Michael Kuhn - Comments

15 EVOLUTIONARY GEMS - http://www.nature.com/nature...

Saturday from delicious - Comment - Like - Share

"Given that the concepts and realities of Darwinian evolution are still challenged, albeit rarely by biologists, a succinct briefing on why evolution by natural selection is an empirically validated principle is useful for people to have to hand. We offer here 15 examples published by Nature over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking. We are happy to offer this resource freely and encourage its free dissemination." - Michael Kuhn

The Life Scientists: Nils Reinton

After three rounds of referee comments and subsequent manuscript revision I get the comment: "we would like you to argue around the concept "you only find what you look for" in the discussion and conclusion". WTF, - in a scientific paper !!! What does that even mean ? Anyone have any ideas on how to respond to this ?

November 6 - Comment - Like - Share

who's asking you to do this? the editors? as for what it means: http://en.wikipedia.org/wiki... – but that wouldn't be a positive thing to put in a paper. I don't know what your findings are, but perhaps you can argue "you only find what your method of detection could possibly find" like in the different methods of looking for protein complexes http://www.sciencemag.org/cgi... - Michael Kuhn

7 more comments

Yes, it's the editors and the paper is a straightforward summary of prevalence of a Chlamydia trachomatis variant (nvC trachomatis). We were only looking for nvC and we found nvC. Finding specifically what we are looking for is kind of a cornerstone in diagnostics (specificity) as opposed to basic research, where you might want to find anything and everything. Nevertheless, like you say... more... - Nils Reinton

how about this pattern: "There are other mechanisms to cause X, for example, A, B, and C [REF]. However, our findings explain XX% of all cases and thus show that Y is an important mechanism in the etiology of X." - Michael Kuhn

That would be ok if there were other "mechanisms to cause X", but here "X" is the presence of this bacteria. Our method is not in dispute, nor is the quality of that method, presumably then, it's agreed upon that our method explains 100% of the cases, and I still do not understand what the editors want from us. I would if this was a question of the specificity or sensitivity of the method, but even then the statement would make little sense to me. - Nils Reinton

Nils, remember that reviewers comments, even editors, don't have to make sense. It sounds to me like they're trying to suggest that they wanted some discussion of sensitivity and specificity, so put that in there and say something like "Detection of other analytes, while of significant diagnostic utility, is beyond the scope of this method." - Mr. Gunn

Mr Gunn FTW. I will just add that I have found some editors to be very responsive to questions like "what the fuck do you mean by this?" -- it might save you some time to ask them directly for a clarification. (Also that I am not in favour of jumping through meaningless hoops to satisfy an editor who *won't* give a reason for his/her requests. There are plenty of journals out there.) - Bill Hooker

Thank you all for valuable advice. I will end up doing a combination of all of the above. I already sent an e-mail reply to ask for clarification, but have also started working in changes such as those suggested by Michael and Mr. dr. Gunn. This is for a national journal which was chosen to reach our clients as effectively as possible, - and it's open access :-) Collaborative studies on... more... - Nils Reinton

So after trying to work in something sensible into the manuscript, in frustration I ended up adding the following to two different sentences (one in the conclusions section and one in the discussion section): "..... emphasizing the point "you only find what you look for"". And....now the paper is approved. Not sure if I am sad or happy about this. - Nils Reinton

Frustrating indeed. I recently abandoned a submission (only a letter to the editor) rather than jump through any more hoops. This is, unfortunately, not an option for anyone still in academia or anywhere else that papers are currency. - Bill Hooker

Paulo Nuin

You drive a big heavy fire truck. Grandma is approaching from the left, on her bike. Do you C) go forward? - http://www.reddit.com/r...

