Pawel Szczesny - Comments

Answer by freesci for custom BLAST db on Galaxy server - http://biostar.stackexchange.com/questio...

December 4 from User freesci - BioStar - Comment - Like - Share

It is possible (or was, as I did it some time ago and don't have access to that installation anymore) using .loc files. See this guide http://wiki.g2.bx.psu.edu/Admin... - there's some info on Megablast customization. However I agree that Galaxy documentation is a bit lacking in administrative areas. - Pawel Szczesny

References Wanted: Pawel Szczesny

Hi, I'm looking for this paper http://onlinelibrary.wiley.com/doi... Please email to ps at pawelszczesny org

December 2 - Comment - Like - Share

Sent. - Torfinn Nome

Got it. Thanks! - Pawel Szczesny from iPhone

Pawel Szczesny

Answer by freesci for Alternatives to Galaxy for wrapping command line tools in a Graphical User Interface? - http://biostar.stackexchange.com/questio...

November 24 from User freesci - BioStar - Comment - Like - Share

You can find comprehensive list on Wikipedia: http://en.wikipedia.org/wiki... Missing software on this list is Knime, for which Pierre and his colleagues have recently recently released set of custom nodes: http://plindenbaum.blogspot.com/2011... - Pawel Szczesny

Pawel Szczesny

Answer by freesci for Making Scientific Movies - http://biostar.stackexchange.com/questio...

November 22 from User freesci - BioStar - Comment - Like - Share

Check BioBlender (http://bioblender.eu/ ). It is a powerful and free molecular animation package. - Pawel Szczesny

Pawel Szczesny

Answer by freesci for What softwares can be used for clustering nucleic acid fragments?? - http://biostar.stackexchange.com/questio...

November 21 from User freesci - BioStar - Comment - Like - Share

For clustering (that is grouping by similarity) I use often cd-hit (http://cd-hit.org/ ). It has a special version designed to cluster fragments/reads from 454 sequencer: cd-hit-454. If more fine grained clustering is necessary, you can use CLANS (visual clustering software on the basis of BLAST similarity - http://bioinfoserver.rsbs.anu.edu.au/program... ). Finally, if the group of sequences is similar you can do MSA, as Larry suggested. - Pawel Szczesny

Bill Hooker

Another competition-based site: http://www.kaggle.com/.

November 4 - Comment - Like - Share

Steve Koch liked this

I must mention Polish alternative (on more sophisticated platform) http://www.tunedit.org - Pawel Szczesny

Egon Willighagen

Going to Maastricht to work on Open PHACTS - http://chem-bla-ics.blogspot.com/

November 2 from chem-bla-ics - Comment - Like - Share

Steve Koch, Bill Hooker, Andrew Lang and 2 other people liked this

Congratulations! - gilleain

4 more comments

Great, congratulations Egon. - Pawel Szczesny

Congrats. - Noel O'Boyle

Great news - seems like a job made for you. - Matthew Todd

Thanx all! Yeah, I think this may be a good move... - Egon Willighagen

Congrats on aligning work with principles! - Bill Hooker

pn

Open Access means people die - http://www.pawelszczesny.org/2011...

October 25 from Google Reader - Comment - Like - Share

Nils Reinton, Yaroslav Nikolaev, Kubke and 4 other people liked this

Central thesis: "open access means that there will be more potentially harmful papers available to general public". We should get rid of the internet too, perhaps? - Noel O'Boyle

8 more comments

Noel, that's not central thesis. That's example of reasoning to which Peter's approach leads. - Pawel Szczesny from iPhone

Pawel, I agree with your point, but I disagree with your example... allowing people to make mistakes I value more than believing you know better and disallow things... your argument is like disallowing freedoms because some cannot handle them... that makes your argument quite different from those of PMR, even though both anecdotal of shape... - Egon Willighagen

Egon, I get the difference very well and that example was chosen on purpose (I had some less "nuanced" as well, but didn't decide to use them). However, if a scientist is using unscientific arguments, the remaining nuances don't make a difference anymore. How we can improve the quality of public discourse if we allow for such argumentation? - Pawel Szczesny

