"Skiff Reader: The Ultimate E-Reader | If you bought an Amazon Kindle DX in 2009, prepare for a heavy dose of buyer’s remorse. The Skiff Reader has overtaken the Amazon Kindle DX as the largest e-reader on the market, but its size isn’t what makes the Skiff so special. The Skiff Reader brings two new technologies to the large-scale e-reader market: a touchscreen e-ink display and “silicon thin-film-transistors on a flexible steel substrate”. The Skiff Reader pushes the e-reader standard by featuring a full touchscreen display spanning 11.5-inches. The Amazon Kindle DX and smaller Kindle models don’t feature touchscreen e-ink, neither does that Barnes and Noble Nook (while the latter has an LCD touchscreen below the e-ink portion). This provides a new, finger-friendly world of navigation as you flip pages, highlight and select content modules and skim through your favorite ebooks."
- AJ Batac
from Bookmarklet
Wow, if that's for real, I'm super jazzed. I've wanted a large high-res ebook reader for ages.
- Joel Webber
Nice. You could fit that inside the case of a MacBook air. I wonder what the update rate on that e-ink screen is though. [edit] Oh... it's not e-ink, it's TFT. Does that mean real-time updates? Wow X 2.
- Matt Mastracci
Morgan's question is most important, followed immediately by what content can you get on it?
- Kevin Pedraja
i'm sitting here ready to buy this sexy beast. but i need to know how muchee. I'm guessing that Amazon.com ain't gonna offer it anytime soon.
- Morgan Haley
As long as it reads PDF, .mobi and HTML formats without extra charge, I'd be OK with whatever proprietary junk they throw on it.
- Matt Mastracci
I'm pretty sure this will not be available up north till you all in the US have it. :(
- AJ Batac
Rumor has it that the company making this thing is owned by the Hearst Corporation, who refer to this cryptically, as the device they expect will save the newspaper publishing industry from being destroyed by free news on the Internet. Expect plenty of DRM. Additionally, the software on the device will allow advertising to be "injected" into content. I am not sure if that means that if...
more...
- April Russo (app103)
Mmmm.. Thanks for the rumors April. But I think they'll crack that baby up (as almost ANYTHING digital or firmware based) in no time after launch, just for me 8)
- ElijahBailey-Zu of FF <0,
Looks like they'll be using Sprint as their cellular provider (which is fine, I guess). If it's reasonably priced and includes a good book library of current titles, I'll probably buy one.
- Jason Huebel
Also has built-in wifi, USB and SD card support. 4GB internal memory (3GB usable for data). The screen is metal, rather than glass, so it will be much more durable that other ereaders. Looks promising.
- Jason Huebel
So here's a question: why doesn't Amazon license their DRM to companies like Skiff? They may make /some/ money on Kindles, but surely they would make even more if Amazon's Kindle format was available on more devices.
- Jason Huebel
That puts the Crunchpad to shame. If they'd come out with one of these that was in color and foldable it would be uber!
- Lindsay is in 20-ten
The only company that's really managed to share DRM across technology platforms is Microsoft I think. Even then, the 'plays for sure' program didn't really last that long. I guess when you have the dream of ultimate control over your end-user's usage, sharing that with others isn't really something people like to do.
- Matt Mastracci
Metal screen is very promising. I'm still curious about refresh rate, cost, DRM, etc. It looks like an awesome e-reader, but it doesn't look like a general purpose computing device (and it really ought to be)
- Jason Wehmhoener
"refresh rate"? I'm sure it's bad, like other eReaders. But I think people are hoping for something that this particular technology just can't deliver. eInk isn't designed for moving images. It's designed for static pages of text. When I look at eReaders now, I don't even consider refresh rate as a factor. Also, I think comparing this to the Crunchpad is comparing apples to oranges.
- Jason Huebel
This doesn't seem to use e-ink though - it's a TFT LCD screen, from the specs. Might mean that it's got an impressive refresh rate, but possibly worse sunlight readability.
- Matt Mastracci
refresh rate for e-ink varies quite a bit from one ereader to another. i bring it up because i have doubts about e-ink as a viable technology, frankly.
