Daniel Jurczak - Likes

The one search company most likely to get purchased by Microsoft to crush Google that I saw in Cambridge UK? PrismaStar.

July 11 - Comment - Like - Share

rowlikeagirl, Sunny (The Geek Lord), Roberto Bonini and 23 other people liked this

Reasons for saying that? - Ahmed

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Why? - Jim Connolly

why ? - Kashif Khan

http://www.prismastar.com/about-u... - ashish

"crush google", wow sounds interesting. - Rich Lazzara

I hope this is the same PrimaStar Robert is talking about - ashish

Rich: Google crush sounds more interesting - like the name of a drink. - Jim Connolly

Why? You'll have to see our Building43 video to see why. :-) But let's just say they did the search technology for several camera stores and the conversion rate went WAY up. Why is that? Because they offer a new way of searching things that really rocks. I can't explain it in text. Gotta show it to you. - Robert Scoble

looking fwd to it - Rich Lazzara

Demo http://www.prismastar.com/our-sol... - Jauder Ho

Primestar's AnswerOil UIX is a good fit for #Bing's decision support platform, combined with shopping cart & checkout optimization products from www.allurent.com would yield further eCommerce results. - Alexander Ainslie

I'm interested.Do they support dynamic search/ads via keywords/tags? I sent them a message, and like what I saw. Very feature driven search. - Mark Essel

Robert: direct link to the building43 video? - James Kuypers

Several people asked which product categories we support -- here's a site that uses over 1000: http://translate.google.com/transla... - Joshua Z. Tabin

(on the right-hand side of that translated page are some samples...) - Joshua Z. Tabin

Also, Mark Essel: YES, we do support dynamic search/ads via keywords/tags. :) - Joshua Z. Tabin

Thanks Joshua, great talking to you. - Mark Essel

Most likely to get purchased by Microsoft with the intent to crush Google, perhaps. But Microsoft intends a lot of things. Maybe they'll buy PrismaStar, then rebrand MSN, er, Live Search, er Bing, and the market will be less confused. - Andy Bakun

But Jessops the camera retailer is losing money: http://www.dailymail.co.uk/money... - Jelly Roll Morton

Jessops has been losing money as long as anyone can remember, which is hardly Prismastar's fault. The point is though that Jessops has a very good search tool with Prismastar's AnswerOil and has seen a substantial increase in its conversion rates since adopting Prismastar's technology. It could be Answeroil which has kept them going this long (nobody would have expected them to still be around in late 2009 eighteen months ago) - John S Cameron

John, did Jessops really see a substantial increase in conversion rates? I respectfully suggest that this is not a fact. Can anyone actually verify this claim? It is on record that Jessops are still around because HSBC Bank saved them, rather than because of their business performance. - Jelly Roll Morton

Posting from another feed: here is the prior art that someone was looking for on Interconnected Sliders : they existed back in 2004 in the public domain - download this FLA file for free and build your own interconnected sliders: http://www.senocular.com/flash... - Jelly Roll Morton

Mr. Gunn

October 12 from Flickr - Comment - Like - Share

Neil Saunders, Brian Krueger - LabSpaces, John Dupuis and 9 other people liked this

Awwwwwwwww. - Bill Hooker

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Congratulations Dr father Gunn - Nils Reinton

Congratulations! - Chris Lasher

Congratulations! - Yann Abraham

Congrats William! - Walter Jessen

So cute! - Stephen Francoeur

The Life Scientists: Chris Patil

Has anyone used Web 2.0 tools like FriendFeed, Twitter, etc. to initiate or implement collaborative science? I'm writing a series of pieces about new technology in scientific communication, and I'd love to talk to someone who's actually used these sorts of tools to do actual science. Let me know!

March 6 - Comment - Like - Share

george, Oliver Schuster, Mary Canady and 22 other people liked this

If you'd rather take it straight to email, you can email me at the address listed here: http://ouroboros.wordpress.com/about... - Chris Patil

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And by the way, this is for a journal, not my blog. - Chris Patil

example: http://tinyurl.com/63vurc - Pierre Lindenbaum

Thanks Pierre. I will definitely follow up with the people involved in that thread. Keep 'em coming, folks! - Chris Patil

I'm not sure this counts but the biogang (http://biogang.openwetware.org/) was sort of founded/created via Twitter/FriendFeed interactions. Lots of projects there. Also, the bioinformatics survey was also propelled by T/FF if I recall. - Ricardo Vidal

Jean-Claude Bradley started a spreadsheet where he wrote this kind of information : https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

See also this post: http://friendfeed.com/e... - Pierre Lindenbaum

This is really amazing, you guys. Thank you. JC, the spreadsheet is incredible. - Chris Patil

There are so many examples on discussion boards like ScientistSolutions, Molecular Station, etc. (Disclaimer, I work for SSI). I could give a you a list of at least 50 specific threads on our site. Here's a recent favorite http://www.scientistsolutions.com/t8853-h... - Rusty Bishop

I just added to the spreadsheet re: the help I got with CSV munging shell scripts earlier. Would discovery of papers through social bookmarking be considered collaborative science? - Mr. Gunn

@Mr. Gunn - no, i don't think so. Collaboration suppose to be productive - if discussion about papers within the group brought all participants to consensus that could be collaboration via social bookmarking with discussions. But bookmarking sites don't provide discussions. Even they would, it will take for a long while for scientists to start discuss about papers online - simple online collaboration. My thoughts also here - http://hematopoiesis.info/2009... - Alexey

Chris - Carmen Drahl made a nice video showing how FriendFeed is used to collaborate with scientists (second vid on the right) http://pubs.acs.org/cen... - Jean-Claude Bradley

Pierre - thanks for posting the spreadsheet - it is nice to see these little projects get re-use - Jean-Claude Bradley

Concretely, the References Wanted room (http://friendfeed.com/rooms...) has really been useful in writing up articles so I can rapidly get my hands on hard-to-come by references in journals to which my institution does not subscribe. But I'm not sure this is a great thing to bring up in your article, except in a vague way; we're not quite clear which side of the law participating re-distributors are on (fair use, or not?) It's not quite the same as discovering papers as per Mr. Gunn. - Heather

Sci-Mate is a very recently opened collaboration to develop Web 2.0 tools for the benefit of researchers. http://www.sci-mate.org/ - Christopher Dyer

Check out: http://www.dental.pitt.edu/informa... - Heiko Spallek

I have recently started a project shared on a wiki + google code + zotero but it is still early days http://openwetware.org/wiki... - Pedro Beltrao

open notebook science should qualify, thinking about usefulchem as example of wiki and google spreadsheets like http://spreadsheets.google.com/ccc... - the list on wikipedia is helpful http://en.wikipedia.org/wiki... - Mike Chelen

I Added the GeneWiki paper in Jean-Claude's spreadsheet https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

Chris - if you are asking for a more technical answer - UsefulChem and the ONSchallenge run mainly on a combination of wiki/blog/Google Spreadsheets - Jean-Claude Bradley

Pierre - thanks for the addition - Jean-Claude Bradley

Maybe this is where Google Wave will turn out to be useful once we all realise that we're not flying around Beginners Island naked like in Second Life ;-) - Sally Church

Sally - do you have a link to the island where everyone flies around naked? Sounds like fun :) - Jean-Claude Bradley

Of course I'm naked but my feline fur hides that pretty well - Jean-Claude Bradley

Jan Aerts to Jan's feed, The Life Scientists

Could we have a list of google wave names somewhere so that I can figure out what Life-Scientists are on there?

