration of models difficult. Discussions will address specific topics including whether a model calibrated under normal conditions be used for simulating cellular and tissue behavior in a patient with several health problems by just shifting parameter ranges, or new model extensions need to be developed? Which models are to be used for simulating chronic diseases in patients treated with a combination of medications?

2. Multi-scale modeling of therapeutic interventions, including pharmaceuticals as well as gene therapy, cell therapy, and physiological therapy. Development of multi-scale models of the key molecular biology, cellular biology, heterogeneous tissue architecture, and physiology, could lead to detailed comparison of many different treatments, including different drugs, routes of administration, doses and schedules by virtual clinical trials that incorporate models of many patients. Due to the multi-scale nature of the models, clinicians could identify emergent therapeutic or toxic effects of treatments, as well as conditions under which therapies fail. These models can translate knowledge from in vitro cell culture to in vivo preclinical and clinical studies, which is important because it is known that observed mechanisms in vitro do not always hold in vivo. These models can help researchers and clinicians translate therapies from animals to humans, or from microphysiological systems (‘body-on-a-chip’) to patients.

3. Multi-scale modelling of biochemical networks personalized with omics data. Combining -omics data, machine learning approaches and other statistical methods with multi-scale modeling approaches to human disease. For example: Integration of statistics, optimization and multi-scale mechanistic modelling of brain metabolism to try to stratify Parkinson's disease patients based on distinct aetiopathegenic origins.

Talks in each of three tracks will focus on the following topics:

1. Key methodologies for different applications. Discussion of whether these methodologies are transferable, and how they can be shared.

2. Specific examples of biomedical applications and diseases studied using multi-scale methods and combining different methodologies. Discussion of how this can be extended to other diseases.

3. Best practices for establishing collaborations with clinicians including development of common language, exchange of data, and application of predictive simulations. Discussion of how to assemble, adopt, and disseminate best practices.

Suggestions of additional topics or extensions of the initially suggested topics will be solicited from the members of the Multi-scale Systems Biology WG and from other members of the MSM Consortium. General information about the Conference will be posted on the WG wiki with several prearranged windows to solicit suggestions on specific subjects.

In the lead-up to the conference, we will organize several webinars to discuss and refine visions for specific conference tracks. These webinars will help to identify and discuss central topics of importance in specific fields and tracks in advance of the conference, so that the conference itself will have well-defined goals for discussions and for outputs of those discussions. A series of webinars will be similarly organized after the conference to finalize white papers, reviews, commentaries and other work products of the conference.

Conference Poster

November 15th Schedule

7:30 - 8:00 a.m. - Coffee and Pastries

8:00 - 8:10 a.m. - Dean Kathryn Uhrich Welcome

8:10 - 8:50 a.m. - Alison Marsden - “Computational investigations of the biomechanical underpinnings of vein graft failure”

8:50 - 9:30 a.m. - Andrew D. McCulloch - “Multi-Scale Modeling and Systems Mechanobiology of Ventricular Hypertrophy and Failure”

9:30 - 9:50 a.m. - Coffee

9:50 - 10:30 a.m. - Denise Kirschner - "Tools for Building and Analyzing Multi-Scale models: TB as a Case Study"

10:30 - 11:10 a.m. - Jason M. Haugh - “Multi-scale modeling of wound healing: progress and challenges in modeling directed cell migration”

11:10 - 11:30 a.m. - Coffee

11:30 a.m. - 12:10 p.m. - Discussion, Track 1: Discussion of the best practices of establishing productive collaborations between scientists, engineers and clinicians to promote transnational research.

12:10 - 1:20 - Lunch

1:20 - 2:00 p.m. - Gary An - "Re-examining the evaluation and use of agent-based models to address the Crisis of Reproducibility, the Translational Dilemma and Precision Medicine"

2:00 - 2:40 p.m. - George Karniadakis - "Stochastic Multiscale Modeling of Hematological Disorders"

2:40 - 3:00 p.m. - Coffee

3:00 - 3:40 p.m. - John Weisel - "Multi-scale methods for studying blood clot and thrombus structure and mechanics from nanometers to patients"

3:40 - 4:20 p.m. - Daniel Beard - "Computational systems analysis to predict and analyze targets for improving mechanicalenergetic coupling in the myocardium in heart failure”

4:20 - 4:40 - Coffee

4:40 - 5:10 p.m. - Discussion, Track 2: Discussion on computational models of pharmaceuticals, gene therapy, cell therapy, and other types of treatment.

6:00 - 6:30 p.m. - Hors d'Oeurvres

6:30 - 8:00 p.m.Conference Dinner for All Registered Participants at theUCR Alumni and Visitors Center, Redmond Dining Room

November 16th Schedule

7:30 - 8:00 a.m. - Coffee Pastries

8:00 - 8:40 a.m. - Laurence Yang - "Expanding the biological scope of multi-scale models of Metabolism and protein Expression"

8:40 - 9:20 a.m. - Danny Bluestein - "A Predictive Multiscale Model for Simulating Platelets Activation and Aggregation in Shear Flows"

9:20 - 9:40 a.m. - Coffee

9:40 - 10:20 a.m. - Melissa L. Knothe Tate - "Translation of Engineering Innovations Discovered through Multiscale, Coupled Imaging and Computational Modeling"

10:20 - 11:00 a.m. - Nathan Lewis - "Capturing a more accurate view of tissue and cell-type specific metabolism"

11:00 - 11:20 a.m. - Coffee

11:20 a.m. - 12:00 noon - Discussion, Track 3: Discussion on Multiscale molecular systems biology: where should we go next?

12:00 - 1:10 p.m. - Lunch

1:10 - 1:20 p.m. - UCR Provost Cynthia Larive's Address

1:20 - 2:00 p.m. - William R. Cannon - "Multiscale Systems Biology: Thermodynamic Methods for Prediction of Cellular Dynamics, Metabolite Levels and Phenotypes"

2:00 - 2:40 p.m. - C. Anthony Hunt -“Scientifically Productive Virtual Experiments"

2:40 - 3:00 p.m. - Coffee

3:00 - 3:40 p.m. - Sunny Canic - “Methodologies to study fluid-structure interaction with mesh- and fiber-reinforced biological structures”

3:40 - 4:20 p.m. - Eric Sobie - "Exploiting mathematical models to predict differences between individuals in cardiac physiology”

4:20 - 5:00 p.m. - Discussion, Summary: Discussion on novel learning/methodology approaches and open problems related to different systems multiscale systems biology modeling methods.