I am shocked how underutilized the undergrads are at mostly-graduate institutions. They're like a second class. I went to a PUI, and we weren't treated as menial labor there. - Donnie Berkholz
This was discussed here sometime ago when someone linked to a PR article that appeared online. - PauloNuin
Here's the structural proteomics example I mentioned previously: http://www.nature.com/nsmb/jou.... "All cloning and initial expression, purification and HSQC/crystal screens were performed at the Ontario Cancer Institute (OCI) over a 12 month period by A.D., D.C. & A.Y. with the help of one FTE technician and (for 4 months) six summer students". - Neil Saunders
On the topic of under-utilisation: we once had a plan to set up something like Condor on machines in the undergraduate computer labs, for number-crunching during vacation. Faculty IT was not impressed, naturally :) - Neil Saunders
I know the people that published the Nature Structural Biology paper. - PauloNuin
The Secretary of State for Innovation, Universities and Skills has today announced the appointment of Professor Douglas Kell as the next Chief Executive of the Biotechnology and Biological Sciences Research Council (BBSRC). - Duncan Hull
Dunno whats going to happen to our lab yet, yikes! - Duncan Hull
Depends on the job, I'd say. A programmer can probably use a portfolio of applications. An academic would look pretty stupid without at least a list of their publications. - Neil Saunders
I have decided I will switch to one of those two when I finish the project I am working on right now, probably python. - Pedro Beltrao
I do envy BioPerls breadth and maturity compared with BioPython .. but not enough to tempt me to switch back to Perl after my early beginnings with that language. I've looked into ways to call Perl functions from Python, but there doesn't seem to be anything that works well and is maintained. - Andrew Perry
BioPerl was essentially my reason for starting out in Perl, about 8 years back. Perl CGI also used to be the way to go for web apps, but the new web frameworks are much more appealing. Increasingly too, I find Perl unwieldy, slow and well...ugly. It's much nicer to write "l = a.length" than to loop through some horrifically complex data structure just to get to a variable. Admittedly, one of my weaknesses is creating horrifically complex data structures :) - Neil Saunders
So, let's kick things off. Who is (a) attending ISMB 2008, (b) attending a special pre-conference but not the main event or (c) not attending, but will be in the area? - Neil Saunders
I'll attend the main conference only. - Roland Krause
(c) - I live in Waterloo, just outside Toronto. If some open-sciency people want to meet up, I'd be keen to meet. The Duke of York is a pretty good pub near the University of Toronto (http://york.thedukepubs.ca/). The Linux Caffe (http://linuxcaffe.ca/) is a slightly longer walk, but also good. - Michael Nielsen
I live in TO but I am not attending ISMB. - PauloNuin
I won't be there, but let's see what the back channel is like - Deepak
I'll be at ISMB only and will be in town July 16-24 - Neil Saunders
I'll be there for the conference and presenting a poster - Daniel Jurczak
would be interesting to know where everyone is staying so we can plan something (pub, restaurant, etc). The conference venue is really close to the entertainment district, but we can always arrange something close to UofT. - PauloNuin
I will be there for the main conference. - Pedro Beltrao
I will be at the 3Dsig satellite meeting on the 18th-19th but not the main event. - Adam Kraut
LinuxCaffe? How deliciously geeky and cool. Must go there. - Neil Saunders
I'll be there, between July 17-23 (main conf. + student symposium). - Michael Kuhn
Neil - it's got free wireless, and stacks and stacks of geeky books piled all around, free for the reading. Plus, it's got a nice atmosphere. - Michael Nielsen
I'm with Neil. Tiresome is the word. That thread is a good example of why I don't bother with NN most of the time. - Bill Hooker
Tiresome? It's Jenny's blog, not conference proceedings, and not even forum thread. People just...chat in the comments. There doesn't have to be a solution for the nomenclature problem right there, or even consensus. And unlike radio, you can skip ahead if it's not interesting to you. (P.S. I find FriendFeed "tiresome") - Eva
The trouble with "if you don't like it, go elsewhere" is that if no one ever speaks up, nothing changes. (Of course, what I dislike about NN isn't going to change, so I'm not doing anything useful here, just letting off steam.) But Eva is doing more: making the criticism where it counts. Eva, what don't you like about FF? It's pretty flexible, so perhaps you could customize your view to suit you better. - Bill Hooker
But I meant - this is just someone's blog, and it's not really fair to extend it to NN as a whole. (Criticism on the forums I get - but even there they're all slightly different). Friendfeed is too fast for me - this was already down on the page now. I already blocked certain people's friends to remove noise, but there's still too much of the same serious discussions flying by too fast to think, and simultaneously people's favourite movies and photos. If I could make friend groups that might work. - Eva
