Tag Archives: PyPedal

PyPedal Release Candidate 4 is Easier to Install

Posted on April 9, 2008 by jcole

I made some changes to __init__.py and setup.py that make PyPedal installable (is that a word?) using the very Pythonic “python setup.py install” method. I also updated the discussion of installation in the manual. However, in order to get this … Continue reading →

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This is a Quick Test of the Google Syntax Highlighter for WordPress Plugin

Posted on April 4, 2008 by jcole

I read about the Google Syntax Highlighter for WordPress in a blog entry by Jacob Gube describing several purportedly-useful WordPress extensions. The plugin sounds like just the thing to pretty-up some entries I’m working on about PyPedal. Here’s a simple … Continue reading →

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An Article on PyPedal May Appear in Python Magazine

Posted on March 31, 2008 by jcole

I received this morning an e-mail from the Technical Editor of Python Magazine asking if I’d be interested in writing an article about PyPedal. I hope to talk with with him soon to get more details and see if we … Continue reading →

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PyPedal Release Candidate 3 Features an Inbreeding Bugfix and Refactored Database Handling

Posted on March 28, 2008 by jcole

The third release candidate of PyPedal 2.0 has been released. It includes a minor bugfix to pyp_nrm/inbreeding_vanraden() and a completely-refactored database backend. After a few days of writing, and a false start with SQLAlchemy, I’ve completely rewritten the database backend … Continue reading →

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PyPedal Release Candidates Feature Fewer Bugs!

Posted on March 12, 2008 by jcole

One supposes that the titles of this entry is not particularly informative because that is, in fact, the point of release candidates: to iron out as many lingering bugs as possible. What do you from a guy with hair like … Continue reading →

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PyPedal now calculates ancestral inbreeding coefficients

Posted on February 13, 2008 by jcole

PyPedal can now calculate ancestral inbreeding coefficients using either the recursion equation of Ballou (1997) or the gene dropping method of Suwanlee et al. (2007). Ancestral inbreeding is the probability of an individual inheriting an allele that has undergone inbreeding … Continue reading →

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PyPedal now calculates partial inbreeding coefficients

Posted on February 8, 2008 by jcole

After sitting on the “coming soon” list for a couple of years PyPedal can finally calculate coefficients of partial inbreeding! As side effect, the pyp_nrm/reorder() routine now moves all founders to the beginning of the pedigree. In the past, founders … Continue reading →

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I’m a code monkey

Posted on March 22, 2007 by jcole

Today has been another three-language day: Fortran [Wikipedia] for the best prediction code, Python for PyPedal, and PHP for my latest side project, Middleton. Oh, wait, I also did some LaTeX in the PyPedal manual and write a one-liner in … Continue reading →

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Working for the Man

Posted on October 5, 2006 by jcole

I know, it’s been a long time since I last blogged. I’ve been busy, what with successfully completing my probationary period and getting my new employee up to speed. I’ve been much busier than I expected this week, but that … Continue reading →

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Perl without tears, the perils of revenge

Posted on September 21, 2006 by jcole

A couple of days ago I needed to install html2latex on the server because it’s part of the documentation toolchain for PyPedal. Which meant a long, strange trip into Perl-land which required that I install packages from CPAN without root … Continue reading →

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