perl, intro, resources

perl
- program - originally developed to transform various dataformats
- useful for data manipulation
- esp. text manipulation by means of regular expressions
- web pages (amazon.com etc)
- cf data manipulation for Human Genome Project
-
- Bioperl - (manipulation and evaluation of genome sequence data)

can be downloaded free from activestate.com as ActivePerl

intro at perl.com, perl.org, where also a library with online books can be found
eg. beginning Perl by S. Cozens
at CPAN - official Perl site with comprehensive documentation-

intro text also here, helps to get first glimpse on the structure of perl + one gets acquainted with some terminology (variable types-scalar, array, hashes, references, subroutines, regular expressions), but not many "aha" feelings so far. however - nicely organized.

PERL INTRO + links to other INTROs and more
Broman´s page - reads very well

Perl code editors - syntax color coding, ....
FREE:
Perl Express - looks trustworthy - last update 2005?
Open Perl IDE looks like OptiPerl - from 2003+patch for Perl 5.8
Perl code editor - basic, webpage rather shabby

shareware
OPTIPERL intergrated environment - looks interesting
DZSoft Perl Editor

ER stress

2007 - Ind J Med Res

ER stress and diabetes. Sundar Rajan



2006 - Science - Hotamisligil.

chemical chaperones reduce ER stress and restore glucose homeostatis in mouse model of T2DM

XXXX - 4-phenylbutyric acid, taurine-conjugated ursodeoxycholic acid

cf XXXXX treatment of ER stressss, cf cited bys



2006 - Phys Reviews
Marinciak S. Endoplasmic Reticulum Stress Signaling in Disease

2005 - JCI
Xu, Bailly-Maitre, Reed. Endoplasmic reticulum stress: cell life and death decisionsJ. Clin. Invest., Oct 2005; 115: 2656 - 2664.


2005 - JBC
Nakatami. Involvement of Endoplasmic Reticulum Stress in Insulin Resistance and Diabetes*

2002 - JCI
David Ron - Translational control in the endoplasmic reticulum stress response J. Clin. Invest., Nov 2002; 110: 1383 - 1388.

quantitative genetics veterinary

quantitative genetics in veterinary medicine - a booklet

http://www.kursus.kvl.dk/shares/vetgen/_Popgen/genetics/genetik.htm

statistics genetics "a must see"

http://www.dorak.info/genetics/notes05.html

European Genetics Foundation
http://www.charite.de/ch/medgen/eumedis/statistics05/genetic-epidemiology.html

article by Kruglyak, Nickerson on the effect of SNP frequency on the LD and a measure of frequency matched SNP correlation.

linear trend ordinal variables

linear trend test for dichotomous(binary) with categorical-ordinal variables
e.g. linear trend of risk (OR) of some disease across genotypes

Cochran-Armitage - in SPSS can be done as - sort of - CROSSTABS - linear-by-linear association

more theory + statsdirect software

statistics resources

statistics resources + accompanying SPSS syntax
as recommended by Marta Garcia-Granero

at www.nabble.com

The book: http://www.bmj.com/collections/statsbk/
The SPSS syntax: http://www.kingdouglasconsulting.com/SPSS/DiverseCultures/Marta/Code/BMJ%20-%20Stats%20Square%20One.txt

statistics resources

XXXXXX
the well known series by dr Bland et ???? that appeared in BMJ
statistics at square one

XXXXXX
very instructive resource (maryland biology) by McDonald

measures of central tendency (location)

1. mean (arithmetic, geometric, harmonic)
2. median
3. mode

anova POST HOCS EG:

http://www.uwsp.edu/psych/cw/statmanual/posthocs.html