Mission: Discuss and share numerical methods, models, and experiments that facilitate integration of subcellular and cellular scales with the macroscopic scales in the human body and other biological contexts, e.g., imaging and geometric modeling, transport within biological fluid flows, tissue properties and tissue mechanics, and uncertainty quantification.

 

Working Group Leads:

Jason Haugh (jason_haugh@ncsu.edu)

Brief History:

This WG can be traced back to WG3 “Cardiovascular and Pulmonary – hemodynamics and fluid dynamics” (lead Rob Kunz) in 2006. In 2009 it was restructured by merging WG3 Macro-To-Micro Scale Imaging and Transport in Biological Systems and WG7 Multiscale Imaging (lead Yoonsuck Choe). At the 2010 MSM consortium meeting, the goals of WG3/7 were discussed and a white paper entitled "Cell Scale to Macroscale Integration" was presented. Four examples of multiscale model integration were discussed: airway defense system, cerebro-vasculature, gastrointestinal tract and tumor growth. One of the major goals discussed was about the publication of special issues on multiscale modeling in archival journals to document numerical methods and strategies for integration of models at various scales through a peer review process. The WG was renamed as the Cell-to-Macroscale WG after this consortium meeting.

Goals and Objectives:

1. Promote IMAG and MSM missions.
2. Organize WG activities leading to concrete outcomes: Publications, proposals, collaborations, recommendations to IMAG, etc.
3. Facilitate communication among WG members.
4. Identify issues (both research and policy) and act on them.

------------------------------------------------------------------------------------------------------

MSM 2018 Activities and Announcements

MSM members Ross Carlson and Herbert Sauro edited a special issue of the journal Processes focused on 'Methods in Computational Biology' (https://www.mdpi.com/journal/processes/special_issues/methods_biology).  The issue included a wide range of MSM associated researchers.

Special Issue Content:

1. Hunt, C.; Erdemir, A.; Lytton, W.; Mac Gabhann, F.; Sander, E.; Transtrum, M.; Mulugeta, L. The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena. Processes 2018, 6, 56, doi:10.3390/pr6050056.
2. Norton, K.A.; Gong, C.; Jamalian, S.; Popel, A.S. Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment. Processes 2019, 7, 37, doi:10.3390/pr7010037.
3. Porubsky, V.L.; Sauro, H.M. Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python. Processes 2019, 7, 163, doi10.3390/pr7030163.
4. Erhardt, A. Early After depolarisations Induced by an Enhancement in the Calcium Current. Processes 2019, 7, 20, doi:10.3390/pr7010020.
5. Pool, F.; Sweby, P.; Tindall, M. An Integrated Mathematical Model of Cellular Cholesterol Biosynthesis and Lipoprotein Metabolism. Processes 2018, 6, 134, doi:10.3390/pr6080134.
6. Farzan, P.; Ierapetritou, M. A Framework for the Development of Integrated and Computationally Feasible Models of Large-Scale Mammalian Cell Bioreactors. Processes 2018, 6, 82, doi:10.3390/pr6070082.
7. Phalak, P.; Henson, M.A. Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota. Processes 2019, 7, 97, doi:10.3390/pr7020097.
8. Roberts, J.; Patterson, D.; King, V.; Amin, S.; Polska, C.; Houserova, D.; Crucello, A.; Barnhill, E.; Miller, M.; Sherman, T.; et al. ADAR Mediated RNA Editing Modulates MicroRNA Targeting in Human Breast Cancer. Processes 2018, 6, 42, doi:10.3390/pr6050042.
9. Rose, T.; Mazat, J.P. FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks. Processes 2018, 6, 39, doi:10.3390/pr6050039.
10. Beck, A.; Hunt, K.; Carlson, R. Measuring Cellular Biomass Composition for Computational Biology Applications. Processes 2018, 6, 38, doi:10.3390/pr6050038.

