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Andrew Perry › Comments
The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000160. Marco Punta, Yanay Ofran
- Andrew Perry
Fold space unlimited - http://www.citeulike.org/user...
Mitchell J Stanton-Cook liked this
Current Opinion in Structural Biology, Vol. 19, No. 3. (08 June 2009), pp. 312-320. You want to know how proteins do it? Take a walk in protein fold space. More often than not you will get a clue if not the answer. If you know what you are looking for and how to find it. In fact, there is more information than we can presently handle. Charting fold space and chasing its creatures has occupied us for the past decades. There is no end in sight. Manfred Sippl
- Andrew Perry
Space Exploration History: The Space Shuttle and the Horse's Rear End - http://www.astrodigital.org/space...
Michael Kuhn and Neil Saunders liked this
Tagged: space bureaucracy funny standards
- Andrew Perry
cool urban legend :) http://www.snopes.com/history...
- Michael Kuhn
Argh .. stung ! And I usually pride myself in not falling for those :)
- Andrew Perry
Unity3D - Zero to Hero!: The Journey Starts Here! - http://marraboy.blogspot.com/2008...
A tutorial blog for Unity3d ... development of an asteroids clone.
- Andrew Perry
TopMatch - Protein Structure Comparison - http://topmatch.services.came.sbg.ac.at/
.. yet another protein structural alignment tool added to my list ...
- Andrew Perry
Postdoctoral Research Fellowship in Computational Biology @ The University of Queensland (Australia) http://research1t.imb.uq.edu.au/bailey...
The holder of this position will be involved in a number of projects studying transcriptional regulation of genes by proteins, non-coding RNA and epigenetic modifications. The focus will be on developing novel computational approaches that integrate heterogeneous data types using hidden Markov models and Bayesian networks in order to predict gene expression. These computational pipelines will be applied to data generated in-house in order to elucidate the genetic regulatory networks of embryonic stem cells and nuclear precursor cells.
- Andrew Perry
Motorola Droid Review - http://blog.jasonhuebel.name/post... (via http://friendfeed.com/jhuebel)
Christoph Studer, ganassa, Haggis (Sean Loyless) and 5 other people liked this
This is my Motorola Droid review. Hope you guys like it.
- Hip-Hop in da House
Nice writeup, Jason!
- imabonehead
Thanks. :-)
- Hip-Hop in da House
Planning to write apps for it?
- imabonehead
I've already downloaded the SDK. But there's a bit of a learning curve to overcome. If anyone has any suggestions on good Android programming resources (other than Google's site), please let me know. I wouldn't even mind killing a few trees for a book.
- Hip-Hop in da House
There's quite a few android books but i never read them myself - http://www.amazon.com/Android...
- imabonehead
I find http://www.androidsnippets.org useful for learn-by-example stuff. Also, the API demos that come with the SDK. The Google docs have improved quite a bit over the course of this year. They are definately a good starting point for the high level fundemental stuff.
- Andrew Perry
from Android
Oh, BTW, great review Jason. Almost makes me want to trade up my ADP-1 for a Droid, since it sounds like an excellent device. Will be interested to know what the average battery life is, and if it has suffered by giving this phone a much larger screen & faster CPU.
- Andrew Perry
from Android
Well, I charged yesterday morning, used the phone all day and didn't charge over night. I'm at >50% battery power. I've done a little power management, so YMMV. So that's about 28 hours without charging.
- Hip-Hop in da House
from IM
Good review!
- Christoph Studer
More regarding battery life: the Droid recharges very slowly. Maybe that and the relatively long battery life indicates a larger battery? Anybody know?
- Hip-Hop in da House
from IM
it might also explain the additional weight of the phone.
- Hip-Hop in da House
from IM
BTW, I've been using the phone heavily this afternoon. Still at 20%.
- Hip-Hop in da House
from Android
I have briefly plugged into my car charger while out running errands. But other than that, no long charging since yesterday morning.