Well, theoretical sciences I guess :) PMR formulated a hypothesis, that is worthy of empirical validation... which effect is larger: that of foolish people, of that of people kept uninformed... (I don't know; I'm not a social scientist...) Where would science be if we cannot hypothesize anymore.... You provided an important alternative hypothesis... null hypothesis, perhaps? - Egon Willighagen

Ok - I get you now. Central thesis: "Anecdotal evidence is irrelevant to a scientific argument." And other things besides OA can help more. - Noel O'Boyle

Egon, the problem I see is that PMR's own words: "I don’t think anyone can deny the truth of that conclusion." are not a formulation of hypothesis, but a populist language. This unfortunately has many implications, none of which I like. - Pawel Szczesny

I agree that PMR's blog posts are often short on links to further detail. I personally prefer linking in my blog to further info to back up my story and improve the 'learnability'... I personally think 'learnability' is the more important aspect, and Open is the means. PMR is an established Cambridge scholar... they can do with bold language, leaving things to be worked out by others.... more... - Egon Willighagen

Egon, you've touched a few very important issues. One thing is that if you don't have a leverage, you use the leverage of the community of which you're a member. So, PMR comments might influence position of people relying on the community in certain situation where trust in a discussion depends on the community's 'brand'. The other thing is that from perspective of people in less... more... - Pawel Szczesny

And finally, the biggest win of OA will be when the general public actually cares about open access to knowledge, not when scholarly communication will be open and still nobody cares. That will translate to _rational_ public discourse, because fact checking and hypothesis testing will be a normal mode of coming to conclusions on public issues. Indeed, there's a place for anecdotal evidence, but they serve as a starting points of coming to conclusions, not end points. - Pawel Szczesny

Pawel Szczesny

Answer by freesci for Searching for proteins that have similar type of residues in binding pocket - http://biostar.stackexchange.com/questio...

October 24 from User freesci - BioStar - Comment - Like - Share

In the past I have used SuMo http://sumo-pbil.ibcp.fr/cgi-bin... by Martin Jambon (also a BioStar user - Martin, where are you? :) ). It will require some modification of your PDB file so you can easily select which residues you want to take into account (for example by marking required residues as belonging to chain X, etc.). See the server for details. Alternatively, you could try to download one of many programs designed to analyze protein structures for binding pocket similarity (ten or so are cited in the introduction of this short paper: http://stat.fsu.edu/~jinfen... ) and then substitute program's database with your own definition of binding pocket. However, I can imagine it's not going to be the most straitforward way. - Pawel Szczesny

Björn Brembs

There is no reason why this needs to be science-fiction - http://bjoern.brembs.net/news...

July 12 from bjoern.brembs.blog : a... - Comment - Like - Share

suelibrarian, Nils Reinton, Kubke and 5 other people liked this

Have an idea for immediate reuse, but couldn't find the page where you state the licensing terms. - Daniel Mietchen

12 more comments

lol :-) no licensing... - Björn Brembs

Bravo sir. - science3point0

I assumed so, but think it would be better to state it somewhere easily findable. - Daniel Mietchen

Is it self-made? - Daniel Mietchen

Self-published ? Without "Peer Review" ? Without "Impact Factor" Holy Cow - I LIKE..... - Graham Steel

Graham, also: "based on self-funded research" ;). - Pawel Szczesny

But where would the funding come from in self-funded research?? - Graham Steel

From a Kickstarter for science (or a Kickstopper for journals)... - Daniel Mietchen

Thread also now under discussion over at G+ https://plus.google.com/1074493... - man, this is getting confusing..... - Graham Steel

Self-made with statement now in the post. - Björn Brembs from iPhone

First reuse: http://en.wikiversity.org/w... - Daniel Mietchen

Love the Beethoven quote!! - Björn Brembs

Can you make the background image available? Would like to reuse it in http://en.wikipedia.org/wiki... . - Daniel Mietchen

Deepak Singh

October 15 from Flickr - Comment - Like - Share

Graham Steel, Ruchira S. Datta and Zu from AOD liked this

My second impression (inspired by the plot on the screen) was that with proper software you could actually "play" the stock market on this stuff. :) - Pawel Szczesny

Lol. Might do better than I usually do - Deepak Singh from iPhone

Pawel Szczesny

Parsing Jackhmmer output - http://biostar.stackexchange.com/questio...

