Posted on: January 9, 2017. Updated on: March 9, 2017
Thanks to renewal of our NIH grant to develop and maintain COPASI, the following position was created in the Mendes group.
Dr. Pedro Mendes, in the Center for Quantitative Medicine (CQM) and also affiliated with Center for Cell Analysis and Modeling (CCAM) and Dept. of Cell Biology, UConn Health, is recruiting a postdoc to undertake research in the area of computational systems biology. The successful candidate will join an International team that are developing the modeling and simulation software COPASI (Hoops et al. 2006 Bioinformatics 22:3067-74). The position, funded by an NIH grant and expected to last 3 years, is to develop and implement simulation and optimization algorithms, particularly focused on large biochemical networks.
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. It is routinely used in biological and chemical research, as documented in many publications from authors around the world (e.g. in 2015 COPASI was used in 79 publications). Development of COPASI thus requires special attention to usability, and extensive testing. The development team also supports the bioscience community of users through online interaction and workshops. The project will continue to support interoperability and standards compliance, particularly regarding the systems biology markup language (SBML) and the simulation experiment description language (SED-ML). COPASI is an International project with a geographically distributed team (with collaborators in Germany and Virginia Tech) and thus requires frequent online communication.
The successful candidate will research algorithms and work on the C++ source code of COPASI, maintaining the existing code and implementing new features. She/he will also provide assistance to COPASI users, organize and participate in tutorials, demonstrations, and other educational and outreach activities. She/he will prepare manuscripts for peer review and present them at specialized conferences. A PhD or equivalent in biology, computer science, mathematics, physics, or related areas is required. Experience of programming in C++ or another object-oriented language, as well as modeling with differential equations, are essential. Previous experience of using COPASI is desirable but not essential.
The environment at UConn Health is particularly rich in the area of computational biology and the successful candidate will be able to interact with other teams at CQM working on systems biology and biomedical informatics, and at CCAM where related computational biology projects are ongoing (VCell, BioNetGen, etc.). Co-located in our campus in Farmington are also the Medical and Dental Schools, and the Jackson Laboratory for Genomic Medicine.
UConn Health is an Affirmative Action/Equal Opportunity Employer