Andrew Perry › Comments

I've seen various programs that do this over the past few years (for example, "Selecton" http://selecton.tau.ac.il/ from the Pupko lab), but I've never used any of them so can't recommend one as good. - Andrew Perry

Codeml from PAML - http://abacus.gene.ucl.ac.uk/softwar... - Marcos de Carvalho

"Protein finder is a gendetector. The program finds genes by performing blastx searches of the input sequence against NR. For each high scoring pair the coverage is calculated. The user can set a threshold for the coverage. Every high scoring pair that meets or exceeds this threshold is reported in an embl file. This embl file can be loaded into artemis together with the DNA sequence." - Andrew Perry

That's awesome. - Bill Hooker

My initial reaction was "how can anyone pipette that quickly !" ... but it seems they have some fancy quench-flow equipment to get around that problem. Very cool. - Andrew Perry

Possums? :-) - Neil Saunders

Yes, we have those running around in there, and the first few times I was woken by the noise I put it down to the ringtail possums. Last night, I was awake when it started, and it was definitely footsteps from some type of heavy bipedal animal, and a distinctly different sound to the scurrying of possums. This time they walked along a single line and then back, over maybe 30 seconds.... more... - Andrew Perry

Trackmate is an open source initiative to create an inexpensive, do-it-yourself tangible tracking system, allowing any computer to recognize tagged objects (and their corresponding position, rotation, and color information) when placed on a surface. - Andrew Perry

Molecular biology and evolution (3 December 2009) beta-barrel proteins are present in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. Their assembly requires a machinery of which the central component, called Omp85 (BamA) in bacteria and Tob55 (Sam50) in mitochondria, is evolutionarily conserved. An open question is whether the signals in beta-barrel outer membrane proteins required for assembly via this multicomponent machinery are also conserved. To address this question, we have expressed in Escherichia coli the mitochondrial porin VDAC from Neurospora crassa fused to a bacterial signal sequence for transport across the bacterial inner membrane. The protein was assembled in the bacterial outer membrane where it formed pores. Assembly of VDAC was dependent on its beta-signal, which is required for assembly in the mitochondrial outer membrane, and on the bacterial Omp85 assembly machinery. These results demonstrate that the basic mechanism of beta-barrel... - Andrew Perry

an exciting turn of events. - Andrew Perry

Now that's interesting...fascinated to see how this plays out now - Cameron Neylon

Congratulations! "We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team." - Paul Buchheit from Bookmarklet

Andrew: I'm just glad Etherpad (probably following the outcry that their earlier post provoked) made public pads possible again and is to be released as open source for anybody to grab the code and create something out of it. I'm not the slightest concerned about the price at which Etherpad would have been acquired had not Wave existed, it's Google we're talking about here. - lelapin

I don't know if there is any point to this ... - Steve Koch

I agree, it's a little pointless putting a Google Doc inside an iframe inside a Wave. It seems inevitable that Google will provide some proper integration for collaborative editing of Google Docs via the wave protocol at some point in the future. There's probably some developers from Etherpad working on it as we speak ... - Andrew Perry

AGen is a new 2D engine and framework specifically designed for the easy and rapid development of games, game prototypes or other visual applications. AGen is completely Lua scripted and allows you to make games with little overhead and without a compiler. - Andrew Perry

This is my Motorola Droid review. Hope you guys like it. - Jason Huebel

I have the car dock, among other things. So I pretty much have charging covered now. - Jason Huebel from IM

"Here are three I bookmarked recently, neither of which I used (yet): The Render Engine: http://www.renderengine.com/index... gameQuery: http://gamequery.onaluf.org/ Also, Raphaël may be an option for vector graphics: http://raphaeljs.com/ And the only one I've actually used - Processing.js: http://github.com/jeresig..." - Andrew Perry

Just discovered there is a locally hosted myExperiment server here in Australia, with a separate database from the main myexperiment.org site. There's not much there yet, and I'm a little puzzled at the purpose of running a separate .org.au server ... it would seem to make more sense to share workflows on http://www.myexperiment.org where they are more likely to be noticed. I'm sure someone has their reasons ... (which I suspect are probably 'because we can'). - Andrew Perry

Seems to be mainly the eResearch crowd from Monash. There seems to be a notion in some quarters that for Australian eResearch to be noticed, it has to be branded as "Australian". Kind of misses the point that in the web of data, you don't care where it came from... - Neil Saunders