September 29 from User freesci - BioStar - Comment - Like - Share

Googel Marketing liked this

What are the options available to parse output (full output with alignments) from jackhmmer? As far as I can test, BioPerl hmmer module isn't able to read it correctly. Are there any ready-to-use libraries (language doesn't matter), or I should write something on my own? - Pawel Szczesny

Pawel Szczesny

Answer by freesci for Parsing Jackhmmer output - http://biostar.stackexchange.com/questio...

October 5 from User freesci - BioStar - Comment - Like - Share

Well, apparently the correct answer is that no library exists that parses full jackhmmer output. Its authors even write: The output format is designed to be human-readable, but is often so voluminous that reading it is impractical, and parsing it is a pain. The --tblout and --domtblout options save output in simple tabular formats that are concise and easier to parse. In case one needs sequences of hits, there are two options. One is to painfully write a parser. The other one is to extract sequence based on coordinates provided by tabular formats. - Pawel Szczesny

Steve Koch to Steve's feed, Science 2.0

Dear Open Science Friends -- I am going up for tenure this semester at the University of New Mexico, Dept. Physics. External letters are one of the most important components of my dossier. I am thinking that a co-signed letter from friends I've met in the Open Science community would be highly valued by those people evaluating my tenure case.

September 2 - Comment - Like - Share

☆彡Jazzy-B, Kubke, Mario Pineda-Krch and 18 other people liked this

I am hoping that some of you would be willing to draft and co-sign a letter of support to be sent to my tenure committe--if so, I would be deeply grateful. Based on e-interactions with me, and in-person at ScienceOnline2010/2011 and ScienceCommons 2010 (Seattle), I think maybe some of you would have positive things to say about my research (I consider our lab's work in open notebook science, open data, etc. to be research) and service (promoting open science being external service). - Steve Koch

32 more comments

The committee wants to see specifically: "..evaluation of the quality, importance, and impact of his research and scholarship, and, if possible, a comparison with other physicists at similar stages in their academic careers." and "...Any comments you wish to make based on your knowledge of his teaching, interaction with students, mentorship, and service will also be appreciated." - Steve Koch

The standard method in our department is to mail letter requests to specific individuals, and to request hard copy signed letters. I've been thinking about this, and while I could ask one of you individually, it seems to me more appropriate, more powerful, and more fun to seek a co-signed letter. This has the risk of the various evaluation committees ignoring the letter, though. One... more... - Steve Koch

If anyone has better ideas, or knows of earlier examples of this from other universities, please post on here, or email me at stevekochscience@gmail.com - Steve Koch

I am really grateful for the years of support I've received from many of you open science supporters in my early career. I know I've been super-lucky to even land the tenure-track job and have always known that. I know that tenure would be a huge gift that is not something I deserve or am entitled to. Instead, I look at it as part of the way things work now, and being awarded tenure... more... - Steve Koch

So what am I asking? Without better ideas for how to do this: I am asking for people in the "open science" community who feel they are familiar with some of my lab's open science or my teaching of open science to state a willingness to be a co-signer of a tenure support letter. Then I am asking that group of people to nominate one person to provide the official letterhead and sign (with... more... - Steve Koch

They are looking at October 1 for deadline. Thank you thank you all! And like I said suggestions for a better process are welcomed! - Steve Koch

Do biologists qualify? If so, count me in. - Pawel Szczesny

@Pawel, absolutely! And Thank you! Everyone counts--all fields of academia (people that come to mind immediately are biology, neuroscience, physics, chemistry, library science), industry, and even those who may not currently have a paid position, but are active open science supporters. - Steve Koch

Count me in, natch. Regarding process: I think you are right to want individual letters from "high status" folks, to stay in the comfort zone of your committee. I suggest that the individual letters be different from the co-signed letter, which is a great idea and could be mentioned in the individual letters as "an instance of the wide web of collaborative opportunity opened up by Dr... more... - Bill Hooker

