Pawel Szczesny - Comments

References Wanted: Iddo Friedberg

Looking for this: http://www.ncbi.nlm.nih.gov/pubmed...

July 23, 2011 - Comment - Like - Share

Please email http://is.gd/Ag43 thanks!! - Iddo Friedberg

On the way. - Pawel Szczesny

Thanks Pawel! - Iddo Friedberg

Björn Brembs

Three weeks mostly offline - http://bjoern.brembs.net/news...

July 23, 2011 from bjoern.brembs.blog : a... - Comment - Like - Share

Enjoy! - Bill Hooker

About to do the same (except I'll be reading books instead of flyfishing). Have lots of fun! - Pawel Szczesny

3-week holiday? Only in Academia ;) Enjoy! - Jan Wessnitzer

References Wanted: Pranab Chatterjee

Paper Needed: http://onlinelibrary.wiley.com/doi... Email Id: pranab AT pranab DOT in. #IcanhazPDF

July 21, 2011 - Comment - Like - Share

On the way. - Pawel Szczesny

THANKS! :-) - Pranab Chatterjee

Pawel Szczesny

Answer by freesci for When and why should short 454 reads be discarded? - http://biostar.stackexchange.com/questio...

July 20, 2011 from User freesci - BioStar - Comment - Like - Share

When you sequence amplicons (samples amplified by PCR), reads below 100bp tend to be just primers, sometimes with a homopolimeric stretches in between. They can be of a high quality and as such, will make it through simple quality filtering. For a decent overview of errors you can stumble across in 454 see http://bioinformatics.oxfordjo... - Pawel Szczesny

Pawel Szczesny

Heard a great story today. Manuscript rejected 4 times (w/o review) because it had "too many Polish names on it". #cultureofscience

July 8, 2011 from Twitter - Comment - Like - Share

Deepak Singh liked this

\o/ - Graham Steel

9 more comments

WTF? - Matt Hodgkinson

Matt, welcome to the world outside of the Commonwealth ;). In case anybody wonders, none of these were PLoS or BMC journals. - Pawel Szczesny

BTW, Neil says it happens down under too http://twitter.com/#!... - Pawel Szczesny

No way!!! - Björn Brembs from iPhone

I've heard similar anecdotes about reflexive dismissal of manuscripts because the authors come from a particular country or region, or because you can tell from the style and grammar that the authors' first language isn't English. I'd argue that this is reason not for hiding author names from reviewers but for making reviewer identities known. - Bill Hooker

how do you know it was because of the names ? - Pedro Beltrao

Pedro, experts in the field praised the idea when received privately the manuscript, yet it's being rejected within at most 6 hours from sending is (the shortest was 45 minutes) - it's clear that a gatekeeper didn't read past the title, author names and affiliations. The quote is actually from one of the experts - he mentioned exactly that reason as a major flaw of the paper. - Pawel Szczesny

My husband's cousin found that he had applications accepted when he wrote "Thor" instead of his real first name, Ihor. I wonder if, as an experiment, you could submit a paper as Paul Chesney - prove that the papers are getting rejected because of the national origin of the authors, and do some sort of expose? By the way, if any of these are US-based journals, you might even be able to sue or something. - Christina Pikas

Here's a study of AJR's acceptance rates by country: http://www.ajronline.org/cgi..., also see this BJP editorial: http://bjp.rcpsych.org/cgi.... If a journal or editor is a member of WAME (World Association of Medical Editors) and they're making decision based on country of origin then they're explicitly breaching their policies:... more... - Matt Hodgkinson

Matt, thanks a lot for the pointers. I've forwarded them to my colleagues. - Pawel Szczesny

References Wanted: Pawel Szczesny

Looking for: Update on fetal hemoglobin gene regulation in hemoglobinopathies. http://www.ncbi.nlm.nih.gov/pubmed... ps at pawelszczesny org Thank you!

July 13, 2011 - Comment - Like - Share

sorry, no access... - Björn Brembs

Sent. - Bill Hooker

Thanks Bjorn. Got it Bill, thank you. - Pawel Szczesny from iPhone

peter murray-rust

What’s wrong with scholarly publishing? Your feedback – Why should journals exist? - http://blogs.ch.cam.ac.uk/pmr...