Wednesday from Reddit - Comment - Like - Share

Michael Kuhn, Yann Abraham, Pierre Lindenbaum and Lars Juhl Jensen liked this

For the lazy people, just go directly to the action: http://bit.ly/4DXwZv - Lars Juhl Jensen

3 more comments

Wow, it seems that Google has decided to censor out the interesting image - Lars Juhl Jensen

When turning 180° later http://tinyurl.com/yh65ojc you can see that grandma was safe, and the truck has gone. So I guess, Google's staff stopped to help her - Pierre Lindenbaum

mirror of the image Google removed: http://i.imgur.com/deTJ8.jpg - Michael Kuhn

Maybe the fire truck had nothing to with the accident. Maybe grandma saw the Google Street View car and go so excited that she fell on her bicycle ;-) - Lars Juhl Jensen

Egon Willighagen

Frequency of a Term via PubMed - http://blog.rguha.net/?p=443

November 11 from Google Reader - Comment - Like - Share

Rafael Sidi, Benjamin Tseng, Frank and 8 other people liked this

Liking this very much! Thanx, Rajarshi! - Egon Willighagen

6 more comments

E.g the rise of "ontology" http://rest.rguha.net/usage... and semantic http://rest.rguha.net/usage... have we reached the peak yet? - Duncan Hull

@Rajarshi a small bug: nothing was displayed with http://rest.rguha.net/usage... whereas the NCBI returns about ~9000 articles http://eutils.ncbi.nlm.nih.gov/entrez... - Pierre Lindenbaum

the site is a little slow, but a while ago I saw this tool for looking at PubMed trends on the internets: http://www.cotch.net/assed... - Michael Kuhn

@Pierre, thanks for the catch. I actually do get the correct data. The absence of bars seems to be a limitation of the Google Charts API and the max size of the chart image. If the X-axis is too long, the bars need to be thinner for it to fit into the plot area, and you can only go so thin and then loose readbility. Like I said - this is a quick hack :) Ideally I'd use matplotlib or R as the backend for plotting, but am lazy right now - Rajarshi Guha

interesting, and very cool. One question/comment, does the Google Charts API by default adjust the image so that the x-axis crosses at a non-zero point on the y-axis? I'm sure that breaks one of Tufte's rules about misleading graphs... - Andrew Su

@Andrew - yes. It took me a bit for me to realize that the count for the first year was not always zero! The Charts API does have a way to set the y range, but I'm going via the pygooglechart Python module which doesn't seem to support that. - Rajarshi Guha

i was about the link to my pubmed trends tool, but i see it has already been done :) it is indeed slow -- a clunky php proof of concept really. (it has been especially slow today because apache filled itself with processes that were trying to do i'm not sure what...) http://www.cotch.net/assed... - Joe Dunckley

Jean-Claude Bradley

Glatiramer Acetate Cheminformatics Problem and Fifth ChemInfo Retrieval Class - http://usefulchem.blogspot.com/2009...

November 4 from Useful Chemistry - Comment - Like - Share

Abhishek Tiwari, Antony Williams, Egon Willighagen and Cameron Neylon liked this

Polymers are where the problem with assuming that chemistry is structure centric come home to roost of course. Nico Adams has been looking at developing ways of describing polymers effectively and it really isn't straightforward. The whole notion of substance, chemical, and structure get very very messy. - Cameron Neylon

13 more comments

What is distressing is that someone added that initial obviously incorrect SMILES and it propagated easily to all those databases. As Tony has said many times curation is a big challenge in chemical databases. - Jean-Claude Bradley

I'd say the cause of everyone blindly copying data, is that they are happy enough to be able to copy data at all... it all starts with Open Data and the right to fix things, and share those fixes... - Egon Willighagen

+1 Egon - Cameron Neylon

I'm not sure that the reason people are copying data are because it's Open. PubChem continues to proliferate yet it is NOT Open. We've had this exchange before..PubChem is NOT Open data but I "judge" it gets copied because people treat it as an authority. It is not a good idea to treat PubCHem as an authority as it is a repository...non-curated and with no efforts underway to curate it... more... - Antony Williams