I'm in. - John Dupuis

Do you have any ppt or whatever of your scio10 or scio11 presentations handy? Was there a recording? I'd be happy to do up a short letter and certainly to cosign a joint letter. - John Dupuis

I'm in. I've served on tenure case and appointments-and-promotions committees, so I suspect a group-signed letter won't have as much weight as individual letters from as high up the academic feeding chain as you can go. Send me out-of-band email at gezelter@nd.edu if you want to discuss. - Dan Gezelter

I tend to agree with Dan. I'm more than happy to sign a community letter, though. - Egon Willighagen

I've never met you personally, so I don't think I should sign any individual letter, but I'd co-sign a letter of course! Just lt us know how you plan on doing that and I'll be there. - Björn Brembs

I'd be happy to help, in any way. I'm so sorry to be a biologist, but at least of a physicist descent (my father), so maybe...? :) - Marcin

I'll happily sign, not high up the feeding chain though I'm afraid :D - science3point0

OK, here's a start: http://piratepad.net/DpuxZJT... I haven't written tenure case letters before so it may need considerable chopping about, but at least we can get started. - Bill Hooker

Great start, Bill! I've co-signed too. - Heather Piwowar

Bill -- That is amazing! Thank you so much! That is wonderfully written and I appreciate it deeply. I've only been in a few departments in my young career, but I can tell you that UNM's physics department is full of faculty that care deeply about education and doing research for the benefit of society. So, I am confident that many of those voting on tenure will be very impressed by the... more... - Steve Koch

@Marcin I love interdisciplinary! Actually our science is focused on biology and have had students in the lab from biology, biomedical sciences, mechanical engineering, biomedical engineering, physics, and optical engineering. Moreover, I don't worry about the departments or academia / industry--with open science, we almost automatically ignore those credentials--while hard-earned,... more... - Steve Koch

@Dan Thank you for the experienced perspective! I've sent you an email with further thoughts / questions. I do accept the reality that I need those high-on-the-chain letters. And will seek those for sure. My gut is still telling me that at least for my department, a co-signed letter will add a lot of value, especially a letter such as Bill has drafted. I think for sure after the dust... more... - Steve Koch

@ John -- thank you for offering to co-sign! This is the only video I'm aware of (I think you were there & also my APOLOGIES for inadvertent slam on library journals!). That was the "data discoverability" session in 2011 and it was a ton of fun for me. Here is the link http://friendfeed.com/kochlab... and here are my notes from the session (with links) http://openwetware.org/wiki... - Steve Koch

Here's slides from 2010 Open Notebook Science presentation http://www.slideshare.net/skoch3... - Steve Koch

Here are my notes (with links) for the ScienceOnline2011 Data Discoverability session: and here are my notes from the session (with links) http://openwetware.org/wiki... - Steve Koch

@others who've piped in--thank you! I am excited to have this support - Steve Koch

Steve - I'm happy to co-sign but I do agree with Dan that individual letters are generally preferred. But if your tenure committee is saying that this is the way to go, definitely follow their direction. - Jean-Claude Bradley

I'm happy to sign as well. Best of luck, Steve. - Mr. Gunn

Now that people are back from science online, *bump* - Bill Hooker

Where do I sign.... - Cameron Neylon

@Cameron: http://piratepad.net/DpuxZJT... - Bill Hooker

added my name - Jonathan Eisen

mine too! - Scott Edmunds

Thank you everyone! Jonathan Eisen has graciously signed and mailed in a snail mail copy of the open letter to my committee. I don't expect to hear anything about it (positive/negative/neutral) until December, maybe January. I will of course update you with any news. Thank you again, everyone: so much support made me feel great! - Steve Koch

References Wanted: Piotr Byzia

Mobile apps for chemistry in the world of drug discovery http://www.ncbi.nlm.nih.gov/pubmed... Anybody? Please send to piotr.byzia (gmail)

September 29 - Comment - Like - Share

On the way (if not the time difference Anthony or Rich would send it before me :) ). - Pawel Szczesny

I'm glad this room still works as it used to, thank you Pawel. - Piotr Byzia

peter murray-rust

Why do we continue to use Citations? - http://blogs.ch.cam.ac.uk/pmr...