July 11, 2011 from petermr's blog - Comment - Like - Share

Daniel Mietchen, Graham Steel, Marcus D. Hanwell and 8 other people liked this

I'd really like to hear some arguments why we should keep journals. BTW, I've no updated my slides on scholarly publishing to contain the most up to date info I could find: http://www.slideshare.net/brembs... - Björn Brembs

16 more comments

Why destroy when you can fix? If we simply ignore all toll-access journals (meaning, never submit there or review for them) they will disappear, leaving a genuinely competitive marketplace of OA journals. Any system you propose to replace journals will have to be better than that alternative, or it's not worth building it. - Bill Hooker

@Bill what is value of having competitive journals? Why not have a single or perhaps slightly fragmented PLoS-like approach? Without journals we would have no impact factors. We can still have scientific editors and referees without journals - peter murray-rust

What would be the need for competition? Innovation? If the architecture of the hypothetical (library-based?) new system is open, any innovation can be brought about by the demand for it. - Björn Brembs

Publishing costs money, and competition reduces those costs. Even PLoS ONE charges more than it costs them, we know this because they are subsidizing the PLoS Glamor Mags. Getting rid of journals means essentially what Peter says, "a single or perhaps slightly fragmented PLoS-like approach" -- who is going to run that? I've seen enough of what happens when scientists run things to NOT want them running the publication business. Frankly I don't want them running a booze-up at my local. - Bill Hooker

I think *some* journals are useful in that they gather together articles of interest to a particular audience. Virtual or overlay journals serve the same purpose. - Christina Pikas

And not to split hairs, but what exactly is "a single or perhaps slightly fragmented PLoS-like approach" except -- a journal? If journals truly no longer exist, what is left -- that is, where do we publish -- on our blogs? How do we arrange for peer review? (And if you think we don't need no stinkin' peer review, head on over to Nils' SciPhu...) And what do we use in place of PubMed --... more... - Bill Hooker

In a perfect world I would imagine that I would be directed to all the most relevant scientific information/projects/results by some automatic algorithm that learns my interests over time and even anticipates potential directions for my research from analogies in other fields. All research should be conducted in the open and these filters would let me cope with the added abundance. In... more... - Pedro Beltrao

all journals are is databases. really... however, we do need these specialized databases for peer review, archiving, better access, and to feed systems like Pedro's ^ - Christina Pikas

In the short term, I think journals will still be around so that articles are grouped by subject area. In the long term, the article is the thing, and they will be floating around in the big cloud, and they will be virtually grouped by tags or subject headings or whatnot. Peer review will be done after the article is published instead of taking so much time before it is published. This... more... - Yo Joe. No, go slow.

Pedro describes exactly the system I've been asking for in the past years. The technology already exists, it only needs to be implemented. What keeps us from implementing it? Publishers with their journals. As long as there are journals in the current sense, there will be no 'Pedro's system'. The natural candidates taking over from publishers are the organizations which have hundreds of... more... - Björn Brembs

Journals exist for two reasons: communication and evaluation. "Pedro's system" is a system for managing information flow, not for evaluation of scholarly output and as such serves communication needs of scientist. On the other hand funders need a quick and relatively hard to gamble measure to evaluate scientists. Journals with their perceived impact are quite good at it (plus funders... more... - Pawel Szczesny

My reply to pmr's original question: http://bjoern.brembs.net/comment... :-) - Björn Brembs

@Bill_Hoooker I am not arguing that peer review should be abolished. I don't see why we need 25,000 different competing places where it happens (or often doesn't happen). And I use PLoSOne-Like to mean a place where discplines are not divided by journal, but where subject expertise exists within the whole. You clearly don't like PLoSONE but I don't know whether this is specific or... more... - peter murray-rust

@Bill_Hoooker "doesnt like PLoS ONE"?? :) - Peter Binfield

@PMR, as Peter B has wryly pointed out, I'm a pretty consistent booster of PLoS ONE. I'm just not convinced (yet -- willing to be) that wholesale slaughter of (Gold OA) journals is a good idea, or that I would want the entire scientific enterprise centered on one giant version of PLoS ONE. I'm a biologist: diversity is a Good Thing (TM) in my world. @Bjoern says "the technology already... more... - Bill Hooker

I think my main point here is that "Pedro's system", even setting aside Pawel's valid concerns about evaluation, is still some way off, and if we try to tear down the current system too fast we are likely to get something that is even further from what we want. Revolution always sounds good but it's usually ugly. Better, I think, to change the current system by killing off just the... more... - Bill Hooker

@Bill: All very valid points of concern - except one: I don't think we are even close to tearing down the current system "too fast", rofl :-) Actually, if I might hazard a prophesy, even if we all worked together and collectively tried to stage a revolution (like that would ever happen!), most likely an evolution would be all that came out of it :-) - Björn Brembs

Heather Piwowar

How about PLoS Currents: Open Science? - http://researchremix.wordpress.com/2011...