- Hip-Hop in da House
from Android
@Jason its a 1400 mAh battery. life of it seems to depend on what you are doing.
- Matt Ellsworth
Yeah, I'm realistic about how long the battery will last. If I'm playing MP3's and talking on the phone, I expect decent battery life. But if I'm watching videos, I don't expect more than a few hours, max.
- Hip-Hop in da House
LANjackal to LANjackal's feed, Security, All Things Google, Android, TheNextWeb Forum, RWW: The Future of Tech, building43
Friendly Security Reminder: If you got a Droid, remember to shred the paper you wrote your Gmail address & password on for the tech rep. I just found mine and fed it to my Fellowes.
Tyson Key and Jeff P. Henderson liked this
Yep. That's what I did when I purchased my G1 last year.
- imabonehead
Wait, what? Buying an Android phone from a carrier's store requires you to compromise your Google identity and all information that flows in and out of it by forking over your Gmail password to a rep?
- David Chartier
from iPhone
You can't get the phone without a Gmail account, and the tech reps are the only ones who can enter that info for you. I thought it was odd too, but if you see Ima's comment apparently T-mobile does it too. TBH I was horrified at the idea, but the rep told me he'd return the paper (which he did). Kinda unnerving though
- LANjackal
from IM
But I mean think of how many times you hand over your SSN (at the doctor, to your carrier/utility provider, etc.) and you never get the paper back. Nothing to freak out about, just make sure you destroy the paper so you don't have your login credentials floating around out there by accident.
- LANjackal
So, no biggie, just go home and change your password after you get your phone.
- Jeff P. Henderson
To elaborate more on my experience, when I bought my G1, I specifically requested to type in my own gmail account and SSN on their keyboard. I purchased mine at a local Costco. I did have to write down my personal information on a piece of paper. I took it home and shredded it.
- imabonehead
I think the reason they're doing it is for expedience. If they allowed everyone to manually enter their own info (bear in mind the average user with a new device) the whole setup process would take forever and picking up a Droid would take several hours on launch.
- LANjackal
The saleslady who sold me my G1 was very understanding. I don't know if other sales paople would do the same.
- imabonehead
I typed my password into the phone myself when they setup the first account for me. No way I'm giving some sales guy my password.
- Hip-Hop in da House
It seems a bit wrong that they don't get you to type your own password. Security #FAIL .
- Andrew Perry
Neo-Futurists at the Neo-Futurarium - http://www.neofuturists.org/
somewhere I'd like to go if I ever end up Chicago again ...
- Andrew Perry
Publisher Item Identifier - http://web.archive.org/web...
Michael Habib, Richard Akerman, Pierre Lindenbaum and 4 other people liked this
The following system for a Publisher Item identifier (PII) to provide unique identification of documents has been adopted by: American Chemical Society American Institute of Physics American Physical Society Elsevier Science IEEE The PII will be adopted by these organisations for all articles published from 1 January 1996. The proponents of the PII wish to encourage its use by other publishers and by secondary information services.
- Roderic Page
Interesting .. I've never noticed the PII in active use. Was it overtaken by the DOI ?
- Andrew Perry
Also, it appears they were thinking ahead: "It is assumed that in the future it will be necessary to identify components of documents (e.g. tables, graphics). PII allows extension to component identification, but does not present a detailed specification for this". This type of identification / linking has been discussed recently around here ....
- Andrew Perry
@Andrew it is referenced by pubmed. e.g. See the XML source of http://www.ncbi.nlm.nih.gov/entrez... ArticleId@IdType="pii"
- Pierre Lindenbaum
Ah, interesting. Thanks Pierre.
- Andrew Perry
Warren DeLano of PyMol fame has passed away :(
Oh no, that's terrible news... how did you hear??
- Shirley Wu
on the ccp4 mailing list
- Deepak Singh
from IM
:(
- Rajarshi Guha
Very sad, I saw Warren introduce an early version of PyMol, it was an excellent piece of software for a one man effort. The mailing list announcement is here: https://www.jiscmail.ac.uk/cgi-bin...
