I’ve been doing a horrible job of jotting things down here when I mean to, so I’m taking a stab at that again. I meant to jot down all my notes on getting GROMACS running with icc, OpenMP, and CUDA on my Mac Pro, but that’s been a few months since I did that now, and it’s drifted out of my head. So. Trying to take a new stab at this when I’m ‘hacking’ things (so to speak)…

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So after a nearly 4 month hiatus from even bothering to look at my coding, I sat down and cleaned up the parsing code I wrote way back when and got some subroutines going for it. Nothing too fancy, but it should discriminate satisfactorily between RIS and BiBTex formatted library exports (based upon file extension). I’ll probably throw in a screener to check the first line or two of the input file just to be on the safe side, but running on extension alone for now should be fine. Click on through for the code!

As I’ve already got the parser and uploader mashed together1, this piece won’t be hard to integrate in. Now it’s just time to write another subroutine or two for the other more common citation library formats, and this script will be ready to rock2!

Added perk: I totally just got my <pre> tags to wrap properly within my frames! Woohoo!
<perma-embed in CSS-file />


1I haven’t put that code up yet, as I got distracted by life in the interim. But, it’s totally functional. Fo’realz!
2Well, on Mac OS X and/or Unix systems at least. I need to verify and/or troubleshoot the script on Windows-based platforms, as I’m unsure how good the uri_escape and File::Spec are at respecting the different operating systems.

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So I’ve toyed around with Plex in the past, but it was in a very limited and limited episode. Using a mouse-free interface was cumbersome and annoying at first. That was a quickly abandoned thought, as I couldn’t really see the implications for using it on my laptop. Since then, I’ve taken a considerably more involved attempt at using Plex, and have thoroughly enjoyed using it since! The rest of this one is a doozy for page length, so you’re going to have to click through to see the rest.

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Have you ever been plagued with a bunch of these errors in your console?

2/8/10 10:51:13 PM osascript[24251] Error loading /Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types: dlopen(/Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types, 262): no suitable image found. Did find:
/Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types: no matching architecture in universal wrapper

iTunes especially likes to choke these out (as my machine did), as shown here:

2/8/10 10:51:13 PM [0x0-0xd4ed4e].com.apple.iTunes[52368] 2010-02-08 22:51:13.952 osascript[24251:607] Error loading /Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types: dlopen(/Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types, 262): no suitable image found. Did find:
2/8/10 10:51:13 PM [0x0-0xd4ed4e].com.apple.iTunes[52368] /Library/ScriptingAdditions/Adobe Unit Types.osax/Contents/MacOS/Adobe Unit Types: no matching architecture in universal wrapper

In order to get rid of these, it’s a relatively easy fix.

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I know I’ve been AWOL a while. Trying to find some motivation to blog again. I’m under the metaphorical weather with stress and haven’t been myself in a while.

However, I was recently pleased to accomplish a successful upgrade (courtesy of some help over at MacForums) of the following into my Mac Pro desktop:

Sapphire ATi HD4870 1GB



It’s upgrading a dated nVidia 8800GT that I received when I purchased the system. I haven’t had the pleasure of really stress testing it yet, but I’m hoping to find some molecular modeling/energy minimization software to experiment with to tax both it and the rest of the system with some thoughts about my protein of interest.

Just recently, I decided to attempt to pick up some manuals and tutorials in order to instruct myself in the ways of Cocoa application construction. Unfortunately, going into this I had no idea how to understand the underlying programming Objective-C in Cocoa. After picking up a text from the local B&N, I’ve found that going through it that it is not all that different syntax-wise from Perl and my really old days of C++ (shoot, about 7-8 years ago I played with teaching myself?). The coding syntax is great…I just need to get my head wrapped around this object-oriented programming so I can visualize this while I code. It’s a bit foreign to me this policy of using classes and objects for modifying data and/or sets of data, but at the same time it all sounds pretty cool.