July 13, 2011 from Research Remix - Comment - Like - Share

Matt Hodgkinson, Graham Steel and Pawel Szczesny liked this

I gather that PLoS Currents could also support discussion-type papers. This could make PLoS Currents: Open Science a cross-disciplinary OA venue for Open Science perspectives. Few and far between at the moment. Other than, you know, *blogs* :) - Heather Piwowar

3 more comments

Discussion on g+ https://plus.google.com/1169568... - Heather Piwowar

Dunno... I can see how it might fit, but I've been thinking of the Open Science landscape as a pretty wild-west kinda place, with one lab on Google Docs and another using PBWiki and someone else blogging and others on OWW and so on and on. If we can find a way to link these disparate systems, rather than looking to centralize things and keep "publishing" "papers" in a "journal", the... more... - Bill Hooker

Bill, the more I look at the scientific community, the more I like Heather's idea. Centralization, at least for some time, would help avoiding a waste time on re-thinking and re-implementing ideas from the scratch, as there could be _easy to find_ foundations to build on. PMR's recent posts (including the one you've commented on) sound pretty much like the discussion this community had two, three, four years ago. - Pawel Szczesny

Hmmm. Thinking again, now it seems I am the one trying to go too far too fast (see my comment here: http://friendfeed.com/petermr...). It will be a while before the "wild west" is tame enough for federated search, so in the meantime PLoS Currents: Open Science would make a good gathering place. - Bill Hooker

Pawel Szczesny

Genome sequence and analysis of the tuber crop potato - http://www.nature.com/nature...

July 11, 2011 from Google Reader - Comment - Like - Share

Dave Lunt and science3point0 liked this

It's been a long story and I'm happy it's finally out. - Pawel Szczesny

Andrew Su

How is it that nobody ever told me about RStudio before? awesome environment for playing in R...

July 7, 2011 from Twitter - Comment - Like - Share

I've commented on Twitter as well, but looks like somebody _tried_ to tell you ;) http://friendfeed.com/search... - Pawel Szczesny

wembley

Incredible amazing awesome Apple - http://www.youtube.com/watch...

July 5, 2011 from YouTube favorites - Comment - Like - Share

Pawel Szczesny liked this

Brilliant. - Pawel Szczesny

Heather Piwowar

Please find me when you get on Google+. I really want it to be awesome... I need a FriendFeed backup plan!

June 30, 2011 from Twitter - Comment - Like - Share

Dave Lunt, Graham Steel, Pierre Lindenbaum and 3 other people liked this

I think Google+ is going to pretty much kill Friendfeed. All the features (plus some) but also with a future ahead of it. Plus absolutely everybody I know from here is already on there. - Mr. Gunn

6 more comments

Interesting assessment, Mr Gunn !! I'm not on Google+ yet, still in the queue. So, could we FINALLY now have the long awaited replacement for FriendFeed ? - Graham Steel

What is really important that with Google Takeout you can easily download your own stuff from G+. Including conversations (!). - Pawel Szczesny

Mr. Gunn... "you incensitive clod!" a slashdotter would say... some here don't have invites yet, OK? :) - Egon Willighagen

So how does Google+ work actually with respect to aggregating content from multiple RSS feeds? - Egon Willighagen

Ah, Mr. Gunn, I should have known you don't know me. You are awfully fond of "death of" pronouncements, aren't you. (Not on Google+, no hurry to be there.) - Walt Crawford

Google+ won't kill Friendfeed until it supports importing. - Victor Ganata

I stand with Heather and agree with Victor: I *want* Google+ to be an adequate replacement for FF, but it is missing vital functions. - Bill Hooker

References Wanted: Iddo Friedberg

Anyone has access to: http://www.nature.com/nbt...

July 4, 2011 - Comment - Like - Share

Please email http://is.gd/Ag43 - Iddo Friedberg

On the way. - Pawel Szczesny

Thanks Pawel! - Iddo Friedberg

Sean McBride

What is the best interface for navigating a few million facts on a single topic, person, organization, etc.?

July 1, 2011 - Comment - Like - Share

I wonder if you find anything freely available. Lots of intelligence software might do exactly what you expect but I didn't find anything to download - only screenshots or occasional videos. - Pawel Szczesny

6 more comments

I think it hasn't been created yet -- not even close. A possible fruitful line of development: Powermarks' incremental search interface, combined with Semantic Web concepts. (Powermarks has been defunct for a few years.) - Sean McBride

The key is to be able to look at an object through a thicket of millions of facts and assertions from any conceivable angle with very little effort and with great speed. To see all the important patterns and connections as quickly as possible. - Sean McBride

Google search results on any topic? Unbelievably primitive and unacceptable for doing serious research. - Sean McBride

DBpedia is nosing around in this area, but it hasn't hit the bull's-eye. - Sean McBride

I'm not sure - it's hard to judge when you don't have direct access to software to play around. I2 (http://www.i2group.com ) sells its solutions to FBI and they are quite happy with them. - Pawel Szczesny

Great pointer -- thanks. - Sean McBride

Analyst's Notebook. Right. I recall that Paul Wolfowitz was using it during the Bush 43 administration. - Sean McBride

Egon Willighagen

Seeking advice: I need a simple platform with OpenID user account support to build a Java web app to run in some cloud. What should I use?