- Greg Tyrelle
Ah i see. Nothing on the google yet. He was relatively young too, wasn't he? Sad...
- Shirley Wu
from twhirl
I met him in August and he seemed fine! very depressing
- Rajarshi Guha
:(
- Ruchira S. Datta
He wasn't much older than me and I knew him a bit back in my modeling days, so this really sucks
- Deepak Singh
Very, very sad. Today in my graduate course on RNA one of the students spent most of the class showing us images of the ribosome that he generated with PyMol. The first thing I introduce to the students in this course is how to use PyMol. This is truly a great loss to the community.
- Tom Tullius
so sad. I only interacted with Warren via email, but it was always a pleasure. I greatly admired his support of FOSS, and was inspired by his ground-breaking work in molecular visualization. such sad news.
- tim
Very sad news indeed... :(
- Egon Willighagen
:-(
- Michael Kuhn
this is a big and shocking loss
- Wladimir Labeikovsky
Wow. I met with him a couple of times. Very, very sad. It will be hard to use pymol now without thinking of him.
- Iddo Friedberg
Very sad. Condolences to his family and friends.
- Neil Saunders
Very sad indeed. His legacy lives on in awesome molecular graphics now and forever.
- Adam Kraut
Oh, that's really, really sad news :(
- Andrew Perry
It was a kick in the head today when I heard that he had passed. A sad day indeed
- Antony Williams
:-(
- Mickey Kosloff
So sad--young guy, met him at a conference about 2 years ago. Accomplished so much--his science and entrepreneurship was an inspiration to me.
- Mary Canady
Anyone else interested in helping continue the PyMol codebase?
- Donnie Berkholz
Donnie, certain hope that it doesn't go away
- Deepak Singh
Last I glanced at the PyMol codebase it was actually pretty scary. Sloccount says: Totals grouped by language (dominant language first): ansic: 477951 (85.93%) python: 65182 (11.72%) cpp: 12928 (2.32%)
- Anders Norgaard
I realize I might get slapped for this but with light comes shadow (very Jungian I know). The upside of Warren releasing code as Open Source is that his work can live on and be continued. This is brilliant. The shadow is what about about his young wife that he has left behind? I talked with Warren earlier this year and PyMol was helping him to create a living. But what does his family...
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- Antony Williams
Please drop your comments here http://warrendelano.blogspot.com/2009...
- Abhishek Tiwari
An open letter to the medical community. - http://synthesis.williamgunn.org/2009...
Steve Koch, Andrew Perry, Bill Hooker and 2 other people liked this
Got some pretty good comments on my blog. Guess those fears expressed by some that friendfeed was stealing comments from bloggers aren't true, at least not for me.
- Mr. Gunn
Exciting debate - made me want to break out the popcorn! ;)
- Shirley Wu
from twhirl
Yeah, I'm finding I have a taste for fiery rhetoric. Maybe I should have been a baptist preacher or something.
- Mr. Gunn
Putting on my 'futurist hat': I expect that if the gatekeepers manage to regulate DTC genomics, making personal genomic information more difficult and expensive to acquire, some consumers will seek 'outsourced' tests provided by facilities in a different jurisdiction. It would be difficult for governments to police the practice of sending a tube of split overseas to an unregulated...
more...
- Andrew Perry
Closure Javascript Tools from Google - http://code.google.com/closure...
A Javascript optimizer and compressor, a Javascript library for widgets and DOM manipulation etc, and an HTML templating system for Javascript.
- Andrew Perry
Gnuplot demo scripts run through the HTML canvas terminal - http://gnuplot.sourceforge.net/demo_ca...
Pierre Lindenbaum, Neil Saunders, Jason Wehmhoener and Tracy liked this
Interactive Gnuplot plots in the HTML 5 canvas element. Now if someone were to write a Gnuplot interpretor in Javascript ...
