AlphaBlog

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!!

So I ranted about my mentor instead of discussing the K grant preamble. Sorry.

What I wanted to discuss is that I had to add a package called parcolumns, which requires processkv.sty as well. The instructions for parcolumns doesn't say that, but if you read the style file it does. Plus, attempting to compile without it throws an error (but only 1/4 times?). Anyway, added it to get a small section to have multiple columns. I thought this was built into LaTeX, but apparently it isn't. I really appreciated it with beamer.cls. You certainly do need it for slides. Anyway, works great, except I still am not able to get pdfsync to work correctly. Perhaps it is the nih2.cls causing the problem, I don't know and certaily don't have time to figure it out right now. Installed twiki on the alpha. Don't have time to configure it just yet. Will have to wait another 13 days. Back to work!

I was able to completely outline a set of objectives last night. I've really had only bits of ideas thrown at me for this grant. When, not if, it finally gets funded, I'll be very happy and proud of myself. My primary mentor's idea was bioinformatics, which I went with from the beginning. This is an area I would really enjoy certainly, working with computers to give you the information that you want. I planned large chunks of my CDP around this theme. However, after meeting with my 'sub-mentor', he reinforced that looking into the clinical aspects may be more rewarding for me. After all, I am a clinician. I think that is a fair assessment and can build upon my strengths. He brought this home by reminding me that publishing another microsatellite paper on falciparum would not really get my name out there like a clinical paper on what we are going to be doing would. Hey, I always wanted to do clinical tropical medicine, but never imagined there was any market for that outside of the military. Perhaps there is. I may even be able to go back to my original plan, many years ago, of evaluating strain differences in virulence. Granted that wasn't with falciparum, but still the same idea. Now it is all tied into these challenge trials and will not likely include any overseas work. That I had to come to terms with due to the financial situation of our group.

Our group. Our fearless leader has not been very encouraging after our initial meeting. I was supposed to call him in Malawi yesterday, but couldn't. So, I wrote more last night, came up with the objectives and sent him a draft version of the entire grant. This morning, he had written telling me that I needn't call him. Turns out, he was just wanting to tell me to ditch the idea of submitting the grant until June! Jesus! I have to have something of my own. Even if it doesn't get funding straight off, and it would only be because of our sour financial situation, which is completely beyond my control, it can be reviewed again in October. If I wait until June, the financial situation is unlikely to be improved and a resubmission couldn't be addressed until February! Too close for comfort. Because at best I'll only have a year of funding starting this June. And that depends upon a certain amount of luck anyway. In the end, he was sufficiently impressed with what I sent him last night to back off and say he would support me. I suspect that part of his hesitancy was that he is writing an R01 now due the same time as my grant, and he didn't want to spend much time helping me. Well, he doesn't need to. I'll do it myself. That way, when I get funded, it will be all me. I will submit a small R grant this year as well, try for the June deadline. This will have to have his name on it, how unfortunate.

I have the format for the K grant down pretty well now. I have the following included in my LaTeX preamble. The nih2.cls if from the sidebar link of LaTeX for NIH Grants, the newer style.

\documentclass[kk,11pt]{nih2} \usepackage[title]{appendix} \usepackage{varioref}% nice with \autoref{label}, use \vpageref[]{label} \usepackage[super,sort&compress]{natbib} \usepackage[smaller]{acronym} \usepackage{hyperref} \usepackage[defblank,neverdecrease]{paralist} \usepackage{hanging} \usepackage{ctable} % \usepackage{pdfsync} \piname{Gregson, Aric L.}

% %%%%%%% 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}}

% %%%%%%%%%% 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}}

\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}{x-irradiated sporozoites} \newcommand{\XS}{X-irradiated sporozoites} \newcommand{\x}{x-irradiated sporozoite} \newcommand{\X}{X-irradiated sporozoite} \newcommand{\TC}{T-cell}

Actually, I didn't end up modifying it that much. I have used many extra packages to make my life simplier. The paralist with is compact forms of listing environment is a life-saver. I don't think I could have done it without that, because of the page requirements. Anyway, better get back to writing something on it! Only 13 days left!!!!! PANIC!!!!

Searching the web again tonight for online references. I find it annoying that you cannot access many journals without a subscription, even ten years after publication. What is the point of publication if people can't actually read the article! I really appreciate the idea that PLoS has developed. Everyone has access to the journal from the get-go! Hey, there we go, aren't we supposed to be spreading this information around for everyone's benefit? Turns out that this is not really the case. Most publishing is done to benefit only the publishing house. Fees continue to increase, while access remains ridiculously limited.

