Bugfix – propogating the makefile generation code. Makefiles are no longer generated separate from the files that use them.
BUG TOFIX – auc computation doesn’t stop on error. Perhaps we should make this a submake, so we can compute all the scores simultaneously?
Computing – gene-genevalues for old
TODO – biopython MDMR compute. Use MDMR data in [...]
Archive for February, 2009
Work Report
Posted in Uncategorized on February 23, 2009 | Leave a Comment »
WIP
Posted in progress on February 20, 2009 | Leave a Comment »
MDMR – Nicholas Schork Multivariate distance matrix regression. Explain a gene distance matrix using parameters (e.g. micro-array chip, or for us, MeSH annotation=disease) BioPython function exists.
http://www.pnas.org/content/103/51/19430.abstract?ck=nck
Profile comparison used to make the distance matrix? Also possible – look for pubmed co-citation (an independant distance matrix, not involving MeSH?)
Regenerating generif.
BG-profiles computed, appear to be less effective. Some [...]
Progress Report
Posted in Uncategorized on February 10, 2009 | Leave a Comment »
Mouse general background compute completed. Disease/GeneBG compute in progress.
cmp-digenei2 for mouse being run
TODO: adapt cmp-digenei2 for BG computes, grep mus results
Reorganise
Posted in blog on February 8, 2009 | Leave a Comment »
Time to clean up the scientific notebook (this blog, in other words). Categories vs. tags make for several organisational methods.
Categories should definitely separate “blog” (organisational notes like this one) from research. The question is whether to separate via topic – disease-gene, motif finding, etc and use tags for whether this is phd-thesis or side project, [...]
Weekend Work
Posted in Uncategorized on February 8, 2009 | Leave a Comment »
GeneBG seems to be OK, trying to get the diseaseBG off the ground. Need to investigate why PMID 9753684 is flagged with MeSH term “Chromosome Aberration” and AGAMOUS Protein, Arabidopsis, but isn’t being picked up by the mesh-disease…
Ah. I see the problem – it’s a matter of odd intersections in the tree – Mosaicism is [...]
New Results
Posted in Uncategorized on February 6, 2009 | Leave a Comment »
Seems pretty similar to the cmp-digenei result. Should note that CTD validation and training validation are unchanged, since those only depend on the predictions.
Mouse direct connections are done. Write a simple cmd-line tool to grep results? What other organisms would be useful use cases – yeast perhaps?
I really need a web interface – somewhere people [...]
Update
Posted in Uncategorized on February 5, 2009 | Leave a Comment »
digenei2 – use this for the new background tweaking
cmp-digenei2 running – added tmp directory stub (for auc.sh)
running mouse version on digenei3
Currently In Progress
Posted in Uncategorized on February 4, 2009 | Leave a Comment »
-mus TAXON_NAME test run in digenei1/ (new TAXON_NAME code)
-hum first compute in digenei3/
TO RUN – cmp-digenei2 once digenei3 is complete
TO FIX – reference to taxon_id=9606 (e.g. in direct_gd_predict.mk)
TO REVISE – maybe use comesh counts (comesh for disease) to get the background stats (save computation)
Mouse Organism Prediction
Posted in Uncategorized on February 3, 2009 | Leave a Comment »
Change organism references from hum to TAXON_FILTER. Hard-code the extraction of mouse genes, but everything else should follow pretty straightforward from that.
Extract the organism-specific filtering from the general computation (get_pval.mk) in direct-predict to the main Makefile, to make switching between organisms possible via simply changing the TAXON_FILTER.