Have you tried the "show best of" links up there on the right? You can even hack the URL to get any number of days you want. I don't use it much but others have commented that it's a good way to get up to speed after a break and/or stay current with the "hottest" topics. - Bill Hooker
I've tried it, but it assumes that I like what *most* people like or commented on, and that's not necessarily true. - Eva
It's tiresome when someone raises an interesting, important issue only for the comment thread to fill with irrelevant, time-wasting crap from people trying to out-do each other and who are oh-so-very-witty and erudite. It seems to be a characteristic of NN and like Bill, it stops me going there. - Neil Saunders
I guess the tendency of any thread to go to waste with irrelevant comments is a characteristic of many online forums. And this tendency increases with the increase on the number of users. I don't access NN that much and based on what you guys said I won't be accessing it. - PauloNuin
@Eva "assumes that I like what *most* people like or commented on, and that's not necessarily true" absolutely, Not all that is famous is important, and not all that is important is famous. Sometimes I find the friendfeed echo chamber too noisy, but on the whole its worth filtering out the noise for the occasionally good signal. - Duncan Hull
It's worth remembering that FriendFeed is searchable. If following in real time is too much, you can always mine it for keywords of interest at your leisure. - Neil Saunders
I've just been pointed here by Corie Lok's blog. I've read your group views before about NN so I'm not surprised. The fact that some people like the conversations there is "tiresome", you think, Neil, and beneath you even bothering to participate, Bill? Why should we be interested in knowing you think this, as you don't bother to provide a reason? (a Twitter post, limited to 140 words, would have been even better for a withering unsubstantiated comment). This old blogopshere sure does make people feel they can be rude about anyone behind their backs, but in public. Well, that whatever faults you damn NN for,it cannot be said to be like some of the comments here and elsewhere in this "little group" about people's personal integrity and intelligence. - Maxine
Maxine, it's just two opinions (mine and Neil's). As several posters have gently, calmly and not at all defensively pointed out on Corie's blog, the optimal solution is for us not to read NN so much. I do post there, usually when someone points me to a good thread. I even recall helping you out the other day, in a NN thread. And I pointed out above that I'm "not doing anything useful" in this thread -- I felt a bit of a heel for the unprovoked jab. - Bill Hooker
But since you asked, I hardly think it out of bounds occasionally to point out that every other thread degenerates into a second-rate Goon show, particularly when Nature is forever trumpeting how web-savvy it is and pointing to NN as an example. - Bill Hooker
I see NN as an Orkut-for-scientists (maybe because I used Orkut for a while to keep in touch with old friends), basically the you have to be a scientist to enter it ("normal" people would find it boring) but in the end the quality of the discussions is not much better than any other social website. - PauloNuin
Apparently the FDA received 10,000 adverse event reports since it has been on the market but against 25M vaccinations, that's a low percentage. The thing people forget is that all vaccines have unknown side effects and can have a severe reaction in some people. - Sally Church
Yes, one can only hope that the vaccine-autism hysteria doesn't repeat. I do notice that I am disturbingly susceptible to scaremongering having a daughter approaching the Gardasil age....... - SciPhu
The thing people forget is that cervical cancer is actually very rare in Western countries. The ones I would worry about are those with a history of cervical or ovarian cancer in the family. - Sally Church
@Sally Church do you think vaccination in western countries is not worth the effort ? - SciPhu
whatever the relative risk of vaccine-related events vs. cervical cancer risk is, the vaccine-related event is going to be preferable to having cervical cancer, right? - Mr. Gunn
I've given a lot of thought to this one and overall, I think the risks of getting cervical cancer are very low unless you have a family history of it. So, no, I would probably pass on this one if I had teenage daughters, but make sure they are educationally aware of the risks and dangers. You have to remember, these vaccines are new and many generations have survived without an increase in cervical cancer. I do agree with vaccinations for tetanus and MMR though. - Sally Church
Mr Gunn: I'm thinking more in terms of the risk of protection from HPV infection vs. the risks associated with a severe reaction leading to paralysis etc. - Sally Church
UniProt is one of the first life sciences databases to distribute all of their data in RDF format (both via FTP and the Web, ~1B triples) -- that ought to count for something :-) - Eric Jain
