Visual Studio and other Microsoft programming tools free

For students, that is. Nevertheless, it does include the brand-spanking new Visual Studio 2010 Pro, which, if your university has annoying IT/software access policies like Brown, can mean less frustration for you. So far I've procured 3 copies of Windows 7 Pro x64, Visual Studio 2008/2010, and Expression Studio 3 for $30 (cost of a student IEEE membership). And there's still plenty more stuff available to play with should I suddenly become inspired.

The weird thing is that Brown University has an MSDNAA agreement (the MSDN Academic Alliance program, which allows schools to provide free and deeply discounted MS software to students). In fact, we have 4+ agreements! Check if your school has a sane policy in place. Here, I'm a grad student in the Dept of Neuroscience, working in a lab that's part of the Engineering Dept. Somehow, I qualify for almost nothing, as far as these MSDNAA memberships go. Oh, wait. I can get a free copy of Windows XP! Woo! The school pays me, through grants to the lab, but I don't qualify as an employee or staff member. Fair enough. But I don't qualify for the CS Dept or Engineering Dept programs because I'm not taking any classes in the departments. I could TA, but even then I'm not technically enrolled. I've fired off a few hot-headed emails, but the responses have been the usual Brown hand-waving/"Wait until we start the Program"/"We're talking with people about that" types. It was easier for me to sign up for the IEEE and hunt down offers like this, rather than deal with my own school, which still gets paid $45k/year for tuition. Amazing.

Aaaanyhow, get yer software at the Microsoft DreamSpark site.

If you're not a student, there are 'Express' versions of many Visual Studio tools available for free. These lack MSDN Library access, which is a great thing to have, as well as 64-bit compilers and some of the more powerful tools, but they're free, legit, and lack alot of the bloat you would usually just throw into a new install. (Am I going to be using SQL Remote Doppleganger USB Ninja FlipFlap elements? I dunno. Meh, just install all of it.) Get them here.

Another school year begins

Ah, the wafting aromatic waves of beer and cardboard boxes could only mean one thing: the kids are back in town. Here are a few minor updates on my end of things (major for me, minor for readers, I suppose)...

Mendeley sadness
My schedule has become too packed and unpredictable to keep up with the Mendeley work, so I decided to leave my Community Liaison job (on good terms). I kept thinking, "As soon as I get over this next time crunch, I'll be ready to really give Mendeley the attention it deserves." But, those crunches just kept coming and I don't see them becoming any less crunchy in the near term. The folks there are great, the product is great, and I really wish I had the time to work on it more. I expect really big things out of that group, and will continue to sing their praises. Okay, maybe not sing. Limericks? Nah. Too many syllables in all the keywords ("There once was a bibliographic... shit, ran out of syllables already").

My Project/Thesis/Thing
I've begun running some of the experiments that I've taken lead on (I don't want to say they're 'my' projects because so much feedback has gone into the process that, like all good experiments, I don't think one person deserves all the credit). I would go into more detail, but you know how it is in research and especially FDA/clinical trial situations. Still, these are 'mah babies' and so far things are looking really good. Now to get to the data! Big thanks to Jessica (my 'med school minion') for putting up with my odd schedule and all the great work. Hrm, I could use another DNI contributor or two...

On the topic of putting together kick-ass experiments, I've been meaning to post that there is a whole field out there that many scientists are completely unaware of called "User Experience", or UX. UX is kinda an amalgamation of user interface, HCI, psychology, feedback, and design that looks at how all those fields converge into the subjective experience of the user. Fascinating stuff, though more on the 'web design' end of the spectrum, and I've been really loving the bits and pieces I've been coming across. This field is set to explode with the continually expanding emphasis being put on web apps, mobile apps, and even OSes in general. Which brings me to another nice tidbit of knowledge.

2 copies of Windows 7 for $30 (for students)

Yeah, right! No, really! Thinking of getting a new PC, but wanna wait for Windows 7? Don't want to reinstall your system halfway through the semester just play with all the fun new built in toys? (Shuddup Mac people. some of us prefer a different flavor of Kool Aid.) Well, you'll love this.

Join IEEE as a student for $30 (1-year membership), and get access to their MSDNAA software library for free. This includes the Windows 7 RTM version. RTM? That sounds like a beta. Nope, RTM stands for 'Release to Manufacturer'. Buy a PC on Oct 23, and this is same version of Windows 7 that will be shipping on it. Not beta, not RC. I've gone through this process, and it works as advertised. Buy the membership, wait about 7 days for the MSDNAA specific email to show up with your login and password (mine took about half that long, maybe because I used my university email address), and go get em, tiger.

Only the Business versions (32 and 64-bit) is up as of this posting (don't waste your time with the RC, and Ultimate isn't much better than Business, unless you need the language packs, which I think can be purchased separately). Supposedly, the 'in place' upgrading has undergone some major upgrades, and Vista users may not even need to do a clean install, though I always recommend it. Mine installed fine - took about 30 minutes and activated without issue.

Here are the linkies:
Source of the info: SlickDeals
IEEE description: here

Data Visualization
I plan to add more on this in the future, but an interesting (free) iPhone app to check out is Roambi, which basically allows you to upload 'data' to their site, and then spit is back in some really visually pleasing, interactive displays on the iPhone.
Try the app's built in demos for a better idea.

While I was gone...

Here are a few stories worth noting from the last few weeks along with some random ramblings.