I agree that PubChem should not be treated as authoritative, but the big advantage it has over ChemSpider is that it can be downloaded and re-used. - Michael Kuhn

I agree that people copying PubChem is indeed not because it is Open... that one is copied merely because it is free and confuse that with Open. That said, I love to see the day that there was a court ruling on that state of the PubChem data, which is at some places claimed to be Public Domain, something refering to the copyright being with the providers, while at other places... a bullet proof statement would be *very* useful indeed. - Egon Willighagen

Michael - there is every intention to provide access to the ChemSpider structure collection in the near future. This will not include all associated information in a record as the associated information has mixed licensing but free to use. - Antony Williams

ChemSpider and Wikipedia have the advantage that errors can be corrected. Are there mechanisms in place to correct errors in DrugBank, PubChem and the many other derivative databases? - Jean-Claude Bradley

DrugBank: yes, David Wishart is said to be quite responsive to comments. Same for KEGG. PubChem: NO. They just aggregate tons of source databases, and you would have to hunt down the source and hope it makes it way downstream... Thus ChemSpider's annotation efforts are invaluable, and I would love to be able to re-use them - Michael Kuhn

Michael...drop me an email at antonyDOTwilliamsATchemspiderDOTcom and let's discuss how you want to use information and what you need to get at and it might be an issue of simply pointing you to the right web services. Lots of people are using ChemSPider through web services at present. We'd love to help you - Antony Williams

thanks Michael - Jean-Claude Bradley

There is also a curated KEGG: http://biometa.cmbi.ru.nl/ - Egon Willighagen

Biometa appears to be static since 2007. The SDF file mostly contains R groups. Seems weird - Antony Williams

Martin Ott moved to Sheffield... (http://www.lhasalimited.org/index...) I'll try to ping Vriend about the future of BioMeta... or the code behind it. - Egon Willighagen

Neil Saunders

STITCH 2: an interaction network database for small molecules and proteins - http://www.citeulike.org/user...

November 8 from CiteULike: neils's library - Comment - Like - Share

Pawel Szczesny, Yann Abraham, Pedro Beltrao and 3 other people liked this

Nucl. Acids Res. (6 November 2009), gkp937. Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. 10.1093/nar/gkp937 Michael Kuhn, Damian Szklarczyk, Andrea Franceschini,... - Neil Saunders

6 more comments

I didn't expect the paper to come out this quickly, I was quite surprised to see it in my feed reader on the weekend. I have now activated STITCH 2 as public website ... hope it's not too buggy :) - Michael Kuhn

this looks like it could be quite useful for our cheminfo retrieval class - I added it to our resources and will let you know if any students make use of it for their term projects http://getcheminfo.wikispaces.com/resourc... - Jean-Claude Bradley

umm .. you are going to make me re-do some work :p - Pedro Beltrao

@Michael - quick questions: I don't think I ever saw homology evidences in the drug-gene interactions. Do you guys avoid doing this or it is just not reported in the evidence info ? - Pedro Beltrao

Congrats Michael! - Ruchira S. Datta

@Pedro: going from STITCH 1 to 2 will change the identifiers of proteins and chemicals, so check first if you run into trouble there - Michael Kuhn

re transfer: if you are in human or mouse, you probably won't see so much transfer. but if you go to e.g. chimp, you'll see a lot of transferred evidence - Michael Kuhn

Michael Kuhn to Michael's feed, The Life Scientists

Fwd: Sites using the StackOverflow engine http://meta.stackexchange.com/questio... includes http://asksci.com http://sciencestack.com http://neuroknowledge.net (via http://friendfeed.com/yokofak...)