For my money, OBO is trying to do semantic web in a big ambitious way, some success already but still a long way to go http://www.obofoundry.org/ - Duncan Hull
WormBase - one of the first model organism databases - is in the middle of a ground up rearchitecture that embraces (some) semantic web principles. All vapor ware at this point but I hope to have a public test site available soon. - Todd Harris
Also, if I remember correctly, EColiHub is also planning an RDF backend (I could be wrong) - Deepak
Agree that OBO are trying to do good stuff with OWL, etc. I think SBML is impressive too. So semantic web == RDF ? If it were that easy, every web service would emit it :) - Neil Saunders
IMO RDF is a sufficient condition for an application to be considered SemWeb. In the end it's a representation of a graph, which is what the SemWeb is all about. Ideally RDF with a SPARQL end point. That's pretty much what the Talis platform offers. OWL is a part of the SemWeb stack, but you don't always have to define a vocabulary. - Deepak
Semantic web (as defined by the W3C) != speaking toasters. It's "just" data (RDF/OWL) that is accessible on the Web. Bonus: Provide a SPARQL endpoint so people can query the data rather than just retrieve it by URI. Challenges: Data modeling, scalability (if you have a lot of data), and creating generic-yet-usable end user tools that work directly with the RDF graph data model (I have yet to see any of these)... - Eric Jain
"generic-yet-usable" you hit the nail on the head :) - Deepak
RDF, OWL, OBO, SPARQL endpoints WHATEVER, doesn't really matter. One of the most important things is agreeing on, defining and sharing vocabularies. Easy to say, much harder to actually do. Despite all the semantic web hot air daydreaming, there aren't actually that many people actually doing it. - Duncan Hull
Some of the Semantic Web standards and tools may be useful for defining and sharing vocabularies, but where they really shine (and stop being overkill) is when you realize that you won't ever agree on one true shared vocabulary, but still need to be able to map/relate concepts from different vocabularies. That, and the generic, graph-based data model is kind of neat :-) - Eric Jain
Thanks folks for giving a little homework for the poor experimental scientist. :) - Attila Csordas
That last comment brought a smile to my face. That's my favorite movie. - Brian Daniel Eisenberg
First, do what Neil said. Then put it out the front on the footpath. someone will take it, and maybe it will get a good home. Or give it to some kids to hack around with. - Andrew Perry
Thanks for the suggestions. I've got about 10ish old Dell PIII desktops and a couple oldish laptops. I've been slowly giving them away, cannibalizing as much as I can, but I've come to the conclusion that for what I am trying to do I will need a lot more processing power. Just don't have the $$$ to upgrade right now. - Brian Daniel Eisenberg
PC Load Letter!?! WTF is PC load letter!? - Hao Chen
Just resharing to my feed, for those not following Life Scientists - Neil Saunders
You mean there are those who don't!!!???!!!##**&& :-) - Deepak
I shall not be there.. Deepak: would have been nice to meet you in person. Just subscribed to the room, virtually I'll be present... - Egon Willighagen
“Yuvi made a comment on another thread about the Metric System in the US. Or lack thereof. It's funny how some things are, like 2 liters of Soda. Go, conversate!”
I live in a US territory where the speed limit is in miles per hour, but the distance signs between towns, cities, and expressway exits are in kilometers. Gas is sold in cents per liter, milk per gallon (plastic) or quart cartons. At least the cars have both miles per hour and km per hour speedometers as they do in USA and Canada, but the odometers are in miles! - Dread Pirate PJ
PJ crying in your beer again-tears/ml beer/fl oz. - Mark Forman
The fact is the the US needs to get with the program. Miles, gallons, pints, pounds? C'mon! It's easier doing things in 10s isn't it? Is it too expensive to change or something? Much of the world has had it for decades now. Suck it up and do it y'all :P - jjprojects
Come now, you know Americans hate change! Our 2 liters of soda is about it. (We do use metric along with american standard, but it's ignored by the people) - Eric Rice
The only reason USA uses metric is because you share some products with Canada and Mexico. The manufacturers and packagers don't want to make separate labels for the same product just because one of the three NAFTA countries isn't metric. So they put both metric and "american standard" on the packaging. That's why your 2 liter bottle of soda says "2 liter 67.6 fl oz (2 qt 3.6 oz)". ;-) - Dread Pirate PJ
Actually, this practice of standardizing on one size and packaging for product shared among the three countries is older than NAFTA, so forget I mentioned it. - Dread Pirate PJ
Forgotten-looking for my .6 fluid ounces of White Out - Mark Forman
I just feel sorry for the kids having to learn all the odd measurements, when they could be just learning decimals instead. What a crazy thing to hold on to. - jjprojects
You used "conversate" just to annoy me didn't you? Jerk. :P - Erica Baker