Now you see it, now you don't (remember)!
First, I'm watching a really interesting piece from 60 minutes on how flawed eyewitness testimony can be. What's most interesting is the way that psychologists can alter the report of an eyewitness in a predictable manner. To sum up one technique, present two faces that are similar to the perpetrator, present the previously chosen face and another that is very different, present the reaffirmed face and the perpetrator. These little psychological tricks provide important clues to the inner workings of memory and an important bridge between experimental and applied psychology. Whether they will be equally useful for neuroscience, we'll have to wait and see. Think of these types of stories as similar to the barrage of visual illusions you would see in an intro to neuroscience course (like these). Part 1 sets up the case, Part 2 is where it gets interesting (those pressed for time can skip to part 2).

Eat it ASIMO!
Toyota has been trumpeting the creation of a noninvasive BCI (EEG) for controlling a wheelchair. Basically, it sounds like a 3 state decoder (forward, left, right), with an emergency stop signal (the user puffs out their cheek). Usually this isn't too exciting (like that Honda media circus the previous month), but the 125ms lag is actually pretty good for EEG. Worth looking into more for those even slightly interested in EEG based systems.

Mendeley-he-hoo!
v0.9 (and now v0.9.1 which fixes a problem with PDF linking), is now available. PDF reader with annotation tools, more control over syncing collections, and a bunch of other features. Go get em, tiger!

Slow goin' and syncing madness

Just a quick note (again) that things over here are changing, which always puts the strain on DNI. Right now my big issue is that all my email is being aggregated by GMail with another account, so I have to log in and out to get to my rss feeds and DNI mail. Plus, a little side project knocked out this weekend + the beginning of the week. Sooooo... sorry about the lag. Also, this Wednesday through next Wednesday will be a brief break, since I'll be preparing and presenting my prelim. Just giving fair warning.

I'm thinking of moving to Thunderbird 3 on a USB key for email, then Neuvasync for iPhone contact/calendar syncing. I'd have a TrueCrypt encrypted file to contain it all. The big problem is that TB, and all email clients for that matter, can only move messages to a single folder, which is picked up by GMail as a tag. In GMail you can have multiple tags, and I would like to be able to move seamlessly between TB and GMail. Poopy. Someone needs to make a GMail tagging add-on for TB. Anyhoo....

Also, if you have a LinkedIn account, there is a BCI group that you might find worth checking out.

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.

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.

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.

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.

http://blag.sebacean.net/wp-content/uploads/2008/07/trucknomnom.jpg

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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.

Categories:

• Starred


• Shared


• Neuroscience and Bioengineering


• Interface and HCI


• Technology


• Science Policy and Perspectives


• Education


• Organization and Efficiency


• Fun and Misc


• Video and Audio
  

A tool and a shout out

First, since Google has released Mobile Sync for iPhones and WinMo devices, I thought I would point out that there are still some annoying bugs. I'm probably going to try out Nuevasync instead, which is more mature (still free, but doesn't do undesirable things like remove pics from contacts, etc.) Thought I would let people know about the option...

And thanks to the interviewing students this past week for a fun time (especially the parts I remember from Friday night). I don't usually say this, but it was a great group, so hopefully we'll see a bunch of you back here in August/September. And hey, it only took 3 Roomba runs and 2 wet Swiffer passes to clean the place, and nothing important was destroyed, meaning the night was a win from my perspective.

Couple quickies

Two things before I return to lurk mode:

1) Stimulus bill looks to be losing science funding, rural broadband, and a bunch of other provisions for schools. The NIH escaped unscathed, but the NSF and NASA got the chop, big time. More details here here here here here.

2) Tech item. I'm getting back into using Miro again (link to the v2 RC3), and thought I would mention it. Miro is a cross platform video and audio rss feed aggregator without the need to really understand anything about rss. Basically, you can browse their catalog of shows, subscribe to any of them (all free), and add websites, making Miro a nice all-in-one video program. I like to keep my video and audio separate, so audio podcasts go with iTunes, vidcasts go with Miro, and the world is at peace. I don't have a dedicated video library program (thinking about using VLC for that).

Quick Notes

My desktop PC is borked right now, so updates may actually be more often in the short term. I tend to post from my laptop more for a couple reasons. Looks like I installed, uninstalled, reinstalled, upgraded, downgraded, and ratcheted things until Vista decided I should be punished by inexplicable freezes. In fairness, I have installed a couple hundred different programs, 2-3 dozen devices for product reviews (man, must have been about 8 keyboards alone!), AND the whole thing is an original, launch day install of Vista on an NVidia mobo 1st gen Intel SLI version with two different generation NVidia GPUs (NVidia's crappy-slow response to Vista's driver changes accounted for almost 1/3 of all crashes, according to the crash reports sent to MS). I'm amazed it lasted this long. There's one more thing I might try, but it is looking like a reinstall is needed, and that ain't happening.