September 16 from petermr's blog - Comment - Like - Share

Steve Koch, Bruno C. Vellutini, Daniel Mietchen and 9 other people liked this

Somebody forgot about funders... Again, and again, and again... - Pawel Szczesny from iPhone

14 more comments

Pawel, what is your point? Should funders use a bad system because there is nothing better that allows them to judge some proposal in 5 minutes? (Because that's what these things are used for...) - Egon Willighagen

Not that they should. They don't have any choice (article views is a joke - it can be gambled in no time). - Pawel Szczesny from iPhone

That's my point: they *have* choice, and the picked something bad. page views is not a better solution; I agree with that. - Egon Willighagen

Egon, what is the other choice funders didn't pick? - Pawel Szczesny from iPhone

I quite like citations. It's +1 old-school style. - Noel O'Boyle

Pawel, actually trying to understand what the contributions of a person to science are. Takes a bit more effort, but at least is fair, balanced, and transparent. No way to hide your decision behind vague metrics, but stand behind your decision. That's what funders should do. - Egon Willighagen

Funders need feedback data to help get traction on understanding the contributions, I think. Citations (lists, rather than counts, particularly) have a role here, the dynamics and distribution of page views might, and lots of other metrics do too. Ideally would hand-curate a bit, then look at clusters, patterns, etc as part of the info that goes in decisions. You know, data mining for decision support, like grown up companies do. - Heather Piwowar

i wonder if PMR knows about the MESUR project and all that. There are people trying to make sense and all out of usages. MJ Kurtz has looked into it quite a bit at ADS, too. - Christina Pikas

@Christina yes I know MESUR. All these projects rely on grace-and-favour handouts from secondary publishers. I believe that what studies there are show that citations are considerably less accurate than usage in showing linkage etween disciplines, etc. - peter murray-rust

Egon, I'm all for reading papers instead of measuring them. But that's what hiring commitees are usually doing, not funders. Funders have too many applications to use manual assessment on all proposals (Gates Foundation has a grant program in which they assess only the idea - author and his afiliation is hidden from the reviewers. The last time I was interested, announcement of the winners was postponed by 7 months, despite the fact that proposal was only 2 pages.). - Pawel Szczesny

And that gets me to the original point - funders are interested in using robust and hard to gamble measures. No such alternative to counting citations exists (I was surprised to hear that funders are aware that if they start to _analyze_ citations, very soon researchers will use negative citations to 'downgrade' competition). Anything relying on clicks, views, usage, search engine results etc. is easy to gamble. - Pawel Szczesny

That's bull. Citations can be faked too; it's harder, but happens too. Just write a review. Write something controversial. Write editorials. The thing here, this gambling is easier by those who are already on top, and have this currency to coin in some extra base level citation. But, I agree, if funders would *only* use citation counts for the papers, I'd be more than happy already.... more... - Egon Willighagen

Egon, we all know that reviewing grant application is a mix of pseudomeasure of impact (whether it's a citation count, H-index or article-level metrics) and individual preferences of reviewers. I'm only saying that choice of pseudomeasurein practice isn't ours - it's funders'. Before NIH OA policy became mandate, comply rate was ca. 4% - now it's 75%. - Pawel Szczesny

Absolutely true. They decide how they do it. - Egon Willighagen

Are funding agencies and proposal evaluation discussed in Moneyball? I haven't seen the movie yet :) If agencies were rewarded for winning, really truly rewarded in a timely manner, then they'd figure out how to use citations, pageviews, everything available to predict impact of proposals. As far as I know we're a long way from this, since we can't even measure winning, really, for a funding agency, can we? - Steve Koch

Pawel Szczesny

Answer by freesci for Analyze genome sequence not published - http://biostar.stackexchange.com/questio...

September 27 from User freesci - BioStar - Comment - Like - Share

The rule of thumb is to postpone any genome-wide analysis until the genome paper is published. On the other hand, using deposited data to perform a vertical analysis (analysis of a single gene family across several species) is usually accepted. However, the best idea is to ask the sequencing lab. You'd be surprised how nice people are usually working there ;) - Pawel Szczesny

Graham Steel

Something outwith my control happened two days ago resulting in my display monitor appearing upside down. I've therefore had to physically turn my monitor upside down in the meantime. How do I change the settings on my PC (Windoze XP) to return things to normal?