- Jason Wehmhoener
Then I guess I'll wait for the next thing after eInk. I looked at a Sony reader the other day, and it took almost as long to refresh the page as it did to read the page (only a slight exaggeration, seriously). I read books on my iPhone and there's no refresh at all. It's right there. Why can't they use that?
- Jandy, ConcertMaven of FF
Regardless, this thing just looks cool :)
- Jan Ole Peek
Jandy, exactly. The only reason people are buying the kindle is because they want cheaper books and they don't own an iphone, think the iphone screen is too small, or don't realize you can use an iphone to read kindle books. e-ink has nothing to do with the popularity of the kindle. ereaders were not considered as a going concern when sony was doing this. the difference is Amazon and...
more...
- Jason Wehmhoener
To say eInk isn't viable simply ignores the popularity of devices like the Kindle. In the proper form factor, it's obviously viable. Also, we're not talking about a device that's meant to be a multimedia player. To suggest that multimedia capability is a requirement for an eReader misses the point of the device entirely.
- Jason Huebel
The iPhone isn't a real alternative to an eReader either. Yes, it can be used to read eBooks. Yes, the Kindle app makes the entire Kindle library available on the iPhone. But would you really enjoy reading an entire novel on that tiny screen? And what of battery life? If I used my iPhone to read an eBook, the battery wouldn't last beyond a few hours. eInk addresses that issue specifically. It sips power-- and only when needed. The iPhone's screen drains power.
- Jason Huebel
I should add that I currently don't own an eReader, but have used the Kindle extensively. I've been waiting for a form factor closer to 8.5x11 that has full PDF support. The DX is nice and i understand that Amazon recently added full PDF support, but it's too expensive. Hoping the Skiff is a bit less so I can justify the purchase.
- Jason Huebel
I'm not saying an iPhone is a direct competitor to a Kindle or Sony reader, just that the time I've spent reading books on it was more enjoyable than the time I spent testing a Sony reader (granted, not that long, but long enough to be dismayed by the screen blinking at me for three or more seconds between pages). Plus, if I were to buy something like this, I would absolutely want it to...
more...
- Jandy, ConcertMaven of FF
Jason, I think you missed my point. The kindle is popular because kindle books are cheap. Period. No other reason.
- Jason Wehmhoener
@Jandy, Oh, well... The Sony eReader is the worst of them, IMO.
- Jason Huebel
@Jason, but that makes it non-viable? Amazon and B&N's sales of the readers prove otherwise. Besides, you pay $400US or more for one of these devices. So you would have to buy quite a few books before you recoup that cost over the hardcover or paperback versions. eReaders have other advantages you're completely ignoring. For instance, they are extremely convenient. You can carry any number of books, periodicals, MP3s, etc in a single device.
- Jason Huebel
They are always connected, too. So any periodicals you subscribe to are automatically delivered. Get up in the morning, grab your Kindle and read several periodicals on a single device. Don't have time in the morning? Grab a single device and walk out the door. When you find time, that single device has all your favorite newspapers and magazines. Ran out of stuff to read? Buy directly from the device and have something new to read within moments.
- Jason Huebel
All that on a device that has a battery life measured in days or weeks, not hours like the iPhone or Crunchpad.
- Jason Huebel
So this statement is completely wrong: "The kindle is popular because kindle books are cheap. Period. No other reason." Period.
- Jason Huebel
Well we're getting there with these e-readers but his one is not colour and still too big. Cut it in half!
- Kol Tregaskes
In fact if there was some way of expanding/collapsing the size then that would be ace! This bendy feature would be good though, it would last longer if I used it. :-)
- Kol Tregaskes
Agreed. If you could collapse a device like this down to a smaller size for storage, that would be nice. But I do want a device that has a larger screen like this.
- Jason Huebel
The size of a paperback reading book is what I'm thinking. That's where I would like to use it (as well as browse the net - if possible - or read newspapers, etc.).
