ggalluvial v0.5.0: A ggplot2 Extension for Alluvial Diagrams, an R package by Cory Brunson, is now available on CRAN

ggplot2 is a very popular R package for data visualization.  When Dr. Jason (Cory) Brunson, a postdoctoral fellow, engaged in a data analysis project with the State Comptroller’s office, he began developing an extension to ggplot2 to create so-called alluvial diagrams, like the one used by Bergstrom and Rosvall in their PLOS One paper.[1]  Dr. Brunson kept working on it intermittently, and a couple of months ago he submitted it to CRAN, which is the primary repository for stable R packages.[2].

Alluvial diagrams can be used to represent repeated categorical measures, classifications that evolve over time, and multi-dimensional categorical data. ggalluvial produces alluvial diagrams using the principles and syntax of the tidyverse packages, including ggplot2 and tidyr.

Please click on the link to an introduction/tutorial that he wrote.[3]

[1]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008694

[2]: https://cran.r-project.org/package=ggalluvial

[3]: https://cran.r-project.org/web/packages/ggalluvial/vignettes/ggalluvial.html

UConn Health/JAX faculty member, Dr. Reinhard Laubenbacher, wins $2.7M grant to develop better tools for biomedical modeling

UConn Health/JAX faculty member, Dr. Reinhard Laubenbacher, has been awarded over $2.7 million over the next four years from the National Institutes of Health (NIH) for “Modular design of multiscale models, with an application to the innate immune response to fungal respiratory pathogens” (1U01EB024501-01). The project aims to develop a novel modular approach to model architecture to improve the usability of multiscale mathematical models. Such tools have emerged as essential tools in the life sciences, especially biomedicine.

https://ip.uconn.edu/news/230/UConn%20Health%2FJAX%20faculty%20wins%20%242.7M%20grant%20to%20develop%20better

Brianna Kozemzak, REU Class of 2016, Named Recipient of the NSF Graduate Research Fellowship Program

Brianna Kozemzak of Saint Mary’s College, Notre Dame, IN receives The National Science Foundation Graduate Research Fellowship Program. The NSF Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master’s and doctoral degrees at accredited United States institutions. Fellows benefit from a three-year annual stipend of $34,000 along with a $12,000 cost of education allowance for tuition and fees (paid to the institution), opportunities for international research and professional development, and the freedom to conduct their own research at any accredited U.S. institution of graduate education they choose.

For more information, visit http://www.nsfgrfp.org.

Anna Konstorum Receives Ruth L. Kirschstein National Research Service Award (NRSA) Individual Posdoctoral Fellowship (Parent F32)

Anna KonstorumAnna Konstorum, a postdoctoral fellow of Dr. Reinhard Laubenbacher’s research group at Center for Quantitative Medicine, has been awarded a F32 Postdoctoral Fellowship by the National Cancer Institute (NCI) of the NIH.

The project titled “Multiscale modeling of synergistic T cell activation for cancer immunotherapy.”

The sponsor is Dr. Reinhard Laubenbacher of Center of Quantitative Medicine, co-sponsor is Dr. Anthony Vella of the Department of Immunology, and collaborator is Dr. Adam Adler of the Department of Immunology.

Dr. Anna Konstorum will develop both intracellular and multiscale mathematical and computational models of combined agonist stimulation of T cell costimulatory receptors OX40 (CD137) and 4-1BB (CD134). The models will be used to decipher the critical mechanisms and scales underlying the experimentally observed synergistic behavior of these two agonists on CD8+ T cell activation, and thus will aide in the development of a quantitative platform from which to examine multiscale drug synergy for application to cancer immunotherapy.