July 1, 2011 - Comment - Like - Share

Not sure if I get the question right, but AWS supports OpenID, doesn't it? - Pawel Szczesny

2 more comments

google apps ? - Pierre Lindenbaum

Pawel, no, I want the web app itself to have openID support.. I want to make a social website.. - Egon Willighagen

Google App Engine just hosts an app, not? I still need a simple toolkit so that I don't have to do any stuff for keeping accounts... - Egon Willighagen

Bill Hooker

Be Slightly Evil - http://www.ribbonfarm.com/be-slig...

June 29, 2011 from Cwhooker's Favorite Links... - Comment - Like - Share

Mickey Schafer and Pawel Szczesny liked this

Tags: venkatesh_rao interestingpeople - Bill Hooker

Thanks Bill for this find. Rao is one of the most original people I've stumbled across recently. - Pawel Szczesny

Graham Steel

The Panton Principles banner is now live over at BioMed Central http://www.biomedcentral.com/ Haven't spotted it yet myself but I am reliably informed !!

June 28, 2011 - Comment - Like - Share

Richard Akerman, Mike Chelen, Egon Willighagen and 4 other people liked this

I take that back - Just spotted it "Panton Principles - Open Data Means Better Science". with a direct link to http://pantonprinciples.org/ RESULT !! (BMC are currently running with abt 30 banners = a one in 30 chance when you look at any page on BMC, this one will show up) - Graham Steel

2 more comments

BTW, you need to stop Adblock to see it ;). - Pawel Szczesny

Any word on how much traffic is coming through BMC? - Mike Chelen

@Pawel - I didn't know that - @Mike - dunno, early doors. Will ask BMC in a week or so. - Graham Steel

Cameron Neylon

Cat...meet pigeons: http://www.wellcome.ac.uk/News... Major funders announce plan to start top-tier journal #oa #openaccess

June 27, 2011 from Twitter - Comment - Like - Share

Cesar Sanchez, Martin Fenner, Graham Steel and suelibrarian liked this

Hmm. This will be HQ because we say it will be HQ. And who are we to doubt. OA is interesting as a kind of clergy push from one end and introduce designedly quality journals while a lot of entrants presumably 'dilute' that (author-pays being the only business model with which they can get new titles off the ground). So can we hit them with sticks to do the right thing (i.e., using candidate standards and best practice docs, not just being open)? - Chris from twhirl

19 more comments

Its no more circular than the same arguments for other "top" journals really. But I think you can probably assume that standards and best practice will be pretty high on the agenda. Wellcome have a good record on that. - Cameron Neylon

Jesus H Christ. They haven't learned anything. "Top-tier journal"? Fuck. We may as well just give up. - Bill Hooker

They've learned some things, just not others...but remember what the core problem here is. Survey after survey tells us that researchers avoid going OA because there aren't sufficiently prestigious journals. This action goes directly to that issue, not really any other. And because it only seeks to change one thing it may well break through that barrier. Then there will be a clear... more... - Cameron Neylon

I don't buy it. After the success (and Impact Factor) of PLoS Biology, I don't see the point in another "prestige OA journal". If PLoS Bio and Medicine weren't enough to kill the "OA != quality" trope, this latest me-too won't help. At least PB/M were supposed to be proving a point; this is just jumping on a bandwagon. (And when is PLoS going to collapse all their journals into ONE? The experiment's done, time for the next step.) - Bill Hooker

An attitude from yesterday. HHMI PR blurb: http://www.up0.net/c... - Björn Brembs from iPhone

No, this is different for a couple of reasons. One it's coming straight from funders. That will make a hell of a difference in a way a third party play like PLoS couldn't. This is the people with the money. The other is that now that PB/M have broken down the barriers on the quality issue there is an opportunity to push further. Yes we know that that difference is meaningless but it matters for most researchers. - Cameron Neylon

Funny thing is of course I was at that meeting saying exactly the same things you are...never had so many Nobel Laureates disagreeing with me at once.... - Cameron Neylon

The other point is that the other message here isn't for researchers, its for publishers. Wellcome &c are saying that they're not happy with the current levels of service so they are going to do their damndest t introduce serious competition. This is a clear statement that the status quo of 6 month embargoes and or NC restrictions or high fees isn't good enough in their view.... - Cameron Neylon

Let's hope they spend the money on a decent, machine readable, semantic, journal platform, that really changes publishing and doesn't destroy scientific data, and let's up their ideal of a top-tier journal is not another Cell, Nature, or Science. - Egon Willighagen

