Tissue Forge: Interactive biological and biophysics simulation environment.

Autor: T J Sego, James P Sluka, Herbert M Sauro, James A Glazier

Publikováno v: PLoS Computational Biology, Vol 19, Iss 10, p e1010768 (2023)

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter

Externí odkaz: https://doaj.org/article/6aac46f100c54ec2bd61f04b2af8d1c7

Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models.

Autor: Xiao Fu, James P Sluka, Sherry G Clendenon, Kenneth W Dunn, Zemin Wang, James E Klaunig, James A Glazier

Publikováno v: PLoS ONE, Vol 13, Iss 9, p e0198060 (2018)

Computational models of normal liver function and xenobiotic induced liver damage are increasingly being used to interpret in vitro and in vivo data and as an approach to the de novo prediction of the liver's response to xenobiotics. The microdosimet

Externí odkaz: https://doaj.org/article/77faf0bce05e48aab4de960dd826f832

PhenoCellPy: A Python package for biological cell behavior modeling

Autor: Juliano F. Gianlupi, T.J. Sego, James P. Sluka, James A. Glazier

PhysiCell, a mechanistic center-based agent-based modeling framework, describes sequences of cell behaviors in a very elegant way with its phenotype submodel. However, its phenotypes are not usable in other frameworks, and the creation of a new pheno

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::27cdd1526b64dcbea5b94a40aaf65d0d
https://doi.org/10.1101/2023.04.12.535625

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Autor: William J. Greenleaf, Sarah A. Teichmann, Margaret Vella, Ajay Pillai, Aviv Regev, Ananda L. Roy, Kristin E. Burnum-Johnson, Cole Trapnell, Yiing Lin, Marda Jorgensen, Gloria S. Pryhuber, Leslie Gaffney, Ken S. Lau, Kimberly Robasky, Jeffrey M. Spraggins, Chuck McCallum, Stavros Michailidis, Randy Heiland, Orit Rozenblatt-Rosen, Allyson Ricarte, Xin bSun, Kevin J. Otto, Amir Bahmani, Zorina S. Galis, James S. Hagood, Monica Nagendran, Gökcen Eraslan, Robin M. Scibek, Jocelyn Y. Kishi, Jay Mulye, Maria Keays, Griffin M. Weber, Caltech-UW Tmc, Charles Ansong, Nicholas A. Nystrom, Vishal G. Venkataraaman, Vladimir Yu. Kiselev, Ucsd Tmc, Ellen M. Quardokus, Tushar bDesai, Bruce Herr, Engagement Component, James E. Anderson, Shin Lin, Lisel Record, Peter V. Kharchenko, Robert F. dMurphy, Stanford-WashU Tmc, Yu Wang, Jian Ma, Sergio Maffioletti, Sarah Black, Matthew Ruffalo, Salvatore Sechi, John C. Marioni, Ziv Bar-Joseph, Richard M. Caprioli, Stanford Ttd, Garry P. Nolan, Marishka Brown, Elizabeth L. Wilder, Maigan A. Brusko, Peter Chou, Tommaso Biancalani, Christian Martijn Schuerch, Julia Laskin, Richard Conroy, Jonathan C. Silverstein, Paula M. Mabee, Dena Procaccini, Pehr B. Harbury, Michael Snyder, Pothur Srinivas, Jennifer Rood, Dana Jackson, Sanjay Jain, Katy Börner, Visualization HuBMAP Integration, William E. Shirey, Sinem K. Saka, James P. Sluka, Agnes B. Fogo, Isabel Goldaracena, Sushma A. Akoju, Raymond C. Harris, Rahul Satija, Sylvia K. Plevritis, Tim Stuart, Shila Ghazanfar, Peng Yin, Harvard Ttd, Aaron M. Horning, Ed Esplin, Amanda Posgai, Michael J. Clare-Salzler, Raf Van de Plas, Aaron Pawlyk, Guo-Cheng Yuan, Benedict aten, DongHye Ye, Hayan Lee, Eyal Fisher, Jay Shendure, Long Cai, Danielle cGutierrez, Carl Kingsford, Ruben Dries, Sara Ahadi, Paul D. Piehowski, Bernd bBodenmiller, Purdue Ttd, Stephanie A. Nevins, Philip D. Blood, Andrew Butler, W. Christopher Lenhardt, Ying Zhu, Alexander J. Ropelewski, Harry S. Nick, Nathan Heath Patterson, Elizabeth K. Neumann, Anna Hupalowska, Samuel H. Friedman, Clive hWasserfall, Qian Zhu, Mark P. deCaestecker, Leonard E. Cross, Mark A. Atkinson, Paul Macklin, Todd M. Brusko, Eeshit Dhaval Vaishnav, Nils Gehlenborg, Kun Zhang

Publikováno v: Nature

Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to de

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a760adbbc42a3cb40fdfb6a51c3f81aa
http://europepmc.org/articles/PMC6800388

Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2

Autor: Juliano Ferrari Gianlupi, Tarunendu Mapder, T. J. Sego, James P. Sluka, Sara K. Quinney, Morgan Craig, Robert E. Stratford, James A. Glazier

Publikováno v: Viruses; Volume 14; Issue 3; Pages: 605

We extend our established agent-based multiscale computational model of infection of lung tissue by SARS-CoV-2 to include pharmacokinetic and pharmacodynamic models of remdesivir. We model remdesivir treatment for COVID-19; however, our methods are g

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fc40b1eaff3e229bf3f1d608d7671b64
https://doi.org/10.3390/v14030605