- Andrew Perry
Android Virtual Reality Goggles [How To Video] - http://phandroid.com/2009...
Andrew Perry and Olka liked this
It looks incredibly silly, but if you replaced the cardboard box with a nicer headset and maybe some lenses, it could make for a good 3D movie viewer (with the movie running splitscreen on the phone).
- Andrew Perry
Avogadro : molecular editor - http://avogadro.openmolecules.net/wiki...
"Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.". You can "sudo apt-get install avogadro" to get it on Ubuntu (although you won't get the latest and greatest version).
- Andrew Perry
ChemDoodle Web Components - http://web.chemdoodle.com/
Pure Javascript components for viewing and editing small molecules.
- Andrew Perry
10.1080/09515088808572924 http://www.informaworld.com/smpp... Neiseer's five kinds of self. mail to sandygautam@yahoo.com- thanks a lot.
Graham Steel liked this
The Monash University library is usually pretty good ... alas, I don't have access to this one.
- Andrew Perry
no access, sorry
- Nils Reinton
no access, sorry.
- Björn Brembs
no can do.....
- Graham Steel
never mind. Thanks for all your efforts. just wanted it for a blog post!
- Sandeep Gautam
on its way
- Kubke
Many thanks!
- Sandeep Gautam
Many thanks to Kubke, I have written a blog post based on this reference paper and you can read it here: http://the-mouse-trap.com/2009...
- Sandeep Gautam
Claudia Koltzenburg, Alexander Griekspoor, Matt G and 4 other people liked this
Why do I see a website in the near future :)
- Deepak Singh
Surely easy deposition has to come first though?
- Cameron Neylon
Perhaps. Ideally all reads and writes would be created equal, but in reality a reasonable amount of heavy lifting is required at one end or the other. Given that data is usually written once and retrieved many times, I wonder if it's easier for those already generating and working with the information to jump through some deposition hoops once, rather than everyone being forced to do it at retrieval, time after time.
- Matt Wood
Agreed that access needs to be easy for users but put barriers in front of depositors and you will only get specific types of data (mostly big and well funded). But I don't know how to square the circle from easy to deposit blob to usefully described blob on a service.
- Cameron Neylon
Cameron, the barriers in front of depositors are cultural or systemic. The barriers in front of retrievers are often technical. But yes, we need to address both problems, but technical challenges of retrieval are real, since we aren't retrieving small data sets any more
- Deepak Singh
The most enthusiastic depositors are those whose peer-reviewed publication is tied to deposition. Get key journals to require deposition of data + metadata prior to publication, under a Public Domain or Attribution-required license, and the rest will follow.
- Andrew Perry
Deepak, absolutely agree - just was uncomfortable with "above all else". Tell you what, I'll let you and @mza get on with the technical challenges while I worry about the social ones. Division of labour and all that. @Andrew - this is absolutely true, but journals will not do this (and I agree with the logic on this) until they get a very strong steer from the community that this is...
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- Cameron Neylon
@cameronneylon it's ridiculous to think you can separate the technical challenges from the social ones, one cannot be understood (and solved!) without the other. Trying to tackle the technical challenges without solving the social ones is like building a car without having the blue print. Trying to tackle the social challenges without the technical ones is like building a rocket ship for the year 2150 and hoping someone will somehow magically solve the technical issues tomorrow.
- Alexander Griekspoor
Alexander, you won't get any argument from me on that, but Matt did start this manifesto with "there are no technical reasons...why an open data platform for science couldn't excel". In my view the technical problems are largely soluble with clear pathways for development, and I don't have the detailed knowledge to make a big contribution at the coalface. The social problems are much larger and require a more multipronged attack - which is directed by but not defined by the current technical capability.
- Cameron Neylon
What are the "social" issues? I'm confused by the use of the word in this context. Are we talking about cultural changes, such as acceptance of a more "open data" world, coercing people into using public repositories and so on? Or is this social as in social network? If the latter, I don't see the relevance to what Matt is discussing.