November 3 - Comment - Like - Share

Daniel Mietchen, Matthew Todd, Frank and 3 other people liked this

Thanks to Pierre for finding this. Math Overflow (http://mathoverflow.net/) actually seems to work and has a community, but the listed sites have almost no audience (yet). Seems Ask Sci is slightly ahead, though. - Michael Kuhn

7 more comments

Here are some recent threads from this room that _could_ also work on Ask Sci (et al.): http://friendfeed.com/the-lif... http://friendfeed.com/the-lif... http://friendfeed.com/the-lif... - Michael Kuhn

re Ask Sci: the homepage listed for the the admin is some kind of shopping portal, which is a bit strange - Michael Kuhn

http://sciencestack.com and http://mathoverflow have LaTex formulas support which is a must for a Science-oriented Q/A site. - Jane Breezler

@Jane: some of us in this room do think that StackOverflow-for-scientists would be a good idea, but please adhere to the guidelines of this room: "Try not to spam and if you are associated with a service (and most don't know that), please say so." – If you're associated w/ sciencestack, we'd love to have a discussion about how such a thing could actually work (or why MathOverflow seems to work, and asksci / sciencestack no [yet]) - Michael Kuhn

Isn't "science" too broad for this? Don't we need smaller units (i.e. chemoverflow, biostack?) Lots of the science questions are very general-sciencey. - Matthew Todd

Despite the fact that sometimes good solution come from people in a different field I would agree with Matthew. More specific sides would reduce the noise for the majority of users. - Konrad Förstner

Well, StackOverflow also has a huge range of topics. The problem with e.g. splitting chemistry and biology is that you then don't know where to put your biochemistry questions. ;) The tagging system (interesting / ignored tags) should help with that. - Michael Kuhn

@Michael: Thanks for the notice. + for mentioning the tagging system! @All: Please direct your discussion and suggestions on Stack Overflow for scientists to http://friendfeed.com/science... - Jane Breezler

Andrew Perry

Space Exploration History: The Space Shuttle and the Horse's Rear End - http://www.astrodigital.org/space...

November 9 from delicious - Comment - Like - Share

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

Michael Kuhn

OpenOfficeMouse: The Multi-Button Application Mouse for OpenOffice.org - http://openofficemouse.com/pr11060...

November 7 from Bookmarklet - Comment - Like - Share

not sure if this is a joke or not: an 18-button mouse for OpenOffice - Michael Kuhn from Bookmarklet

The Life Scientists: Deepak Singh

Warren DeLano of PyMol fame has passed away :(

November 5 - Comment - Like - Share

Oh no, that's terrible news... how did you hear?? - Shirley Wu

23 more comments

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... more... - Antony Williams

Please drop your comments here http://warrendelano.blogspot.com/2009... - Abhishek Tiwari

Michael Kuhn

Edgetic perturbation models of human inherited disorders. - http://www.ncbi.nlm.nih.gov/entrez...

November 6 from Google Reader - Comment - Like - Share

"Here we investigate [...] interaction-specific or edge-specific ('edgetic') alterations." 'edgetic'? seriously? Looks like it has precedence, also by Marc Vidal: http://www.ncbi.nlm.nih.gov/pubmed... - Michael Kuhn

Neil Saunders

How to reject a scientific paper - http://bytesizebio.net/index...

November 5 from Google Reader - Comment - Like - Share

Joe Dunckley, Jo Young, Michael Habib and 4 other people liked this

*giggle* - D0r0th34

2 more comments

I like #4. The "pretend to be British" wouldn't work for whoever wrote that -- their examples of "British usage" are terrible. - Bill Hooker

I don't know, Bill. I knew a Mancunian who often used those very phrases. - Mr. Gunn

so are the German phrases :) - Michael Kuhn

Jonathan Eisen

OMG this is the best paper in years - http://isotropic.org/papers... - HT to Jessica Green for pointing this out

November 5 - Comment - Like - Share

Dan Gezelter, Bosco Ho, Mickey Kosloff and 6 other people liked this

...and here's the presentation of the paper: http://www.youtube.com/watch... - Michael Kuhn

5 more comments

it is excellent. I'm not so sure about that part about chicken though. - Richard Akerman

What a great find! - Chris Lasher

Certainly seems to refute earlier work by C. Sanders. - Matthew Todd

Chicken. Chicken chicken chicken. - Bosco Ho

Rhubarb Rhubarb - http://en.wikipedia.org/wiki... - Andrew Lang

http://itre.cis.upenn.edu/%7Emyl... This gives links to fill in the back story. - Chris Lasher

Michael Kuhn

Python in the Scientific World - http://neopythonic.blogspot.com/2009...