And I am clueless how they will get *active* *top* scientists do a decent review in 1-2 weeks... - Egon Willighagen

By having topper activer scientists as editors to ride herd on them? No I don't know either... - Cameron Neylon

Late to this - been at work. I'm all for OA as y'all know. Have mixed views on this one though as matters stand and from the discussion above. I guess the bit that irk's me (and I'm with Bill on this one although I also see where Cameron is coming from too) is the "top-tier" thing. We know about Gold/Green/Gray OA. This sounds to me like bringing the lurgy of IF back into the equation and creating a new brand of OA Publishing - let's dub it "Polished Gold" OA. Do we really need that - SRSLY ?? - Graham Steel

Coming from a different side, I think that such move might do much more for spreading the OA in countries in C&E Europe than most of the things done so far (because PB/M hadn't been sufficiently prestigious here, while anything branded by Wellcome, MPG and HHMI is perceived much better). At the fundamental level it's all wrong, but in short term it may translate into way quicker adoption, as it (as Cameron notes) significantly changes dynamics in the system. - Pawel Szczesny

I like "polished Gold OA" as the name for this. I understand Cameron's argument and Pawel's European corollary but I am still firmly on the curmudgeonly side of this one. How many Polished Gold journals will it take? How many more concessions and accomodations to publishers and to the Way It's Always Been Done? I don't care for this bit either -- "The long-term business model will be... more... - Bill Hooker

A couple of comments on this. First, regarding "impact" I'll keep re-stating my position that until we have a working sorting mechanism for post-peer review publishing we need the tiered journal system. Just imagine doing research with pubmed but no journal tittles. The flood of papers is really impossible to manage without filters and the tiered journals is our currently poor but... more... - Pedro Beltrao

Bill, while I again agree fundamentally with you, I think there's a small catch in here in the issue of expensiveness of prestige. PLoS had virtually no prestige when they started and I tend to think (but I have no data) that $3K per article wasn't enough to cover all the aggressive marketing they were doing to become prestigious. Institutions involved in here don't need to spend... more... - Pawel Szczesny

So where (physically) will it be based, if anywhere? I suppose Cambridge is too much to hope for as I look for jobs :\ - Chris from twhirl

More seriously, is there a limit to demand for OA? Presumably PLoS looked at that before starting. I just wonder if there'll be a squeeze. I also think that this enterprise's backers need to be stumping up for some serious storage for supplementary data deposition / sharing. - Chris

Apparently they will (anonymously) publish review comments... - Chris from twhirl

And while not on the subject, would this be a +circle or a +spark..? - Chris from twhirl

Pawel Szczesny

One step closer to open science - http://www.pawelszczesny.org/2011...

June 29, 2011 from Circle of Complexity - Comment - Like - Share

Amira, Andrew Lang, science3point0 and 3 other people liked this

Comment in blog... - Egon Willighagen

Thanks. Replied. - Pawel Szczesny

The Life Scientists: Benjamin Tseng

Question: given Google+'s "circles" and active development, have we finally found a FriendFeed replacement worth using?

June 29, 2011 - Comment - Like - Share

Sally Church liked this

We will see once it's open for signups. - Pawel Szczesny

What are you doing posting this on FF? Circle it up! - Joseph Rosario

Hope so. Can't believe facebook never did it as it was always the missing feature / big issue (mates / colleagues / family / other parents / etc. all in one group). I'm guessing hangouts will just end up replacing the seedier functions of craigslist... - Chris from twhirl

Pawel Szczesny

SPORE series winner. Computational experiments for science education. - http://www.ncbi.nlm.nih.gov/entrez...

June 28, 2011 from PawelSzczesny's starred items... - Comment - Like - Share

Egon Willighagen and Ruchira S. Datta liked this

Content is CC-something... not sure about the source code yet... - Egon Willighagen

The site says "Free and open source". The code available in SVN repo https://svn.concord.org/svn... EDIT: found license, it's GPL. - Pawel Szczesny

Models are CC-BY-NC, though. Could be better. - Pawel Szczesny

Pawel Szczesny

I wouldn't mind if OpenAccessMap.org had an API or a way to download the data (what about sharing on on GitHub?). #oai7

June 23, 2011 from Twitter - Comment - Like - Share

wasn't aware of http://www.openaccessmap.org/ ! - Graham Steel

2 more comments

Graham, it has been announced today, just a few hours ago :) - Pawel Szczesny

Ahh, so that's why ;-) Ill alert Stuart Lewis who maintains the Repository 66 map http://maps.repository66.org/ - Graham Steel