- Neil Saunders
Maybe cultural issues is better. But basically the fact that we have an entire social edifice built around control and secrecy driven by the need to publish. Fundamentally the problem that we need to rebuild the reward systems so that people actively take advantage of the potential of available technology. So yes, cultural rather than social perhaps, but I do think social networks or...
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- Cameron Neylon
22 Resources to Easily Create CSS Layouts | Vandelay Design Blog - http://vandelaydesign.com/blog...
a good list of many of the better free 'skeleton' CSS layouts around the web.
- Andrew Perry
Refactoring Home - http://www.refactoring.com/index...
"Refactoring is a disciplined technique for restructuring an existing body of code, altering its internal structure without changing its external behavior". This site contains a catalog of common refactoring operations.
- Andrew Perry
Ubuntu mirrors already slow as sludge - and Karmic is still 6 days away http://insidesocal.com/click... #linux
Mike Chelen liked this
change the #ubuntu repository mirror to another one: software sources > select best mirror
- Mike Chelen
here is a helpful guide: http://www.addictivetips.com/ubuntu-...
- Mike Chelen
debtorrent is another interesting option, it actually gets faster during high usage http://bit.ly/23NHCE
- Mike Chelen
Yep, debtorrent sounds like a good solution here, assuming enough other people use it too (and assuming you aren't on some touchy University network, where the sysadmin will physically turn up in your office within minutes of Bittorrent connection being detected, irrespective of the data being transferred).
- Andrew Perry
The trouble with getting a domain name is that I actually need to figure out how to organize my online life...
Khader Shameer, Dan Hagon, Jason Winget and 3 other people liked this
I've been at it for years and still haven't figured it out
- Deepak Singh
It's a lot of work. Probably easiest to have a clear landing page that says "here are all the other places to find me".
- Neil Saunders
Yes, more or less figured that out. Question of how to set that page up at the moment. I do want to aggregate some stuff back to one place though. OpenIDs, FOAF, draft documents, that kind of thing, and some view of the streams that I'm generating. Aside from anything else I need to learn how to actually run/deploy/setup these things.
- Cameron Neylon
On a related note: It seems you used to be able to generate FOAF for your Friendfeed subscriptions using http://friendfeed.com/<username>/subscriptions?output=foaf .. but unfortunately it doesn't seem to work now.
- Andrew Perry
A domain name is just a name so if you've got some content hosted elsewhere already you can just use it as an alias - however I think the problem you're actually talking about is hosting that content. Assuming you're not already tied into one particular hosting company (as part of the domain name registration) I'd advise looking at a few content management systems (although they're...
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- Dan Hagon
Wait, friendfeed FOAF doesn't work anymore? Data portability fail there! I hope that's not a facebook-mandated change.
- Mr. Gunn
Cameron, I'd look into delegating your domain URL as an OpenID URL. Verisign has a pretty cool profiles service: http://williamgunn.pip.verisignlabs.com/ and there's also Google Profiles.
- Mr. Gunn
@Mr. Gunn - fancy stuff, this, very cool. Coverflow-style scrolling borrowed from OS X. Methinks I should switch from MyOpenID (http://mummi.myopenid.com)...
- 'Mummi' Thorisson
Yep, openID is coming. Think I'll be doing something quite simple with a Wordpress install as a starting point.
- Cameron Neylon
PlayOnLinux - Run your Windows applications on Linux easily ! - http://www.playonlinux.com/en
"PlayOnLinux is a piece of sofware which allows you to easily install and use numerous games and softwares designed to run with Microsoft®'s Windows®."
- Andrew Perry
Dealing With Big Data In Bioinformatics - http://www.bioinformaticszen.com/softwar...
george, Ricardo Vidal, Michael Kuhn and 7 other people liked this
Good comments on the post too ... a few interesting counterpoints from the fans of flat files.