So, second note, related to the first. The Intel Core i7 CPUs and chipset are out, and expensive. There is no upgrading from the previous generation - CPUs have different pins and some (I think all as of right now) motherboards support only DDR3. Important to note: If you are planning on buying/upgrading anytime soon, be aware that there is another major socket introduction in ~6 months. By socket, I mean the physical shape and number of pins that mount the CPU to the motherboard. These, too, will neither be compatible with the current (now 'old') crop, NOR the current i7 boards. The current i7 is Socket1366. The upcoming is something like Socket1066. The two i7 sockets will exist at the same time, with the 1366 marketed at enthusiasts and workstations (read: awesome pwnage machines), and the 1066 aimed at consumer and general use machines (read: nublet, whiney l00sorZ). Both will be major upgrades from the current architecture (Socket775). The 1366 has an on dye memory controller, similar to AMD's Hypertransport, meaning massively fast communication between CPU and memory, and no dealing with the rest of the device bus. I believe the 1066 has the memory controller on the mobo, but still dedicated to CPU-RAM communication only. Basically, on dye means faster performance, more upgradable, more transistors on the CPU wafers, and more complexity to manufacture, hence the two lines. So, if you want a blazing fast computer but heard that there is a new upgrade coming out in 6 months, unless you want to wait for the price drops (and that is a legit concern, since mobos are running AT LEAST $200, and the top of the line CPU is $1500 alone), the current 1366 i7 is the way to go. The mainstream 1066 will still be very fast, still outpacing the current architecture (775 that is), so don't think of this as a "Pentium versus Celeron" situation at all. It is more along the lines of the Xeon versus Pentium (not really, but you get the idea). I'll be upgrading to it within the next month, and no, I'm not aiming at the $1500 CPU, thank you very much, but I will post my experience. Maybe a few build pics to go along with it?

Next, as I said, Mendeley is on top of things, and they snuck out an update - 0.6.1 - which resolves the file renaming issue and a couple other bugs. I'd bet that the syncing has been addressed as well, but haven't tried that feature. The site doesn't list it prominently, so just download the installer that is listed in the usual download section. Oh, and the metadata extraction is at least 100x's faster than the 0.5.X versions. Nearly instantaneous. And I didn't notice before, but now you can query the DOI identifiers for metadata that is incorrectly identified. Again, haven't tried it yet, but there seems to be some type of new online check that runs after the metadata extraction that cleans up a ton of minor errors and inconsistencies. I dropped 40 papers in and it failed to extract data from 2, and had slightly messy recognition for 2. The others were perfect. Also, more accurate metadata means less chance of renaming files to ridiculous lengths, though it doesn't look like there is a check in there yet (still gives the fill title name).

Aaaaand... today's SPF will be the last for the year, probably.


Aaaaand... I will be in Iceland for the New Year's celebration, and giving a talk. Details will be posted as I get them. Probably at a nice bar, with drinks to follow. General audience. Come help the Icelandic krona rebound!

Aaaaaaaaand... oh! Almost forgot. Another computer bit. If you want to try a really spiffy music program with all the slickness of iTunes, plus the add-on capabilities of Firefox, and the responsiveness and limited resource use of Notepad (okay, lil more memory, but still great), definitely check our Songbird. This open source, Firefox code based, cross platform, iPod supporting, iTunes library syncing bundle of awesome is, um, awesome! After using iTunes for so long, I forgot what it was like to open my music program in 2 seconds and have buttons click as I click the mouse, rather than 5-10 seconds afterwards (Apple software on Windows machines sucks goat nads). And, it doesn't need 3 different background processes loaded into memory when not in use, oh, AND you don't have to download a crappy video player *coughQuicktimecough*, oh, and it integrates with a bunch of major music services, like Last.fm. No, there is no iTunes store, so iPhone users are stuck there. When my desktop gets working again, I will try syncing my iPhone's music to see if the only issues are app installing and Outlook syncing. I'd expect Outlook syncing to come in the form of an add on sometime within the next 4 months, or so. Anyhow, very excited about this app, as you can tell. I tried it in early beta and was less than impressed, but it has really matured.

Publishing beyond the scientific paper realm

I talked with John D yesterday for a bit about publishing, online resources, and the general structure of the scientific literature world, which was interesting since we come from different backgrounds and generations. He emphasized the importance of the different 'levels' of journals, for instance, that Nature Neuroscience papers are generally better than EBR, etc. I think that can be something that gets wrapped in or emerges from an online community (ala Digg, Reddit, etc.).

Well, fresh off my rss of doom (you should have seen the librarians faces when I said, "Yeah, 900 unread items right now. I'll get through that in about 30-45 minutes." Google Brain FTW), is this bit from The Urban Elitist (via Polymeme) on good ole book publishing, which I often forget about. In the wake of the Kindle's success and Google's agreements with universities and now magazines, the author asks how they will remain a viable business.

Books are significantly different from papers in many, many ways, but they share some similar problems. We still have another 30-50 years before a truly paperless society is possible, and current media have a much shorter lifespan that good ole paper and clay tablets (a topic for another day, but I would not be surprised to see a major project get funded for looking into storage devices that last 10's of thousands of years). Books are unidirectional and stylized, while research papers are really made to be discussed. But, books aren't the TV to primary lit's video games because they, too require active participation, and focused attention.

Anyhow, something worth a few minutes of meditating on.

Oh, and SPF is still coming today...

Online and software options

I met with the university e-resources people yesterday for a couple hours to go over some of the lesser known, start-up type services and programs out there. Below is an excerpt from a follow up email.

For software products, W=Windows, M=Mac, L=Linux.

http://www.mendeley.com/ (WML) (My favorite :) )
http://www.labmeeting.com/signin (Also has a Firefox plugin.)
http://laboratree.org/pages/home
http://ologeez.stanford.edu/
http://jabref.sourceforge.net/index.php (Used by engineering students)
http://www.pubmedreader.com/
http://pubget.com/search (Nice for browsing a journal at a time, but duplicates much of what PubMed does already - email alerts, saved searches, etc. Does allow tagging individual articles and filtering by tags.)
http://www.connotea.org/ (Also has a Firefox plugin, requires disabling Firefox plug in security checks)
http://www.easybib.com/ Bibliography maker
http://www.scribd.com/ Didn't mention, but worth noting. Online, unlimited storage of documents (doc, pdf, txt, ppt, xls + a few more). Can be public or faux-private (the url to the doc can be shared, it just doesn't show up in searches by site visitors or Google).
http://www.nextbio.com/b/home/home.nb Another option I forgot to mention. Has a nice iPhone app that pulls down full text of articles. More about searching through databases and raw results from published datamines.