Nice find Graham. I wasn't aware of that. - Pawel Szczesny

Pawel Szczesny

On the technical tutorial on accessing prior versions of resources using Memento http://mementoweb.org/ #OAI7

June 22, 2011 - Comment - Like - Share

Tutorial will have two parts: Memento and Open Annotation. - Pawel Szczesny

12 more comments

Slidedeck is available here: http://www.slideshare.net/hvdsomp... - Pawel Szczesny

If the prior version of the resource is available somewhere (any compatible archive or versioning system) the system will pull it out transparently. - Pawel Szczesny

International Internet Preservation Consortium http://netpreserve.org/about... - Pawel Szczesny

Prior versions can be also accessed from search engines caches. - Pawel Szczesny

Archiving systems are usually self-contained and do not know if the other archive contains complementing material. - Pawel Szczesny

Possible issue of spamming time archives or attempts to rewrite the history. - Pawel Szczesny

Branding the archives issue - user should know which archive provides the page (it doesn't need to be obvious, as the time negotiation goes through HTTP protocol, not API). - Pawel Szczesny

Memento provides a timemap (list of versions with timestamps) for any kind of resource, not only Wikipedia/Mediawiki (which has similar feature in its API). - Pawel Szczesny

Applications available now: FireFox plugin and Android application. Iphone/Ipad/IExplorer (?) in experimental stage. - Pawel Szczesny

Internet Archive is Memento-compatible. - Pawel Szczesny

After adding Memento to a service, one doesn't need to present links to prior versions within the page. - Pawel Szczesny

One could apply Memento to linked data. Already implemented in DBpedia. - Pawel Szczesny

You could do time-series analysis across DBpedia versions. - Pawel Szczesny

Pawel Szczesny

Obviously PLoS ONE's appeal process doesn't work.

June 14, 2011 - Comment - Like - Share

Pedro Beltrao, Bill Hooker and Egon Willighagen liked this

For the background see this thread http://friendfeed.com/freesci... Two months after sending the appeal in my colleague wrote directly to the editor because nobody form PLoS got back to him. The editor sent him reviews again, without answering the complains. My colleague sent an email to PLoS ONE _again_ and yest another two weeks of silence. - Pawel Szczesny

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Given the no-so-great experience people (including me) have with P1 recently, I must conclude that is not ready yet to become Mega Journal it aspires to be. - Pawel Szczesny

Growing pains? Or do you think there is something intrinsically wrong with their workflow? - Egon Willighagen

I wish I knew... Could be that in quality scientific publishing you can have only two of three: fast, inexpensive, low barrier. - Pawel Szczesny

My guess: faced with rapidly increasing submissions that outpace any and all attempts to increase the size of the "editorial engine", and still lumbered with the need to finance PLoS Everything Else, P1 is something of a victim of its own success. Rate limiting step is increasing the power of the editing engine: you can only add so many AE's, they can only handle so many mss each. - Bill Hooker

I would say that that is a fair assessment, Bill. - Graham Steel

So, something wrong with the design of the workflow then, causing it to not properly scale. - Egon Willighagen

Bill, I think it's only part of the problem. Jan's issues http://friendfeed.com/jwessni... had nothing to do with AEs. However I could only speculate, because I simply don't know (PLoS hasn't been very open on its internals). PLoS should open its processing workflow to the community, so the community could help fixing it. - Pawel Szczesny

One of the manuscripts I handled as AE had a similar problem. I had requested an additional control experiment to rule out an alternative explanation that the authors did not find reasonable. The appealed, got a reply saying "we'll get right on it" and then didn't hear from them, for two months. Eventually I got copied on their complaints (apparently that's what some staffers there do... more... - Björn Brembs

We're working on improving the appeals process. We know there have been delays, but these should be improving. One factor is that we are more lenient in considering appeals than most other journals, so we handle many more. Generally, appeals are considered by a consulting editor, who then coordinates with the academic editor who made the decision to reject and/or a new academic editor. Because we routinely involve a second academic editor to act as a neutral editor for the appeal this can cause some delays. - Matt Hodgkinson

Pawel Szczesny to Pawel's feed, The Life Scientists, Science 2.0

This is The Open Science: https://github.com/ehec-ou... Annotation of E.coli O104:H4 Genome on GitHub, sequence data under CC0.

June 15, 2011 - Comment - Like - Share

joergkurtwegner, Mike Chelen, Scott Edmunds and 7 other people liked this

Contributions come from industry and academia. - Pawel Szczesny

2 more comments

Some of the analyses are of very low quality, or simply wrong (mainly from the company that set up this wiki). Nevertheless some consensus appears to emerge, as more experts join in. - Pawel Szczesny

Well, fork off then! :) - Egon Willighagen

The analyses are in the wiki? GitHub Wikis can be forked, though only through Git itself. - Mike Chelen

Daniel Mietchen

Anyone know of examples of extensive amounts of supplements to published papers? Especially looking for multimedia supplements.