- Andrew Perry
from Android
Come to supercomputing. My whole talk is on this subject ;). Trying to figure out if I should start writing about it before or after
- Deepak Singh
I understand the points in the comments about using flat files for better speed. However compared to when I used to use miscellaneous scripts and data files to do my research I find that using a 'Ruby on Rails' type of database-backed approach is much better for me because of the shorter development time and how much easier the code is to maintain.
- Michael Barton
@Deepak I did consider mentioning Hadoop/NoSQL (see last paragraph of earlier draft http://bit.ly/ztjS9) as it's obvious to discuss these types of approaches when dealing with very large datasets. However I think these tools do still require a fair amount of work for maintain and use compared with a more standard kind or MySQL approach. I say that because I tried using map/reduce across the university cluster and had quite a few teething problems.
- Michael Barton
More generally, "any DB + any ORM" is A Good Thing. I can see why people stick with (My)SQL. It's tried and tested. I find a lot of the newer developments interesting, exciting, fun - but often, "too agile" for real work. Libraries change too fast, documentation (if any) goes out of date, code moves to new repositories, in the space of 3 weeks.
- Neil Saunders
@Neil I originally tried using DataMapper instead of ActiveRecord but so many Rails centric libraries assume ORM == ActiveRecord. This meant using DataMapper precluded the use of the factory_girl and shoulda libraries which I have come to find very useful. I think Rails needs to be is truly ORM agnositic and that the current changes in Rails 3.0 doesn't go far enough to address this.
- Michael Barton
I agree. I really like DataMapper (and other ORMs - sequel, mongomapper), but using them with Rails components = ugly, not fully-functional hacks, as things stand. Be interesting to see how the new ActiveSupport looks. I'm even considering abandoning Rails for now and just plugging together components myself as required (e.g. ramaze/sinatra if web frontend required).
- Neil Saunders
Michael, I am not talking just about Hadoop/NoSQL, but the fundamental challenges of operating at high scale. How you handle disk failures, node failures, approaches to managing that data, etc. The rules change once you are working in the multi TB range (and when I talk Big Data I am mean several TB's).
- Deepak Singh
The Render Engine - Javascript Game Engine - http://www.renderengine.com/index...
Michael R. Bernstein, Marcos de Carvalho and Pierre Lindenbaum liked this
"The Render Engine is a cross-browser, open source game engine written entirely in Javascript."
- Andrew Perry
Giftag – Pick Anything | Andrew Perry - http://www.giftag.com/pansapi...
A wishlist service running on Google App Engine. Pretty snappy little web app, although I'm sure there are tons of competitors (Amazon's 'Universal' wishlists for starters).
- Andrew Perry
(web.py) - http://webpy.org-simplewebappf...
"web.py is a web framework for python that is as simple as it is powerful. web.py is in the public domain". A barebones simple web application framework for Python. Similar to Sinatra for Ruby, or the "webapp" module used by Google App Engine. I like the way it keeps the code close to the HTTP protocol - the method to handle a GET request is called ... you guessed it ... GET().
- Andrew Perry
Here Comes Science - http://science.easternblot.net/...
I watch/listen to this pretty much every day
- Rob Shillingsburg
website problems? sounds like they need to ssh tunnel through another server first
- Mike Chelen
Yep, Eva has been having some harrowing issues with her web host - seems to be moving hosts now. The key part of her post was a link to the album on Amazon: http://www.amazon.com/Here-Co...
- Andrew Perry
Starting to get the hang of Wave. I compulsively copy-edit other peoples text and add formatting for clarity. Is this considered rude ?
no, but then they might get annoyed if you stop ;D
- Mike Chelen
Please continue.
- Chris Lasher
Agree - very good practice! :)
- Allyson Lister
Thanks all. I felt like that was the right approach. I'm guessing that eventually some type of Wave "netiquette" will evolve for large Waves with many participants. It's one thing to 'improve' a shared document, but another to modify someones personal comments to change the meaning of what they were trying to say (as I've seen people having fun with ... changing "rox" to "sux" with much...
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- Andrew Perry
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