Tuesday, March 31, 2009

Two new Mendeley tools! Part 2

The second, and arguably the most awesome tool new to Mendeley is.... Me!
(Tool? Get it? I'm so punny!)

I was waiting for this to be posted on the Mendeley blog before saying anything, but I will be joining the Mendeley team as a Community Liaison. Victor Henning and I came up with the idea when we met for coffee during his US east coast tour. We thought that designing a reference managing program/system should really be driven by the potential users, and that this was almost a full time job in itself. Like most problems, this one could be solved with minions. Or 'Mendions', if you prefer.

What does this mean to you, dear readers?

1) First, yes I will be mentioning cool Mendeley items. And yes, I am a paid consultant, so, depending on how you want to see it, I am a little biased. BUT...

2) I am working with Mendeley because I think the program has significant potential and the folks there have the vision, resources, and talent to do great things. Also, I can't believe that after leaving academia in 2001, I came back in 2005 to find almost no change in the tools for managing information. Seriously, EndNote looks the exact same as when I used it on my Power Mac 9500/120 running System 7. Sad.

3) My job is not to 'sell'. My job is to get feedback from users, librarians, and labs on how to make Mendeley work the way they do. There is a nice feedback and bug reporting system in place, so the Community Liaisons are more the 'big picture' folks and web presence crew. Yes, we'll be 'promoting' the program and web service but, like I said, I'm doing this because I do think it's a great program. So, if you have any insights you can provide, check the feedback system (it's very easy to use) and let me of any other the other CLs know! If you think I'm being unfair or too 'rah-rah', call me on it.

I'm really excited about this, and after dealing with all the papers and other literature I've amassed with my thesis project and DNI, I have a vested interest in helping make Mendeley awesome.

Monday, March 30, 2009

Two new Mendeley tools! Part 1

Today: The awesome tool. Tomorrow: The total tool.

One of my suggestions to Mendeley has been put into action, and it totally rocks. It's a very simple idea: a bookmarklet that you can click when you are in PubMed or IEEEExplore that directly imports the publication into your paper library (they added a number of other sites, like Google Scholar, too). Well, it's a reality, and it totally rocks. Just one word of caution. There is still some wonkiness with DOI vs PMID queries that they are aware of, so just be aware of that. Once that is ironed out, I may switch Super Paper Friday over to be a shared Mendeley library. Here's the info, from the source:
It’s here! The Mendeley browser “bookmarklet” allows you to import documents from websites and academic databases into your Mendeley library with a single click. At the moment, the following sites are supported: ACM Portal, Amazon.com, arXiv.org, CiteSeer, IEEE Xplore, IngentaConnect, Google Book Search, Google Scholar, PubMed, NASA Astrophysics Data System, and ScienceDirect. We’ll be adding support for further sites continuously.

This is how it works: Say you’re on PubMed and you’ve just discovered an interesting paper. Now, all you need to do is click the “Import to Mendeley” bookmark in your browser - Mendeley does the rest: The paper is automatically added to your Mendeley Web library with metadata, abstract and (if available) the PDF. All of this happens in the background, so you don’t have to leave the PubMed page you’re on.

It also works on search results pages, so you can import multiple documents at the same time - a small pop-up allows you to choose which ones.

Friday, March 27, 2009

SPF resuming next week

No sleep makes Brandon l0o0o0o0opy.

EEG consumer BCIs spanked by the Schwartzinator

Forbes has a fun little story on the state of consumer BCIs that hits on the major consumer players, but also throws real BCIs researchers John Wolpaw and Andy Schwartz into the fray. Each echos the officially sanctioned position of their respective scalp electrode versus implanted microwire/fancier probe electrode camp.

I prefer to call this the Head-Computer Interface versus Brain-Computer Interface debate. I try to be even keeled on the subject. EEG is obviously a worthwhile endeavor because there's none of that messy surgery involved, and thus appeals to a very large audience (at least in the near term). Hey, if you get a signal that can be controlled by the user reliably and with an acceptable level of precision, you have something useful. BUT, EEG is a degraded, garbled, sloppy signal prone to nearly limitless interference sources. Anything that can bork an implanted BCI can bork an EEG-based system, but EEG throws the doors open to the world because you are essentially wearing an antenna (or several).

One major problem with EEG is the fallacy that somehow destroyed information can be recovered by some form of fancy filtering. This is simply not so. Think of the electrode as a point of convergence for all electromagnetic signals of a measurable intensity. Even after narrowing frequency bands and implementing funky probabilistic decoders, any squiggle can be the convergence of several squiggles of indeterminable sources. In other words, at a specific time, a signal of amplitude +5 can be two signals of +4 and +1, -2 and +7, or 5 signals of +1-4-2+3+7. And don't even start with harmonics.