November 5 from Google Reader - Comment - Like - Share

Benjamin Tseng, Bruno C. Vellutini and Neil Saunders liked this

"Yesterday I [Guido van Rossum] attended a biweekly meeting of an informal a UC Berkeley group devoted to Python in science (Py4Science), organized by Fernando Perez." - Michael Kuhn

References Wanted: Text Savvy

Looking for the following: Gelman, R., and Meck, E. (1983) Preschoolers' counting: Principle before skill. Cognition, 13, 343-359.

November 5 - Comment - Like - Share

Sorry. E-mail is jaydamion@gmail.com. - Text Savvy

sent - Michael Kuhn

Dank' schoen. - Text Savvy

Lars Juhl Jensen

Predicting new molecular targets for known drugs - http://www.nature.com/nature...

November 1 from Google Reader - Comment - Like - Share

Ed Millard, Khader Shameer, Matthew Todd and 10 other people liked this

The title is a bit generic, isn't this what Phil Bourne's been doing? - Ruchira S. Datta

8 more comments

I think this is an extension of their (Kieser et al) previous work with SEA - Rajarshi Guha

Nature has a story on this in their news section: http://www.nature.com/news... - Michael Kuhn

Is this using Lasso or similar program? Interesting appearance of DMT as a molecule of interest - I have a student doing a report on it this term http://getcheminfo.wikispaces.com/Adam+My... - Jean-Claude Bradley

Uses SEA http://sea.bkslab.org/ - Rajarshi Guha

Thanks Rajarshi - looks like another cool online resource to explore - Jean-Claude Bradley

That's cool. How likely is the top match to be a real inhibitor? - Andrew Lang

We're trying to run our virtual library of Ugi products we can make in my lab http://usefulchem.wikispaces.com/UClib00... I hope that isn't too large a task - Jean-Claude Bradley

We did some of this validated cross-target prediction also http://www.nature.com/doifind... - Matthew Todd

That's awesome Mat! What would be the next step to processing our Ugi product library on the TDI kernel? - Jean-Claude Bradley

Duncan Hull

Authors beware, and protect your online identity - http://www.citeulike.org/user...

November 5 from CiteULike: dullhunk's library - Comment - Like - Share

Michael Kuhn liked this

errr - authors who give out their user details deserve what they get! - Jo Badge

I'm not sure I've understood the implications of this, but isn't just like an account on any other service? - AJCann

well, another option would be for journal submission systems to drop the requirement that only the corresponding author can submit. it should be enough to let the PI verify the submission. - Michael Kuhn

Pedro Beltrao

DRYGIN: a database of quantitative genetic interaction networks in yeast. - http://www.ncbi.nlm.nih.gov/entrez...

November 3 from Google Reader - Comment - Like - Share

Pawel Szczesny and Ruchira S. Datta liked this

umm .. everything is password protected. Not a very useful database if you cant actually use it. - Pedro Beltrao

2 more comments

they might have been aiming for January 2010, when the NAR db issue officially comes out - Michael Kuhn

It makes sense, since the data they have on this database is part of paper that Boone talked about and that I assume is currently under review. Still .. annoying :) - Pedro Beltrao

yep, I just got the email response back. They will remove the password protection when the other paper describing the data is published. Bummer :) - Pedro Beltrao

NCBI ROFL

Shrew pursue taboo dew brew. - http://www.ncbirofl.com/2009...