October 12 - Comment - Like - Share

Tom Tullius, Jeannette Høvring, Daniel Jurczak and 21 other people liked this

toddwharris@googlewave.com - Todd Harris

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just added you to Life Scientists wave - Cameron Neylon from twhirl

A Google Wave might be appropriate for tracking such a group. - Shiran Pasternak

shiranpasternak at the same domain. - Shiran Pasternak

search "with:public research" and you will find the "Research collaborations in Wave" wave endre.sebestyen@googlewave.com - Endre Sebestyen

yann.abraham@googlewave.com - Yann Abraham

Searching Google Wave with "tag:the-life-scientists" will get you to "Research collaborations in Wave", a good starting point for life scientists. - Martin Fenner

b.brembs@googlewave.com - Björn Brembs

mndoci - Deepak Singh

I also missed out on the invites .. if anyone knows someone .. :) - Pedro Beltrao

I'm firstname.lastname - Ruchira S. Datta

firstname.lastname here too - Andrew Clegg

I don't get how you search in public waves. I've tried searching for tag:the-life-scientists and it gets no hits -- I think it's just searching my own waves - Andrew Clegg

there was a thread by Kol about wave usernames couldn't find the link - ffcode

Aha -- with:public . They really should include a button for that - Andrew Clegg

anna.k.croft - Anna Croft

Lots here: http://ff.im/91NZC - Kol Tregaskes

thanks Kol - ffcode

attilacsordas - Attila Csordas

I never got invited to the party :( - Lars Juhl Jensen

AndrewJamesPerry - Andrew Perry

avijitguharoy@googlewave.com - A Roy

allyson.lurena@googlewave.com - Allyson Lister

@Endre: You can link to waves, eg: https://wave.google.com/wave... - Nick Lothian

mbembee@googlewave.com - embee

000.cacarr@googlewave.com - Christopher A Carr

cassjohnston - Cass Johnston

plindenbaum - Pierre Lindenbaum

firstname.lastname också - Egon Willighagen

diegomorelli76@googlevave.com - diego morelli

abhishek.twr@googlevave.com - Abhishek Tiwari

Would like to be added to life scientists wave, please! david.rothman@googlewave.com - David Rothman (☤)

@David: done - Pierre Lindenbaum

Many thanks, Pierre. :) - David Rothman (☤)

churchsg - Sally Church

life scientists wave: me too, thx - Attila Csordas

Don't know if I actually put myself here :-) jan.aerts@googlewave.com - Jan Aerts from email

Count me in: matt.j.wood - Matt Wood

jeanclaude.bradley at googlewave dot com - Jean-Claude Bradley

chrisamiller@googlewave.com - Chris Miller

Matt: added. - Jan Aerts from email

inspiring2designllc@googlewave.com - Justin H. Johnson

somebody please add me too attilacsordasat... - Attila Csordas

Attila: can't seem to find attilacsordas@googlewave.com. - Shiran Pasternak

it does exist I can tell ya :) - Attila Csordas

@Attila: tried a different way... yer in. - Shiran Pasternak

Done. - Jan Aerts from email

An undergraduate student in our lab, Caleb, just got his wave invite. I told him to look at this thread for possible people to connect with. - Steve Koch

+1 skhadar@googlewave.com - Khader Shameer

got it, thanks - Attila Csordas

murvine - thanks! - Christopher Murvine

Afternoon all. I've written my first robot, which hopefully will embed an interactive mass spectrum into a blip whenever a UniProt name is encountered in the text, and corresponding mass spec data is found for this protein. I say "hopefully", as I've not been able to test it for real, as, alas, I have no account. When are the next batches released? If it's not for ages, does anyone fancy testing it anyway? - Neil Swainston

Am now Waving as ben.blackburne. - Ben Blackburne

Now waving as lars.juhl.jensen - Lars Juhl Jensen

waving too: sciphu@googlewave.com - Nils Reinton

waving as fgibson - Frank

aemonten@googlewave.com. How can I get started with the life scientists wave? - Alejandro Montenegro

my wave ID: macmanes@googlewave.com - Matthew MacManes

dan.swan@googlewave.com searching is sloooooow trying to find the life scientists wave right now! - Daniel Swan

chris.lasher@googlewave.com - Chris Lasher

sjcockell@googlewave.com - Simon Cockell

jwhabig@googlewave.com - Jeff Habig - Jeff Habig

comprendia[at]googlewave[dot]com Mary Canady - Mary Canady

rebeldad@googlewave.com Brian Reid (PR guy for life science types ... I promise to behave) - Brian Reid

bronxman - Jack H. Pincus

I'm trying to get a Solexa/Illumina Sequencing Wave going. Search "with:public Illumina" or add me macmanes@googlewave.com - Matthew MacManes

waving as georgkam - george

For some reason, I'm stevekoch3 but glad to finally have a preview account! - Steve Koch

And I found the research collaborations wave by the following search: "with:public tag:the-life-scientists" - Steve Koch

mine is pedrobeltrao@googlewave.com (thanks to Mr Gunn) - Pedro Beltrao

In case there is still someone with spare invitations: piotr.byzia at gmail.com - Piotr Byzia

tom.sante@googlewave.com - Tom

Im steelgraham7@googlewave.com - Graham Steel

sametstalker@gmail.com - Samet Güngören

michael.kuhn - Michael Kuhn

Requesting for life scientists wave, abhishek.twr@googlevave.com thanks in advance - Abhishek Tiwari

The usual, neilfws. - Neil Saunders

now that I am finally on board: danjurczak@googlewave.com - Daniel Jurczak

i'm mightyfib(at)gogglewave(dot)com Your most welcome to add me...:O) - Jeannette Høvring

mine is dave.lunt - Dave Lunt

michael.chelen@googlewave.com or @gmail.com can't see any way to check :D - Mike Chelen

is there any good way to import contacts? it seems to work through the google contacts system like gmail - Mike Chelen

pengwen.not.penguin@googlewave.com - Parvez Halim

mstalnos@googlewave.com - Tresterling

I'm on (thanks to Steve Koch!): tom.tullius@googlewave.com - Tom Tullius

Alexey to Alexey's feed, Regenerative Medicine, The Life Scientists

YouTube - Johns Hopkins Medicine: A Century of Stem Cells - http://www.youtube.com/watch...

September 21 from Bookmarklet - Comment - Like - Share

Daniel Jurczak, Mackenzie Cowell and Ami Iida liked this

Jim Till to The Life Scientists, Science 2.0

Fwd: Canadian Stem Cell Foundation launched, http://www.stemcellfoundation.ca/ (via http://friendfeed.com/tillje...) #stemcell

September 22 - Comment - Like - Share

Daniel Jurczak and Alexey liked this

It's actually the CSCF website that was launched today. "The Canadian Stem Cell Foundation is a non-profit organization founded in 2008. The goal of the foundation is to advance the field of stem cell research, raise public awareness and simulate public discussion about stem cell issues. The foundation is headquartered in Ottawa, Ontario": http://en.wikipedia.org/wiki... Disclosure: I'm a member of the Board of the CSCF. - Jim Till

Khader Shameer to Khader's feed, The Life Scientists

Its time for me to prepare a CV for my post-doc applications, any suggestions ? What are the must haves in a bioinfo post doc CV ?

