Literature DB >> 29296510

Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches.

David E Stone1, Elizabeth S Haswell2, Elizabeth Sztul3.   

Abstract

In classical Cell Biology, fundamental cellular processes are revealed empirically, one experiment at a time. While this approach has been enormously fruitful, our understanding of cells is far from complete. In fact, the more we know, the more keenly we perceive our ignorance of the profoundly complex and dynamic molecular systems that underlie cell structure and function. Thus, it has become apparent to many cell biologists that experimentation alone is unlikely to yield major new paradigms, and that empiricism must be combined with theory and computational approaches to yield major new discoveries. To facilitate those discoveries, three workshops will convene annually for one day in three successive summers (2017-2019) to promote the use of computational modeling by cell biologists currently unconvinced of its utility or unsure how to apply it. The first of these workshops was held at the University of Illinois, Chicago in July 2017. Organized to facilitate interactions between traditional cell biologists and computational modelers, it provided a unique educational opportunity: a primer on how cell biologists with little or no relevant experience can incorporate computational modeling into their research. Here, we report on the workshop and describe how it addressed key issues that cell biologists face when considering modeling including: (1) Is my project appropriate for modeling? (2) What kind of data do I need to model my process? (3) How do I find a modeler to help me in integrating modeling approaches into my work? And, perhaps most importantly, (4) why should I bother?

Entities:  

Keywords:  National Science Foundation; computational biology; modeling; processes; workshop

Year:  2017        PMID: 29296510      PMCID: PMC5739093          DOI: 10.1080/21592799.2017.1382669

Source DB:  PubMed          Journal:  Cell Logist        ISSN: 2159-2780


  8 in total

1.  Flagellar length control system: testing a simple model based on intraflagellar transport and turnover.

Authors:  Wallace F Marshall; Hongmin Qin; Mónica Rodrigo Brenni; Joel L Rosenbaum
Journal:  Mol Biol Cell       Date:  2004-10-20       Impact factor: 4.138

Review 2.  Modeling transcriptional networks in Drosophila development at multiple scales.

Authors:  Zeba Wunderlich; Angela H DePace
Journal:  Curr Opin Genet Dev       Date:  2011-09-01       Impact factor: 5.578

3.  Detyrosinated microtubules buckle and bear load in contracting cardiomyocytes.

Authors:  Patrick Robison; Matthew A Caporizzo; Hossein Ahmadzadeh; Alexey I Bogush; Christina Yingxian Chen; Kenneth B Margulies; Vivek B Shenoy; Benjamin L Prosser
Journal:  Science       Date:  2016-04-22       Impact factor: 47.728

4.  Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.

Authors:  Max V Staller; Ben J Vincent; Meghan D J Bragdon; Tara Lydiard-Martin; Zeba Wunderlich; Javier Estrada; Angela H DePace
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-06       Impact factor: 11.205

5.  Rule-based modeling with Virtual Cell.

Authors:  James C Schaff; Dan Vasilescu; Ion I Moraru; Leslie M Loew; Michael L Blinov
Journal:  Bioinformatics       Date:  2016-06-09       Impact factor: 6.937

Review 6.  Modeling cellular processes in 3D.

Authors:  Alex Mogilner; David Odde
Journal:  Trends Cell Biol       Date:  2011-10-27       Impact factor: 20.808

7.  PI(4,5)P2 regulates myoblast fusion through Arp2/3 regulator localization at the fusion site.

Authors:  Ingo Bothe; Su Deng; Mary Baylies
Journal:  Development       Date:  2014-05-12       Impact factor: 6.868

Review 8.  Theory in Biology: Figure 1 or Figure 7?

Authors:  Rob Phillips
Journal:  Trends Cell Biol       Date:  2015-11-13       Impact factor: 20.808

  8 in total

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