1.1 --- a/grant.html Mon Apr 20 17:13:37 2009 -0700 1.2 +++ b/grant.html Mon Apr 20 17:16:11 2009 -0700 1.3 @@ -324,16 +324,15 @@ 1.4 Figure 1: Top row: Genes Nfic and 1.5 A930001M12Rik are the most correlated with 1.6 area SS (somatosensory cortex). Bottom row: 1.7 -Genes C130038G02Rik and Cacna1i are those 1.8 +Genes C130038G02Rik and Cacna1i are those 1.9 with the best fit using logistic regression. Within 1.10 -each picture, the vertical axis roughly corre- 1.11 -sponds to anterior at the top and posterior at 1.12 -the bottom, and the horizontal axis roughly 1.13 -corresponds to medial at the left and lateral 1.14 -at the right. The red outline is the boundary 1.15 -of region SS. Pixels are colored according to 1.16 -correlation, with red meaning high correlation 1.17 -and blue meaning low. Format conversion between SEV, MATLAB, NIFTI 1.18 +each picture, the vertical axis roughly corresponds 1.19 +to anterior at the top and posterior at the bot- 1.20 +tom, and the horizontal axis roughly corresponds 1.21 +to medial at the left and lateral at the right. The 1.22 +red outline is the boundary of region SS. Pixels are 1.23 +colored according to correlation, with red meaning 1.24 +high correlation and blue meaning low. Format conversion between SEV, MATLAB, NIFTI 1.25 We have created software to (politely) download all of the SEV files from 1.26 the Allen Institute website. We have also created software to convert 1.27 between the SEV, MATLAB, and NIFTI file formats, as well as some of 1.28 @@ -362,7 +361,7 @@ 1.29 ∙ For each gene, a 2-D matrix whose entries represent the average expres- 1.30 sion level underneath each surface pixel 1.31 1.32 -Figure 2: Gene Pitx2 1.33 +Figure 2: Gene Pitx2 1.34 is selectively underex- 1.35 pressed in area SS. We created a normalized version of the gene expression data by subtracting each gene’s mean 1.36 expression level (over all surface pixels) and dividing each gene by its standard deviation.

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3.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 3.2 +++ b/nih-blank.cls Mon Apr 20 17:16:11 2009 -0700 3.3 @@ -0,0 +1,96 @@ 3.4 +% vim:tabstop=4 expandtab syntax=tex: 3.5 +% This is nih.cls by Alan Shields, May 2003 3.6 +% email: Alan-Shields2omrf.ouhsc.edu 3.7 +% Heavily based upon (read: copied almost exactly from) 3.8 +% nih.sty by Bruce R. Donald and Matthew L. Fidler 3.9 +% 3.10 +\NeedsTeXFormat{LaTeX2e} 3.11 +\ProvidesClass{nih-blank}[2005/05/24 NIH PHS 398 as of November 06] 3.12 + 3.13 +% includes needed for preliminary code 3.14 +\RequirePackage{ifthen} 3.15 + 3.16 +\pagestyle{empty} 3.17 + 3.18 + 3.19 +% Preliminary code 3.20 +\newcommand{\nih@kk}{~} 3.21 + 3.22 +\newboolean{nih@blank} 3.23 +\setboolean{nih@blank}{true}% not strictly necessary, but let's be clear about it 3.24 + 3.25 +% Options 3.26 +%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu) 3.27 +%%%% NIH suggests Helvetica or Arial 12pt. Use Helvetica Postscript fonts for 12pt also. 3.28 +\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{helvet}\renewcommand{\familydefault}{\sfdefault}}} 3.29 +%\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{times}}} 3.30 +%\DeclareOption{12pt}{\AtEndOfClass{\RequirePackage{arial}}} 3.31 +\DeclareOption{11pt}{\AtEndOfClass{\RequirePackage{helvet}\renewcommand{\familydefault}{\sfdefault}}} 3.32 +\DeclareOption{nihblank}{\setboolean{nih@blank}{true}} 3.33 +\DeclareOption{kk}{\renewcommand{\nih@kk}{\small KK}} 3.34 +\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}} 3.35 +\ProcessOptions\relax 3.36 + 3.37 +% The class we're overwriting 3.38 +\LoadClassWithOptions{article} 3.39 + 3.40 + 3.41 +% Begin Requirements 3.42 +%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu) 3.43 +%%%% PHS 398 allows 0.5in magins everywhere. Simplify page layout using geometry package. 3.44 +%\RequirePackage{fullpage} 3.45 + 3.46 +%% Page Margins 3.47 +%% Use standard paper size (8 ½" x 11). 3.48 +%% Use at least one-half inch margins (top, bottom, left, and right) for all pages. 3.49 +% Leaves enough room on all margins: 3.50 + 3.51 +% 0.5 inch top 3.52 +%\RequirePackage[letterpaper,left=0.5in,top=0.5in,bottom=0.575in,right=0.55in,nohead,nofoot]{geometry} 3.53 + 3.54 +% 0.49 inch top 3.55 +\RequirePackage[letterpaper,left=0.5in,top=0.49in,bottom=0.575in,right=0.55in,nohead,nofoot]{geometry} 3.56 + 3.57 + 3.58 + 3.59 +% 0.45 inch top 3.60 +%\RequirePackage[letterpaper,left=0.5in,top=0.45in,bottom=0.575in,right=0.55in,nohead,nofoot]{geometry} 3.61 + 3.62 +% Ideal but Doesn't leave enough room on some margins: 3.63 +%\RequirePackage[letterpaper,left=0.5in,top=0.5in,bottom=0.5in,right=0.5in,nohead,nofoot]{geometry} 3.64 + 3.65 +% the command below simply deletes the headers and footers and makes 3.66 +% the geometry exactly like the paper grant application: 3.67 +%\RequirePackage[letterpaper,margin=0.5in,includeheadfoot]{geometry} 3.68 +\RequirePackage{fancyhdr} 3.69 +\RequirePackage{amsmath} 3.70 +\pagestyle{empty} 3.71 + 3.72 + 3.73 +%%%% More code 3.74 +% preamble stuff 3.75 + 3.76 +\renewcommand{\headrulewidth}{0pt} 3.77 +\renewcommand{\footrulewidth}{0.75pt} 3.78 + 3.79 +%%%% Changed by M A Lewis, Ph.D. (mal11 at alumni.cwru.edu) 3.80 +%%%% Simplify page layout by using geometry package above. 3.81 +% page dimensions (note: assumes 8.5x11) 3.82 +%\setlength{\oddsidemargin}{31pt} 3.83 +%\setlength{\textwidth}{8.5in} 3.84 +%\addtolength{\textheight}{0in} % 0.5in margins on both sides 3.85 +%\addtolength{\textwidth}{-1.1in} 3.86 +%\setlength{\oddsidemargin}{-1in} 3.87 +%\addtolength{\oddsidemargin}{0.505in} 3.88 +%\setlength{\evensidemargin}{\oddsidemargin} 3.89 +%\addtolength{\textheight}{0.2in} 3.90 +%\addtolength{\topmargin}{-0.2in} 3.91 +%\renewcommand{\baselinestretch}{.9} 3.92 +%\headwidth=\textwidth 3.93 + 3.94 +\addtolength{\headheight}{2.5pt} 3.95 + 3.96 +% rename the bibliography section 3.97 +%\AtBeginDocument{\renewcommand{\refname}{Literature~Cited}} 3.98 +\AtBeginDocument{\renewcommand{\refname}{Bibliography \& References~Cited}} 3.99 +%FIXME: something is going on with the bibliography style. Dunno what.