September 21 - Comment - Like - Share

<gently bumps> - Graham Steel

2 more comments

Does ctrl+alt+up work (or ctrl+alt+down)? - Pawel Szczesny

If the shortcut above doesn't work, try changing the registry key HKEY_LOCAL_MACHINE\SYSTEM\GDI\ROTATION "Angle"=dword:changehere to 0. Software to edit registry is called regedit (type in "run" box). - Pawel Szczesny

TOP MAN, Pawel. ctrl+alt+up and/or down didn't initially do anything. Investigated option two but unable to find the sub directory I was looking for. Tried option one again and BINGO !! My life is no longer upside down.... Cheers ! - Graham Steel

References Wanted: Björn Brembs

Am I really cited in this article? I can't verify it without access: http://www.ingentaconnect.com/content...

September 22 - Comment - Like - Share

No access. - Egon Willighagen

3 more comments

There's an abbreviated references list http://www.ingentaconnect.com/content... - Pawel Szczesny

I saw that and it didn't contain our paper - that's why I posted it here :-) - Björn Brembs

Yes, you are :-) Sent! - JJ

Many thanks! - Björn Brembs

Pawel Szczesny

Science Commons is closed and it seems that the focus of that part of Creative Commons shifts from (open) science to (open) educational resources.

September 18 - Comment - Like - Share

Alex Holcombe and Kubke liked this

I have an impression that it will disconnect scientific community from important discussions again. - Pawel Szczesny from iPhone

John had reassuring thing to say about CC's continuing role in science: http://del-fi.org/post... - Bill Hooker

CC community at the CC global summit (last weekend) remained unconvinced. We'll see. - Pawel Szczesny from iPhone

Egon Willighagen

but seriously... $35 for a single paper? I wonder what buying a single, print issue would cost... #fail

September 3 from identi.ca - Comment - Like - Share

Graham Steel, Todd Hoff and Björn Brembs liked this

If you count only papers you actually read, having a journal subscription makes individual papers much more expensive. $35? What about $50-$60 in a subscription? (numbers based on individual deals with large publishers of the institutions I worked at - "big deals" look quite different) - Pawel Szczesny

6 more comments

Pawel, I don't understand your math... 50-60 is per paper? for the institute, for you personally? - Egon Willighagen

If your institute pays for subscriptions of the whole journal, but you actually read only small portion of what's published, the cost per paper read is ca. $50-$60. Last time I checked it was true for a single institution and for a large society as well. - Pawel Szczesny

It would be great to see statistics on that, although I guess these numbers are not widely shared. - Marcus D. Hanwell

So, those are journals of which a whole organization reads about 100 papers, without depublication? With duplication that would go down to perhaps 25 papers, for one journal. Cancel, I'd say. You don't buy a newspaper just to read the front page either... Seriously, such a journal would fail the 'we think this journal has something interesting to say' bar, not? But I cannot imagine this to be the case for the average journal? How is this counted anyway? Like Marcus said, please, more detail. - Egon Willighagen

These are almost always "back of a napkin" calculations, because deals with institutions or societes are usually negotiated individually, so it's hard to compare notes. Also, with subscription you don't only buy papers, but also convenience. That said, the number I've seen twice were quite similar - ca. 10-15% of available content actually being read by subscribers. Given the deals that were signed, that ratio elevated cost of a single paper to $50-$60 range. - Pawel Szczesny

I guess that makes ~ $35 the best estimate. After all, the publishers have access to *all* needed information. - Egon Willighagen

Yes, I'm sure all prices are not out of thin air, which makes me wonder if stats were the reason for publishers to sharply raise prices (MPG/Springer in 2007 or last year's UoC/NPG). - Pawel Szczesny

Heather Piwowar

RT @cboettig: "What would scholarly comm look like if it were built from scratch today?" Priem's ans: Doesn't matter, can't do that #datacite