The second problem is population size. I know we like to think that motor cortex responds to only movement. It makes life easier. What life? Life in La-La-Land. MI responds to visual stimuli, movement preparation, auditory stimuli, imagined movements, movement related words (heard, internally rehearsed or spoken), reward, attention, cutaneous and proprioceptive feedback, and a bunch of other factors I'm not even mentioning. Until the impact of these influences is understood and quantified, there will not be any BCI that translates the neural activity for "move my arm to point x,y,z". EEG will never have the fidelity to isolate the differences feedback has at the single neuron level, so the nature of the recorded signal will never allow the 'direct' mapping of neural activity to output. That is, the activity that once gave rise to movement can never be harnessed with an acceptable degree of control to recreate the movement. Yes, I am using the word never. Never. There, I said it again.

Like I said, this isn't an attack on EEG, just reality. Different uses for different technologies. I can drive a car on a road. That doesn't mean I can drive a road, or that a road has no use.

Thursday, March 26, 2009

A story about a child named Notepad.exe

Little Notepad.exe was always the quiet type of child; he never complained, talked out of turn, or crashed for that matter. But, he also never played with the other children, instead opting to spend recess inside, content with a single font and word wrap. The other children left Notepad.exe alone, for he was too plain and boring, and while flaunting their fancy ribbons and spell checkers they would giggle about which mail merge feature was better on standard 9x12 manila envelopes.

[insert more blathering literary setup here, maybe a plot, too]

The alien exploded from Notepad.exe's chest, a freakish monstrosity barely reminiscent of the shy creature it inhabited. As the creature's vessel collapsed to the ground with the sickening thud of dead flesh, the patrons at the motorbike and baby stroller emporium froze in horror. Before anyone could scream, the fearsome being, pulsing with raw energy of a million suns, spoke. "I am Notepad++, destroyer of worlds!"

Anyhow, I wanted to point out that Notepad++ is a great alternative to Notepad, and can be used to completely replace Windows's built-in, underpowered app. It has a ton of fancy tools, like code highlighting/collapsing if you are using it as an editor for any number of different languages, all sorts of text manipulation settings, tabbed and side-by-side document viewing, plugin support, and really too many features to even attempt to explain here, so do check it out. Oh and it's free.

Font trivia

Filling out grant stuff, and I thought it would make sense to match the font in Word 2007 to the PDF I'm filling out. So I go to check for Helvetica in Word, and... it isn't there!?!? Hel-friggin-vetica? Okay, okay, maybe a bug or something. Let's see if I can download it... $300!?!?!

Needless to say, this mystery just sucked down about an hour of my time. I briefly explored the seedy underworld of typeface worship, following the twisted lies of stroke terminators and outfoxing the glyphs of despair. All I can say is that I can never look at Ariel again. *shudder*

I did find this ancient, sacred text, though.

Oh, and no, Office 2007 does not have Helvetica, no matter how many movies they make about the damn font. And yes, barring the usual alternatives, you have to pay out the nose for a 52 year old typeface.

Feeds updated (final update on these, I swear!)

I'll update the post below as well, but I have the feeds now finalized, and I'm adding them to the sidebar after this is post is up.

For those of you wondering how I'm categorizing the news items with minimal pain, here's how...

I'm using Google Reader for my usual news reading. To keep from having to type tags, I'm using a free program called AutoHotKey, which is an AMAZING piece of software. Sounds simple, but basically it lets you create simple scripts that can do just about anything. Kinda like Windows meets the bash prompt, but easier to use, low on resources, and a $^$&-ton of really useful scripts out there. In fact, many of the little utility programs that you use right now may have an AHK script equivalent, especially if you got them from Donation Coder. AHK scripts can be compiled into executables, or you can let them run in the background, or you can drop files onto them. Want a script that randomizes your desktop icon placement every 15 seconds? 30 seconds of coding (if you don't know what you're doing).

In this case, I have a simple AHK script that changes Alt+F1 into the "t" keystroke (opens the 'tag' section in GReader), Alt+F2 into "Neuroscience and Bioengineering, ", etc. So, I see something I like, I drop my thumb on the Alt, hit F1, consider the categories it falls into and hit those F-keys, and then Return. My hands don't have to move, except in a few cases (which is why I used Alt+F1 for t, when I could just hit t).

If anything is wonky, please please please let me know.