September 14 - Comment - Like - Share

Daniel Jurczak, Lucas Brouwers, Mike Chelen and 5 other people liked this

Focus on the position requirements, and do not add in minor stuff not required, unless where it serves as topic for the interview. - Egon Willighagen

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Keep it short. Use a template. Spelling/grammar errors look bad. Focus on the cover letter, not the CV. Say why you want the position and what you will bring to it - generic applications look very bad. Rather than listing skills, give examples of problems that you've faced and how your skill set solved them. Publications, presentations posters etc. can be a separate section in a smaller font, after the other stuff. - Neil Saunders

Agree with both the above. You can tailor the CV itself to the job you're applying for -- don't have a one-size-fits-all. Emphasize different skills and experiences depending on where you're applying -- some could be left out for brevity in some job applications, but left in for others if they're more relevant. Plus it doesn't hurt to ask a slightly more senior friend or colleague if you could see theirs, to have something to work from. - Andrew Clegg

Thanks Egon, Neil, Andrew for the different, yet important points. - Khader Shameer

Agree with above about the cover letter. On the CV, one URL pointing to your publications (via citeUlike, zotero etc), another pointing to your LinkedIn profile.One URL for your blog. Restate your relevant skills, as appropriate for the job and thats about it. - Frank

Pawel built nice tag cloud for his resume: http://www.flickr.com/photos... - Pierre Lindenbaum

Frank: Do you think listing your pubs on your CV is out of date these days? Personally I think a link to a comprehensive online list would be better, but I'd worry about old-fashioned employers thinking that "wasn't the done thing". Also that puts the onus on the reader to actually fire up a browser and put the link in (esp. if it's a printed CV) - Andrew Clegg

If it's a PDF CV, include links to the pubs? - Rajarshi Guha

Frank : I am not yet an active blogger - is that an absolute requirement for a compbio postdoc or job :| ? - Khader Shameer

I am planning to put a link to my publications in PubMed as suggested by Rajarshi, but some of them are conference abstracts / non-pubmed publications, so I need to use a combination of both. - Khader Shameer

Don't forget to mention about you computational and programming skills in a detail, I guess most of Post-doc potions need programming skills well advance so just open up - Abhishek Tiwari

Thanks Abhishek, will have a section dedicated to tech skills. But at the same time I don't want to enumerate n number of technologies / bioinfo tools am familiar with. That would easily fill 2 pages of my CV. - Khader Shameer

Compliment @all. Nice crowd sourcing. Found via search for zotero. Trackback: http://identi.ca/notice... - Markus Merz

@Andrew. I think it depends on the job, if you are going for a research position, they generally want to see what you have been doing, a non research position a reference list is probably irrelevant. I would agree that producing a list of your publications actually on the CV is outdated and would probably extend the page limit, I did suggest adding a link rather than listing them :). They would have to navigate to Pubmed to "read" them anyway.. or at least check the dates - Frank

@Khader, wether you blog or not is your decision, I doubt it would be a deciding factor. I probably would expect to see some online activity, opensource project, link to research code, etc. However, I do understand this largely depends on the work you have actually been doing and is not a given - Frank

Regarding publications: how about a handful of key relevant papers on the CV itself, plus link to full bibliography on one's website (w/ links to PubMed).? - 'Mummi' Thorisson

Mummi: Dunno what Khader's CV is like, but if it was me applying for my first postdoc, those two lists would have been the same :-) - Andrew Clegg

Frank, Mummi, Andrew - Thanks for the points. My thesis related papers are in different stages of review, so I may not be able to provide a link to full list of publication as of now. I am planning to provide list of publications within the CV as of now, once I get my papers accepted, I can substitute it with a link to PubMed. I think Chris Millers CV is a good template for an online CV http://www.chrisamiller.com/cv... . Now need to find one good template for an offline version. - Khader Shameer

Thanks guys. Prepared my CV and cover letter with your suggestions and send the application yesterday. Today, I just finished my first post-doc interview. It was a nice experience. - Khader Shameer

Publication list is the most important thing on a CV. One gets so many applicants, all of whom write their cvs so well, that one inevitably distinguishes between candidates on their publication record. - Matthew Todd

Good luck, hope the news is good - Andrew Clegg

Andrew, thanks ! It went on well - now waiting for the next steps : reco, thesis submission, etc. - Khader Shameer

Alexey to Alexey's feed, Regenerative Medicine, The Life Scientists

YouTube - Sean Morrison, UM Center for Stem Cell Biology: Part 4 - http://www.youtube.com/watch...

September 20 from Bookmarklet - Comment - Like - Share

Daniel Jurczak and yuriandre liked this

i still agree that scientists should pursue research on SC bio. - Summer of http://www.soloden.com - yuriandre

Neil Saunders

roo - http://roo.rubyforge.org/

September 17 from delicious - Comment - Like - Share

Rob Syme, Daniel Jurczak and george liked this

This gem allows you to access the content of: Open-office spreadsheets (.ods); Excel spreadsheets (.xls); Google (online) spreadsheets; Excel’s new file format .xlsx. - Neil Saunders

Bora Zivkovic

Why Exercise is Not the Best Prescription for Weight Loss http://www.theexaminingroom.com/2009... #PLoS

August 7 from Twitter - Comment - Like - Share

Colby, Daniel Mietchen, Re Zookeeper and 8 other people liked this

that's a nice review, too bad he didn't use the ResearchBlogging tags :( - Christina Pikas

24 more comments

That was my first thought as well and I am going to ask him to do it and thus be eligible for the Pick Of The Month.... - Bora Zivkovic

If the mean weight of the 12 KWW according to the table was around 83kg. This means that they burned around 12*83 kcal (996 kcal) in a week. This is the amount I burn when I go running for about 80 minutes (at least according to my running watch). So is this really surprising that this rather low amount of burned calories didn't translate into more weight loss ? - Daniel Jurczak

It's nice when a study appeals to personal preconceptions :-) I'm a big believer in exercise as a part of daily life (= moving around a lot, walking), as opposed to a special, extra activity (running, gyms). - Neil Saunders

I really don't understand why people find it so important to use the ResearchBlogging icon. I never put it on my own blog posts about peer-reviewed research. Is it not obvious when a blog post supports its statements with proper sources? Why should I put an icon from someone else on my blog posts to point out the obvious? - Lars Juhl Jensen

I agree with Daniel, the study might not represent the ppl who actually do something during their 200min/week workout. If they were to run 7mph for 30min a day they would burn 3000+kcal. - marcin

@Lars - it's not (only, just, really) so we trust you more, it's so we can find you more easily! The point is to list these things together so that a journalist or patient or teacher or random lay person can find them - Christina Pikas

Correct - not just that you get more traffic, but that traffic is of high quality: people who are actively looking for high-quality blogging. The aggreggator is highly regarded and valued by the non-blogging community as a portal into high quality blogging. For example, I give my monthly Blog Of The Month award at PLoS ONE only to posts aggregated at ResearchBlogging.org. - Bora Zivkovic

I guess what I have against ResearchBlogging is that I feel it will highlight the least important posts on my blog. I'm allowed to slap the icon on a post where I write a commentary on some already published research, but when I do what I think is real research blogging - namely to blog primary research results before they are published elsewhere - then I'm not allowed to put the icon on the post. - Lars Juhl Jensen

highlighting certain posts will also bring more attention to your other posts, in my experience. I'm glad you mention this, because I've not heard this complaint before. Your primary research posts are probably more relevant for those in your research area whereas your ones on published research might have a wider appeal and could benefit from wider attention maybe? - Christina Pikas

Whereas any traffic to my blog will obviously tend to bring in a few extra hits to other posts (although not many in my experience), I don't think that my commentaries are aimed at a broader readership than my other posts. I generally blog about science for scientists in the same field - my aim is not to do outreach and try to make papers accessible to a broader public. Maybe that simply places me outside the scope of ResearchBlogging? - Lars Juhl Jensen

I don't find myself using the #researchblogging service either... I like the idea, but it is just too much work - Egon Willighagen

Another problem I have is that I am not sure which of my posts live up to the guidelines of ResearchBlogging. Most of my posts related to peer-reviewed papers present also my own additional analyses of the primary data published in the paper I discuss. The posts are thus a mix of peer-reviewed and non-reviewed results. It is not clear to me if I would even be allowed to put the icon on them, so I decided to not bother with it. - Lars Juhl Jensen

sounds like the right choice for you, so no reason to question it. - Christina Pikas

Deepak said it better than I: "it’s equating *serious* with peer review that I have a problem with" (http://mndoci.com/blog...) - Lars Juhl Jensen