It's worth noting that for every 'serious' app mentioned in this article, an Android equivalent is available. Based on the use case discussed, an Android phone with a physical keyboard would be a much better choice for anyone who might need to do any significant amount of typing, such as administrating a server or tweaking some HTML. I really should comment on the original article, but I don't think I can handle the yapping and rationalizations from the iPhone fanboys. - Andrew Perry from Android

A very simple, high level overview of the methods in a typical protein crystallography pipeline, from recombinant DNA manipulation to protein production and crystallization to 3D structure determination. Includes cheezy 'corporate induction video'-style soundtrack. - Andrew Perry

Bob Hitchings presentation about emerging trends and techniques for using geolocation on smartphones. - Andrew Perry

Journal of molecular biology (19 November 2009) The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrel, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow "constriction zone". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets... - Andrew Perry

Looking sharp Don ! - Andrew Perry

Another plus for agile development? :) - Benjamin Tseng

Ah .. but "muck around" really means "iterate" or "tweak" .. so the app may end up taking the same amount of time as a non-agile app, but it will have been through more rounds of iterative improvement. - Andrew Perry

Now that I think about it a little more, 454 would be best, as I want to re-sequence a genome. - Alejandro Montenegro

Thanks to everyone for their comments. I've been sending emails and getting quotes from all of the recommended companies. I'll keep you posted. In the meantime, if you know of any other companies, please share. - Alejandro Montenegro

The GIFT is a Content Based Image Retrieval System (CBIRS) which enables you to do Query By Example (QBE) on images, giving you the opportunity to improve query results by relevance feedback. It includes a tool which lets you index whole directory trees containing images, which you can then browse and search using the GIFT server and its clients. - Andrew Perry

Excellent. A tick in the plus column for the government. - Neil Saunders

There is a lot of dross on Channel 31 in Melbourne, but there are a few gems too - namely "Chartbusting '80s", "Champagne Comedy" and "The Shambles". The disability talk show with the lesbian midget was pretty good too. I'm pleased that they are being allocated spectrum and given some help transitioning to digital before the analog network gets turned off, since up until this announcement their future has been uncertain. - Andrew Perry

Our house is rather fond of "Vasili's Garden". - Neil Saunders

I think our designers/developers for BioGPS use http://www.balsamiq.com/product...... - Andrew Su

If you have a mac machine, I would highly recommend OmniGraffle. There are many good stencils available at http://graffletopia.com/. I had some good success with it in my previous gig :) - Satish Bhat

Finding and picking apart code that may work, but is not completely optimal, is a pretty easy game, and some of this article is a little petty. It shouldn't be a huge surprise that "OMG some Google engineers wrote some suboptimal Javascript !!1!" - however the good part about this article is that they provide lots of examples of common Javascript optimizations that can be applied. - Andrew Perry

Raphaël is a small JavaScript library that should simplify your work with vector graphics on the web. Raphaël uses SVG and supports Firefox 3.0 , Safari 3.0 , Opera 9.5 and Internet Explorer 6.0 . - Andrew Perry

finally a little cross-compatibility for svg :) - Mike Chelen

gRaphaël is a Javascript library that helps create attractive charts - Andrew Perry

javascript is a helpful tool any time the browser comes into usage - Mike Chelen

The Ubuntu and Debian EC2 images published on http://alestic.com allow you to send in a startup script using the EC2 user-data parameter when you run a new instance. This functionality is useful for automating the installation and configuration of software on EC2 instances. - Deepak Singh

I used this feature last year - it's really handy to be able to pass a script to "apt-get install" various things after startup. In my case I also pulled a BLAST database from s3 using s3cmd. - Andrew Perry

user-data scripts are compatible with official ubuntu amis, and can be used to boot strap other startup utilities like runurl - Mike Chelen

It seems this could be used to avoid maternally inherited diseases caused by 'defects' in the mitochondrial genome of the nuclear-genome-donor-mother. - Andrew Perry

Multicore and MPI FTW !! - Andrew Perry

Some amazing acrobatics / gymnastics here, once it gets going. I wonder why we rarely see people doing these moves today - I doubt it is due to lack of skill or training. Maybe certain moves have just gone out of vogue, or are now considered too likely to cause serious injury ? - Andrew Perry