October 2, 2010 - Comment - Like - Share

Euan and Martin Fenner liked this

http://dx.plos.org/10... seems to be the current record holder at PLoS ONE, with 43 supplementary files. No multimedia, though - just figures and tables. http://dx.plos.org/10... has 27 supplementary files, of which 24 are videos. - Daniel Mietchen

4 more comments

Yes, Neil, and thanks. I was asking a bit in the other direction because the Neanderthal genome paper was already on our list. If anyone knows of a supplement exceeding these 175 pages (which includes 51 figures and 58 tables), though, please share it here. - Daniel Mietchen

Thanks for pointing me to the Neanderthal paper. Used the info in a presentation today. - Martin Fenner

Just noticed that the above comment by @neilfws is gone. I was sad to see him leave, but I understood the reasoning behind that. I do not understand why he deleted the account. For the record, the paper he mentioned is at http://www.sciencemag.org/content... . - Daniel Mietchen

What happened to neilfws? - Björn Brembs

Bjorn, Daniel I assume he simply forgot the lesson of Eva Amsen (she also left FF deleting account) assuming that it's like the Facebook - you delete account and everything stays anyway. - Pawel Szczesny

The Life Scientists: Pierre Lindenbaum

I'm looking for a cartoon published here on friendfeed TLS, a few years ago. On one side we could see some scientists "2.0" having fun and on the other side, the "gray" scientists "1.0" not having fun BUT writing some papers. Any link ? Thanks.

June 16, 2011 - Comment - Like - Share

Mike Chelen and Egon Willighagen liked this

Did you mean this one http://www.sciencehumor.org/2007... ? - Pawel Szczesny

yes! Many thanks Pawel (and Neilfws on twitter) - Pierre Lindenbaum

Pawel Szczesny

Talked to nice people on the internet. Found them on the OKFN Open Science Working Group conference call.

June 15, 2011 - Comment - Like - Share

Deepak Singh and Graham Steel liked this

Was great to have you on the line for the first time, Pawel. Please do come back again. - Graham Steel

Thanks Graham. I will definitely try. - Pawel Szczesny

:) - Graham Steel

References Wanted: Walter Jessen

Looking for a Nature Genetics paper: http://www.nature.com/ng... Please send to walter@highlighthealth.com - Thanks!

June 13, 2011 from FreshFeed - Comment - Like - Share

On the way. - Pawel Szczesny

Thanks Pawel! - Walter Jessen from FreshFeed

Daniel Mietchen

What would research funding look like if it were invented today? Let's start collecting materials. (via http://friendfeed.com/danielm... ).

October 15, 2009 - Comment - Like - Share

Mr. Gunn, Iphigenie, Chris Rusbridge and 11 other people liked this

The basic structure for this part iii of the "what would X look like if invented today" series is in the mind map at http://www.mindmeister.com/3016825... , with background via http://friendfeed.com/search... . Main points: More flexibility in the models of funding, more attention to technological shifts in the way people (including scientists) communicate. Such has also been argued at http://ff.im/9GGRn and http://2020science.org/2009... . - Daniel Mietchen

36 more comments

Just noticed that we used different notions of "public funding environments" in the mind map so far. What I had in mind was to have "funding environments" in public, much like what fundscience.org plan to do. Some of the added comments seem to have used the term in the sense of environments for "public funding". Both notions are certainly valid, and we should think of ways to keep them apart. - Daniel Mietchen

good point re making this difference clear(er) in the map - Claudia Koltzenburg

I would like to see a lot more funding of contests - Jean-Claude Bradley

Yes, Jean-Claude, contests and prizes with a competitive element are definitely on the list. If you have good examples from the recent past, please post them here. - Daniel Mietchen

"More money for science is always good. Or is it? Six experts tell Nature what concerns them most about the US stimulus spending and suggest ways to ensure that it benefits research and society in the long term." - http://www.nature.com/nature... - Daniel Mietchen

Daniel -for a recent example of a contest for research: http://onschallenge.wikispaces.com/ - Jean-Claude Bradley

Thanks, Jean-Claude. It is noted along with http://www.claymath.org/millenn... and http://www.xprize.org/ as an effort to make the chain from achievement to award both shorter and more transparent than currently usual. - Daniel Mietchen

Daniel - the thing I like about contests is that barrier to participation is orders of magnitude lower than traditional funding - there is no need to convince anyone that what you are attempting will actually work before doing anything. Of course this limits the type of projects that can be run but it still applies to a large number. - Jean-Claude Bradley