This endeavor to teach myself how to program for Cocoa stemmed from a problem in the lab that I’m trying to negotiate and remediate. We have a massive collection of bacterial strains frozen down in our -80˚C storage freezers. In order to keep track of everything in there, we obviously have some kind of log/database for this. Over the years, the electronic database that was established has become more and more unkempt due to the flawed design when they set it up. The file was originally setup as a flat-file database in FileMaker, and the searching capabilities of the database/software is horrendous. It’s nigh impossible to find anything in the database unless you enter just the exact piece of text. So, logically, we want to clean this electronic database up to a standard we find fit (everything is recorded by hand as it’s created in a massive binder as a working hardcopy) with adequate amounts of information and good to exceptional searching capabilities (basically searching any string/entry for a piece of text).

Playing around with some other software, and reading up on relational databases, it seems that FileMaker was just an overkill piece of software for what the lab was using it for…a flat-file spreadsheet. It’s a relational database tool, and it was far from being used as such. Granted, I could try to reconstruct a FileMaker database and beat my head against a wall until I found out how to properly integrate a search function into the database, but that just would not be any fun! FileMaker/Apple’s home-entry database software Bento is a really simplistic database tool, using a simple flat-file setup with a bunch of flashy Mac OS X 10.5 features, as it’s Leopard-specific software. The searching in this software is fantastic for how we query it to find our entries, but it lacks so blasted much in what we want the database to eventually do. I’m thinking this will serve as an interim tool for managing our database until option three has made itself ready.

Yes, option three is me trying to write a small Cocoa app that will create, manage and interface with the database. I’m relatively impressed with the Core Data capabilities to date, just in what I’ve seen from Bento and iBank (despite iBank’s sluggish response when its database gets large) and I’d like to utilize it if I could. In addition to all this, I just think it’d be far more fun to write my own application for this kind of thing. I can ultimately add or remove features at will (provided I don’t spontaneously forget how to code it), and it’s free! Well, it’s costing my time, but it’s time I’m wiling to give up for it. I think I’m comfortable enough with the Apple platform that I’d be willing to learn how to write small apps for it to carry on with me over time. It’s just a matter of taking the time to suck it all in, get my head around object-oriented programming, and then learn how to interface it all with a user interface. That last part is what I think may ultimately kill me…I sure hope Xcode has some wimpy simple tool for building and interfacing with a UI setup.

Luck will have it, I’ll get this all finished before I graduate, and then Apple will restructure Cocoa so much that I will not have a clue what I’m doing anymore in it. I’m crossing my fingers that this doesn’t happen!

P.S. I don’t think there’s enough researchers out there willing to write their own applications for tools…at least I never meet enough that aren’t already computationally-focused.

I’m not sure how many of you use Macs, but since I’ve purchased my MacBook Pro I have become a pretty adamant fan of the Mac operating system. One of my few gripes is the choice of web browsers. Safari is the default for Mac OS X. It looks nice, goes well with the OS, but it has a tendency to stall or not tell you when it’s actually done loading a page. Overall, didn’t like it. I went back to FireFox, since I was pretty comfortable with it on the PC. I toyed with a few others while I was familiarizing myself with FireFox again.

Shiira was slick and smooth looking, but I couldn’t figure the damn thing out. Eventually I gave it up, as their support isn’t nearly as forward as some other browsers. I haven’t tried out their latest build, so I can’t vouch for that.

Opera was a pull-over from my older days on the PC when I first enjoyed tabbed browsing. Opera on the Mac really didn’t impress me.

OmniWeb was attempted a couple of times, and none of those times I really enjoyed it that well. It integrates nicely into Mac OS X, shares much of the same looks, but I can’t stand the blah look to it, and it seems to have similar stalling issues like Safari did.

To the present day, I kept Camino around as it was designed to be a Mac-specific rebuilt Mozilla based off of FireFox. I really didn’t care for the limited looks of it, but man it was a speedy loader of pages. I could live without the plugins and the simple look, but the buttons and fonts didn’t look very good.

I read that Camino is going to use a new renderer for fonts called Cairo, designed to make better use of the Mac’s OS features. Regardless, the latest nightly build of Camino appears to incorporate this. My webpage fonts look awesome now. I can’t believe how crisp the text looks now!

I’d encourage any Mac users to give it a try if they’re a fan of FireFox and want to give something a little more Mac-like a try.