Few of the old standards:
http://www.citeulike.org
https://www.refworks.com

General web services to note:
http://www.getdropbox.com/ (WML)
Public and private documents. Desktop client syncs indicated folders automatically. Direct link for each file, which can also be accessed from the desktop app side without internet connectivity.
http://www.mediafire.com/about.php?type=1
Unlimited media-only storage. Links to website, where the file link resides (forces other people to visit their site to download, but they don't have to sign up. Can be removed by purchasing a pro account). Provides embedding code for websites.
https://www.mesh.com (WM)
I didn't mention this specifically, but it is part of the Microsoft online universe, and they have done a great job with it. Integrates with the other Live services, which is MS's big push towards cloud computing. Mesh allows the creation of a 'webtop' (web based desktop in the browser) where files can reside. Files can be synced to any computer with the Mesh client installed. The Mesh client also allows the user to log on remotely to any PC in their 'Mesh' that is online and use it as if they were sitting in front of it. Supports Mac, works in Firefox, allows sharing and syncing between any computer (so Mac -> PC and PC -> Mac). Comes with 25GB of remote storage. Mesh is the center around which MS is building their web based applications, so expect it to be everywhere eventually. It is also from their new research division, which actually makes good, interesting, and creative software, and not at all similar to the 'old Microsoft'.
https://www.foldershare.com/ (WM)
Part of the MS Live universe. Automatically syncs folders between computers directly (no Mesh desktop syncing) More online storage options broken down here:
http://lifehacker.com/5064688/online-storage-feature+by+feature-comparison-chart

http://www.evernote.com (WM +iPhone +WinMobile +FF Plugin)
Simple but powerful note taking app. Built in OCR, tagging, syncing between all PCs, free for 40MB, premium account allows 500MB. Allows txt, voice, and picture notes, along with web clippings and files.
http://www.zoho.com/
Before Google Docs, there was Zoho. They are considered neck-and-neck with Google Docs, but Google Docs has the luxury of being integrated with Gmail and all the other widely adopted Google services.
http://feedrinse.com/
I didn't get to talk about this one, but this service filters RSS feeds, repackages them, and then sends them off as a new feed.

RSS in general
Plenty of clients people can download, plenty of web based clients (Google Reader is still ranked as one of the best, and what I use). Open standard, and far more ubiquitous than thought by almost anyone I've talked to in the sciences. Implementing RSS for university services would not be enough - there would have to be a serious push to make faculty and students aware of it.

Software only products:
Bookends: http://www.sonnysoftware.com/ (M)
Papers: http://mekentosj.com/papers/ (M)
IdeaMason: http://www.ideamason.com/default.htm (W) (More of a brainstorming, organization program.)

Mendeley news items

First, I've been messing with the latest Mendeley release, and the performance/speed issues are much improved. Unfortunately, there are several new nasty bugs, which the company is aware of and working on. These problems stem from the complete rewrite of the code that finished just prior to public release (more on this later), so I'd expect them to be in working order very soon (I assume version 0.6.1 will be at the bug-free level of v 0.5.9). The most significant issue is the inability to sync libraries to the server, which will be addressed first. Auto-renaming on Windows (at least) is broken as well, which isn't really a bad thing, since a previous bug could cause trouble for less savvy Windows users - see my post about the file name length issue.

Now, the good/big news is that I got to meet with Victor Henning, one of the two co-founders of Mendeley. Awesome guy, and we ended up talking for about 4 hours about various topics, from research to Mendeley business.

On the topic of the bugs in 0.6.0, Victor mentioned that there were several setbacks in the schedule due to all the non-coding workings which took time from the bug squashing. They promised the new version by the end of November and wanted to deliver on it, which they did, but needed about 2 weeks to work out the new code's kinks. There were some other things, but overall they needed this version out when it was released and getting everything up to the functionality of 0.5.9 is priority #1, and should be a matter of weeks. What's reassuring is that it isn't a case of not knowing what is wrong, or the problems being unexpected. They're on top of it all. Figuring out how to optimize the code and make things run smoother is MUCH more difficult from a coding perspective, so the fact they they addressed that so impressively means the smaller bugs should be cake.

The vision of the program and service, and some of the collaborations (sorry, all hush hush, but the details are very sweet), make me truly excited about the future of the project. The next post will cover some of the similar, but either more unstable or less usable options, and none of them hold a candle to where Mendeley will be in a year, or so. Victor and company are very interested in keeping the system features responsive to users' needs, and the push is far more towards openness and adoption than hoarding and proprietary knowledge. So, I had high expectations and they were all met or exceeded by what I heard.

Oh, and Victor was toting a few interesting books, which I need to look into: Quantum Enigma, Physics Encouters Consciousness by Rosenblum and Kuttner and The Quest for Consciousness by Koch

As a slightly random aside...

