People involved
in creating TangleSolve
Mariel is a post-doctoral fellow at the Department of Mathematics, U.C. Berkeley. She has worked in the field of DNA topology since 1994 and has specialized in the tangle model for site-specific recombination. Mariel was a student of De Witt Sumners , in her PhD dissertation [T4] she used the tangle model to analyze various site-specific recombination reactions. During all her student years, while trying to reconcile the mathematics of the tangle model with the molecular biology of site-specific recombination, she realized the need for a computer implementation that would make this wonderful mathematical tool accessible to experimental molecular biologists. TangleSolve is the realization of this dream accomplished in collaboration with a few wonderful students.
Yuki is a graduate student at Florida State University. Yuki started working on TangleSolve in 2001. He was then a 3rd year undergraduate student at UC Berkeley majoring in both Mathematics and Physics. Yuki was selected as an Undergraduate Research Apprentice (through the URAP program at UC Berkeley) by Prof. Rainer Sachs and Dr. Mariel Vazquez. Yuki developed TangleSolve as a result of this research experience.
Wenjing is a 3rd year undergraduate at UC Berkeley majoring in mathematics. Stefanus graduated from the UC Berkeley Math Department in Spring 2005 and is starting Graduate School at Stanford in Fall 2006. In Spring 2005 Wenjing and Stefanus were URAP students and worked with Mariel on a second version of TangleSolve. The new version includes reference to known theorems which ensure that for systems of tangle equations satisfying specific conditions the set of solutions computed by TangleSolve is complete. Wenjing did the computer implementation and wil continue working on this project in 2005 and 2006.
Acknowledgements
We want to thank the Undergraduate Reseach Apprentice Program ( URAP) for encouraging undergraduate research. Yuki Saka's research during the summer 2001 was funded through the URAP Summer Stipend Program.
Mariel's research at Berkeley was funded by NSF grant DMS 9971169 and NIH grant GM68423. We also want to thank the Burroughs Wellcome Fund Interfaces in Science Program that, through the Program in Mathematics and Molecular Biology (PMMB), funded Mariel's research from 1997-2000; and, in particular, the DGAPA-UNAM fellowships that funded Mariel's research and education from her undergraduate years until her PhD completion (1993-2000).