AlphaBlog

Looks like I found my error! There is no fortune file named fortune, only fortunes. See! Easy mistake. So I put the following into my fortunes.sh file

fortune 50% fortune 50% limerick

Clearly, this didn't work. Before I realized my mistake however, I thought that the code suggested on the mailing list was wrong. But I don't think so. We shall see! :P

Still can't get the symlink to my user directories to work with the Apache server. Frustrating.

Aargh! I had modified the suggested fortune.sh code, thinking that was the problem. It does work, but receive complaint from nanoblogger as it is running the script. So let's see what happens now.

I'm having fun exploring the goofy fortune files on this machine. I managed to read quite a few last night during the slow times at work. So I changed this one here to take 50% from fortune and 50% from limerick. Also, there were gaps and holes in the original one yesterday, so I modified the fortune.sh file as someone on the NB mailing list suggested, basically taking out all the sed. We'll see!

OK. It didn't work. There may have been a typo on the suggested instructions that were posted. I have now modified the file, so we'll see what happens now. There was no fortune output with the above post.

I had placed the MOODS_DIR in the blog.conf instead of the URL. Of course, the little pictures can't replace text if the pictures cant' be found! I didn't really think hard enough about it, but obviously the moods directory must be uploaded to the website. I copied the entire moods directory to the main blog directory and updated the entire site. So let's see if it finally works!

Nothing is as simple as it sounds. ;P Like attempting to get moods working.

Let's see. Perhaps now it is working? I have figured that you need to place MOODS_URL in the blog.conf file for nb to find the moods configuration. Hopefully it works now.

Oops! Trying to get this symlink to the web directory working has not proved very easy. I managed to destroy my index.html page in the process. I'll try to rebuild it now and see if I lost the last entry.

I thought I would just check to see if entry moods were working. I think they should be, but I have never given them a try, so here goes.

I have been trying to set-up the alpha here to display the pages of this blog, but I've been having difficulty. I am attempting to use a symlink from my user directory into the web directory, rather than copying all the files over. It looks like you should be able to do that from what I have seen on the web, but I have failed thus far. I don't see a big problem with copying everything over to the we directory, but that seems like a waste of space. We'll see.

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!!