Ovcharenko Group Wiki

2012-02-06

• Made software requests for Mac

2012-02-04

• Got ECHO classifier to run with sample data.

2012-02-01

• Gave brief presentation on group CiteULike? page
• Spoke with Leila about working with the classifiers available to the group. There are at least three classifier pipelines in the group
  • Leelavati Narlikar's ECHO classifier, which includes Markov chains of the sequences as features and relies on PRIORITY to find motifs de novo
  • Leila's classifier, which contains many similar elements rewritten from Leelavati's classifier, uses MAST in the MEME suite, and does not include the Markov chain as features
  • CLARE, which is modeled after Leila's pipeline, but uses tfSearch for finding motifs de novo, has pre-calculated control sequences, and may not be as accurate as the other two pipelines.
• Determined the first thing to do is to use the data sets that are packaged with Leelavati's ECHO
  • The ECHO software won't work out of the box. I need to figure out how to fix it so that it runs.
• Attended Workplace Dynamics I workshop.

2012-01-31

• Downloaded PEAK file for GSM807734, from the publication May, Dalit et al. "Large-scale Discovery of Enhancers from Human Heart Tissue." Nat Genet 44, no. 1 (January 2012): 89-93.
• Obtained liftOver to convert the coordinates from HG18 to HG19
• Mapped GSM807734 from HG18 to HG19

2012-01-30

• Identified a ChiP-Seq paper by Visel, et al. from 2009 for enhancers from P300, for mouse embryos with a focus on brain and limb development
• Had NCBI postdoc orientation at 2PM
• Obtained ID badge