- Kol Tregaskes
It would even be nice if it folded in half or something. That way, you could turn it landscape and read two smaller (approximately paperback-sized) pages or you could turn it portrait and read a single PDF-type letter-sized document. Fold it in half and put it in your bag to carry it around.
- Curtiss Grymala
If it's crippled with DRM'd and doesn't support popular open formats, it'll be another pass for me. I actually don't mind minimal DRM too much for purchased books, but I shouldn't be restricted in any open formats I wish to view and there definitely shouldn't be any passing of data back to the mothership.
- Phil Ashman
I'm not sure that I'd for sure name it best (it's kind of unfair to compare all different sorts of TV shows together in one category), but it's certainly the one I return to over and over and over again. (Too bad not all of the seasons were of equal quality, though.)
- Spidra Webster
Part of the impact of West Wing was the marked contrast between Josiah Bartlett's administration and the real-life version under Bush and Cheney.
- Mark It's 2000-Oh-1-Oh J
That may account for some of its popularity, Mark, but I think West Wing was popular for what marks a lot of Sorkin shows: excellent dialogue, fantastic mix of comedy and drama, supernal ensemble casting...and the extra for West Wing was being able to geek out over all that governmental stuff. The dialogue was so thick with it that repeat viewings reward you. Takes several times seeing an ep before you really feel you've gotten everything out of it.
- Spidra Webster
Without looking at other answers: Homicide, particularly the first year.
- AJ Kohn
First season of Miami Vice... unfadeable baby!
- Adrian
The West Wing was so awesome I remember bit characters. Like the guy in records or something who had the best line ever. "Well you're a strange little frumpy man, aren't you?" Of all the series I've loved, this one lasts the longest.
- Heather
People are so serious about their TV! People are yelling at me on Twitter, too! Geez. LOL
- Mona Nomura
from iPhone
None of the above. But. Mad Men is climbing the charts fast. Still. WW is in the stratosphere, and nothing will touch it.
- Christopher Galtenberg
from iPhone
I've been watching it again on DVD. In fact, watching it right now... Jean-Paul just spiked her drink, Tae Diggs is talking to a bunch of folks about to get it... uh oh... aaaaand.... poor Molly...
- Ken Sheppardson
Plus most of the rest that ya'll listed. Good picks! :-)
- Mathew A. Koeneker
better than TWW: Arrested Development, Futurama, Veronica Mars, The Simpsons (uh, stopping somewhere between end of season 9 and season 12 at the latest), 30 Rock, Community, and Newsradio. Action, Pushing Daisies, and Life, too if we can sneak in those shows that were "cancelled before their time". Buffy up to S5 but not past it. Esp considering the relative doldrums of TWW s3 - s6.
- Andrew C
That's easy, 24 and X-Files are far better. :-)
- Kol Tregaskes
Guess I'm just one of those peeps who think the west wing was boring. Couldn't get through an episode. Was more interested in ER at the time.
- Jon, the Beartato of '10
from Android
Rome series 1, BSG reimagined, Sportsnight, Buffy, Farscape, Magnum PI, Red Dwarf, Thundar the Barbarian, Underdog, M.A.S.H., Password, What's My Line?, I Love Lucy, The Carol Burnett Show all rank pretty high with me. I'm sure I missed some. Loved West Wing in doses, but it became taxing for me to watch.
- Michael W. May
West Wing is a tough show to compare shows to. As far as must watch TV: Damages, Flash Forward, Rescue Me, Dark Blue, Fringe, Lie To Me... This would be easier if I was near my DVR!
- amarquart
The West Wing might be my FAVORITE series but I think the BEST series was The Wire.
- Akiva Moskovitz
Good show, but best ever? Don't think so. The Wire and Rome, for instance, are way better. Heroes Season 1 (only), Kings, The Black Donnellys, Babylon 5, New BSG before season 4 are some more. Andrew C names a bunch more that I agree with.
- Chieze Okoye
Buffy the Vampire Slayer. (sorry, @Ha3rvey.)
- edythe
from iPhone
Nobody's mentioned The Greatest American Hero? *sings* Believe it or not, I'm walking on air. I never thought I could feel so freeeee-eeeeee-eeeee!
