According to my Wordpress dashboard, this will be the 100th post here at PA.  I’m fairly pleased with the response that the blog has gotten so far, and I feel like my decision to keep the focus tightly on Open Access was a good one.

I have to admit feeling a bit like I’m both preaching to the choir and shouting into the wind at the same time.  Most of the comments come either from a dedicated core (awesome) or others in the OA movement who I presume are getting pings from Google hits (also great).  At some point though, I’d like to start hooking into that next layer; people who might be interested in doing more things with OA but don’t know how or are unfamiliar with all of the great options.  We can sit here all day and pat one another on the back for a point well made, but it’s the public-facing products and discussions that will really make a difference.  By this I mean the things that you’re already familiar with; sites like OpenWetWare, journals like PLoS, public talks by proponents of OA, etc.

You might say I’m interested in expanding PA’s deliverables.

At the moment I’m sort of investigating some of the projects that are already out there.  To be honest, I do feel like the OA movement is in some ways disjointed, in that there are many projects which are being maintained by small groups and have relatively narrow impact.  This isn’t necessarily bad - this is the sort of “grass roots” community-based enthusiasm that many causes would love to have.  I’m more interested, however, in applying whatever minimal force I can bring to bear in a way that has more widespread effects.  I’m not sure what this is yet, but I’m thinking hard about it.

Once again, thanks for reading.  It still amazes me that one person pecking away at a laptop keyboard can engage in these discussions in a (hopefully) productive way.  I look forward to continuing the conversation with all of you.

I have been trying to post once a day, but I’m actually working on something that’s taking me a bit of time.  I’d rather get something useful before posting it here, so that’s why it may be a bit before I get anything online.

I’m planning on doing sort of a three-part post:

1. Generating a more realistic scene in POV-Ray
2. Rendering (protein) structures in this type of scene
3. A python script combining molscript and POV-Ray for setting up the render

Stay tuned.  I’m hoping that by at least posting the agenda, it will give me enough motivation to actually get it done :)

I recently installed the WP-Cache plugin in order to reduce the server load due to PlausibleAccuracy’s massive (double digit!) traffic.  Because of this, it may take some time for the “Latest Post” and “Latest Comment” feeds on the front page to update.

This was more of a proactive move than a strictly necessary one.  I’d rather have things squared away on the back end just in case.

It was actually a really easy upgrade.  The new backend will take some getting used to.

Off to scour the wordpress codex and figure out how to program a mini latest comments feed for the front page.  I’ll probably edit this post when it’s done (hopefully in short order, unless I run into major problems).

EDIT: I think I’ve gotten a comment feed working on the front page.

Ever since John Wilbanks had emailed me to say that his comment didn’t show up on the site, I’ve been wondering what happened to it.  Today I sifted through the mass of crap in the Akismet filter that comes with Wordpress and found several comments (his as well as a couple from McDawg) that were erroneously getting tagged as spam.

If you have been bitten by the filter, or think your comments are disappearing into the ether, feel free to contact me and I’ll try to get it fixed.  Comments are my favorite part of blogging, and I don’t want anyone to feel slighted.

As long as I’m talking about site news, I should mention that Wordpress 2.5 is out now, and I’ll probably be updating the blog over the weekend.  Hopefully there will be limited interruption, but I’ve done enough upgrades to know better.  As part of the upgrade I plan on adding a “latest comment” feed to the front page, just below the “latest blog post” item that is currently there.

In addition to muttering about how everyone needs a little more ‘net in their lives, I’ll also be doing reviews of interesting papers that I come across in the literature.  I’ve applied to register at BPR3, so these posts should be accompanied by a nice little icon to indicate when the verbage is going to get dense.

I’m working on the first of these posts now.  I’m going to put some time into it, because I’m probably going to submit it as part of a “job interview”.

Even though the design for PA is pretty minimal, that doesn’t mean that it isn’t complicated enough to throw my CSS skills like a colicky bronco.

The latest issue that I (seem to have) squashed is the positioning of the search box in the top right of the page.  Originally I had tried to place the box in the header section, in line with the site logo and name.  I put the search box inside of a span and floated the whole thing right.  When I loaded the page in my browser, however, the box ended up in line with the navigation links.  It was a bit odd, but I thought it actually probably looked better that way so I didn’t fix it immediately.

When I loaded the page in Internet Explorer, the search ended up between the header and the navigation.  It didn’t look very good.  It was time to sort this out.  I started getting a sense of the problem when I moved the HTML code for the search box down into the <div> it was displaying in, the navigation bar.  When I did this, the search box moved below the nav bar.  Ok, so it seems to always shift down for some reason.  Next I removed the float:right line from the relevant CSS, and sure enough it displayed in line with the nav text, but aligned left.  This is where I want it to be, minus the right justification.  After continuing to try to wrestle the float into place, I finally decided that the position property was what I needed.  Applying position:relative to the parent navigation <div> and some absolute positioning to the search span, it seems to be where it is supposed to be.

The HTML snippet:

<div id=”nav”>
<span class=”navlink”><a href=”http://plausibleaccuracy.com/”>Home</a></span>
<span class=”navlink”><a href=”http://www.plausibleaccuracy.com/about/”>About</a></span>
<span class=”navlink”><a href=”http://plausibleaccuracy.com/blog/”>Blog</a></span>
<span class=”navlink”><a href=”http://plausibleaccuracy.com/gallery/”>Gallery</a></span>
<span class=”navlink”><a href=”http://plausibleaccuracy.com/blogroll/”>Blogroll</a></span>
<span class=”navlink”><a href=”mailto:plausible.accuracy@gmail.com”>Contact</a></span>
<span class=”search”><?php include (TEMPLATEPATH . ‘/searchform.php’); ?></span>
</div>

The relevant CSS:
.search {
position: absolute;
right: 0;
top: 0;
padding: 0.5em 0;
}
#nav {
position: relative;
width: 100%;
margin-top: 5px;
border-top: 1px solid black;
border-bottom: 1px solid black;
padding: 0.5em 0;
}

There are instructions for doing this on the web, but for some reason it took me just a bit of tweaking to get them to work in Wordpress 2.3.3.

First create a new page (in my case I called it “Home”) and include the static content. For this site it’s the welcome message you see on the front page.

Next create an empty page (I called it “Blog”)

Now go to Options–>Reading and make it look like this:

Now, http://yoursite.com/ will link to the static page, and http://yoursite.com/blog/ will go to the latest posts.