The special issue was published in July 2019 as an open access book available at:  https://www.mdpi.com/books/pdfview/book/1403

______________________________________________________________________________________________________________________

MSM 2017 Activities and Announcements

The Metabolic Pathway Analysis 2017 conference was held in Bozeman, MT July 24-28 2017 (http://www.chbe.montana.edu/biochemenglab/MPA2017.html). The conference series focuses on computational approaches to decode biological principles found in ‘omics’ data sets and spans the gamut of fundamental and applied biology including multicellular systems, environmental nutrient cycles, and human health. The MPA conference series integrates a highly interdisciplinary group of international biologists, computer scientists, engineers and mathematicians for formal and informal discussions focused on state-of-the-art advances in metabolic network analysis methodology, theory and application.  A number of lectures were recorded, including a session on computational methods.  The presentation files can be found at:

 

https://montana.app.box.com/s/79scbn5osjg901xjvoryznn1xwaqkqxe

 

The conference is sponsoring a special issue in the MDPI Publishing journal Processes with a focus on computational biology methods.  Please see the following link if you are interested in submitting a manuscript:

 

http://www.mdpi.com/journal/processes/special_issues/methods_biology

 

------------------------------------------------------------------------------------------------------

MSM 2017 (10^th Anniversary) meeting Discussion Items

If you have not already done so, please take a moment to fill out the following survey:

https://uiowa.qualtrics.com/SE/?SID=SV_54MqRl0bkocoGup

 

Discussion Topics: (Please feel free to add and modify any topics below)

1. Brief introduction of participants
2. Review the current WG mission, goals, and objectives
3. Review progress of last year's plans
4. Review survey results

Summary of Discussion from the Breakout Session:

2:00-3:00pm, March 23, 2017

Introduction

• Read the revised mission statement to be more inclusive so that it also references experiments and a broader range of biological phenomena
• Brief statement about the role of the steering committee from Jeff Holmes and the history and function of the working groups.
• Brief introduction from each participant on their research interests. Roughly 2/3 of participants were attending the working group for the first time.

2016-2017 achievements

• Hosted two webinars:
  1. April 20, 2016 - Dr. Sanghun Choi, University of Iowa
  2. October 20, 2016 – Dr. Melissa Knothe-Tate, University of New South Wales

• Conducted and reviewed a survey of WG members to help identify interest

WG Discussion Items

• Encourage participants to present at a future webinar or recommend colleagues whose work would be of interest.
• Thoughts on doing shorter media presentations similar to the "Three Minute Thesis" pitch and providing more to the general public.
• Seek new co-leads to take over the working group.
• Ideas for content, focus, audience, and publisher for a special issue on MSM that appeals to the end users.
• Repositories for code and data that could link to the wiki and approaches taken by other groups on this issue (e.g., GitHub, simTK)

2017-2018 Proposed WG activities

• Host at least two webinars over the next year

Put together a special issue that features a series of technical briefs that clearly outline methods with clear examples. Bookend the briefs with two opinion pieces, starting with the perspective of the modeling community and ending with the perspectives of the end users, e.g., biologists/clinicians. Perhaps link code and data to the articles.

 

2015 WG Breakout Session:

Discussion Topics: (Please feel free to add and modify any topics below)

1. Review and revision of the current WG mission, goals and objectives
2. Brief introduction of participants
3. Review progress of last year's plans
4. 2015-2016 WG plans:
5. Host two IMAG MSM webinar scientific presentations (any volunteers and/or potential speakers): John Dallon, BYU - tentatively speaking in Spring

• Support “New Index of Predictive Models” by encouraging WG members to enter their model indices.

• Better connect WG members, via, facebook, ResearchGate, LinkedIn etc.

• Plan special sessions at major conferences.

• Consider a publication to achieve long-term goals: Position paper publication, collaborative projects, etc.

 

Summary of Discussion from the Breakout Session:

2:10-3:00pm, September 8, 2015

1. Mission Statement

• Read the mission statement and discussed expanding the WG focus from numerical methods to also include models and experiments.
• Discussed what subcellular actually encompasses and how to define the range of scales of interest to the group.
• Also should consider expanding the scope to extend beyond human health, and to consider biofilms and other areas of interest that fit the WG.
• There was also a suggestion that we provide examples of what cell-to-macro scale is.

 

2. Introduction

• Each participant introduced himself or herself and summarized their research interests. It became apparent that certain topics had some density, such as wound healing, biofilms, mechanobiology, cell-matrix interactions, cancer, transport phenomena, relating in vitro data to animal models.
• It was suggested that forming subgroups centered on keywords such as these might help foster actionable items for the WG.

