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Lars Juhl Jensen
Protein networks: A basis for large-scale data mining - http://www.slideshare.net/larsjuh...
Protein networks: A basis for large-scale data mining
Benjamin Tseng
Amazing gel shows Ubiquitin is transferred one-at-a-time and on a millisecond timescale! - http://www.iayork.com/Mystery...
Amazing gel shows Ubiquitin is transferred one-at-a-time and on a millisecond timescale!
That's awesome. - Bill Hooker
Ian York rocks, as do the scientists who did this. - Mr. Gunn
Gels still speak, even without lasers... - Mark A Jensen
My initial reaction was "how can anyone pipette that quickly !" ... but it seems they have some fancy quench-flow equipment to get around that problem. Very cool. - Andrew Perry
Pawel Szczesny
Finished a proposal for three lectures on practical aspects Science 2.0 targeted towards PhD students.
The overview of the proposal is already on my blog: http://freelancingscience.com/2009... - Pawel Szczesny
novoseek
Pawel Szczesny
Genome sequence data: management, storage, and visualization. Biotechniques. [PDF] http://www.biotechniques.com/multime...
nice and brief overview-- thanks Pawel - Mark A Jensen
Marcin Wojnarski
Data mining / bioinformatics challenge: analysis of DNA microarray data - http://tunedit.org/challen... (prizes for best solutions)
Attila Csordas
Let's organize an EMBO (un)Conference Series based on The Life Scientists community here! - http://www.embo.org/program...
"Organizers can apply to hold a series of three conferences that may take place over a six-year period in an EMBC Member State. These conferences should cover different and evolving aspects of a relatively broad subject area of major importance to the scientific community worldwide. They may alternate with corresponding meetings in North America or Asia, facilitating interactions between scientists based in Europe and beyond. A minimum of 100 participants should be accepted. The maximum funding provided by EMBO for a conference series is 30,000 euro per conference" - Attila Csordas from Bookmarklet
'Organizers are therefore required to justify all major costs in the budget section of the application form. It is expected that participants (other than the speakers) will pay for their travel, accommodation, subsistence and registration fee. EMBO funds can be used to cover: • travel (Apex / Economy), accommodation and subsistence costs of the speakers • reasonable administration costs... more... - Attila Csordas
'How to apply: Organizers can apply to hold a series of three conferences that may take place over a six-year period in an EMBC Member State. Funding for all three conferences in the series is set aside upon approval of the first conference. However, organizers are required to submit a new application form for the second and third conferences (in the year preceding the follow-up conference).' http://courses-workshops.embo.org/SubmitA... - Attila Csordas
EMBC Member States http://www.embo.org/aboutem... can we pick 1 for the 1st? UK, Spain, Portugal, Finland...? What about Prague? (I love Prague) - Attila Csordas
application deadline 1st August - Attila Csordas
Sounds great! Will you be lead organizer? I'm up to contribute! - Björn Brembs
yes, I am able to write the 1st draft of the application proposal - Attila Csordas
'minimum of 100 participants; I assume we have >100 subscribers here from EMBC Member States :) - Attila Csordas
I know that the BioSysBio organizers are looking for financial support for the 2010 ByoSysBio conf so maybe we can join the 2 endeavors, as BioSysBio's profile: Synthetic Biology, Systems Biology and Bioinformatics & The Life Scientists' profile are overlapping, alerting them - Attila Csordas
sent an email to BioSysBio organizers and lifescientists@googlegroups.com - Attila Csordas
If you organize as an unconference where everyone speaks, you could just subsidize the travel for everyone. - Donnie Berkholz
But then you have to have a list of (travel-subsidized) speakers, which sort of undermines the unconference principle. - Heather
Pawel Szczesny
It's confirmed: I will be speaking at the conference on Open Science organized by CC-Poland here in Warsaw in May. Biogangers, I will try to make you famous (in Poland) :)
Very cool - who else is on the programme? - Cameron Neylon
I don't know details yet. I hoped to meet some of you in person, but it looks that all guests from abroad are involved in Open Access projects (which is the main focus of the conference). It's short, one day event, so I don't expect lots of speakers. - Pawel Szczesny
Really too bad that I won't be in Poland then :-( Good luck and I hope to finally meet you later this year. - Piotr Byzia from twhirl
Pawel Szczesny
Eric Von Hippel's book - Democratizing Innovation - http://web.mit.edu/evhippe...
Pawel Szczesny
We never invent anything new, yet progress is made! - http://www.daniel-lemire.com/blog...
Pawel Szczesny
20 Useful Visualization Libraries : A Beautiful WWW - http://abeautifulwww.com/2008...
Java, java, java....hmm methinks there is a message in there somewhere... - Cameron Neylon
I'm looking into the processing language right now. Seems quite versatile. - Sung W. Lim
processing also has implementations in python, ruby, and javascript. simile is cool because it works with RDF. google charts and vis is pretty well documented and widely compatible. all the node graph stuff is great however it seems limited to one type of visualization. - Mike Chelen
Can you point me to the Python implemnentation? - Rajarshi Guha
Rajarshi, I haven't found python implementation of Processing, but here's a quick recipe how to use Processing libraries via Jython: http://processing.org/discour... - Pawel Szczesny
+1 like for Cameron's comment ;- - tim
hmm jython may be the best option, the next closest suggestion would have been shoebot http://tinkerhouse.net/shoebot... - Mike Chelen
Mike, Shoebot looks nice, I haven't seen that before. - Pawel Szczesny
go2web20
Maxine
Music that's bound to be interesting - Reciprocal Space - Stephen Curry's blog on Nature Network - http://network.nature.com/people...
"The Yu group have created a ‘home-made’ micro-array on a music CD that just needs an ordinary CD player to scan the disk for the results of the binding assay. They did what!?! You heard right – and their system is impressively flexible since interactions involving DNA and protein can both be analysed." - Maxine from Bookmarklet
"The disk can be inserted into a standard CD player to analyse the results! Because music CDs have been designed to play back smoothly even when they get scratched or dirty, the music is encoded in a way that allows error detection and correction. The software analyzing the readout from the disk knows precisely where the errors on the disk lie. Now, normally you don’t care about the... more... - Maxine
imabonehead
Hackszine.com: Linux Tip: super-fast network file copy - http://www.hackszine.com/blog...
"The problem is that there is a certain amount of per-file overhead when using scp or rsync to copy files from one machine to the other. This is not a problem under most circumstances, but if you are attempting to duplicate tens of thousands of files (think, server or database backup), this per-file overhead can really add up. The solution is to copy the files over in a single stream, which normally means tarring them up on one server, copying the tarball, then untarring on the destination. Unless you are under 50% disk utilization on the source server, this could cause you to run out of space. Brett Jones has an alternative solution, which uses the handy netcat utility..." - imabonehead from Bookmarklet
Antony Williams
This is a request for guidance to help make ChemMantis better. ChemMantis is a document markup technology we have built on the ChemSpider platform. I've posted a presentation here. Look at slide 75 (I recommend full screen mode). To help us enable the system I am looking for lists of bacteria, viruses, fungi etc. I welcome guidance. - http://www.chemspider.com/blog...
also...lists of fungi, viruses etc... - Antony Williams
Someone needs to download the NCBI taxonomy database - Neil Saunders
Left a comment at your blog about getting species lists from NCBI. - Neil Saunders
Neil..great source of information. Thanks - Antony Williams
No worries; by the way, taxonomy files at NCBI FTP site are at: ftp://ftp.ncbi.nih.gov/pub/taxonomy/ - Neil Saunders
You can also get the (more or less same) taxonomy data here in tab-delimited format or RDF: <http://www.uniprot.org/taxonom...> - Eric Jain
Eric, cool! Thanks for that link. - Neil Saunders
Bill Hooker
This is a bold prediction, but it feels pretty solid to me. Glyn Moody: "Soon ... America will become one of the most fervent advocates for *minimalist* intellectual property regimes. Yes, you read that correctly: just wait." - http://opendotdotdot.blogspot.com/2008...
as other countries continue to develop technology and we begin to fall behind? Not so sure about that one, but I'd welcome the IP policy change. - Mr. Gunn
Andrew Perry
Neil Saunders
I love DokuWiki too, didn't know about the PubMed plugin - neat :) - Daniel Swan
It is neat - the same developer has plugins for PDB and PubChem too. Demo page: http://predikin.biosci.uq.edu.au/bacpath... - Neil Saunders
is that your remote key that you're broadcasting in the Friendfeed example? This might not be such a good idea, given that one can share things using the remote key: https://friendfeed.com/account... - Michael Kuhn
that is very cool - Cameron Neylon
Hi Neil. I like how you went for the mediawiki skin. Can you tell me how you got the gnuplot plugin working? - Mitchell J Stanton-Cook
Mitch: don't recall any issues with gnuplot. Just followed the link off this page - http://www.dokuwiki.org/plugin:..., downloaded, installed. Worked fine, once gnuplot was installed on the server :) - Neil Saunders
Lars Juhl Jensen
Tanath
Slashdot | (Useful) Stupid Unix Tricks? - http://ask.slashdot.org/article...
No Unix trick is ever stupid. - Rishabh Mishra (p248)
But all of them _are_ awesome. - i80and
Alexander Griekspoor
PLoS Computational Biology: Defrosting the Digital Library: Bibliographic Tools for the Next - http://www.ploscompbiol.org/article...
Great review by Duncan Hull et al describing scientific literature repositories and bibliographic tools. Disclaimer: very happy obviously with the attention for Papers! ;-) - Alexander Griekspoor from Bookmarklet
Yu-Jie Lin
Visualizing Linux package dependencies at noumena - http://blog.thejit.org/2008...
Visualizing Linux package dependencies at noumena
Anyone would like to put some efforts for RPM? - Yu-Jie Lin
Egon Willighagen
A lot has certainly happened in 3 years - we're almost the same "age" - Jean-Claude Bradley
Congratulations!!! and yes a lot has changed. I am right behind you :) - Deepak Singh
Egon Willighagen
GitToDo support for Freemind: graphical mapping of important things on my schedule - http://chem-bla-ics.blogspot.com/2008...
GitToDo support for Freemind: graphical mapping of important things on my schedule
Neil Saunders
How I landed my alternative career in science writing - http://alternative-scientist.b...
Neil Saunders
Love that tip on scaling - Deepak Singh
The last point feeds back into the first point. - Michael Barton
Love the connection between #1 and #10. Open Everything FTW! - Bill Hooker
Pawel Szczesny
Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. - http://www.ncbi.nlm.nih.gov/entrez...
Andrew Perry
Setting up NCBI wwwblast on Ubuntu 8.04 (Hardy), Apache 2 - http://blog.pansapiens.com/2008...
Ian Mulvany
Markov Chains using CouchDB's Group Reduce - http://www.connotea.org/user...
Oh nice - Deepak Singh
Love markov chains. - Mike Reynolds
Lars Juhl Jensen
After realizing that SlideShare is not good for posters, I decided to simply upload high-resolution images of the posters to a Picasa web album. At least it allows zooming and ensures that everything is rendered correctly. - Lars Juhl Jensen
Talking a closer look at the images, it is clear that Picasa seriously degrades the quality relative to the jpeg files that I uploaded. So neither SlideShare nor Picasa seem to be good solutions for storing posters online. - Lars Juhl Jensen
So is there a market for a dedicated poster sharing site? I only know of eposters: http://www.eposters.net/ - Neil Saunders
What about scribd ? saving your poster as pdf should keep all the information/quality ? BTW , you can also handle your pdf's with google docs. You could also try .https://www.acrobat.com/ . - Pierre Lindenbaum
I could obviously just upload the images to my Wordpress.com blog and make a page with captions, thumbnails of them and links to the full versions of the posters. But then I would have to be editing HTML every time I add a poster and they would not show up on FriendFeed. There must be a better way to do this ... - Lars Juhl Jensen
Pierre, thanks for the suggestions - I do have PDFs of the posters. But do any of the resources you mention play nicely with FriendFeed? I would like to see thumbnails here like I get from Picasa and SlideShare. - Lars Juhl Jensen
did you select 'actual size' when uploading to picasa? - Thomas Lemberger
@Lars, oh, i did not understood you wanted something FF-compatible :-) - Pierre Lindenbaum
@Thomas, yes I uploaded it in "actual size" and if I download the jpeg then I get exactly the same file that I uploaded. So it is Picasa's web viewer that degrades the quality. - Lars Juhl Jensen
@Neil, just took a look at ePosters. As far as I can tell, the only service they provide is to host a PDF file for you and assign a unique id (ISSN?). They obviously mention tons of advantages of submitting your poster, but as far as I can see I would achieve the same by just putting the PDF on my blog: anyone can see it, anyone can print it, it becomes searchable, etc. - Lars Juhl Jensen
I just enabled the RSS feed of my downloads section (I use e107.org). Now any file I put in my download section will be in this RSS feed: http://bjoern.brembs.net/e107_pl... (where the 4 denotes the RSS version, in this case Atom). It doesn't seem this is FF compatible, is it? - Björn Brembs
Eh, imported the feed to Google Reader and then shared it. No good, too complicated - Björn Brembs
In an ideal world, what do people want in a poster sharing site? An embeddable flash viewer with zooming/panning? RSS feeds with thumbnails? I work on Nature Precedings and we're actively looking for ideas to encourage the sharing of posters. Please feel free to post thoughts in our forum: http://network.nature.com/group... or use our feedback form to submit ideas: http://precedings.nature.com/contact - Hilary
I'd say that if you took SlideShare, added zooming and panning to the flash viewer, and fixed the bugs in the rendering of PDFs then you would have exactly what I'm looking. - Lars Juhl Jensen
You can try a postercast in scivee (example: http://www.scivee.tv/node/5798) but it will not be FF friendly. I don't even know if they have RSS feeds for users. The same was as presentations, you can sinc parts of a video to zoom in sections of the poster (click show poster on the video). - Pedro Beltrao
Hi Lars, would Smugmug work for your purposes? FF does include it. - Ruchira S. Datta
What about things like Scribd or similar. For things like posters they might work out quite well. - Deepak Singh
pdfs and amazon s3? - mjc
Maybe a simple Flickr pool? Here's one called "poster sessions": http://www.flickr.com/groups... - Neil Saunders
Flickr will scale down your image to less than 1024x1024, unless you have a Pro account (for which to pay). S3 you also have to pay for, and it doesn't play well with FriendFeed either (see Lars' comment: "But do any of the resources you mention play nicely with FriendFeed?"). - Michael Kuhn
FWIW, FriendFeed will display an image along with the post if the RSS item contains a media:thumbnail tag of the right dimensions (http://groups.google.com/group...). However, getting your standard blog platform to include this won't be easy. - Michael Kuhn
Thanks for clarification; that explains why Tumblr media are not displayed, Tumblr's fault not FF. - Neil Saunders
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