- Jason Huebel
I've never seen West Wing, but that's how I feel about Six Feet Under.
- Alix Whitmire
ditto what Alix wrote. and I'll add The Wire.
- jbrotherlove
"The West Wing might be my FAVORITE series but I think the BEST series was The Wire." - Akiva
- Mona Nomura
West Wing is a great series. Period. BUT NYPD Blue was better.
- Louis Gray
The Prisoner (the original 60s series, not the remake).
- Parody
I saw a clip. It showed a person being cowed into standing for the president. That was enough for me.
- SuezanneC Baskerville
What does cowed into standing for the president mean?
- Mona Nomura
intimidated - one is "supposed" to stand up when the president enters a room, at least according to the show. it's a statist ritual, like singing songs of praise to governments. i find it offensive.
- SuezanneC Baskerville
Respect != intimidation. Besides, what's wrong with showing respect to ranked officers? POTUS is the Chief of Staff.
- Mona Nomura
I'm thinking of trying to simulate covering a talk by simultaneously watching the same video, e.g. this one by Gary Bader: http://www.youtube.com/watch... Follow link above to a Doodle date finding poll
- Michael Kuhn
from Bookmarklet
I've proposed the afternoon in Europe, so that people from the US can join in the morning
- Michael Kuhn
I've put in my availability. Should be interesting - we can compare (subjectively) the experience on that as compared with our known experiences on FF. Btw, if anyone wants a wave account, just let me know. We all have loads of invites now, it seems.
- Allyson Lister
thanks Allyson, Roland and Graham. I agree with Ally that we should compare Wave to FF, so I'd like to give priority to people who have covered ISMB. Also, I'm just curious to see how well Wave handles Ally's writing speed. :)
- Michael Kuhn
I'll be covering the Recomb Satellite via FF for now; given the limited number of people who have access to it so far that seems to be the only venue.
- Oliver Hofmann
I'm giving a talk on Wave in a few weeks - was thinking I might put the slides in as images, then work through them using the slideshow function - if I can stream audio out and people could leave comments on the slides as we go...but collaborative note taking with a relatively small number of people seems to work really well - if you can pull the video/slides in even better.
- Cameron Neylon
The talk is supposed to be 3:30 on Tuesday 15th but is late in the day so would probably be later. Will looking into what networks facilities are available...
- Cameron Neylon
@Michael, nothing can handle Ally's writing speed :D
- Benjamin Tseng
@Cameron, forgive me if this is a dumb question, but how would a talk like that work? would you interrupt it to answer comments/questions as they came in?
- Benjamin Tseng
@Michael, @Benjamin - you're really bigging me up there! :) FF seemed to be able to keep up, so hopefully so will Wave :)
- Allyson Lister
@Benjamin - thinking I would have the slides in a Wave, webcast video, people could comment next to the slides as appropriate (or inappropriate) and then at the end you have an annotated version of the talk as it happened. Could certainly answer questions - people often interrupt inside the room anyway - but there wouldn't be a simple mechanism to get speakers attention. Anyway I don't...
more...
- Cameron Neylon
looks like Wed, Dec 16 at 4 pm UT / 5 pm CET will be it. (Sorry Roland.) Any other nominations than for what to watch instead of Gary Bader: Predicting Protein Interaction from the Genome, http://www.youtube.com/watch... ?
- Michael Kuhn
@Cameron: I also think having slides and comments in the same Wave is a separate experiment, also streaming live can have its own problems. so let's keep this one simple :)
- Michael Kuhn
Yep, that's cool. I should be available on 16th as well anyway
- Cameron Neylon
Just saw this thread and plan to be there on 16th. My suggestions for videos to watch are at http://en.citizendium.org/wiki... . Alternatively, we could also go for 2-3 TED talks where the change of subject may provide for additional testing functionality.
