Pawel Szczesny › Likes

Daniel Mietchen
Open Science and Citizen Science: A Research Communications Strategy Project (176) -
Just noticed that this had not been posted to Friendfeed yet, so I thought I'd just do it, as I think this page provides a usefully organized set of resources. Seen at . - Daniel Mietchen from Bookmarklet
Konrad Förstner
Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods -
Björn Brembs
Honoraria from for-profit organizations? -
Are you being payed for *all* hours you work? - Egon Willighagen
Like most others, I'm being paid a lump sum each month, regardless of "work hours": - Björn Brembs
But the tax payers only pay you for about 40 hours. Per law, I'm sure. Us academics created a rat race, rewarding those with more output, so that we ended up working 80 hours, and even on holidays (... is my CDK work today part of my academic output? likely...)... the whole world allows a Gates tax, and we worry about a honoraria ... - Egon Willighagen
I see your point. However, for me the issue is more to make them pay rather than me getting anything. I get by fine, I don't need any money. But I'd very much like to make them pay for what they get regardless :-) - Björn Brembs
It's worth balancing off the benefit you get from the exposure as well. But where I've been asked to advise for profits or do more than give a short talk I've started asking for a day fee. Partly as a way of doing less but also because I need to justify the time away from "real" work. And when they do pay its a nice bit of money to pay for travel or other things that usually end up coming out of my own pocket. But I also usually work on the basis that the "first one is free" - Cameron Neylon
Björn, you don't have to keep the money! You can spend it for the better cause... That's what happens with a few percent point of the Gates tax... - Egon Willighagen
@Egon: which is why I will either donate the money to charity or buy lab equipment. I only wonder: should I charge and if so how much and to charity or lab? - Björn Brembs
You should charge. If the company in question does not have much money but you like the people or the ideas, then don't charge much -- but always charge something. If you don't, you risk being under-valued: the point is not about pride but that if you are going to give advice or information you want it taken seriously, otherwise why bother giving it? After two years in biotech, my... more... - Bill Hooker
Oh, and you should charge *at least* the same as you get in your normal job. That is, if your job pays X per year, work that out as an hourly rate (based on 40hrs/week not what you actually work!) and charge that for the hours of work you will be putting in (both preparation and presentation time), plus expenses (travel, accomodation, etc). - Bill Hooker
Rob Syme
2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles -
Heather Piwowar
How about PLoS Currents: Open Science? -
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
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: 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
The Brain Is Not Made of DNA -
The Brain Is Not Made of DNA
Great post ! - Nils Reinton
Ian Holmes
ECHO: A reference-free short-read error correction algorithm [RESOURCES] -
Daniel Lemire
Carl Boettiger
Segue: Easy cloud computing in R, now with custom packages -
Got custom functions with extra dependencies working now, just updated the notes. Thanks to JD for helping me debug this. - Carl Boettiger
Seb Paquet
Why should scientists practice open science? -
Seb Paquet, B. Sc. in Physics, Ph.D. in Computer Science Because we can't afford to conduct closed science. See question on Quora - Seb Paquet
all good responses - Jean-Claude Bradley
Finally, finally, finally submitted our friendfeed manuscript :-)
Looking forward to it! :) - Berci Mesko, MD
Where did you submit it? - Björn Brembs
Alex Holcombe
A journal editor wrote (in a comment at bottom of that some of the comments people have written on my blog constitute defamation against him and his journal and are therefore illegal. I believe strongly in free speech, and therefore don't want to delete the comments "just to be on the safe side". What should I do?
I don't think I am liable, but don't want to support such commenting activity if it is illegal. - Alex Holcombe
Example comment: "Glossing over greed with syrupy intentions is corrupt." The others are here: - Alex Holcombe
Added comment on the thread. I've never met GE but my impression is that he's a straight arrow -- but that doesn't mean all publishers are as honest! Regarding liability, surely that is a settled question by now -- if bloggers were liable for comments, where would that leave Wordpress, political bloggers, facebook, etc etc etc? - Bill Hooker
Thanks Bill for your helpful comment! BTW, although I don't like GE's aggro stance, and certainly mentioning libel/defamation has a somewhat chilling effect, he may not have intended to threaten or chill my speech, so I wouldn't want to accuse him of that. About the comments he say are defamatory, I certainly didn't like their tone and maybe developing a good comment policy for my blog will reduce them in future and give me cover for deleting the ones that are particularly ad hominem. - Alex Holcombe
Can anyone point me to a good blog commenting policy? (for someone like me who is a big believer in free speech) - Alex Holcombe
I also agree: if comments would make blog authors liable, the judicial systems in any country wouldn't be doing anything else :-) - Björn Brembs
Thanks guys- also if any of you disagree with GE's points, feel free to comment on my blog ( ), because GE writes as if I'm the only one with my "illogical" views that "make no sense" regarding the possibility of fast-track fees biasing the journals - Alex Holcombe
Michael Nielsen
Documents as geometric objects: how to rank documents for full-text search | DDI -
Useful for data mining, clustering, document classification, full-text search and other applications. - Michael Nielsen
Abhishek Tiwari
Big-Ass Servers™ and the myths of clusters in bioinformatics -
I like this post, cause he makes some great points, but it also makes me want to cry because it admits that we don't know how to write software - Deepak Singh
I couldn't resist a response :) - Deepak Singh
Matt Wood
Great cloud sessions at BOSC in Vienna: Good to see Sequencescape, a project I started at Sanger, get some airtime.
Nature: why scientific programming does not compute -
FigShare now allows multiple file data 'sets'. Oh, and what file types does your research come in? List them below or in the comments at the latest blog post:
Space Oddities
PLoS ONE: Citizen Science Reveals Unexpected Continental-Scale Evolutionary Change in a Model Organism -
peter murray-rust
Why Openness Matters to me and to you: The Architecture of Access to Scientific Knowledge -
Dave Lunt
PLoS Biology: Darwin's Theory of Descent with Modification, versus the Biblical Tree of Life -
Talking about Darwin and the Tree of Life? Better read this first. Title almost put me off, glad it didn't. - Dave Lunt from Bookmarklet
Yann Abraham
A case study in personal genomics « Genomes Unzipped -
Incredible amazing awesome Apple -
Incredible amazing awesome Apple
Brilliant. - Pawel Szczesny
Björn Brembs
Mr. Gunn
[huge win for open science!] Fifty-year search for calcium channel ends: Cell's power generator depends on long-sought protein (via @phidias51) -
""But thanks to the Human Genome Project, freely downloadable genomic databases, and a few tricks -- we were able to get to the bottom of it."" - Mr. Gunn from Bookmarklet
Can you please post this to that BioStar where they wonder what bioinformatics is good for? - Egon Willighagen
Bill Hooker
peter murray-rust
Publications from the “Visions of a Semantic (Molecular) Future” Symposium -
Who said data repositories were boring? Just found db of people accused of witchcraft in Scotland, 1563 to 1736:
Simon Cockell
Bayesian vs Frequentist. A pragmatic bioinformatician's view -
Cameron Neylon
Open Research: Pipedream or growing reality -
Open Research: Pipedream or growing reality
That's why I couldn't find it. Imported with the wrong date... - Cameron Neylon
Egon Willighagen
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics -
BMC Bioinformatics, Vol. 11, No. Suppl 12. (2010), S1. BACKGROUND:Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce.DESCRIPTION:An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.CONCLUSIONS:Hadoop and the MapReduce programming paradigm... - Egon Willighagen
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