10:00a – 7:15p
Other
- Reply to BJ with final corrections / proofs
Deep sequencing analysis
- scatterplot correlations on log10 scale
Coding
- Interesting matlab fact: Nested functions have access to the parent workspace.
- Got CIGAR and MD parser from Jeff to ID deletions, deletion locations, mutations etc.
- Cloned Hazen’s storm-analysis repository
- Worked out path syntax for calling new repository
- Syntax for calling new DaoSTORM from matlab:
% Location of the New Repo, the DaoSTORM folder, and the windows dlls.
stormAnalysisPath = 'C:\Users\Alistair\Documents\Research\Projects\General_STORM\matlab-storm\External\storm-analysis\storm-analysis\';
newDaoPath = [stormAnalysisPath,'3d_daostorm\'];
sampleDataPath = [newDaoPath,'\sample_data\'];
windowsDllPath = [newDaoPath,'windows_dll\'];
% The necessary file paths
SetPaths = {[PythonPath,';'];
[windowsDllPath,';']};
% The new DaoSTORM command.
DaoSTORM = ['path=',SetPaths{:},' & ',' & ',...
'python.exe ',newDaoPath,'mufit_analysis.py',' '];
dax = ['"',sampleDataPath,'comp.dax','"'];
mlist = ['"',sampleDataPath,'comp_mlist.bin','"'];
xmlfile = ['"',sampleDataPath,'3d_zfit.xml','"'];
call = [DaoSTORM,dax,' ',mlist,' ',xmlfile];
eval(['!',call])
Polymer simulations
Ph Project
- running simulations
Mentoring
- Getting Bogdan setup with EDAC MES with beads