AlphaBlog

Grant LaTeX Preamble

I finally finished!!! After a month of hard work and doing nothing but writing, I managed to write an entire K23 in 30 days. I received receipt confirmation that the NIH has it! Using AlphaX as the LaTeX editor was a lifesaver. The only problem I have is that the spell check is broken in my beta16 release. Worked fine in the previous release. I continuously receive a broken pipe error. I haven't had time to figure out how to debug it. Aside from this minor inconvenience, I just spell-checked it in the end using Emacs on this computer and comparing the two windows, all was fast and flawless. I detailed more of the tortuous process over at my Aorchid blog. The other issue came up when constructing the Resouces and front matter pages for the grant, which I didn't make in LaTeX. I should have, but instead used the MSWord fill-in documents provided on the NIH web site. This was a huge mistake and it led to a couple of small errors in the submitted grant, things that shouldn't hold back review or approval. Still, I, we (Xochitl and I), put a tremendous amount of time into this grant for it not to be as near to perfect as possible. I found, after the submission, that the PDF fill-in pages from the NIH web site work MUCH better than the M$ crap. Oh well. Next time!

The preamble for the document is as follows:

\documentclass[11pt]{nih2}
\usepackage{processkv}
\usepackage{parcolumns}
\usepackage[title]{appendix}
\usepackage{varioref}% nice with \autoref{label}, use \vpageref[]{label}
\usepackage[authoryear,colon]{natbib}%[super,sort&compress]
\usepackage[smaller]{acronym}% printonlyused -- didn't work
\usepackage[defblank,neverdecrease]{paralist}
\usepackage{hanging}
\usepackage{ctable}
\usepackage[pdfauthor={Aric Gregson, MD}, pdftitle={Career Development Award Proposal (K23), P. falciparum Challenge Trials and Molecular Analysis},pdfborder={0 0 0}]{hyperref}
% \usepackage{pdfsync}
\piname{Gregson, Aric L.}


\includeonly{coursedescriptions,malaria-rx}


% %%%%%%% My own edits:
% %%%%%%%
% % Usage: \mc{number of columns spanned}{Major column heading}
% Note: different from standard usage, included Left justification
\newcommand{\mc}[2]{\multicolumn{#1}{l}{#2}}


% supress the ugly colored boxes around the active parts of the % text. But it doesn't work!!
\def\pdfBorderAttrs{/Border [0 0 0] } % No border around Links
% Some further Color tuning. Use xcolorsel for help with the colors
% \def\pdfborder{/Border [0 0 0]}
% \definecolor{links}{rgb}{0.2116,0.0104,0.7716} % BlueViolet
% \def\LinkColor{links}
% \definecolor{anchors}{rgb}{0.5812,0.0665,0.0659} % IndianRed
% \def\AnchorColor{anchor}


% %%%%%%%%%% Heading Modifications for RCA PHS 398
\renewcommand{\thepart}{\Roman{part}}
\renewcommand{\thesection}{\thepart.\arabic{section}}
\renewcommand{\thesubsection}{\thesection.\Alph{subsection}}
\renewcommand{\thesubsubsection}{\thesubsection.\roman{subsubsection}}


\numberwithin{equation}{subsection}
\numberwithin{figure}{subsection}
\numberwithin{table}{subsection}


\renewcommand{\bibname}{Literature Cited}

%%%%% Aliases for this paper - shortcuts
\newcommand{\PF}{\emph{Plasmodium falciparum}}
\newcommand{\pf}{\emph{P.\ falciparum}}
\newcommand{\cs}{circumsporozoite\ }
\newcommand{\ab}{antibody\ }
\newcommand{\abs}{antibodies\ }
\newcommand{\xs}{irradiated sporozoites}
\newcommand{\XS}{irradiated sporozoites}
\newcommand{\x}{irradiated sporozoite}
\newcommand{\X}{irradiated sporozoite}
\newcommand{\TC}{T-cell}




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Document begins below %
\begin{document}

As you can see, I tried to include pdfsync, but it never worked properly with TeXniscope. I have found this to be true with beamer.cls as well. I also tried, but failed, to remove the boxes from around the hyperlinked text. I have the line included above to do so, but it just doesn't work. I even tried what is supposed to work according to hyperref documentation. Not a huge distraction, however I would much prefer that printed copies do not have this distraction and then I could include the colors for on-screen versions to make links easier to find. I may continue to play with this, because this is an important feature that needs to work if I am going to push to use LaTeX for all protocol and grant development.

I'm not sure how other people have created their Biosketches in LaTeX, so I have included a copy to download for others to see. It looks OK. I think it could be improved. I will note that it looks at least 100 percent better than the MSWord versions others have submitted. You can download it here. At nearly 100 pages, this was some work! Here's to it getting a fundable score on the first go-round!!