November 3 from NCBI ROFL - Comment - Like - Share

Michael Kuhn liked this

"Here, we provide a detailed account of chronic alcohol intake by mammals as part of a coevolved relationship with a plant." - Daniel Mietchen

"Therefore, we hypothesize that moderate to high alcohol intake was present early on in the evolution of these closely related [primate / human] lineages." :) - Michael Kuhn

Pierre Lindenbaum

Sites using the StackOverflow engine http://meta.stackexchange.com/questio... includes http://asksci.com http://sciencestack.com http://neuroknowledge.net

November 3 from Twitter - Comment - Like - Share

cool! I've re-shared it to the Life Scientists room http://ff.im/aVeLG - Michael Kuhn

Michael Kuhn

Wired: Mob Rule! How Users Took Over Twitter - http://www.wired.com/magazin...

November 2 from Bookmarklet - Comment - Like - Share

shared mainly for the cute illustration :) - Michael Kuhn from Bookmarklet

AJCann to AJCann's feed, The Life Scientists

OK, I give in -anyone got a spare Wave invite for me? Thanks.

October 19 - Comment - Like - Share

Carl Fulp, Mike Chelen, 'Mummi' Thorisson and 3 other people liked this

I'd be happy to receive an invite, too :-) thanks - Claudia Koltzenburg

24 more comments

Oh is this where the Wave queue is? *stands in line* - Bob O'Hara

No cutting in! :-) - AJCann

Can I have your email address - please. I have 5 invites. - Khader Shameer

steelgraham7 AT gmail DOT com - Graham Steel

AJCann and Graham : both of you are invited. Got 4 more to share - pls send email address. - Khader Shameer

Thanks Khader. - AJCann

sent you a direct message w/ my email address - Michael Kuhn

If anyone in Wave has spares can they also check the Life Scientists invite list? Drop me you're Wave address (I'm cameronneylon@googlewave.com) and I can add you - Cameron Neylon from twhirl

Khader or anyone nice, here's mine: ctt.journal at googlemail.com - Claudia Koltzenburg

Khader, if you still have some, I am mikael dot huss at the same domain as Claudia above - Mikael Huss

@ajcann ha!! Knew you couldn't last - are you ajcann? I'll attempt to add u to some stuff.... - Jo Badge from iPod

Hi Khader. neil.swainston_AT_manchester.ac.uk if there are any spares. Thanks. - Neil Swainston

andrew.sid.lang AT gmail DOT com if you can - thanks! - Jean-Claude Bradley

Send invites to Michael, Claudia and Huss. Sorry Neil and Bradley. - Khader Shameer

that's ok Khader - we'll keep trying - Jean-Claude Bradley

For the public record, I didn't receive a Wave invite from Khader :-( - Graham Steel

Graham, that was a too early announcement :|, usually wave takes a day or two to send the invitation. In Wave's own words "Invitations will not be sent immediately. We have a lot of stamps to lick. " - Khader Shameer

"usually wave takes a day or two to send the invitation" I was not aware of that, thanks for pointing this out, Khader. Thank you kindly for sending out the invites... - Graham Steel

Yeah, See you on wave Graham :) ! - Khader Shameer

Thanks anyway, Khader. - Neil Swainston

I'll add myself to the list of the currently waveless: carlfulp AT gmail DOT com - Carl Fulp

May as well add my name to the list of those left behind ! elbuono AT gmail DOT com - Ian Simpson from twhirl

still holding out - I know that if I get one of these, I'll get sucked into the Waveome and my thesis will soo *never* be done in time! - 'Mummi' Thorisson

Got few more invites: added Ashish, Lucas, Andrew, Carl, Ian :) - Khader Shameer

Mummi send me your gmail ID. - Khader Shameer

Rich Apodaca

Why I don’t use Google Reader anymore - http://scobleizer.com/2009...