Has there been any recent follow-up study to "Activities, costs and funding flows in the scholarly communications system" at http://www.rin.ac.uk/our-wor... ? - Daniel Mietchen

The Wellcome Trust weighs in on reforming science funding: http://www.timeshighereducation.co.uk/story... - see also http://ff.im/bljS1 . - Daniel Mietchen

thanks for the pointer, Daniel - Claudia Koltzenburg

Let's not forget that http://www.submeta.org/ provided funding for http://onschallenge.wikispaces.com/ - certainly a "basic research" funding model that looks promising - Daniel Mietchen

One more: http://ff.im/cHoa5 on HHMI's focus on "people, not projects" - http://pazoulay.scripts.mit.edu/docs... . - Daniel Mietchen

Daniel, not that I have anything against HHMI, but that mantra is not exclusive to them. For example Max-Planck Society has exactly the same approach (and I would say that at 10% of HHMI's budget and having twice as much Nobel prize winners, MPG looks a bit more effective ;) ). - Pawel Szczesny

Didn't mean this to be exclusive, and I am well aware of MPG approaches (been there for a while). - Daniel Mietchen

"I wish there was a universal format for submitting grant proposals; authors could post proposals (once!) & then the funders bid on them." (rephrased from http://ff.im/5VwEI ). I would add that the process should be public. fundscience.org plan to go this way. - Daniel Mietchen

How do funders and scientists rank "more attention to technological shifts" against the "scientific expertise they have"? One says "change" the other "keep doing what you know"! Are those two things not disagreeing each other? In other words, who would you fund first, the "crazy new idea" or the "conservative stuff"? - joergkurtwegner

I would think funders should have (as they do now) the liberty of choosing their priorities, and in many cases this will be a mixture of many incremental projects and some revolutionary ones. The main shift in the system would thus be to have just ONE avenue for proposals, and to make it public. - Daniel Mietchen

On the role of rules in creativity and innovation: http://ff.im/cRs7K . - Daniel Mietchen

Interesting collection of thoughts on peer review, much of it relevant to funding: http://post.queensu.ca/~forsdy... . - Daniel Mietchen

Another interesting one: http://scienceblogs.com/cortex... . See also http://ff.im/cEiof . - Daniel Mietchen

Interesting: There is a chance that funders may actually listen: http://ff.im/fEqJG . - Daniel Mietchen

I'll let you guys know what their feedback was - I know Moshe Pritsker from JoVE will be at the NSF panel - other panelists TBA - Jean-Claude Bradley

Thanks, Jean-Claude. Further relevant post: http://ff.im/fGr3B . - Daniel Mietchen

thanks Daniel - excellent post - Jean-Claude Bradley

One more: http://ff.im/fI1oI . And yet another one: http://scienceblogs.com/drugmon... . - Daniel Mietchen

An image: http://ff.im/giuen and another preparatory post: http://ff.im/gpry3 . Plan to write this part III up over the next two weeks or so. - Daniel Mietchen

I am homing in on this one and think it would have greatest chances to have an impact if it could be provided in a format of a poster or a few slides that funders could be encouraged to reuse. Any suggestions as to formats suitable for this? The text will of course also be blogged (or co-blogged if anyone is interested) but I really want to make an effort to reach the target audience because that is where the most important changes have to happen. - Daniel Mietchen

One way to do this would be to take a depiction of the research cycle and add comments on every way in which funders could interact with it - perhaps colour-coding the long-term suitability of each strategy. - Daniel Mietchen

Anyone know a collaborative platform to edit posters, other than Google Docs? - Daniel Mietchen

"add comments on every way in which funders could interact with it" great suggestion, Daniel - Claudia Koltzenburg

I have started a Google Doc presentation on this at http://docs.google.com/present... . Everyone welcome to join in! - Daniel Mietchen

Document is all set up now (cf. http://ff.im/hc4YL ) and shall serve as one of several bases for discussion at http://ff.im/gaWDe . - Daniel Mietchen

An experimental description of the current state of research grant peer review is at http://ff.im/hsSJO . - Daniel Mietchen

Further finger training at http://ff.im/hsSJO and http://ff.im/hylRU and http://ff.im/hzyWW - these posts shall be linked from http://docs.google.com/present... to provide background information on individual aspects of research funding. See also http://ff.im/kipeU and http://ff.im/m39l9 . Further suggestions much welcome. - Daniel Mietchen

4 July @Torino: http://www.esof2010.org/schedul... - Claudia Koltzenburg

Planning to submit a proposal for an ESOF 2012 session on "Research funding 2.0" (or so; cf. http://ff.im/EhgP5 ), largely based on the materials collected here. Collaborators welcome! Some more food for thought: http://www.slate.com/id... . - Daniel Mietchen

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