One question, of course, is why not go open source? From my perspective (my thoughts only), this is a big project that requires full time resources. Firefox, Linux, and a few other projects are always pointed to as if they are the norm, but there are 10's of thousands of projects that are crap, dead, or updated at a glacial pace, and those are the real norm. We did talk about how a project this size requires investment from outside sources to get off the ground, and those sources are rarely OSS friendly (not unreasonable, especially in the current economic climate). This flies in the face of the official OSSI standing, so you end up in a situation where you are controlled entirely by outside interests. IMO, the OSSI is remarkably close minded for being about 'openness', and abiding by their requirements seems unreasonable.

Get it while it's hot!

New version of Mendeley is out (0.6.0) - a big rewrite for the folks there - so go grab it. MUCH snappier, much more refined, nicer looking, easier to use, etc. Overall, a very nice improvement. Word of caution - I haven't had a chance to confirm that my database corrupting bug has been squashed, and the file renaming can still cause the issue I posted about earlier (easy enough to remedy). I'll probably try for a full migration later this week.

Speaking of Mendeley, I'll be meeting with one of the creators this weekend, which should be fun. I'm also meeting next Monday with the university task force for enhancing Brown's electronic resources, so hopefully I will learn about some bits and pieces that slipped by my radar. I'll be preparing a rundown of all the various options out there, so once that is compiled, I will post it here.

Sorry about the lack of updates - duty calls...

SPF format follow-up

I've heard back from a few people, and I think the new format works much better than the previous ones. I am posting the EndNote libraries (ENL files, not papers) to my DropBox account, which seems to work well - just a quick right click for me and no accounts needed for everyone else. If you don't have a drop box account, no need to get one, but it does rock. Personally, I like Microsoft's Live Mesh more, but there's no option to share with people outside the service (now with Mac and Linux Clients).

One person posted that fewer items with a brief rundown would be helpful. The only reason for the long list this tome was that it was the first SPF in over a month, so wading through the papers should be easier when I am good about posting weekly. As for abstracts, there are two options:

1) The links are to the PubMed entry, usually, which means that you can find the papers that look interesting from the titles and stack up a bunch of tabs in the background (hold down control in FF or IE when clicking the link, and if it opens as the active tab, check your preferences). So, the easiest thing to do is just control-click down the list when something piques your interest and load up a bunch of tabs. Do a quick perusal of the abstracts and close the tabs for those that don't interest you.
2) Alternatively, use the EndNote file, which has the abstract included (usually).

I'll try to single out a top 5 or 10 and post them at the top with a brief 1-3 sentences, but they are going to be the ones that I like, meaning they might not mesh with your interests (particularly, there will probably be few EEG/ECoG papers). I do read all the abstracts for these, and they all hit on something worthwhile or of personal interest, so it isn't like I just dump my feeds into the list. The 30 or so weekly papers are chosen out of around 500-1000 that make it to my aggregator, so a great deal of filtering is already in place. I have expanded the criteria a little since beginning in the interest of the site, but that means I no longer read all the papers posted. (I also have a few each week that I don't post for person interest and to keep everyone's idea of my exact project purposely murky.)

So, things will keep evolving, but this is a good start, IMO.

Super Paper Friday!

I declare today to be Friday!

New setup: Using boring old EndNote, filtering the feeds in Google reader, and then copy and pasting the PMIDs. Use EndNote to remove the duplicates and download the PDFs. The PDF download in EndNote is okay-ish - only missed 36 out of 188 items. And no, no idea why each citation has [pii] at the end (probably interpreting the new line character weirdly).

Oh, and here's the EndNote library file. Thanks Remy for the suggestion! Post a quick comment to let me know if it works.