- Daniel Mietchen
SDwildgene has added a photo to the pool: This male Peregrine Falcon was drooling at the yummy birds flying by down below. :-) Or not. See the pictures in the comments for what's happened. First, I noticed this perching male Falcon showing sign of discomfort. He hung his head and wagged it from side to side with the beaks open as if he was choked. As I was about to jump up to perform the Heimlich maneuver him, I suddenly realized that he was in a process to regurgitate the casting (the pellet of indigestible material). Sure enough, there it came. This seemed to be a painful process as the falcon continued to show sign of discomfort and there's slimy liquid (saliva or gastric juice) hanging down on his beaks. He recovered in a minute or so, wiped his beaks on the stick and took off. He is ready again for the next meal :-)
- burdr
That would be a great place to party when Friendfeed will shut down :)
- Jérôme Flipo
Very cool! What kind of LED lights are you using? We have old rope lighting that we are planning to change out for color changing LED rope lighting in in several rooms, but we have a bunch or research before we begin that project. Any tips from your experience?
- Rachel Lea Fox
Also, are the color changes tied to any data or just rotating on a cycle?
- Kevin Fox
We're using Color Kinetics: http://www.colorkinetics.com/. Beti actually ordered these, and I haven't investigated them deeply. There are two types of controls, one which is a dial on the wall that changes color, modes, and frequency of change. The other is an ethernet/RS-232 solution. We don't have the advanced one right now, but we may upgrade to it sometime after I look into it. I'm not sure how much work needs to be done to time the lights to something like Sonos.
- Cristo
I want one that ties to my brain according to my mood
- Jesse Stay
Rachel, also I think you like hidden doors, right? I don't think I've taken a photo of our finished hidden door, but I'll try to upload one soon.
- Cristo
Cristo. The doors look awesome. And I love the use of light through them. It really gives the space a beautiful and fun feel!
- Rachel Lea Fox
Rachel and Kevin: I agree with you that the special lighting effects really do add a lot to a room. It makes it magical and otherworldly. I bought the lights from one of the largest distributors, Wiedamark, of the Color Kinetics products and they were very helpful. Their website is: http://www.wiedamark.com/colorki... -- they can help determine which product is best for your...
more...
- Beti Cung
So what does agarose taste like? I once had a dessert that looked and felt like 4% Metaphor but was in fact strawberry flavour...
- Richard Badge
from Nambu
Agarose tastes like a less tasty version of agar-agar, which is basically what it is. Just a set gel of sugar.
- Cameron Neylon
At least if you're a chorister and notice the details of the rough edges. The thing that is not working here is the sense of psychological locking that you get in a good performance. Subtle time differences everywhere. I wonder how much post production they did.
- Cameron Neylon
it's hard to give lines shape this way -- the dynamics generally are kinda muted. neat experiment, though!
- D0r0th34
it also selects for a particular type of chorister: one willing to "sing solo" on YouTube. that's an OMG NO from me.
- D0r0th34
Yeh, its all the stuff you get from the rest of the choir that is missing. But nonetheless the fact that this can be done with what are presumably for the most part webcams is pretty impressive. And yes, it clearly selects for exhibitionists to a certain extent.
- Cameron Neylon
That's what I also found interesting - it's rather the opposite for normal chorists - they like to blend in, they tend to be anti-soloists. So, secret handshake, Cameron?
- Heather
Or not so secret... :-) Quite a few of us around these parts though...well three anyway...
- Cameron Neylon
Interesting observation on singing scientists - would chorists embrace open science more/ earlier than soloists?
- Daniel Mietchen
I'll survey our Choral Union and ask. :) I think there's a few scientists in our bunch. (I have Haydn earworm right now like you WOULD NOT believe. Benedictus...)
- D0r0th34
quoniam tu sooooooolus datus... oh, this could get bad (even worse because "datum" is a neuter, bad me)
- D0r0th34
I suspect there are huge numbers of non-soloists out here. Back when I was in Berkeley Community Chorus, I co-soloed (the lead quartet in a requiem, with two people taking each part) *only* because I was the least terrified of the baritone-basses. And swore I'd never do it again. (Being the only sight-reader in the baritone section was bad enough.)
