Difference between revisions of "A stochastic simulator for growing single cells: software extensions and realistic simulation"

From Master Projects
Jump to: navigation, search
Line 3: Line 3:
 
|Contact person2=Timo Maarleveld
 
|Contact person2=Timo Maarleveld
 
|Contact person3=Anne Schwabe
 
|Contact person3=Anne Schwabe
|Master areas=Bioinformatics, Systems Biology
 
 
|Fulfilled=No
 
|Fulfilled=No
 
}}
 
}}
 +
 +
|free text=}}
 
When a population of cells is growing at steady state, so at a fixed growth rate, then surprising differences occur between single cells. For instance, cells do not progress through their cell cycle in synchrony and stochastic events cause cells to differ in their molecular make up. To understand how these two causes of cell variation underlie variability of populations of cells we have recently developed a simulation software package (http://stochpy.sourceforge.net) that can simulate stochastic cell growth. In this project, the student will extend this software package with methods for the simulation of DNA replication and plasmid dynamics. This requires programming of StochPy in Python. With these extensions the student will study the differences between genes expressed from the genome and plasmids as function of cellular growth rate. If the students would like to do a limited number of experiments then we can generate experimental data of growing cells under the microscope using plasmid and genome expressed fluorescent reporter constructs.
 
When a population of cells is growing at steady state, so at a fixed growth rate, then surprising differences occur between single cells. For instance, cells do not progress through their cell cycle in synchrony and stochastic events cause cells to differ in their molecular make up. To understand how these two causes of cell variation underlie variability of populations of cells we have recently developed a simulation software package (http://stochpy.sourceforge.net) that can simulate stochastic cell growth. In this project, the student will extend this software package with methods for the simulation of DNA replication and plasmid dynamics. This requires programming of StochPy in Python. With these extensions the student will study the differences between genes expressed from the genome and plasmids as function of cellular growth rate. If the students would like to do a limited number of experiments then we can generate experimental data of growing cells under the microscope using plasmid and genome expressed fluorescent reporter constructs.
  
 
* Simulation & Programming
 
* Simulation & Programming
 
* Estimated duration: 4-6 months
 
* Estimated duration: 4-6 months

Revision as of 09:51, 24 August 2016


About A stochastic simulator for growing single cells: software extensions and realistic simulation


Description

|free text=}} When a population of cells is growing at steady state, so at a fixed growth rate, then surprising differences occur between single cells. For instance, cells do not progress through their cell cycle in synchrony and stochastic events cause cells to differ in their molecular make up. To understand how these two causes of cell variation underlie variability of populations of cells we have recently developed a simulation software package (http://stochpy.sourceforge.net) that can simulate stochastic cell growth. In this project, the student will extend this software package with methods for the simulation of DNA replication and plasmid dynamics. This requires programming of StochPy in Python. With these extensions the student will study the differences between genes expressed from the genome and plasmids as function of cellular growth rate. If the students would like to do a limited number of experiments then we can generate experimental data of growing cells under the microscope using plasmid and genome expressed fluorescent reporter constructs.

  • Simulation & Programming
  • Estimated duration: 4-6 months