Hi folks -- Excellent debate going on here. A couple points. First, you should realize that our current requirement of discussing peer-reviewed work is just a first step. We're working on a way to aggregate posts about conference presentations, and posts on ongoing research shouldn't be far behind. It's true that "serious" <> "peer-reviewed," but discussions referencing peer-reviewed literature are very likely to be serious, so this is an easy first pass at sorting the chaff from the wheat. - Dave Munger

Second, our interface has gotten much easier to use. If the last time you tried the site was more than two months ago, you should definitely give it another shot. - Dave Munger

The important thing is that you have the correct markup in the page, not that you're displaying some icon. Anyone can display that image and not be aggregated by your site. Dave, that's why we've been stressing, even before the site was running, that it's not about the icon, but the markup. - Mr. Gunn

To return to the topic at hand, however, I think the study is obviously flawed and in fact quite irresponsible to be making such a claim. The major fuck-up, and I mean that literally, was allowing the exercising group to eat more. Still, they lost a full inch of abdominal fat, which isn't useless. Again, this is a classic example of what not to do when reporting scientific results. They must have known the media would pick up on this and relate only the headline and not the subtleties. - Mr. Gunn

The topic is now the homepage Buzz on scienceblogs.com - Bora Zivkovic

Mr. Gunn, I agree -- in fact you don't have to display the icon, just use the markup and the post will be aggregated. And, as we've talked about on twitter, it's in COinS (if not on our site, at least on the original blog post) - Dave Munger

At risk of dragging this back on topic - Mr. Gunn, you should leave a comment with your observations on the paper. Unlike this FF thread, comments on our site won't be 'acquired' and will thus form a permanent part of the record. :) - Peter Binfield from iPhone

Seriously, Peter, if someone came along and offered $50M, comments on your site would be acquired, as well, no? I'll leave a comment anyways, along the line of "the whole freaking thing is invalid because they let the heavy exercisers eat more!" - Mr. Gunn

Actually I seriously doubt it. Did you meet our Founders? I don't think they started PLoS to make a buck... What I do know is that Mission Driven Not For Profit organizations rarely sell up. - Peter Binfield

Once science communication has emancipated from the paper era, not even ONE journal may be necessary. So even if PLoS ONE were given $50M to shut down, there are lots of things you could do with that money to fulfill your mission of providing open access to research results. - Daniel Mietchen

@Mr Gunn: I wouldn't call the study flawed, just the ridiculous media interpretations. It is important to not restrict the food intake in a study like this because the point is to see whether according to recommendations, simply exercising will induce weight loss. And the results corroborate other research; if you just tell people to exercise they will compensate or overcompensate... more... - Colby

The Life Scientists: Donnie Berkholz

Writing the conclusion of my dissertation. Anyone else who's been through this got any advice?

July 28 - Comment - Like - Share

Daniel Jurczak, Todd Hoff, Mickey Schafer and 3 other people liked this

Advice in writing conclusions? Well, I just go back over what I wrote about, discuss some things a little too speculative for the results section, and then talk about what the followup would be. - Mr. Gunn

22 more comments

remembering that if everything else is good, then in all likelihood very few (if any) will actually read the conclusion... - Andrew Su

I tried not to write one, but my supervisor wasn't having that :-) It need only be a very few pages. Just briefly review your findings from each chapter, highlight what's good (novel findings, strong evidence for hypotheses) and suggest ways to improve what's bad (weak evidence, further experiments). - Neil Saunders

I still think it's the best part of my thesis. Pan in with the introduction, show detail in results, pan back out in the conclusion. A well-written discussion section should place what you've done in a broader context and also allows you a soap-box to give your vision of the future: important questions for the field, how your techniques/results help to (partially) answer them, perhaps... more... - Chris Cotsapas

+1 Chris: this is the time to think about the big picture for your field: what are the important questions, where should the field be headed, etc. It's where the real *thinking* goes. (If you've done any. I hadn't, so I just wrote a half-assed summary that wasn't worth reading, especially if you'd already read the damn thesis. That'll work too.) - Bill Hooker

Are we talking PhD thesis or Masters level? My PhD conclusion turned into a longish essay about what was wrong with the field and why people weren't asking the right questions. Only chance you ever get to get that kind of thing in print - Andrew Clegg

It's a PhD thesis. But I'm also trying to keep in mind that the average number of readers of a thesis is 1.5 (including the committee), so I consider it more of a personal exercise than anything else. - Donnie Berkholz

It *is* a personal exercise. But it might also force you to think about what (and how) you want to proceed for the next few years. Really thinking about where your field is, what's wrong with it now and where it's likely to go at a high level gives you a lot of clarity on where you should be going. And that's a habit you should get into. - Chris Cotsapas

In your conclusion, you want to conclude your work. Therefore you should state that you did or did not answer your research questions that you listed in your introduction :) - Frank

Thanks all for the advice. I ended up doing a bit of a meld, first summarizing some general conclusions useful to people who don't care about my proteins, then generalizing out to talk about a few approaches I used and plan to continue using to approach scientific questions of all kinds, and how at least one of them is underappreciated and underutilized. - Donnie Berkholz

If you make your thesis available online, the number of readers might reach even higher numbers (say, 4.5), particularly for passages that contain popular key words. - Daniel Mietchen

Following Daniel then, the key question is how to work the words "naked" and "sex" into the conclusion of a biochem thesis...? - Bill Hooker

If my advices were good, I would sell them. - Paulo Nuin

I agree with Daniel that if you make it available online, it becomes more meaningful -- like many above, my concluding chapter was somewhat hastily written, but also included the most important critique of the discipline in general -- not a single person reacted to it, and from what I can tell skimming current linguistics literature, that critique still holds (and would likely invite... more... - Mickey Schafer

@Mickey - I'm curious: if your critique still holds, then why not submit a slimmed-down version to a journal, as a short commentary piece or whatever? Just never got around to it, or other reasons? - 'Mummi' Thorisson

@ Mummi -- Most excellent question...at the time, was totally burned out, ready to jump ship, struggling through financial chaos, and suffering from being stupidly young/angry -- now, since I've killed most chances of doing serious linguistics again, am considering scanning portion of my dissertation and some earlier work to make available online. Have to find it in the garage,... more... - Mickey Schafer

I don't have any helpful advice, just wanted to let you know I"m going through the exact same process right now :) - Philip McDermott

My conclusion was a single page with "THE END" in 10 point font - Jonathan Eisen

@Philip - same here, working on my Introduction and will remain in this mode for probably another coupla months [sigh]. It's fun though. Definately looking forward to the discussion, when I can get on the proverbial 'soap box'. - 'Mummi' Thorisson

I read a lot of papers and I always appreciate a good intro and a good conclusion. I like to see a passionate summary of the heart of what you were trying to say, how you think you did, some deeper and broader implications of your work, what other people think, and where it will go in the future. Pretty much assume no one will understand the middle part and this is really your chance to connect and say something people will understand and care about. - Todd Hoff

I checked what I wrote: One page, consisting of six small paragraphs (one introductory, one final, and one for each of the experimental chapters) - p. 104 in pdf at http://bit.ly/q8r8i . - Daniel Mietchen

Bill, just stumbled upon this one and thought citing it may be one option to achieve that: http://www.ncbi.nlm.nih.gov/pubmed... . - Daniel Mietchen

Re electronic copies, that's problematic because I no longer own copyright on published chapters, and I don't have permission to republish, just for personal use. - Donnie Berkholz

a bit late to the party, but I am also about to write the conclusions section of my master's thesis. After all those suggestions here I will rethink my approach (lazy overview) a little bit. - Daniel Jurczak from iPhone

Chris Miller to Chris's feed, The Life Scientists

Encouraging good development practices for non-professional programmers? - Stack Overflow - http://stackoverflow.com/questio...

August 6 from Bookmarklet - Comment - Like - Share

Daniel Jurczak, Konrad Förstner, Abhishek Tiwari and 8 other people liked this

"I collaborate with a number of scientists (mostly biologists) who develop software, databases, and other tools related to the work they do. . . . Does anyone have any suggestions for how to persuade people whose primary job isn't programming that it's of benefit to their community for them to be more open with the tools they've built?" - Chris Miller from Bookmarklet

5 more comments

I wish I had enough karma to vote down that first answer (the one about Perl) - Deepak Singh

I wish I remembered my password to my other account to vote up that answer (the one about Perl) XD - Paul J. Davis

lol - Deepak Singh from IM

People shouldn't be getting grants without having a plan for sustainable software development and long term data storage. I wonder if grant reviewers have gotten more clueful about such issues in the past few years? - Eric Jain

Eric ... Alas no. Although they are beginning to ask the right questions - Deepak Singh from iPhone

Sure would be interesting to see the funding agencies require posting code developed using public money to a repository somewhere and then have journals require links to code before publication similar to genome papers. Even something as simple as versioned tarball hosting. - Paul J. Davis

The Life Scientists: Khader Shameer

Looking for a list of integrated resources (web servers or database similar to STRING, iHOP, STITCH etc ) to quote in my thesis.

August 5 - Comment - Like - Share

Daniel Jurczak liked this

I'd start with the latest NAR webserver and database issues. - Neil Saunders

True. But just curious to know if there is any blogs or review articles available on the topic. - Khader Shameer

Searched pubmed using keyword 'integrated database' got some good references, also cited resources from Bork Group, Biomart, Phylofacts, Taverna etc - Khader Shameer

Deepak Singh

Bowline - http://github.com/maccman...

August 4 from delicious - Comment - Like - Share

Daniel Jurczak and Neil Saunders liked this

Ruby desktop application framework - Deepak Singh

Paulo Nuin

To all who Think Themselves a Programmer - http://sfbay.craigslist.org/sfc...

July 7 from Google Reader - Comment - Like - Share

Marcos de Carvalho, Pierre Lindenbaum and Daniel Jurczak liked this

I want to "hate" for the attitude of the ad, but "like" for some of the cool "Hello World" programs, especially the ninja scroll one, which must use a dynamic programming algorithm in JavaScript. - Chris Lasher

The Life Scientists: Wladimir Labeikovsky

The pleasure and importance of printed journals : Nature - http://www.nature.com/nature...

July 1 from Bookmarklet - Comment - Like - Share

Bora Zivkovic, Jason Tsai, Mary Canady and 17 other people liked this

Someone needs to upgrade from dial-up...... And get off their ridiculously high horse. - Wladimir Labeikovsky from Bookmarklet

29 more comments

and learn about print on demand. - Pedro Beltrao

Liking the comments rather than the letter, obviously :-) I guess they're entitled to their (ridiculous, wrong-headed, irrelevant) opinion. - Neil Saunders

The only thing I can identify with is this act of discovering while browsing. There is no very good equivalent online for this (yet) - Pedro Beltrao

The quality comment is what kills me. As if somehow cellulose and ink enhance the quality of the peer review... - Wladimir Labeikovsky

All his points are killing me: You want to browse during breakfast? Has the guy ever heard of a "browser"? Been reading my news et al. during breakfast for the last 10 years. Laptops FTW! And yes, Wladimir: how does cellulose and ink make a journal any better, I wonder? I think we should get together and write a pointed reply to Nature! - Björn Brembs

Wow, Bjorn, feel free to include my name on the letter, but I wonder if it's worth the bother. It's not like we'd even have any common ground to discuss. - Mr. Gunn

@Mr. Gunn: Worth smorth. Consider the fun! :-) - Björn Brembs

It would be fun! - Mr. Gunn

Only problem may be that the letter which is the most fun writing won't be the one getting published, lol :-) - Björn Brembs

I've had a letter published in the print edition. I know to what degree those things are edited before they hit the page. - Mr. Gunn

'Until Nature comes up with a new business model, to read this story in full you will need to login or make a payment' - Andrew Spong

@Mr. Gunn: So you'd think "upgrade from dial-up" and "ridiculously high horse" would be edited out? :-) That cracked me up :-) - Björn Brembs

Here's my first draft: http://etherpad.com/FZ2N9FKECI - Björn Brembs

As for random browsing, wikis have it by default, and it's the outcome of many a search on a journal's site or on other parts of the web. - Daniel Mietchen

Despite the fact that printed journals contribute only a small fraction of the total amount of paper I think it is a question of mind set and awareness. Why get hundreds of printed pages of a journal if you only skim through a small part of it and read only a tiny part at all? That's quite a waste of resources (paper, ink, energy for production and transportation). Yes, paper... more... - Konrad Förstner

One more on random browsing: http://search.twitter.com/search... . - Daniel Mietchen

Yes, Konrad. See also http://ff.im/4GRMM. - Daniel Mietchen

After the fall of Genset in 2006, they started to put their whole library in the garbage. I've tried to save a part of the journals (see this picture http://www.flickr.com/photos... ). I sent some e-mails to the local libraries, to the centers of research, etc... Nobody asked for those journals and at the end, all those books ended into the bin. - Pierre Lindenbaum

@Pierre - Really a shame, maybe try next time bookcrossing.com or freecycle.org at least for the books. I had a similar experience when I wanted to donate some books in quite good shape to the local library. They didn't take them for whatever reason. - Konrad Förstner

That's pretty good, Björn, but I wouldn't even concede the point about discovery. I think discovery through re-sharing of bookmarks (connotea/citeulike/Mendeley(soon)) and through article use stats (Mendeley, PLoS) works better than randomly paging through a magazine. - Mr. Gunn

@Mr. Gunn, I don't know about that. We pick topics and people tend to be somewhat close to what interest us. I can't understand half of what is in a regular issue of Nature but I guess that if I ever browsed it in print I would spend more time on articles that I would never even look at the abstract. I am not even saying that one way is better than the other .. just that my online browsing habits are much more focused than would be if I had to check paper versions. - Pedro Beltrao

Yeah, I'm definitely more focused online, but the serendipity of print limits you to that one article, whereas recommendation online can come from the whole body of work. Maybe we need a good way to browse recommendations? - Mr. Gunn

Is there an analogy about paging through a set of recommendations from trusted people rather than through someone (the editors) with whom you have no direct connection? - Cameron Neylon

I page through F1000 listings, FF bookmarks (citeUlike and connotea) from others, and my broad search terms. Would that count? My subjective impression is that this leads to a broader sample of the literature than if I were just browsing the hip journals. But it certainly also feels less leisurely and comfy :-) - Björn Brembs

Great conversation. I am a strong believer that social bookmarking and networking tools can do a better job of nudging serendipity along than flipping through a paper journal. Use of these tools increases the chances of coming across relevant discoveries in adjacent fields. (shameless plug: http://2collab.com/ is designed with this goal in mind.) That said, my former position at Lulu.com left me a firm believer that print-on-demand is the way to go whenever print is prefered. - Michael Habib

"the proportion of reading by U.S. science faculty from browsing decreased in recent years, replaced by other means of learning about articles that are read. While the proportion of readings decreased over the years, however, that number of readings found by browsing remains about the same: 88 readings in 1977 and 95 in 2005. Readings from searches increased from 17 to 78 readings between these two years." - Tab. 1 in http://www.dlib.org/dlib... . - Daniel Mietchen

"the quality of these prestigious journals could gradually decline to the standard of many of today's web-only journals." What a flippiant remark, as above how does the medium of information transfer effect the quality of the content. What a dinausaur, lets start a charitiable fund to buy them an iphone - although will will have to advertise this via a telegram - Frank

And indeed given some effort they might actually rise to the standard of several of today's web-only journals, one can at least hope... - Cameron Neylon

I'll play devil's advocate here. My first reaction was rather like those above, but there's room for all, no? I liked getting American Scientist in print, though have now opted for online. But there are places laptops aren't very practical. Breakfast isn't one. I don't want my serendipity forced on me, either, cf Pedro. Comment about quality might have to do with the lower cost barrier for a new journal to enter web-only vs print, but didn't like idea that quality for established journals would decline! - Heather

From a practical standpoint I find that when I'm reading something in print, my mindset is different and I have a longer attention span and can actually get through a long article without realizing there's something else I need to look at or do online. I think there is still a place for printed journals, but more for reviews or 'popular' science such as GEN or the Scientist. If it's a primary research paper you really need to read for your work or research, I think the media doesn't matter. - Mary Canady

The Life Scientists: Shirley Wu

The All Results Journals - "Because all your results are good results" - http://arjournals.com/ojs...

March 4 - Comment - Like - Share

Mike Chelen, Bruno C. Vellutini, Chris and 28 other people liked this

Just got an email from them to be on the SAB for the Biology journal. Do they typically ask people without Ph.D.s (yet)? I like the concept but have concerns about legitimacy, etc... - Shirley Wu

40 more comments

If it were me, it would boil down to who else is on the SAB, and could I see myself publishing there. If it's not something I'd normally want to be associated with, then I don't think the cool title is worth it. my two cents... - Andrew Su

Shirley: erm... no, that doesn't sound typical. looking at the few members of the board who have joined up and are displayed on the site, they look to be all prof or assoc prof level (no names i recognise, but...), which seems pretty standard... - Joe Dunckley

It actually looks pretty good to me -- OJS, LOCKSS, CC-BY and a founding concept (publish all data) that I agree with. It's a definite plus in my book if they don't care about formal degrees and just want to get the best people. I'd like to know more about the business model/support framework, esp since there's no mention of author-side charges. I've registered as a reader/potential author/available reviewer. - Bill Hooker

If I could double-like this, I would. - Chris Miller

Let us know what you find out, Shirley. I'm a grad student who wouldn't mind reviewing either, if it's kosher. - Chris Miller

I replied with some questions, we'll see what they say - Shirley Wu

Quoting Feynman: "If you've made up your mind to test a theory, or you want to explain some idea, you should always decide to publish it whichever way it comes out. If we only publish results of a certain kind, we can make the argument look good. We must publish BOTH kinds of results." [http://wwwcdf.pd.infn.it/~loreti...] - Eric Jain

It will be interesting to see how this plays out. My main concern is that it is a lot of work to write a paper based on failed experiments and I don't know how many researchers would be willing to do that. I don't have a problem with sharing my failed results from within my lab notebook, which I have to maintain anyway. But if scientists do contribute I think it is fantastic. - Jean-Claude Bradley

Key questions are business model and what they are offering beyond what is already available. Also not confidence inspiring that two of the web pages provides for SAB members seem to lead to dead ends which don't have their name listed. Happy to give benefit of the doubt but presentation of these things is important. - Cameron Neylon

@Jean-Claude: I see two kinds of papers ending up in these journals: 1, "this didn't work" papers reporting pretty much only failed expts; and 2, regular papers that simply include extra information on the stuff that failed, as well as the stuff that didn't. Even when the failed stuff is useful information, trad. journals usually tell you to leave it out. So this model seems to be a sort of compromise between ONS and normal science -- a "gateway drug" for ONS, perhaps? - Bill Hooker

@Bill: A bit of an aside, I'm currently reviewing a paper for Neuropharmacology, a journal which is a tad out of my usual reading. Scanning the author instructions, I was struck by this line:Results. The results should be fully illustrated. Negative findings should also be noted to avoid unnecessary replication by others. - NatBlair

Bill - I appreciate the motivation and the utility if they get submissions - I am just wondering if they can get enough people to put in the effort. It will be interesting information about the scientific community either way. - Jean-Claude Bradley

Haven't heard back from them yet. The morning after I sent my response with questions, however, I got a verbatim copy of their original email sent to me again by the same person. So I don't know what's going on but like Cameron said, not exactly confidence inspiring - Shirley Wu

Does anyone have an opinion on the Journal of Negative Results? - Mr. Gunn

@Jean-Claude - I think your concern is well founded. We get good feedback for JNR-EEB (http://www.jnr-eeb.org/index...), but few submissions. - Bob O'Hara

I got a reply from the section editor that contacted me. They do want Ph.D. scientists, and he didn't know I was still a graduate student (not that hard to click on the "about me" page of my blog, especially if you mention that you've seen my blog and that's why you're contacting me...). Anyway, the other things he mentioned were that there are no author fees (in addition to no access fees), and everything is done in a volunteer fashion because the people involved want to improve science. - Shirley Wu

I'd still be concerned about whether it's possible to sustain high quality without a business model but then again, that's what this open stuff is all about, right? So it would be great if it worked long enough to get something behind it to maintain it. Of course, J-C's concern is also a big one - who will write and submit papers to it? - Shirley Wu

I'd be very worried - getting papers is a big enough problem - but to do it with no business model just isn't sustainable. The business model can be volunteer but then you've got to explicitly worry about how to support and retain your volunteers. But in general I think I'm coming to JC's point. No-one has the time to write full papers on material that isn't up to the grade for existing journals - I don't think they are going to start just because the journals are there. The barrier has to be much lower. - Cameron Neylon

People who start writing their papers before doing the actual work and keep them in sync with the latest progress should be glad to be able to submit them somewhere (even if a few more days of effort are required to clean up the paper and answer reviewer questions etc)? This approach also seems more effective than spending weeks after the fact going through unreadable lab notebooks and... more... - Eric Jain

Which one of the two Eric? I think the latter is more common...but even with a good record the hassle of going through a peer review process is a big disincentive - Cameron Neylon

Kind of journal of negative data. More likely to fail, or at least what people claim as "all results" will be the tip of iceberg. - Dean Johns

"They do want Ph.D. scientists" -- that grates my cheese. Suppose you read Shirley's blog and think "smart person, want her on board my project" -- well, what has changed when you find out she's a grad student? This feeble reliance on a piece of paper is why universities are less and less focused on actual education, and more and more on certification -- a product, bought and sold. [/rant] - Bill Hooker

I certainly agree with you, Bill, but I think there was some validity to what they said; they went on to ask me what my plans were after graduating, whether i was going to remain in the sciences. I would assume that they wouldn't be recruiting folks with Ph.D.s in mol bio that were now working as management consultants on wall street, for example. But they didn't exactly do a great job of vetting if they didn't know I was still a student. - Shirley Wu

@Cam: I think this is basically another "journal of negative results", not so much about material that isn't up to scratch. Eric's comment about people who keep notes in sync with benchwork makes me think that journals that are willing to take negative results are likely to be a boon to anyone who keeps an open or semi-open notebook. (I disagree that peer review is a hassle or a disincentive. Sure, some reviewers are jerks, but overall the process is fun.) - Bill Hooker

I've never looked at the journal of negative results. But it strikes me as quite weird to think about peer-reviewed negative results. I think it's sufficient to just publish your notebook and an informal summary ("we were hoping this would happen, but instead this happened and we don't feel like publishing it in a peer-reviewed journal. Hope these results are helpful!") It's tough to see what peer-review would add w/o asking the researchers to do extra experiments? - Steve Koch

I'm also unclear on whether there is a definition of "negative result." Does the term originate from pharma stuff? I.e., drugs that didn't work? In other fields is "negative result" a synonym for "less-interesting result?" That's sort of what I was thinking and why peer review would seem weird. - Steve Koch

Steve, I think there does need to be some degree or review, or they could end up with a bunch of "Bigfoot was not discovered in Alaska" kinds of submissions. Negative, in the sense of isn't something that will support a grant application, is how I imagine it to be used. - Mr. Gunn

Mr. Gunn, yeah I agree with that. I was really saying I don't see the point of having a journal like that. It seems like a waste of peer-review resources. Self-publishing seems to make more sense to me...but I'm probably not thinking about the right examples of negative results. - Steve Koch

What the journal adds over self-publishing is editing, review, and discovery. Pretty much the same as other journals. I see what you mean about a waste of resources, though. Some people consider Friendfeed to be a waste of resources, too, so there's that. - Mr. Gunn

This is all fascinating. Mr. Gunn says, "What the journal adds over self-publishing is editing, review, and discovery. Pretty much the same as other journals..." But it is the same as other journals? This one would be specifically devoted to secondary findings—that would set it apart, wouldn’t it? If this journal were well run (which doesn’t seem to be the case, based on Shirley’s... more... - Hope Leman

Hope, my comments were directed towards Steve's question of what value publishing negative results in a journal would have over simply self-publishing them. Of course the journal would be set apart from others in terms of content. - Mr. Gunn

I can't make much comment about how organized they are other than that they didn't know I wasn't a Ph.D. despite having been to my blog. Even if they do have a committed and organized core of people, the bigger concern is whether they can sustain a purely volunteer effort. If they can't, they need an actual business model, and the arguments here (and elsewhere: http://tinyurl.com/c2b3xm) are of the mind that a full-fledged journal of negative results isn't cost effective. - Shirley Wu

Thank you for your patience, Mr. Gunn. Thank you for the link to Cameron's post on the topic. That is an outstanding, asute bit of analysis. - Hope Leman

Another possible use for the open journal system model would be using it for well-done student publication -- another venue of practice before hitting the bigger journals -- individual schools/labs could put OJS to use, students learn not simply to write for publication but also how to act as reviewers -- provides a neat continuing reinforcement of how to read science (stats, design, etc) -- basically a more finished open notebook product -- also useful for initiating new people into the lab - Mickey Schafer

Hey all -- I got an email invite from All Results Journal:Physics today for the scientific advisory board. I reread my comments above and still agree with my own skepticism. On the other hand, wouldn't mind supporting it to see if it can fly. Did any of you end up getting invovled? Jean-Claude, I see your name on the SAB for ARJ:Chem ... any opinions? - Steve Koch

(As an aside: is this thread sufficiently public that the majority of reasonable people wouldn't mind if I linked it to the editor who sent me the invite? I think definitely yes, but given the hoopla that ensued several weeks ago, figured I'd ask first.) - Steve Koch

I'm still skeptical - I don't see evidence of awareness of the magnitude of the job they're taking on. But then anything that starts from the assumption "publication should basically be free" sets my alarm bells ringing. Happy to see this made public but then I would be I guess :-) - Cameron Neylon

It'd be good if it did take a role as a dumpster for drug research -- stuff failing at any stage might be usefull from discovery on. - Chris from twhirl

Pity is that it's not what I thought at first, which is a journal that publishes just data sets with structured annotation (rather than a full paper being needed, shortcutting the idea of the paper-writing robot) to really get people to clear out their lockers. Just a tab-format form answering the kinds of questions listed in projects linked to by MBBI (ref.... more... - Chris from twhirl

Call it ' Kudos Convertors -- "Free you data. Boost your citations*." ' [* Subject to funders counting it]. How about some kind of data copyright statement while we're at it, to assist with enforcement. - Chris from twhirl

Yeah, I agree, Chris. It'd be much better w/o need for formal paper and "rigorous peer review" as they state now. Editorial or peer review should just make sure that necessary info has been included. Wonder if SAB members can change any of these decisions before they go "live?" - Steve Koch

Michael Kuhn

Apparently live-blogging at ISMB is so popular that FriendFeed banned our IP address (via http://friendfeed.com/ismbecc...)

June 29 - Comment - Like - Share

David G. Pisano, Benjamin Good, Jean-Claude Bradley and 12 other people liked this

DM Brett or one of the other FF staff. They're usually helpful and I'm sure happy about the usage once they know what's going on. - Neil Saunders

3 more comments

Could have been anticipated. I guess next year in Boston it is going to be Google Wave anyway. - Daniel Jurczak

wow :) - Pedro Beltrao

Excellent. Well, sort of. - Michael Nielsen

Well I guess that answers the concern that without some of last year's ring leaders it wouldn't take off huh? - Cameron Neylon

The Life Scientists: 'Mummi' Thorisson

OmicBrowse: a Flash-based high-performance graphics interface for genomic resources - http://dx.doi.org/10...

June 29 - Comment - Like - Share

Daniel Jurczak and Khader Shameer liked this

"OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. It is an open source tool capable of regulating multiple user data access to each dataset to allow multiple users to have their own integrative view of both their unpublished and published datasets, so that the maintenance costs related to supplying each collaborator exclusively with their own private data are significantly reduced. OmicBrowse supports DAS1 imports and exports of annotations to Internet site servers worldwide. We also provide a data-download named OmicDownload server that interactively selects datasets and filters the data on the selected datasets. Our OmicBrowse server has been freely available at http://omicspace.riken.jp/ since its launch in 2003. The OmicBrowse source code is downloadable from http://sourceforge.net/project...." - 'Mummi' Thorisson

Lars Juhl Jensen

The pleasures of bioinformatics: moved the lab from Lyngby to Copenhagen in 2 hours including packing and unpacking.

June 29 from Twitter - Comment - Like - Share

Piotr Byzia, Khader Shameer, Daniel Jurczak and 2 other people liked this

Paulo Nuin

Establishing a successful bioinformatics core facility team. - http://www.ncbi.nlm.nih.gov/entrez...

June 28 from Google Reader - Comment - Like - Share

Daniel Jurczak liked this

Robert Scoble

I haven't looked at Netbooks lately. Is the Asus 1000HE still the best for under $400? Which is the best to run OSX on? Answer on FriendFeed

June 27 from iPhone - Comment - Like - Share

Derryl Beukes, Jack Nork, Daniel Schildt and 24 other people liked this

Yeah, the Asus 1000HE still gives best bang for your buck. That, and it can run games decently. - Sam Goldfield

44 more comments

would love to load osx on my netbook i have the acer aspire one d150. decent only if brought up to 2gb of ram. battery runs atleast 6+hrs - Jay Martinez

Robert, you should wait for next lineups which include Nvidia Tegra and ION chipsets that run 1080P videos smoothly. Otherwise, Asus 1000HE is definitely one of the best nowadays, specially in terms of battery life. - Nir Ben Yona

I love OS X on my MSI Wind, plus the battery options are very nice to have in a netbook. - Aaron Dyer

1000HE works fine for me---thrilled about battery life, but haven't moved to OS X on it. You *know* if you buy something, something better is announced the next day... - elspmdi

Nir: when are those coming? - Robert Scoble

I have the MSI Wind and am very happy with it. - Tendonitis' Bitch

I'm waiting for the Asus 1005HA (out this week) - the fully loaded version. I believe the Dell Mini is still the easiest for running OSX tho - Andy Sternberg from fftogo

I was personally looking at the HP Mini (fully loaded, bluetooth, the works), and Newegg is having a sale for $329.00? - Sam Ferry

depends. some people hate the msi wind. i got it because at the time it was one of the *only* ones that you could overclock. some people get other kinds for the keyboard size but does not have the overclock feature. my msi wind runs the default xp, windows 7, and os x. i have unbuntu on usb and backtrack 4 on sdhc. it's a great little machine for the price with great battery life. it... more... - sɹǝɥʇɐǝɟʞɔɐןq

one of the better compatibility charts floating around regarding OSX and Netbooks. http://gadgets.boingboing.net/2008... - Jerry Schuman

been using the Acer Aspire One 531 for a while now, the inbuilt 3G module makes it very interesting but today switched to the Samsung N110,what a machine, running windows 7 ultimate is the only way to go - Patphelan

Robert, the new Lenovo IdeaPad S12 with ION chipset is already up for pre-order and scheduled for shipment on July http://bit.ly/kXgMw. Other netbooks with Tegra chipsets are expected to make a debut on Q4. - Nir Ben Yona

What is the benefit of a Netbook over, say a 13-inch MacBook or an iphone? - Curt Mercadante

the boing boing link jerry gave shows the msi wind works well with it. however, there's a hack for the audio i/o -albeit not very elegant but they are working on it and it's getting there. - sɹǝɥʇɐǝɟʞɔɐןq

Curt: price over Macbook. Screen resolution and flexibility over iPhone. - Robert Scoble

You can put OSX on the 1000HE? I'm posting this with a 1000HE, and I must say I really love the device. - Robert James Massey

Curt, I was considering the MacBook Air and asked Robert for alternatives. Have iPhone. Want keyboard, practical screen and multi-tasking. - Conor Ogle

curt, a netbook isn't for everybody. i have an iphone, netbook, and macbook pro. you take your netbook when you need to travel on the go but don't want to lug around your primary 3+ grand laptop, risking theft or damage. it has a bigger screen and capabilities than the iphone. they are supposed to complement your existing computing experience -not necessarily replace anything. - sɹǝɥʇɐǝɟʞɔɐןq

The Dell Mini 9 is supposed to be the most Hackintoshable netbook. - nick

tbh I've never been a fan of the atom processor. It made no sense in buying the equivalent of a 5yr old centrino. A beefed up battery on a centrino benchmarks the same as a netbook. However as others have suggested the ION chipset is the way to go if you want to offload DXVA videos on to it. - Shaf

Ive had the HP Mini 1000, The Acer Aspire one, and the 1000HE. The 1000HE is hands down the leader. - Kyle Nas

shaf, it would be interesting to see what happens when the dual core atoms come out in q4 and how they will stand in regards to the ion. will they integrate the ion some how, or will they compete? the tech is getting better. - sɹǝɥʇɐǝɟʞɔɐןq

Use my 1000HE now as I write this and I love it. It's great as an extra especially when travelling, but I would not choose it as my main computer. The screen & keyboard is too small for bigger tasks and more hours of work. That said, I do use it a lot! Great when in the kitchen and you need a recipe from Google, or just need to check your email in the living room & don't want to go upstairs to the mainframe station :-) - Morten Blaabjerg

sɹǝɥʇɐǝɟʞɔɐןq indeed - I'll just wait in the meantime ;) - Shaf

Morten, I actually replaced my touch screen HP with my 1000HE and just hook it up to a 22" monitor when I'm at the house. The ability of the computer to quickly change resolutions makes it even better. Although I am preparing to buy a Mac soon. So... Where can I find details on OSXing my 1000HE? Maybe I should google it. - Robert James Massey

robert scoble, (i just saw your question up there), the ions are supposed to come out near the end of summer. the dual cores by intel released at october at the earliest -meaning netbooks a month after that. - sɹǝɥʇɐǝɟʞɔɐןq

I run OS X on my Acer Aspire One, works wonderfully and software update works too! - James

James: do tell how you did it? - Jay Martinez

We've had excellent results with the $200 Acer Aspire One's. They make an awesome PBX platform. - Ward Mundy

I've had OSX installed on my Lenovo s10. Ran just fine. The problem was that OSX's UI is not well suited to the little screen -- particularly compared to Win7. - Christopher A Carr

PIAF on an Aspire One is just hilarious. Ward gets bored easily. - Jerry Schuman

I wish that boingboing chart had a video column. - John Bachir

Does anyone have heat issues on netbook(running macos x) particularly when running flash? - ashish

Curt: Ever since I bought my iPhone, I rarely use my Asus netbook anymore. The iPhone effectively replaced it for me. However, when away from home, there times when my netbook is needed. I just wish the video was faster. That is my biggest netbook complaint. - Mark Davidson from BuddyFeed

Ward, off topic... PIAF in VirtualBox on Mac mini. Along with a few other virt machines. - Jerry Schuman

sɹǝɥʇɐǝɟʞɔɐןq ION is just the platform there are already Atoms using the platform albeit mini-ITX and smaller(see the Zotec boards). Mixed reviews so far, think it can handle 720p but struggles at 1080p and you can forget blu-ray - Shaf

good question, I've been wondering the same thing or considering the Ipod touch - freedom fighter mom from twhirl

shaf, the zotac is a mini itx motherboard i've being drooling over for some time. in regards to ion netbooks, the ideapad is the first *netbook* to have ion and plans to be released in a month or two... hence my safe estimate of august for the netbook: http://www.liliputing.com/2009... :) - sɹǝɥʇɐǝɟʞɔɐןq

ah, i see the ion netbook (from my previous link) has been now set back to october. this is around a month or two when the atom dual cores plan to be released. both attempt to trackle the prob of smooth hidef playback 720p, not quite 1080p or i yet. - sɹǝɥʇɐǝɟʞɔɐןq

i hear that Dell mini 9 is the best netbook to run OSX on. I just bought one and going to attempt it. - drinktale

The Dell Mini 9 is the best, Robert. I have one, and it's wonderful. I've installed OSX two different methods that worked quite well. I even blogged it: http://www.trevorcarpenter.com/2009... - Trevor Carpenter

Why not use Ubuntu instead :) - Manuel Mas

The 1000HE is a nice piece of kit, however it (or maybe just mine) had a pretty loud fan (a clearly audible "rrrr" noise at all times). Has anyone else got the same issue? - Martin Häger

Netbooks still Taboo in my opinion, until Neo platform from nVidia shows up. Without decent 3D, I don't call it a computer...Even iPhone has better 3D capabilities than current netbooks... - Adi Rabinovich

I have always been a fan of the Samsung range, check out more here: http://www.sammynetbook.com - Winston

Pedro Beltrao

Science journalism: Breaking the convention? : Nature News - http://www.nature.com/news...

June 24 from Bookmarklet - Comment - Like - Share

Chris Lasher, joergkurtwegner, Konrad Förstner and 19 other people liked this

I still think they should have interviewed other people than me, though. It is not like I was the main person behind what happened on FriendFeed at ISMB in Toronto. - Lars Juhl Jensen

5 more comments

I guess you had the best sound-bites Lars :-) - Neil Saunders

@Neil @Lars "bloggers don't need icebreaker events ;-)" heh - Duncan Hull

Some of these comments confuse me slightly. The definition of "publishing" is the process of production and dissemination of literature or information (http://en.wikipedia.org/wiki...) why do some scientists confuse publishing only to be a peer-reviewed journal publication and assume other methods- giving talks, posters, slides, open notebooks are not "publication"? - Frank

@Frank absolutely, publication is "to make content publicly known." public-ation - Duncan Hull

That's a long story, Frank, but it boils down to the currently dominating definition of scientific "publication" stemming from the pre-web era when journals were more widely circulatable then the other kinds. And, for the last five decades or so, all major scientific journals have used pre-publication peer review to decide which content comes into the journal, since printing on paper was (and still is) expensive. - Daniel Mietchen

Repost of my comment on the Nature web site: I also find it ironic that people go to conferences to present their work and at the same time want to keep their discoveries secret. On the other hand, if people abstain from presenting new results then why would anyone want to participate in conferences? In some fields, computer science comes to mind, the best work is published in... more... - Lars Juhl Jensen

michaël rosseel

PhotoshopDisasters - http://photoshopdisasters.blogspot.com/

June 25 from delicious - Comment - Like - Share

Daniel Jurczak and Berci Mesko, MD liked this

Roderic Page

“Installing `libgd` from source on OS X” — Mike West - http://mikewest.org/2007...

June 24 from delicious - Comment - Like - Share

Daniel Jurczak and Neil Saunders liked this

Using Matías Giovannini’s great instructions, I was (finally) able to get the GD library installed on OS X so I can build some charts in Perl. I've condensed his instructions into the shell commands that I actually needed to get everything installed, and record them here just in case I ever have to do it again. :) - Roderic Page