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10.1016/j.cub.2008.04.061 (2008).
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Ajemian, R., Green, A., Bullock, D., Sergio, L., Kalaska, J. and Grossberg, S. Assessing the function of motor cortex: single-neuron models of how neural response is modulated by limb biomechanics. Neuron 58, 414-28, doi:S0896-6273(08)00221-3 [pii]
10.1016/j.neuron.2008.02.033 (2008).
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Alaerts, K., Heremans, E., Swinnen, S. P. and Wenderoth, N. How are observed actions mapped to the observer's motor system? Influence of posture and perspective. Neuropsychologia, doi:S0028-3932(08)00380-1 [pii]
10.1016/j.neuropsychologia.2008.09.012 (2008).
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Amici, F., Aureli, F. and Call, J. Fission-fusion dynamics, behavioral flexibility, and inhibitory control in primates. Curr Biol 18, 1415-9, doi:S0960-9822(08)01096-8 [pii]
10.1016/j.cub.2008.08.020 (2008).
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Antal, A., Begemeier, S., Nitsche, M. A. and Paulus, W. Prior state of cortical activity influences subsequent practicing of a visuomotor coordination task. Neuropsychologia 46, 3157-61, doi:S0028-3932(08)00295-9 [pii]
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Asaad, W. F. and Eskandar, E. N. Achieving behavioral control with millisecond resolution in a high-level programming environment. J Neurosci Methods 173, 235-40, doi:S0165-0270(08)00337-3 [pii]
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Badets, A. and Pesenti, M. The effects of intention and practice on a non-motor duration estimation task. Acta Psychol (Amst) 129, 243-8, doi:S0001-6918(08)00088-7 [pii]
10.1016/j.actpsy.2008.06.006 (2008).
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Barriere, G., Leblond, H., Provencher, J. and Rossignol, S. Prominent role of the spinal central pattern generator in the recovery of locomotion after partial spinal cord injuries. J Neurosci 28, 3976-87, doi:28/15/3976 [pii]
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Bartels, J., Andreasen, D., Ehirim, P., Mao, H., Seibert, S., Wright, E. J. and Kennedy, P. Neurotrophic electrode: method of assembly and implantation into human motor speech cortex. J Neurosci Methods 174, 168-76, doi:S0165-0270(08)00386-5 [pii]
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Bedny, M., Caramazza, A., Grossman, E., Pascual-Leone, A. and Saxe, R. Concepts are more than percepts: the case of action verbs. J Neurosci 28, 11347-53, doi:28/44/11347 [pii]
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Belin, D., Jonkman, S., Dickinson, A., Robbins, T. W. and Everitt, B. J. Parallel and interactive learning processes within the basal ganglia: Relevance for the understanding of addiction. Behav Brain Res, doi:S0166-4328(08)00535-4 [pii]
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Berens, P., Keliris, G. A., Ecker, A. S., Logothetis, N. K. and Tolias, A. S. Comparing the feature selectivity of the gamma-band of the local field potential and the underlying spiking activity in primate visual cortex. Front Syst Neurosci 2, 2, doi:10.3389/neuro.06.002.2008 (2008).
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Berryhill, M. E. and Olson, I. R. The right parietal lobe is critical for visual working memory. Neuropsychologia 46, 1767-74, doi:S0028-3932(08)00011-0 [pii]
10.1016/j.neuropsychologia.2008.01.009 (2008).
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Bestmann, S., Harrison, L. M., Blankenburg, F., Mars, R. B., Haggard, P., Friston, K. J. and Rothwell, J. C. Influence of uncertainty and surprise on human corticospinal excitability during preparation for action. Curr Biol 18, 775-80, doi:S0960-9822(08)00537-X [pii]
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Bhattacharya, S., Samanta, D. and Basu, A. Performance models for automatic evaluation of virtual scanning keyboards. IEEE Trans Neural Syst Rehabil Eng 16, 510-9, doi:10.1109/TNSRE.2008.2003377 (2008).
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Birbaumer, N., Murguialday, A. R. and Cohen, L. Brain-computer interface in paralysis. Curr Opin Neurol 21, 634-638, doi:10.1097/WCO.0b013e328315ee2d
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Blankertz, B., Losch, F., Krauledat, M., Dornhege, G., Curio, G. and Muller, K. R. The Berlin Brain--Computer Interface: accurate performance from first-session in BCI-naive subjects. IEEE Trans Biomed Eng 55, 2452-62, doi:10.1109/TBME.2008.923152 (2008).
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Bohannon, J. The Gonzo Scientist. Flunking Spore. Science 322, 531, doi:322/5901/531b [pii]
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Bohannon, J. Video games. 'Spore' documentary spawns protest by scientists who starred in it. Science 322, 517, doi:322/5901/517a [pii]
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Borroni, P. and Baldissera, F. Activation of motor pathways during observation and execution of hand movements. Soc Neurosci 3, 276-88, doi:780817558 [pii]
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Brawn, T. P., Fenn, K. M., Nusbaum, H. C. and Margoliash, D. Consolidation of sensorimotor learning during sleep. Learn Mem 15, 815-9, doi:15/11/815 [pii]
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Bridgeman, B. and Hoover, M. Processing spatial layout by perception and sensorimotor interaction. Q J Exp Psychol (Colchester) 61, 851-9, doi:790357931 [pii]
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Brown, L. E., Wilson, E. T. and Gribble, P. L. Repetitive Transcranial Magnetic Stimulation to the Primary Motor Cortex Interferes with Motor Learning by Observing. J Cogn Neurosci, doi:10.1162/jocn.2009.21079 (2008).
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Brown, S. D. and Steyvers, M. Detecting and predicting changes. Cognit Psychol, doi:S0010-0285(08)00060-1 [pii]
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10.1016/j.jneumeth.2008.06.026 (2008).
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Calton, J. L. and Taube, J. S. Where am I and how will I get there from here? A role for posterior parietal cortex in the integration of spatial information and route planning. Neurobiol Learn Mem, doi:S1074-7427(08)00181-0 [pii]
10.1016/j.nlm.2008.09.015 (2008).
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Candidi, M., Urgesi, C., Ionta, S. and Aglioti, S. M. Virtual lesion of ventral premotor cortex impairs visual perception of biomechanically possible but not impossible actions. Soc Neurosci 3, 388-400, doi:783046525 [pii]
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Cao, X., Wang, H., Mei, B., An, S., Yin, L., Wang, L. P. and Tsien, J. Z. Inducible and selective erasure of memories in the mouse brain via chemical-genetic manipulation. Neuron 60, 353-66, doi:S0896-6273(08)00768-X [pii]
10.1016/j.neuron.2008.08.027 (2008).
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Carp, J. S., Tennissen, A. M., Mongeluzi, D. L., Dudek, C. J., Chen, X. Y. and Wolpaw, J. R. An in vitro protocol for recording from spinal motoneurons of adult rats. J Neurophysiol 100, 474-81, doi:90422.2008 [pii]
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Carrillo-de-la-Pena, M. T., Galdo-Alvarez, S. and Lastra-Barreira, C. Equivalent is not equal: primary motor cortex (MI) activation during motor imagery and execution of sequential movements. Brain Res 1226, 134-43, doi:S0006-8993(08)01369-3 [pii]
10.1016/j.brainres.2008.05.089 (2008).
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Chaminade, T., Hodgins, J. and Kawato, M. Anthropomorphism influences perception of computer-animated characters' actions. Soc Cogn Affect Neurosci 2, 206-216, doi:10.1093/scan/nsm017 (2007).
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Chowdhury, S. A. and DeAngelis, G. C. Fine discrimination training alters the causal contribution of macaque area MT to depth perception. Neuron 60, 367-77, doi:S0896-6273(08)00749-6 [pii]
10.1016/j.neuron.2008.08.023 (2008).
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Coello, Y., Bartolo, A., Amiri, B., Devanne, H., Houdayer, E. and Derambure, P. Perceiving what is reachable depends on motor representations: evidence from a transcranial magnetic stimulation study. PLoS ONE 3, e2862, doi:10.1371/journal.pone.0002862 (2008).
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Cohen, M. R. and Newsome, W. T. Context-dependent changes in functional circuitry in visual area MT. Neuron 60, 162-73, doi:S0896-6273(08)00675-2 [pii]
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Cohen, M. X. and Frank, M. J. Neurocomputational models of basal ganglia function in learning, memory and choice. Behav Brain Res, doi:S0166-4328(08)00542-1 [pii]
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Cohen, R. G. and Sternad, D. Variability in motor learning: relocating, channeling and reducing noise. Exp Brain Res, doi:10.1007/s00221-008-1596-1 (2008).
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Corey, D. P. and Movshon, J. A. Sensory systems: from molecules to percepts. Curr Opin Neurobiol 18, 355-6, doi:S0959-4388(08)00129-3 [pii]
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Costantini, M., Committeri, G. and Galati, G. Effector- and target-independent representation of observed actions: evidence from incidental repetition priming. Exp Brain Res 188, 341-51, doi:10.1007/s00221-008-1369-x (2008).
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Da Cunha, C., Wietzikoski, E. C., Dombrowski, P., Bortolanza, M., Santos, L. M., Boschen, S. L. and Miyoshi, E. Learning processing in the basal ganglia: A mosaic of broken mirrors. Behav Brain Res, doi:S0166-4328(08)00554-8 [pii]
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de Lange, F. P., Jensen, O., Bauer, M. and Toni, I. Interactions between posterior gamma and frontal alpha/beta oscillations during imagined actions. Front Hum Neurosci 2, 7, doi:10.3389/neuro.09.007.2008 (2008).
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de Lange, F. P., Roelofs, K. and Toni, I. Motor imagery: a window into the mechanisms and alterations of the motor system. Cortex 44, 494-506, doi:S0010-9452(07)00114-1 [pii]
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Di Filippo, M., Picconi, B., Tantucci, M., Ghiglieri, V., Bagetta, V., Sgobio, C., Tozzi, A., Parnetti, L. and Calabresi, P. Short-term and long-term plasticity at corticostriatal synapses: Implications for learning and memory. Behav Brain Res, doi:S0166-4328(08)00528-7 [pii]
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Dias, N. S., Kamrunnahar, M., Mendes, P. M., Schiff, S. J. and Correia, J. H. Comparison of EEG pattern classification methods for brain-computer interfaces. Conf Proc IEEE Eng Med Biol Soc 2007, 2540-3, doi:10.1109/IEMBS.2007.4352846 (2007).
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Dinstein, I., Gardner, J. L., Jazayeri, M. and Heeger, D. J. Executed and observed movements have different distributed representations in human aIPS. J Neurosci 28, 11231-9, doi:28/44/11231 [pii]
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Donaldson, Z. R. and Young, L. J. Oxytocin, vasopressin, and the neurogenetics of sociality. Science 322, 900-4, doi:322/5903/900 [pii]
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Draganski, B., Kherif, F., Kloppel, S., Cook, P. A., Alexander, D. C., Parker, G. J., Deichmann, R., Ashburner, J. and Frackowiak, R. S. Evidence for segregated and integrative connectivity patterns in the human Basal Ganglia. J Neurosci 28, 7143-52, doi:28/28/7143 [pii]
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Dunlop, S. A. Activity-dependent plasticity: implications for recovery after spinal cord injury. Trends Neurosci 31, 410-8, doi:S0166-2236(08)00147-1 [pii]
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Engel, A., Burke, M., Fiehler, K., Bien, S. and Rosler, F. What activates the human mirror neuron system during observation of artificial movements: bottom-up visual features or top-down intentions? Neuropsychologia 46, 2033-42, doi:S0028-3932(08)00060-2 [pii]
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Enticott, P. G., Johnston, P. J., Herring, S. E., Hoy, K. E. and Fitzgerald, P. B. Mirror neuron activation is associated with facial emotion processing. Neuropsychologia 46, 2851-4, doi:S0028-3932(08)00190-5 [pii]
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Enzinger, C., Ropele, S., Fazekas, F., Loitfelder, M., Gorani, F., Seifert, T., Reiter, G., Neuper, C., Pfurtscheller, G. and Muller-Putz, G. Brain motor system function in a patient with complete spinal cord injury following extensive brain-computer interface training. Exp Brain Res 190, 215-23, doi:10.1007/s00221-008-1465-y (2008).
