Welcome

 

Dixy is a web application for producing Dynamic, Interactive XY plots of data.
To use and interact with the data, click Datasets in the menu bar above.
Alternatively, here is an example visualisation of a number of QFA datasets.

 

Background (QFA)

 

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel. QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA.

 
 

For more information about QFA, and the data presented on this site, see the following publications:

 
  • Banks, A., Lawless, C., Lydall, D. (2012) A Quantitative Fitness Analysis Workflow. J. Vis. Exp. (66), e4018, doi: 10.3791/4018
  • Addinall SG, Holstein E-M, Lawless C, Yu M, Chapman K, et al. (2011) Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects. PLoS Genet 7(4): e1001362. doi: 10.1371/journal.pgen.1001362
  • Hsin-Yu Chang, Conor Lawless, Stephen G. Addinall, Sarah Oexle, Morgan Taschuk, Anil Wipat, Darren J. Wilkinson and David Lydall (2011) Genome-Wide Analysis to Identify Pathways Affecting Telomere-Initiated Senescence in Budding Yeast. G3 1(3): 197-208. doi: 10.1534/g3.111.000216
 
 

An R package that implements Quantitative Fitness Analysis:

 
qfa: the R toolbox for carrying out Quantitative Fitness Analysis
 
See also:
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar