Samuli Eldfors › Likes

Can't argue with any of those - Chris Miller

Picked up by Genome Tech's DailyScan ;) - Shirley Wu

:) - Deepak Singh

Genome Tech DailyScan sends traffic skyward, anyone know who is behind http://www.genomeweb.com/newslet... (one person or a group of people? they don't say on their website or in the feed) - Duncan Hull

yes, it is a pity that the traffic is not being directed by a place like postgenomic. The editors of genome tech daily link to a lot of blogs but it would be great to create the same dynamics of the tech world (that has techmeme) in science blogs. Traffic could then flow to where the conversations are happening and not specifically because of editor decision. - Pedro Beltrao

I'm curious about the kill-the-flatfile. I agree in principal, but I think often one invents complicated schemes in some cases where a simple tab-delimited works okay. It is the evolution/flexibility of the data (since many of problems/tasks are often ill defined at the outset) that XML helps with, and of course as data scales from thousands to {m|b|tr}illions BDB,SQLite, become critical. What is crazy is how much effort (my experience) is spent worrying 'bout formatting data from one format to another. - Jason Stajich

Genomeweb is a fairly widely read trade mag. We used to call it people magazine for genomics :). Their newsletters are quite widely read as well - Deepak Singh

@Deepak ta, but *who* is behind it, no names are given, its all a bit anonymous - Duncan Hull

Don't know who the primary publisher, but do know some of their journalists. Don't have a copy of the mag on me, but the masthead should have info. - Deepak Singh

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

You could go to your "me" page, then click "Edit/add" on the right. Clicking on your blog you can refresh the feed. - Michael Kuhn

Yes, I tried that, but nothing happened. I wondered if it was perhaps something related to FF's recent break down. - Michael Barton

@Michael, I was thinking this morning on what you commented about anonymising the data. Do you mean removing the country affiliation from every entry from a country with less than x number of entries? - Michael Barton

I didn't read the original discussion, but I'd like to see some kind of obfuscation - I don't know how much entries is there from Poland, but I'm pretty sure I could recognize what my friends and colleagues have entered. This wouldn't be fair. - Pawel Szczesny

I guess the most obvious solution would be to remove the data about country from the public dataset, which would make it pretty difficult to identify anyone. The other option would be to convert country to macro-region, then make the data available. - Michael Barton

Yes. I don't know what value of x would be reasonable (5? 10?). You could add another column for the macro-region to the data so that the geograph doesn't get totally lost. (We should learn from the AOL search data disaster and be careful... http://en.wikipedia.org/wiki...) I don't know what other characteristics in the dataset could be used to personally identify people. - Michael Kuhn

On second thought, x (the cut-off for showing the country) should be fairly high as you'll have some further sub-divisions. Perhaps 25? - Michael Kuhn

No, it really was. Haven't enjoyed ISMB as much in recent years, the coverage made me want to be there! - Daniel Swan

Yes, it was brilliant advertisement for the conference! It only lacks the second layer of authors who summarize blogs, into human readable 'scientific american' level pieces. - Egon Willighagen

I thought it was by far the best example of this that I have seen so far. Combined with a live video feed it would make a compelling case for not bothering to go to conferences :) - Cameron Neylon

@Egon - We are writing a conference report based on the notes so there might still be a longer and more readable version :) - Pedro Beltrao

Can I like this again? :) - Neil Saunders

Ah, so I have a lot of notes that I want to write up too. How do I contribute them? - Ruchira S. Datta

I should mention that I took them the old-fashioned way, with a fountain pen. But of course my plan is to type them up. - Ruchira S. Datta

~ 85 sRNA known from E.coli; targets and function often unknown, but often conserved - Neil Saunders

miRNA regulators in eukaryotes: mechanism still unclear (inhibition/degradation/both) - Neil Saunders

> 500 miRNA in humans; also conserved; also few targets or functions known - Neil Saunders

Comparing sRNA regulation to other types; transcriptional, PPI - Neil Saunders

Modelling and simulation of regulation: regulator may be (1) always expressed, (2) switched on by external signal - Neil Saunders

sRNA regulation advantageous where fast response required - Neil Saunders

Next: how does this integrate with transcriptional regulation? - Neil Saunders

Finally, someone provides a clear, succinct summary of what a network interaction graph is - Neil Saunders

Where 2 TFs required, feed-forward loop = AND gate - Neil Saunders

May be mixed loops: combination of ncRNA and protein factors - Neil Saunders

Example mixed feed-forward loop: OmpR + MicF (sRNA) -> ompF - Neil Saunders

Other examples known in bacteria and human - Neil Saunders

Mixed negative feedback loops: e.g. RyhB -> Fur, E. coli; stochastic simulation. - Neil Saunders

Summary: mixed regulation extends possible regulation dynamics - Neil Saunders

Moving onto predicting miRNA targets in genomes - Neil Saunders

Use known targets to narrow the solution space; miRNA "seed region"; conservation at target site; repeat binding sites - Neil Saunders

RepTar algorithm: starts with 3'-UTR, HMM profiles repetitive signals, matches to miRNAs - Neil Saunders

Validation using shuffled sequences and experimental data; not over-selling the method - Neil Saunders

Predicted miRNAs: seed match (84%), 3'-compensatory (11%), nearly-full match (5%) - Neil Saunders

Moving on to applications of RepTar: viral miRNAs - Neil Saunders

Significant overlap of predicted targets for different viruses: GO annotations make sense - Neil Saunders

Second set of targets are immune system-related; do viruses use miRNA to down-regulate immune system? - Neil Saunders

HCMV: evades NK cells by mimicking MHC-I to make cell appear "self" - Neil Saunders

MICB - top target for HCMV miRNA UL112; experimental validation by over-expressing UL112 in cell lines; MICB down-regulated, controls are not. Also use luciferase reporter assay with 3'-UTR and mutagenesis of binding site. - Neil Saunders

Viral infection of UL112 deletion mutant confirms results - Neil Saunders

Describing further experimental confirmation. Obviously quite excited about her results :) - Neil Saunders

Viral miRNAs may therefore be therapeutic targets; e.g. for antisense RNA, or mimic miRNA effect for immunosuppression - Neil Saunders

Great talk. Wrapping up now - running through almost to 10 am. - Neil Saunders

Good coverage too, Neil - Roland Krause

Feel free to suggest or modify topics, volunteer to demo something, etc. I'm hoping this will be very interactive - Shirley Wu

Two years ago we already talked about Web 2.0 and actually gave a talk series at EMBL. Back then, we had RSS, delicious, citeUlike, but of course not twitter/friendfeed. I actually think that (as we've proven here) FriendFeed is a really effective way of forming an ad-hoc community, so I guess we should give another talk at EMBL. :) Anyway, we should give people this link as it's a Web 2.0 introduction for scientists: http://van.embl.de/cb... - Michael Kuhn

Hmm, I thought publishing it would make it editable by anyone but apparently not. Is there a way to do this? - Shirley Wu

This invitation link should work for anyone: http://docs.google.com/Doc... (I hope there are no spam-bots trawling for google docs links...) - Michael Kuhn

Cameron had an excellent blog on Friend Feed introduction for scientists (http://blog.openwetware.org/science...). I have a few other links related to the use and impact of FF on the blog (http://wildtype.wordpress.com/2008...) - Shannon McWeeney

If someone asks about Second Life we could show them Second Nature's homepage (http://www.nature.com/secondn...) where Nature hosts talks. A good example of a recent talk was the 23&me talk (http://scienceroll.com/2008...). I don't have a lot of experience in Second Life but I don't mind flying around if the connection is good enough. - Pedro Beltrao

One nice example of the use of second life in science is for archeology http://www.digitalhumanities.org/dh2007... - Pedro Beltrao

Session starting now - Pedro Beltrao

The google doc was updated as the session was going on with the gist of the discussion - Shirley Wu