AlphaBlog

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??

OK! I got the picture in there about as good as I can. I like the look. I used Gimp to take the raw tif file and convert it to png for the web. The photo is from Xochitl's most excellent film Countdown.

Not my strength as you can see. I'm trying to get this picture into the banner, but I'm having a bit of trouble getting it into the right place. I'll leave it like it is for now; better than nothing. I would like the image to be within the grey banner only. Plus, I need to crop the black frame. Waiting for vegetable risoto to finish.

I changed the last entry's categories to make it correctly under only Alpha. I wasn't clear on how to delete entries from categories. I had to ask for help. Maybe the directions were in the help section, but I didn't notice them. Anyway, this is how you do it:

• nb -l all to get the categories of all entries
• nb -c 1 -l all to get the entry numbers on a per category basis (important for deleting entries from categories)
• nb -c 1 -d 1 will delete the entry number 1 under category 1

This will delete the entry only from that category, not delete it entirely. You must repeat steps two and three for each category that you want to delete the entry from.

On a side note, I'm beginning to like vi more as I play with it.

I didn't realize that what I needed to be looking at was the host name, not the domain name to get the correct domain for the host. I suppose that it really is the host name not the domain name, though the domain name needs to be set correctly for the yp configuration, but I don't think I'm using that at the moment. So, after reading through several more man pages and using the apropos command to find related pages, I came across the hosts file. This still had the computer name, i.e. host name, as my.domain. This is the default when you install the system. I wasn't quick enough during installation to realize that I would need to change this to something more realistic. I hope, now that I have the host name set correctly sendmail will now have the correct host name. Just for good measure, I'll restart sendmail, but I don't think I need to do this, though not sure why. Maybe because my mail server asks who sent the mail, sendmail doesn't tell it that? Not sure. Not much time to work on this now.

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.