Wednesday, March 25, 2009

The feeeeeddddssssss must be fed!

He we go...

Starting today, the RSS feed structure will follow the structure from this previous post. Old feed items are not being updated, so for everything before today, starred = BCI, shared = technology. Side bar links updated, too.


TED talks worth noting

Of course almost all TED talks are worth noting, but three are particularly rocking. The first two are by Aimee Mullins. The first is more of a show and tell Q&A session, discussing the various legs she has and the stories behind them. The second is a formal talk with an interesting story about her interactions with children.

The third video, featuring Pattie Maes, discusses what her lab calls a "sixth sense" - a combination camera and projector system and is location and context aware. If you've seen some of the MIT 'cyborg' types before, think of this as the iPod-ization of that concept. Though I don't really consider this a new 'sensory' experience, the demo is pretty amazing.

Monday, March 23, 2009

Back on the attack Wednesday

Alright, Wednesday is going to be 'relaunch day', so stay tuned. No major redesign or anything like that, but hopefully the RSS changes will be implemented.

Saturday, March 14, 2009

Mendeley releases v0.6.3

Run, do not walk, and get the new Mendeley v0.6.3! The file organization features are awesome! Control the folder structure using extracted metadata, add watch folders (open Mendeley - boom! Any papers in this folder are automagically imported), PMID queries for metadata, and a ton more (translation support, integrated Word plug in installer, speed improvements, bug fixes - including that Windows filename bug, and more).

Very cool improvements. More Mendeley news to come, too, but I'm waiting to say exactly what that news might be...

Adding a new feed (or 20)!

So, if you have followed/subscribed to the RSS feeds, you know that they are updated several times/day (yes, I am actually doing that manually, and yes, I do read what I mark, except papers, though I read all abstracts). You probably also noticed that I mark a decent amount of stuff related to data analysis junkie related items under the BCI feed, including hard drive tech, CPU updates, and general organization/efficiency stories.

To better serve my dear, dear readers and and reduce the chance of myself developing a schizotypic disorder when trying to find material, I am going to restructure the whole feed setup sometime within the next week.

Site feed:
If you just let your browser or reader autodetect feeds, this is what you get. It is only stories I actually write. If that's all you want, then cool beans. But, there is much, much more available through the below feeds!

Starred items:
Broader implications, greater importance across 2+ fields or specifically to my research/lab/general situation/jobs/etc. This will include some papers, but not all, some tech, but not much (and no more multiple tagging of the same stories on different sites when one happens to add a small detail I find interesting - those will go in my private feeds). I'm hoping this will be a lower volume feed with greater signal-to-noise. High blog topic correlation with low variance is the aim.

Shared items:
My posts and strictly BCI related news items. Other blogs can add Blogger feeds as drop in items, and in general, the 'Shared' designation is meant to be the most topical to the readers. Now it should be. This will include NO papers, only media coverage of BCIs, NISs, BMIs, prosthetics, neural implants, some EEG/EOG/ECoG/MRI, and robotics/material science/neuroethics/neuroinformatics. Tech items will be limited to major, and only major items, like significant architecture changes, wireless transfer, CCD/CMOS advances, and new power/battery tech.

Tag: Neuroscience and Bioengineering
These items are specifically neuroscience related, and will include all papers. Papers will be purged each week in the Super Paper Friday post, leaving only media articles referencing them.

Tag: Science Policy and Perspectives
Political, social and generally interesting science bits. A paper might slip in here or there, but not many.

Tag: Video and Audio
I love the io9 sci-fi site, but they tend to post 20 YouTube clips in a single story, which brings most browsers to a crawl. This feed will contain only video and audio items. This way YOU can enable a script blocker or Flash blocker to read stories as usual, and then quickly scroll through these items. Since there aren't many, maybe 5 per week, you should be able to find stuff fast as long as you don't wait 3 months to look for it.

Tag: Organization and Efficiency
This will be the most 'eclectic' feed, covering data organization (physical and virtual), working space design, neat-o desks, software (like Mendeley and Firefox), notetaking, and other random bits to make life easier.

Tag: Technology
All the techy goodness that I find rockin'.

Tag: Education
Items related to education/PhD life/books/notetaking/etc.

Other feeds and tags may follow, but I think this covers the bulk of the material on the site.

Tuesday, March 3, 2009

Allllllmost back

Basically waiting for my prelim to be completed before getting back to DNI. I have a tentative date, which is very soon, so once that is packed away things here should normalize.

Don't forget about the RSS feeds. They are still updated daily with nuggets of neuro-robot-computer goodness!