- Walt Crawford
"I’ve gone back to using another wonderful visualization package, PyMol. I find that it hits the sweet spot between easy setup of the scene I’d like and generating nice figures. The specific feature that I’ve come to rely on quite heavily is the built-in ray tracer. There are three available ray tracing modes in addition to the default, each of which has its uses. Mode 1 will place a black outline around your structure, which can help make the secondary structure elements visually distinct. Mode 2 is really interesting, in that it only renders the outline. I find this especially helpful if I want to show something in an overlay without obscuring what is behind it. Mode 3 produces “quantized” color in addition to the outline, giving your figure a very cartoonish appearance. I find that this one has to be used with care :) "
- Mike Chelen
from Bookmarklet
I'll have to do some tests to see if this is any faster than my local ISP DNS.
- Benjamin Golub
hmmm... and the reason behind this offer?
- MikeAmundsen
They will then know every single domain name that every user is trying to resolve, and how often, etc.
- Glen, Bespectacled Elder
DeWitt that doesn't mean they aren't copied elsewhere or they will actually follow through with the policy.
- Todd Hoff
anyone know what appears when the domain request is invalid? i.e. will i see a google search page w/ ads?
- MikeAmundsen
Yay! This is super cool. I'm using it to work around my ISP (Comcast) hijacking DNS requests.
- Joe Beda ()
Another cool thing are the vanity IP addresses that were obtained for this: 8.8.8.8 and 8.8.4.4. '8' is a lucky number, you know.
- Joe Beda ()
@Todd: Actually, the privacy policy is pretty clear about what's temporary and what's permanent. If temporary logs were "copied elsewhere" as you suggest, it would be a pretty obvious violation of this policy. And I think it's pretty unreasonable to suggest that Google wouldn't "actually follow through" on its own privacy policy.
- Joel Webber
Joe, do you know who had 8.8.8.8 prior?
- Micah Wittman
Fast, doesn't seem to hijack 404s in any way. But I will have to go over the privacy policy carefully, in the context of Google's broader privacy policy. I wish we knew if the NSA had direct access to Google's traffic like they do for ISPs. This will certainly give Google a lot of data about web use.
- LogEx
Joel, it's just a policy. If the NSA or some other agency says Google won't get this slice of spectrum etc then don't be surprised of all that traffic is split off some switch somewhere into total information awareness.
- Todd Hoff
@Todd - half the company would quit in protest on the spot if Google even contemplated doing something like that. Including our own founders. But here's a question -- what could a company do that would reduce your fear? Clearly you use the Internet, and DNS, today. What assurances did your ISP make that cause you to trust them? Personally speaking, I find the Google DNS privacy policy a heck of a lot more reassuring than my ISP's. At least Google is promising in writing to do the right thing.
- DeWitt Clinton
People don't know DeWitt. All those fat internet pipes hook into switches that have tap lines on them. And are there any examples of people quitting en masse in protest? I've not seen it. There's nothing people can do to reduce my fear because I know too much about it. Those promises don't matter. They can change at anytime and there's no external verification and as I said, the data is...
more...
- Todd Hoff
I wonder how much this gets traction beyond things like Chrome OS where Google can require the client to use their name servers. DNS is an abstract concept to most people, and for businesses, Google Public DNS doesn't offer the level of control other managed DNS services offer (like OpenDNS, for example). As an IT guy, one thing that I see missing is the ability to manually refresh the cache. I'm also interested to see how Google respects TTLs.
- Mark Trapp
BTW, here's the Speakeasy Privacy Policy: http://www.speakeasy.net/tos.... Here is Comcast's: http://www.comcast.net/privacy.... Here is AT&T/SBC's: http://www.att.com/gen.... Guess what? None of them publish a log deletion policy and ALL of them reserve the right to do nearly whatever they want (even sell) your personally identifiable information, including IP addresses. Those ISPs are seeing every bit of traffic from our machines today.
- DeWitt Clinton
DeWitt, I went through that, and I'm still left wondering what Google's caching does. It doesn't explicitly say that Google will always respect the TTL on a record, and I don't see a remedy to resolve an outdated cache (for example, if Google fetches a record with a TTL of 86400 10 minutes before I change that record, if there's no way to force a manual lookup, even changing the TTL to...
more...