October 29 from Google Reader - Comment - Like - Share

tldr: he's following lots of people, therefore GR is slow for him and he gets all the news he wants from Twitter - Michael Kuhn

2 more comments

It's funny how just as for many Google == search, GReader == feed reader. - Neil Saunders

yep. has anyone here tried Fever? http://feedafever.com/ For me GR is working fine, but I only have ~50 new items each day in my feeds. I'm guessing to take advantage of the "prioritizing" Fever does, you'd need more input (and be interested in more input) - Michael Kuhn

I use Bloglines to follow about 200 blogs, mostly scholarly communication/OA/open science stuff. That's pretty much the limit though -- and many of those 200 are very infrequent posters. What I really want is a reader that has a "related" function like FF's. - Bill Hooker

Michael Kuhn

Google Maps Navigation on your mobile phone - http://www.google.com/mobile...

October 28 from Bookmarklet - Comment - Like - Share

Richard Akerman liked this

...and it'll show you where the next In-N-Out Burger place is :) - Michael Kuhn from Bookmarklet

Heh. OpenStreetMap blog asks: "Is there anyone left to compete with?" http://www.opengeodata.org/2009... - Michael Kuhn

Michael Kuhn

More on Amazon’s Relational Database Service (RDS) - http://www.allthingsdistributed.com/2009...

October 27 from Google Reader - Comment - Like - Share

via @gruber: "Amazon CTO Werner Vogels on where Amazon’s new hosted MySQL Relational Database Service fits in with their other cloud storage services." - Michael Kuhn

Michael Kuhn to Michael's feed, The Life Scientists

BBC NEWS | Asia-Pacific | S Korea clone scientist convicted - http://news.bbc.co.uk/2...

October 26 from Bookmarklet - Comment - Like - Share

Andrew Perry, Greg Tyrelle, 'Mummi' Thorisson and Maxamad liked this

"He was given a two-year sentence suspended for three years." - Michael Kuhn from Bookmarklet

Michael Kuhn

The Reverse Geocache Puzzle | Arduiniana - http://arduiniana.org/project...

October 22 from Bookmarklet - Comment - Like - Share

Yaroslav Nikolaev, Pedro Beltrao, Cameron Neylon and 2 other people liked this

cool idea: a wedding gift w/ built-in GPS: it'll only open at a specific location, and it only tells you the distance to wherever that is - Michael Kuhn from Bookmarklet

Genius. "At one point a friend of the family, a charming gentleman from up the street, said to me with a thick accent, “You are — how you say in English? — a BASTARD!” That one comment made this whole project worthwhile." - Bill Hooker

References Wanted: Pedro Beltrao

From evidence to inference: probing the evolution of protein interaction networks http://dx.doi.org/10... to pedrobeltrao at gmail. com

October 19 - Comment - Like - Share

can't help you with that, but maybe you could ask directly Carsten Wiuf as he has all his articles in pdf on his site - http://www.daimi.au.dk/~wiuf/ - Andrej

sent - Michael Kuhn

thank you - Pedro Beltrao

Michael Kuhn

HHMI Lab Management: Making the Right Moves - http://www.hhmi.org/resourc...

October 19 from delicious - Comment - Like - Share

Pedro Beltrao, Abhishek Tiwari, Khader Shameer and Ruchira S. Datta liked this

"Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty" (should the time ever come) - Michael Kuhn

It is a very interesting read. I received a copy from HHMI last year. - Khader Shameer

Definitely an essential read - the questions to ask when interviewing candidates to hire is really helpful. - Jason Stajich

Michael Kuhn to Michael's feed, The Life Scientists

Does anyone know of studies/estimates for the coverage of mouse phenotype dbs like MGI (http://www.informatics.jax.org/)?

October 20 - Comment - Like - Share

Mike Chelen and Carl Fulp liked this

in particular, I'm wondering how exhaustive the phenotyping for any given gene is. I.e.: If a phenotype is not listed, how high is the chance that it does occur but wasn't recorded? - Michael Kuhn

Michael Kuhn › Comments