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Esopenko, C., Borowsky, R., Cummine, J. and Sarty, G. Mapping the semantic homunculus: a functional and behavioural analysis of overt semantic generation. Brain Topogr 21, 22-35, doi:10.1007/s10548-008-0043-8 (2008).
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Felsen, G. and Mainen, Z. F. Neural substrates of sensory-guided locomotor decisions in the rat superior colliculus. Neuron 60, 137-48, doi:S0896-6273(08)00769-1 [pii]
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Fisher, L. E., Miller, M. E., Bailey, S. N., Davis, J. A., Jr., Anderson, J. S., Rhode, L., Tyler, D. J. and Triolo, R. J. Standing after spinal cord injury with four-contact nerve-cuff electrodes for quadriceps stimulation. IEEE Trans Neural Syst Rehabil Eng 16, 473-8, doi:10.1109/TNSRE.2008.2003390 (2008).
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Flegal, K. E. and Anderson, M. C. Overthinking skilled motor performance: Or why those who teach can't do. Psychon Bull Rev 15, 927-32, doi:15/5/927 [pii]
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Frey, S. H. Tool use, communicative gesture and cerebral asymmetries in the modern human brain. Philos Trans R Soc Lond B Biol Sci 363, 1951-7, doi:V31P786790X1M102 [pii]
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Gabbard, C., Cordova, A. and Lee, S. A question of intention in motor imagery. Conscious Cogn, doi:S1053-8100(08)00116-5 [pii]
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Gangitano, M., Mottaghy, F. M. and Pascual-Leone, A. Release of premotor activity after repetitive transcranial magnetic stimulation of prefrontal cortex. Soc Neurosci 3, 289-302, doi:780817109 [pii]
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Glenberg, A. M., Sato, M., Cattaneo, L., Riggio, L., Palumbo, D. and Buccino, G. Processing abstract language modulates motor system activity. Q J Exp Psychol (Colchester) 61, 905-19, doi:790266283 [pii]
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Gorostiza, P. and Isacoff, E. Y. Optical switches for remote and noninvasive control of cell signaling. Science 322, 395-9, doi:322/5900/395 [pii]
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Gottlieb, J., Balan, P., Oristaglio, J. and Suzuki, M. Parietal control of attentional guidance: The significance of sensory, motivational and motor factors. Neurobiol Learn Mem, doi:S1074-7427(08)00172-X [pii]
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Gueugneau, N., Mauvieux, B. and Papaxanthis, C. Circadian Modulation of Mentally Simulated Motor Actions: Implications for the Potential Use of Motor Imagery in Rehabilitation. Neurorehabil Neural Repair, doi:1545968308321775 [pii]
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Haber, S. N. and Calzavara, R. The cortico-basal ganglia integrative network: The role of the thalamus. Brain Res Bull, doi:S0361-9230(08)00342-0 [pii]
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Han, F., Caporale, N. and Dan, Y. Reverberation of recent visual experience in spontaneous cortical waves. Neuron 60, 321-7, doi:S0896-6273(08)00767-8 [pii]
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Harel, R., Asher, I., Cohen, O., Israel, Z., Shalit, U., Yanai, Y., Zinger, N. and Prut, Y. Computation in spinal circuitry: lessons from behaving primates. Behav Brain Res 194, 119-28, doi:S0166-4328(08)00356-2 [pii]
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Hayden, B. Y., Nair, A. C., McCoy, A. N. and Platt, M. L. Posterior cingulate cortex mediates outcome-contingent allocation of behavior. Neuron 60, 19-25, doi:S0896-6273(08)00760-5 [pii]
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Herman, P., Prasad, G., McGinnity, T. M. and Coyle, D. Comparative analysis of spectral approaches to feature extraction for EEG-based motor imagery classification. IEEE Trans Neural Syst Rehabil Eng 16, 317-26, doi:10.1109/TNSRE.2008.926694 (2008).
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Hernandez, A., Nacher, V., Luna, R., Alvarez, M., Zainos, A., Cordero, S., Camarillo, L., Vazquez, Y., Lemus, L. and Romo, R. Procedure for recording the simultaneous activity of single neurons distributed across cortical areas during sensory discrimination. Proc Natl Acad Sci U S A 105, 16785-90, doi:0808702105 [pii]
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Holmes, P. and Calmels, C. A neuroscientific review of imagery and observation use in sport. J Mot Behav 40, 433-45, doi:75597KN814K11N17 [pii]
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Hudson, T. E., Maloney, L. T. and Landy, M. S. Optimal compensation for temporal uncertainty in movement planning. PLoS Comput Biol 4, e1000130, doi:10.1371/journal.pcbi.1000130 (2008).
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Huo, X., Wang, J. and Ghovanloo, M. A magneto-inductive sensor based wireless tongue-computer interface. IEEE Trans Neural Syst Rehabil Eng 16, 497-504, doi:10.1109/TNSRE.2008.2003375 (2008).
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Ikegami, T. and Taga, G. Decrease in cortical activation during learning of a multi-joint discrete motor task. Exp Brain Res 191, 221-36, doi:10.1007/s00221-008-1518-2 (2008).
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Imamizu, H. and Kawato, M. Neural correlates of predictive and postdictive switching mechanisms for internal models. J Neurosci 28, 10751-65, doi:28/42/10751 [pii]
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Izawa, J. and Shadmehr, R. On-line processing of uncertain information in visuomotor control. J Neurosci 28, 11360-8, doi:28/44/11360 [pii]
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Jain, N., Qi, H. X., Collins, C. E. and Kaas, J. H. Large-scale reorganization in the somatosensory cortex and thalamus after sensory loss in macaque monkeys. J Neurosci 28, 11042-60, doi:28/43/11042 [pii]
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Johnson, A. P., Cleaves, H. J., Dworkin, J. P., Glavin, D. P., Lazcano, A. and Bada, J. L. The Miller volcanic spark discharge experiment. Science 322, 404, doi:322/5900/404 [pii]
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