 

3. 2014-2015 achievements

• Hosted two webinars: (1) Jie Liang, University of Illinois at Chicago and (2) Keith Gooch, Ohio State University.
• Co-hosted a s Special Session on Multi-scale Modeling featuring MSM members from Biomechanics (primary) and Cell-to-Macroscale (secondary) Working Groups at the 12th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (CMBBE), Amsterdam, The Netherlands, October 13-15, 2014. http://www.cmbbe2014.com/

 

4. Review of last years plans

• Mentioned Predictive Model Index for new participants
• Discussed ideas of trying to foster more interactions between WG members and with non-modelers and decided that might be best handled by subgroups with focused interests or via social media, e.g. ResearchGate.
• Still need to conduct a survey of WG members

 

5. 2015-2016 Proposed WG activities

• Host at least two webinars with the idea of one in the Fall, one in the Spring, and two in the Summer.
• Have a tentative commitment from John Dallon from BYU for the Spring
• Welcome volunteers from the WG to present their research as well
• Will conduct a series of brief surveys over the course of the year to better define the interests of the group in an attempt to create focused subgroups and to develop actionable items for next years meeting.

-------------------------------------------------------------------------------------------

2014 WG Breakout Session:

2013-2014 Achievements:

• Published a special Issue on Multi-scale Modeling and Simulation of Biological Systems, Journal of Computational Physics, 244, 1-336, July 1 2013. Guest Editors: Ching-Long Lin, Grace C.Y. Peng, and George Karniadakis: 21 papers with applications to one of the following six biological systems: (1) Cardiovascular systems, (2) Respiratory systems, (3) Cells/proteins, (4) Biochemical processes, (5) Bone mechanics, (6) Predicting surgery outcomes.
• Hosted two WG webinars; WG member gave a new grantee webinar.
• Participated in special session CMBBE 2014.

Discussion Topics: (Please feel free to add and modify any topics below)

1. Review and revision of the current WG mission, goals and objectives
2. Consolidate active members across different WGs to form vibrant, reorganized WGs.
3. Discuss transfer of leadership.
4. 2014-2015 WG (tentative) plans:

• Host two IMAG MSM webinar scientific presentations (any volunteers and/or potential speakers).

• Support “New Index of Predictive Models” by encouraging WG members to enter their model indices.

• Better connect WG members, via, facebook, ResearchGate, LinkedIn etc.

• Plan special sessions at major conferences.

• Develop a new white paper to achieve long-term goals: Position paper publication, collaborative projects, etc.

 

Summary of Discussion from the Cell-to-Macroscale Breakout Session:

1:00-2:30pm September 3, 2014

1. History of Working Group (12:10 – 12:12)
2. 2013-2014 Achievements
3. Mission Goals and Objectives
4. Who are we? We went around the room and briefly introduced ourselves, spoke about what our research interests are, and why we thought cell-to-macroscale was the right working group. We found a wide range of interests that all seemed to meet at the interface of the cell. Some of us are interested in the role of solid mechanics, fluid mechanics, while others are interested in biochemical signals and molecular pathways. Some are interested in tissue-level phenomena but need to incorporate some level of abstraction at lower scales that stops at the cell. Some are interested in subcellular phenomena, microtubule dynamics and the cytoskeleton and linking it to whole cell behavior.
5. Went over recommendations from last time.
6. General Discussion: Mentioned that there was a lack of nanoscale mechanics represented so we will make an effort to incorporate this into the Wiki and future discussion.
7. Want to conduct a survey to find out more details about the working groups expertise and interest using a collection of key words.
8. Predictive Model Index  - discussed what the index is and then larger community discussions that have been occurring over feelings about releasing code along with publications.
9. Separation between biologists and modelers. How to attract more of the data collected by biologists to modelers, e.g. by creating more of an online community?
10. Resolve to create a better sense of community maybe on Research Gate or some other online community that will foster more collaboration within the working group and bring traffic and communication from outside
11. Explore setting up a session with a biologist conference to emphasize what multi-scale modeling can do for them. Possible candidates AJP, American Society of Cell Biology, Nature Editors – Frontiers Meeting

Suggestions from Jim Bassingthwaighte via emails dated September 4, 2014:

1. Model indexing: provide a brief description for each model listed, and put a paragraph at the top of the model list about the instructions for submission and review (any committe to review and approve submissions).

2. Develop a set of examples that utilize Uncertainty Quantification, e.g. by collecting a set of e.g. 20 papers on this topic and even putting them into a special issue of a journal or a WG-sponsored book.

 

(Tentative) Plans for 2014-2015:

1. Incorporate nanoscale mechanics into the WG scope and future discussion.
2. Conduct a WG survey to better position ourselves.
3. Bridge biologists and modelers and foster more collaboration within WG members by creating an online community.
4. Promote multi-scale modeling by setting up a session with a biologist conference.

--------------------------------------------------------------------------------------------------------------------------------------------------------------