- Mark Trapp
@Mark -- I can't see how to force a manual refresh either, but I'll find out. I agree that it's necessary in some situations.
- DeWitt Clinton
Mark, that page DeWitt linked to seems to infer that they respect TTL for prefetches: "The complexity of the name selection problem makes it impossible to solve online, so we have separated the prefetch system into two components: a pipeline component, which runs as an external, offline, periodic process that selects the names to commit to the prefetch system; and a runtime component, that regularly resolves the selected names according to their TTL windows."
- Matt Mastracci
@micah Level3 owns 8.0.0.0/8 and Google has 8.8.8.0/24. BTW, 7.7.7.7 is owned by the US Dept. of Defense.
- Joe Beda ()
Matt, what concerns me about that is it seems they interpret the TTL as a range of times they're allowed to ask for a new record; that is, if they automatically refresh records faster than the TTL, that's okay, as long as they don't hold onto it for longer than the TTL. A TTL shouldn't be a guideline: if I set a TTL to 86400, unless I manually tell you to fetch it again, you shouldn't...
more...
- Mark Trapp
Cool, added them to my list of servers that dnsmasq is to use.
- Grant Bierman
The RFC does specify TTLs as "a 32 bit unsigned integer that specifies the time interval ... that the resource record *may be* cached before it should be discarded" I don't know if there's ever going to be a rock-solid guarantee that a resolver will cache your records (its cache could always overflow or become corrupted). Jumping TTLs isn't half as annoying as the broken resolvers that cache one of your round-robin DNS responses for all their customers for days, though. ;)
- Matt Mastracci
Oh yes, checking too quickly is definitely a better problem than checking too slowly. One of the things we used to deal with was managed DNS that charged by the record lookup; in cases like that, you absolutely want people to respect the TTLs you specify or it can wind up costing you dearly. I don't really know if companies still get away with that (we get managed DNS for free now), but...
more...
- Mark Trapp
I'm not happy with this. I feel it is a step too far. They could know and control way too much... from the OS Chrome to DNS/ mweh! And then what about a system fail! Laugh! I'm sure Murphy is working on it. How much of the network could go down with it. #don't-put-all-your-eggs-in-one-basket
- DC Crowley
I am working on a docking experiment to see interactions between phosphorylated peptide(s) with a receptor. I am looking for a reliable tool (software/ web server) for protein-peptide docking - any suggestions ?
As far as the docked complexes from the tool provides known interactions (from literature) and minimization values are in good range (-ve), I can consider the docking as reliable. Neil, thanks for the suggestion - but am afraid this server is designed exclusively for Kinases, Class-I, and MHC Class-II - am working on phosphatases.
- Khader Shameer
1) Dock (full options, difficult to implement), 2) AutoDock (less options, but faster to implement), 3) HEX (even less options, but perhaps the best tool to start). These are all free. In addition, depending on your institutional subscription there are other (expensive) options.
- genereg
Thanks. I already tried AutoDock with different parameters, but doesn't seems to be a good choice for protein-peptide docking. GRAMM-X is not able to recognize the phosphorylated residues in my peptide. I will try DOCK and HEX.
- Khader Shameer
According to this link [ http://tinyurl.com/cp5t9b ] DOCK is not recommended for Protein-Peptide docking. Now am going to try different programs ranked well in CAPRI.
- Khader Shameer
if it is not for protein-peptide docking, what it it for :) BTW you do not need the whole protein, you just need to consider its reactive center and the peptide. Also you may wish to try Molegro. It is not free, but you can get a free copy for a 1-month evaluation. The problem is that all commercial programs use their unique output formats not compatible with the standard PDB format and not easy to transform to view and analyze in the external software.
- genereg
Ah right, the forgotten phosphatases :) I'd start with a review article; someone must have benchmarked the most-used packages. I've played with zdock, hex and autodock over the years, all with their pros and cons: zdock - 'quick and dirty', hex - easy to use GUI, autodock - the most comprehensive but last time I checked, under very active development and hence poorly documented.