August 24 from Twitter - Comment - Like - Share

Christina Pikas and suelibrarian liked this

OH HELL YES. Thank you. - RepoRat

3 more comments

That misses the point of the question, imo. It's a thought-experiment meant to help set goals, like asking "what would a perfect scholcomm system look like?". We can't build one of those either, but designing it on paper is a useful exercise. - Bill Hooker

Bill, that was my reaction at first, too. But upon further reflection, I think that the point of the *answer* is that it's too easy to get lost in fantasies about what things should be like without really engaging with the real situation in real life. If I were trying to reform some large complex system that had many competing real-world interests, and people kept wantint to talk about the "perfect system," I suspect I'd lose patience with that line of thinking pretty quickly. - Your Neighbor Steve

I wonder who will be the first to write a post entitled: "What's wrong with scholarly communication today? Wannabe stakeholders." ;) - Pawel Szczesny

Steve++. Elements of the OA movement have a bad habit of bandar-loggist "Something noble and grand and good/Won by merely wishing we could." - RepoRat

Deepak Singh

Stanislaw Lem- Philip K. Dick: A Visionary Among the Charlatans - http://www.depauw.edu/sfs...

August 21 from Instapaper: Unread - Comment - Like - Share

Deepak, have you read any book by Lem? - Pawel Szczesny

Pawel Szczesny to Pawel's feed, Science 2.0

Quite interesting: automated list of Twitter experts on "open science" at Topsy.http://topsy.com/s... Found a few new names.

August 21 - Comment - Like - Share

Ahmet Yükseltürk and Egon Willighagen liked this

Cool feature! It doesn't get the quotes right for me, finding hits for open and science separately too... - Egon Willighagen

2 more comments

Strange, every time I click on "mentions" the phrase is right. Do you have an example? - Pawel Szczesny

Oh, ic... maybe it's just the list where single words are highlighted... :) - Egon Willighagen

Just checked: you're 100% right! the second col in the sum page are the account 'about me' bits, and there it highlights the single words :) - Egon Willighagen

References Wanted: Graham Steel

Institutional Repositories, Open Access, and Scholarly Communication: A Study of Conflicting Paradigms doi:10.1016/j.acalib.2011.07.002 http://www.sciencedirect.com/science...

August 19 - Comment - Like - Share

no access - Wolfgang S

Check your email. - Pawel Szczesny

Thanks, Pawel ! - Graham Steel

Pawel Szczesny

Comment by freesci - http://biostar.stackexchange.com/questio...

August 18 from User freesci - BioStar - Comment - Like - Share

Bacteria only? Pathogens to human or in general? - Pawel Szczesny

peter murray-rust

Figshare meets Open Drug Discovery - http://blogs.ch.cam.ac.uk/pmr...

August 7 from petermr's blog - Comment - Like - Share

Graham Steel, Steve Koch and Egon Willighagen liked this

Quote: "Figshare has been developed with zero cash (but a lot of love from Mark). That will scale as far as establishing that the concept works and scientists like it." Indeed, lots of love (and way more work) from Mark, but please Peter, get your facts straight. It's not that anybody else deserves credit for FigShare (nope - it's all Mark's work), but I think it's important to remember that zero cash approach _doesn't scale_. - Pawel Szczesny

@Pawel I said "as far as". I believe that that point has already been reached. You may tell me different. I did NOT say it scales indefinitely - indeed I intended to imply that it would not scale automatically when it got beyond proof of concept. If you think it has not reached proof of concept say why and what it needs to achieve - peter murray-rust

Mateusz Koryciński to Mateusz's feed, Bioinformatics Central, Biology, The Life Scientists

Looking for good Ca-binding site prediction method or server. Any ideas? I need to predict it from sequence.

July 22 - Comment - Like - Share

If it's a known protein, Uniprot may have that feature already in the annotation. http://www.uniprot.org/manual... - Pawel Szczesny

Thanks! I actually found a paper about identying EF-hand domains and I've already got idea what to do. But thanks for the link! It will be helpful. - Mateusz Koryciński

References Wanted: Iddo Friedberg

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

July 23 - 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 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

Pawel Szczesny › Comments