Another annoyance this evening has been the horrible web interface designs of many of these on-line journal access sites. You have to wade through lots of loaded garbage, often requiring loading more than one page to get to the article. Now, in Safari that sucks, because it is so damn slow. I am not able to use Camino, because it doesn't play correclty with the UCLA proxy server, which by the way I will be losing soon as Xochitl is officially graduating from UCLA soon. Then I will be stuck with the vastly inferior, hardly worth having UMB version. Boy, talk about a shitty library. Well, I wouldn't mind living in the building, it is very nice, but they can't afford to fill the library with any current journals relevant to my research. Even Hopkins sucks compared to UCLA. The UMB library insists that their proxy only works with Netscape on the Mac. I'll have to look into that as soon as the UCLA proxy expires. I seriously doubt their claim. Who uses Netscape on the Mac anymore??

Still not working. The I've set domainname to a correct and valid domain name. That name however, is being forwarded to one of the Mac domains at the moment. When I restarted Apache, it gave me a complaint about an invalid domain name. The domain name has stuck, as evidenced by running domainname. Maybe this will clear up when I use this as the main server for the web sites, not sure yet. Also, I have not been able to get Sendmail to believe it is from xochitlfilms.org. I still get the errors in my received mail that the sender has an invalid domain name. I finally figured out how to restart Sendmail (pathetic, yes I know). OpenBSD FAQ had kill -HUP 'head -1 /var/xx/sendmail.pid', which just didn't work. Running kill -HUP pid worked just fine. We'll see what is up with the domain name and sendmail later today.

The MoinMoin wiki has not made me very happy. It is not as straightforward as I thought it would be to set-up. For instance, I have not been able to change the theme and the editing box in web browsers is unacceptably small. I'll give twiki a try on this computer. The Vanderbilt site uses it and I like their site, plus it's in the ports. I don't have time to play with it now, since I'm being a good boy and working on my K grant rather than playing with the computer (much anyway).

Trying to get the K grant to look different (somewhat) and nice with Latex. I started with the template from this site, using the newer nih class file. Using ctable, paralist, hanging styles, I've got a nice looking Biosketch template, though I need to get paralist to bring in the wrapped lines further and haven't yet messed with that. I also need to get \autoref to capitalize the word 'section' and refer to sections in the appendix as 'Appendix A' instead of 'section A'. These things can wait, because more importantly I need to get something substantial written down by the end of this week. A great package called acronym, part of the default install on the Mac is invaluable when writing something containing so many acronyms. Much easier than trying to guess where the first occurrence of an acronym is located. The only problem I have found, is that when defining an acronym with a short name, \acro{DEPM}[Department of Epidemiology]{fullname}, I can only get the package to place the short name in text, not the acronym.

Anyway, lots of good dinners, relaxing over wine and movies and getting up late to write.

Post-call today after a longer than normal shift. After the dog walk I was too tired to do any real work. I've been looking into using Emacs for more, since if I can integrate more work into one application, it would be much easier. But neither emacs nor vim are particularly straightforward to use, so I have hesitated several times before on further exploration. Last night, during some down time, but not enough to sleep, I searched out more info on using Vi. I think it is manageable, at least when OBSD drops me into it by mistake I can maybe edit the file and easily quit now.

I started a simple emacs wiki on the powerbook in an effort to keep track of projects and how much time I spend on each project. I worked way too much these last few months, but I didn't do a good job of tracking how much time on each project. At this point it seems wise to do so---I have to prove my time spent on projects and need to estimate how much percent effort goes into each project. The problem I am having with emacs wiki is that each time I tell it to update the pages, it creates another page with the same name, but a further .html in the file name. Not sure why. The documentation for emacs is better than Vi, though I'm having trouble with this particular point. I've found MoinMoinWiki and it looks very happy. I may give this a try very soon to compare to emacs wiki.

Need to try the NB upgrade soon. Not brave enough just yet.

I can't believe it! I feel like I have been trapped inside the auto-formatting 'feature' of MSWord for the last hour! I must be tired. I forgot that there is a substitution error in electric menu of AlphaX on the G4, which turns \frame{ into {\frame. This caused me serious wasted time and annoyance for the last hour. I even compared to an old document and didn't notice. Damn! Plus, the dogs pissed in the house again, after an hour and a half walk! I was mad. I'm sure that didn't help with figuring this out either.