Born in early-seventies UK, I am fully conversant in both forms of measurement. Other people, however, sometimes look at me sideways when I ask them to cut something 3 feet by 180mm. Even more so when I tell them to make it half a digit thick! - Slippy Lane
Running events: 5K 10K races. I've spent my whole life metric so I'm always a little confused about distances in miles. - melmcbride
I survived the change from Imperial to Metric in Canada and like Andrew Smith I still use pounds and ft/in for personal measurements. Strangely enough my (now adult) children who grew up only knowing metric do as well. - Brian Sullivan
In the third grade, 1978, in Georgia my math teacher said "OK, we've got to learn the metric system, because the US is going to switch over to it SOON!" Apparently we had plenty of time to learn it. :-) - Joey Gibson via twhirl
When you're a kid in the U.S., you don't think of it as hard to learn. You don't know anything different! You learn it just like you do your ABC's. There's 12 inches in a foot, 3 feet in a yard, and 5,280 feet in a mile. The hard part is when you get to high school science classes. That's when I learned there are 2.54 cm in an inch and how to convert from C to F. - Matt
It's kinda hard to visualize distance in metric, even though I know the math is easy. I kinda have a grasp on how big 100 yards is, or 1/4 mile, etc. Only lately, have I started to realize the distance of 256 m. - Eric Rice
just curious - how do you see that kind of functionality improving your experience? I personally haven't thought about it much - Julian Baldwin
I mean if I really like a comment, that way I can vote for it ... not every comment is equally relevant in a coversation - Nick O'Neill
@nick should that feature be public or private then? what's not equally relevant to you, may be highly relevant to myself or someone else - Julian Baldwin
I often want to like a comment, rather than or as well as the original post. I'd also like something more than "like": sometimes it's not clear if "like" means "I like what you posted" or "I'm glad that you posted this but I don't agree with the content". - Neil Saunders
Then the conversation would be all screwy. Nevermind I see what you're saying. I thought you meant vote comments up. That would be nice. Maybe a star next to the comment or something. - Corvida
We can't expect other cultures to respect our mores if we don't respect theirs, so I'm all for honoring the request. On the other hand though, I can't fathom why the Ngarrindjeri want the remains returned. I'm an atheist, and anybody's welcome to my scabby bones if they want 'em after I'm done with 'em (med research and educational projects get first dibs). - Bill Hooker
Though the RMS response was a nice contrast to the British Museum's "yeah, we've had these in a drawer for 150 years but we need to do more research before you get them back". Let's face it, more or less everything these guys had has been destroyed: we can at least give them this. - Neil Saunders
I find sites with "remember me" boxes very confusing - it's never clear exactly what they remember. Usually to do with cookie storage, I think. - Neil Saunders
It's pretty much permission for the site to store a cookie, although I agree, the NN cookie doesn't seem to work - Deepak
It was working for me for a while. Now it doesn't always remember me. Guess it's because I've been neglecting it so much... :( I'm sorry NN!! Please remember me again... I promise I'll come around more often. - Ricardo Vidal
Remember to also check the "remember to remember me" checkbox... - Eric Jain
It remembered me today, but usually I just use Firefox's remembering powers so my info is at least filled out and I only have to click a button. - Eva
It remembers me for longer than claimID does - who was it who recommended me claim ID for an openID? - Maxine
I also rely on Firefox so it is easier to login, otherwise I would have to type everytime I access it. - PauloNuin
I'm using the Sxipper Firefox extension to remember my login information. It has some nice features for automatic form filling. - Yuval Langer
Maxine, not too late to switch to myopenid.com. They do a great job - Deepak
"On WordPress.com it is used to store all images and other web page components from the admin area to the user’s PC, speeding up access and reducing unnecessary web traffic." - Neil Saunders via Bookmarklet
Worked for me in FF3 but not Flock 2 - Neil Saunders
I'm sure that promiscuous, non-functional phosphorylation occurs to a degree. Not sure that I buy the evolutionary argument. Phosphorylation may consume a tiny fraction of cellular ATP, but it's like the "what use is half an eye" question. Over time, would we expect selection for efficient use of ATP and against wastage, no matter how small the differences? - Neil Saunders
that depends on the selection pressure (effect on fitness plus population size). I don't think that there is enough selection pressure to purify most wasteful phosphorylation for the energy it costs. There is also a high turn-over of phospho sites so at any given moment (i.e. present time) there must also be a large number of sites that are under transition. - Pedro Beltrao
