Test post with mtcolorer/colorer

Here’s a block of multiline code…


foreach my $person (@people) {
my %tags = (Supervised => ‘pi’,
# Supervised_by => ‘student’,
Worked_with => ‘collaborated’);
foreach my $tag (keys %tags) {
# next if ($limit_to && $tag ne $limit_to);
if (my @data = $person->$tag) {
my $year = $lineage->discover_year_appeared($person);
next if ($year eq ‘unknown’ && $lineage->purge_unknowns);

# Save a node for this primary person
$lineage->save_node($person); # use different glyphs/colors for supervisors

And here is some code that is s/\/argh\/\/toothpicks\/g inline.

modENCODE RFAs announced

The National Human Genome Research Institute (NHGRI) plans to initiate a model organism ENCODE (modENCODE) Project that will try to identify all of the sequence-based functional elements in the Caenorhabditis elegans and/or Drosophila melanogaster genomes. The project will be run as a Research Network called the modENCODE Consortium which is supported by two RFAs. The first RFA (RFA-HG-06-006) solicits applications for a set of projects that will conduct experiments to identify functional elements in the target genomes and the second RFA (RFA-HG-06-007) solicits applications to participate in the Research Network as a Data Coordination Center. Both experimental and computational approaches will be part of modENCODE and the project will be associated with, but separate from, the human ENCODE (ENCyclopedia of DNA Elements) Project that was launched by NHGRI in 2003.

New genetic map almost complete

I’m almost done putting the finishing touches on a new Genetic Map display. Intended as a drop-in replacement for the Acedb GMap, the new Genetic Map leverages the GBrowse infrastructure providing a familiar user interface as that for browsing the genome.

I still need to fix a few small things (what in the hell is a centi-centi-Morgan?) ๐Ÿ™‚ RD also asked if it might be possible to display mapping data. I think some small modifications of my code that I use for calculating confidence intervals should be sufficient for generating spans for both 2- and 3- factor crosses. The display might get a little complicated displaying separate spans for each experiment – it might be better to aggregate like-experiments together?