- Neil Saunders
Thanks Neil. zdock is always my best friend. but I spend a lot of time with AutoDock as it was ranked as one of the best docking tool in different benchmark reviews. I was hoping that my AutoDock clusters will show nice -ve values for every other docking I tried - but it never happened. Now I am running ZDOCK and planning to get some energy values using minimization routines of Ghemical.
- Khader Shameer
Just to update : Due to some inconsistencies in the energy of complexes generated using ZDOCK, I contacted the authors of the program and got to know that ZDOCK consider the phosphorylated-tyrosine as normal tyrosine during the docking process. Now am working on developing an approach similar to that of MODPROPEP specific to phosphorylated peptide. Will update If I get some promising results.
- Khader Shameer
I just found this thread. Khader, is this question still relevant ? we've just finished the development of a high-resolution peptide docking algorithm within the Rosetta package... If it's still relevant I could try and model that peptide for you...
- Nir London
Nir : Thanks for your note. I proceeded with the superposition approach, but am not so happy with the results. We are still looking for better options. I will be happy to try it if the program can take up *phosphorylated peptides* and perform protein-peptide docking.
- Khader Shameer
It works with *phosphorylated peptides* :) or any other kind of short peptides. The code isn't released yet though, as the paper is still under review, If you send me some background, ref. PDBs etc.. I could easily do the docking for you.
- Nir London
Thanks, This is great, Nir. I will send you an email with details.
- Khader Shameer
usage of open source software, and application of its principles, advances science research & publishing by allowing faster and more efficient replication and modification of new ideas
- Mike Chelen
Interested in the contrast between open science and distributed science - can you have "closed" distributed science? Or is that just collaboration?
- Richard Badge
from Nambu
That last "leafy sea dragon" image is actually a weedy sea dragon. And they're found from the SW to the SE coast, rather than 'around the coastline" of Australia.
- Neil Saunders
Thanks Neil for this information, I reference it.
- Ami Iida
These pictures are gorgeous -- will show these to my kids.
- Mickey Schafer
This interview with Founder and Ultra-Marathoner Danny Dreyer provides a glimpse into the life-changing and pain-eliminating running technique quickly becoming the standard for marathon runners around the globe: ChiRunning. - http://www.youtube.com/watch...
he gave a class to a few groups of us doing a triathlon with Team In Training (The Leukemia & Lymphoma Society) years ago. pretty interesting stuff.
- metalerik
from iPhone
The video says almost nothing about what the method actually is. I guess it's a promotional video for the book?
- Evan Parker
Yeah, it's a promotion. I found the book kind of hard to follow, but the dvd is pretty good -- I'd start there.
- Paul Buchheit
Evan, We listened to Dreyer once and our running club had a trainer who trained with Dreyer. No one actually says anything on the method. They both said, "Well have you'll have to take the ($$$$) class or buy the DVD. I guess it's more visual than anything.
- Admiral Anika
It's a long drive to Atlanta and back; this is usually when I catch up on my podcasts (Stack Overflow, This American Life, and most importantly C2CBio). Unfortunately, I'm all caught up with C2CBio. Thus, my drive would be full of win if one or more new episodes become available before the trip late this month. My stimulated brain cells will thank you from the interstate.
- Chris Lasher
We'll try and get at least one out that week
- Deepak Singh
"Yesterday I attended a biweekly meeting of an informal UC Berkeley group devoted to Python in science (Py4Science), organized by Fernando Perez. The format (in honor of my visit) was a series of 4-minute lightning talks about various projects using Python in the scientific world (at Berkeley and elsewhere) followed by an hour long Q&A session. I was blown away by the wide variety of Python use for scientific work. It looks like Python (with extensions like numpy) is becoming a standard tool for many sciences that need to process large amounts of data, from neuroimaging to astronomy... [see list of very interesting TOPICS and projects]." \\ see also http://fperez.org/py4scie... which includes links \ Video at http://www.archive.org/details...
- Adriano
from Bookmarklet