Pawel Szczesny - Likes

Mr. Gunn to Mr.'s feed, The Life Scientists

I need some feedback/career advice.

Graham Steel, Andy Bakun, Allyson Lister and 18 other people liked this

Many of you know I've been working with Mendeley as a sort of ambassador/community liaison. I started this because I've always felt a little shut out from contributing to open science/open access/open data because I don't work for a publisher, don't really write code, and wasn't in a job where I could openly share data. This was a way to influence how things develop by promoting the people who "get it". - Mr. Gunn

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I had to quit for the "real job" a little while back and found not only that I had more time to work for Mendeley, but that I started getting other offers/opportunities also. - Mr. Gunn

Now I've got a newborn daughter and am liking the time I can spend at home with her, which raises the following conundrum: Can I do more of this community liaison work for companies that support/promote open access and put my research career on hold, or is there not any future in this? - Mr. Gunn

Can I trust the friends and colleagues I've met on here to be able to have a real discussion with me, keep me honest, and tell me if I'm backing the wrong horse as I take on more clients, or would I be considered a sell-out? Would people believe that my opinions still come from me and my experiences, or would people just think "You're only saying/supporting that because they're paying... more... - Mr. Gunn

Do you think there's room to grow in this kind of role or am I just wishfully thinking that I can make my own job in this tough economy and get to spend time with my daughter too? - Mr. Gunn

I really believe this is a way I can contribute to changing how science is being done, opening up the process, disintermediating scientific discovery, and all those noble sounding things, but do you buy it, or do you think I'll not only become corrupted by money but lose my relevance because I'm not really doing science anymore? - Mr. Gunn

Can I help companies that don't quite get it to improve and become better and more responsive to their community of users or will I lose touch? - Mr. Gunn

I will be saying nothing works better than inspiring people by setting examples, I will not go with holding my research career even it is not working well as long as I have passion for discovering something. But there are certain realities and money is one of them. Ambassador/community liaisoning is other way to contribute back to the science, but it will be too early to give up your... more... - Abhishek Tiwari

Mr. Gunn. You can absolutely do so, but as you note, you cannot do this with one client. It will have to be a consulting/pundit role (you should probably have a chat with Paul Miller at some point http://cloudofdata.com). The life science industry will be challenging given the limited opportunities, and in this economy, this will not be a walk in the park. As to whether you have to be... more... - Deepak Singh

And we'll tell you if you're being an idiot. It also depends on what you really want to earn. You're not going to get rich doing this, at least not quickly. - Deepak Singh

Abhishek, I could cite all the times when I've recommended Papers or Zotero instead because it really was better for what the person was looking for as evidence that I don't always have to say what the official line is, but that wouldn't illustrate all the discussions I've had where the company point of view _became_ my point of view. This is exactly the kind of discussion I want to be... more... - Mr. Gunn

Thanks Deepak. I know you will, and I'm not looking to get rich. I'm looking to do work for people I believe it, be a force for good, and at least for the moment, spend more time at home with my daughter. - Mr. Gunn

Mr. Gunn, it will only taint it if you let it, although there will people who'll always be skeptical. As long as you are honest and present your point of view rationally, you'll be fine - Deepak Singh

I'd like to think that being open and transparent online helps illustrate my biases, too. - Mr. Gunn

Way outside my area of expertise, but I would think the "consulting/pundit" thing that Deepak mentions would involve lots of travel, especially to start. Not sure how conducive that is to spending more time at home... - Andrew Su

Andrew, missed that bit. There would be a fair bit of travel - Deepak Singh from iPhone

Tough call MrG. I'm not concerned about you selling out, plus I will call you out if I think you are sliding into that trap (as, I'm sure, will the rest of the FF posse). My larger concern would be whether you can make a living that way. Is there a more regular (but part-time) gig that you could get to buffer the difficulties of forging a new path? For instance, do you write easily and... more... - Bill Hooker

Having a part-time gig would allow you more freedom to take risks and experiment, and could be phased out as and when your liaison/consulting work grew. - Bill Hooker

Bill, that's a really great idea. My current commitments are only part-time, so having something more steady would both help the bottom line and insulate me from selling-out criticism - "I don't need to do this." Please, put me in touch. - Mr. Gunn

the ultimate evidence for or against bias is behavior, would such a position restrict or inhibit assuming a critical perspective? - Mike Chelen

What fun would that be, Mike? I just wanted to do a sanity check against my friends and colleagues here to make sure that at least some of them would promise to call me out if I started to not make any sense or drift away from the principles of openness this community takes as a fundamental principle. - Mr. Gunn

Interesting situation! My take is that people who have no history of interaction with you, will not spend a lot of time looking you up online. As soon as they know you're being paid to do this, you'll be a sales rep - which means there isn't even any need to look you up, they already know who/what you are. Thus, IMHO, no online history will get you out of the sales rep box. - Björn Brembs

I agree with Bill's suggestion, and also his non-worry about bias. Or rather, we're all biased, but you don't come across as a sell-out company mouthpiece to those who know you, so you can let that slide. Bjorn isn't tender, but he's right. Either way, you won't change it by adding on more opportunities to be a facilitator. And forging your own path to be more with your family - having been there, I would say you won't regret it later. One always has career regrets, but that's because we only have one life. - Heather

Mr. Gunn. A full time liaison for a company will effectively make you sort of a sales rep. I have been a sales rep myself - which was a valuable learning experience, but I suspect, like me, not one you would fit comfortable into for a longer period of time (several years). When I left university, my friends and colleagues told me that I had a time-limit of 1-2 years to get back into... more... - Nils Reinton

Thanks, Nils, Heather, Björn. My intent is not to work full-time for a specific company, and I'm not doing that now. My intent is also to talk more about ideas and trends and less about specific products. Although I do spend a fair amount of time recommending Mendeley, I think Zotero shares their mission and I just personally prefer Mendeley. I used Zotero to write my first paper and it came down to me just wanting a desktop, full-screen app instead of their browser add on. - Mr. Gunn

Björn - We all have our various reasons to believe what we do and say what we do. In my role, I'm not being paid to say anything or to have a certain opinion. In fact, I think where I disagree with the Mendeley guys is more valuable to them than where I agree, because what they're basically paying me for is my insights as a scientist who knows the field and keeps current with... more... - Mr. Gunn

I know I can't speak for anyone, and I'm not appointing myself spokesperson, but if I spend a lot of time listening to, talking about, and synthesizing ideas, and I can also effectively market those ideas to people who need to hear them (that is, companies who want to listen and adapt), isn't that a win? Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in? - Mr. Gunn

"Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in?" YES, absolutely, you are already doing this very well. If you can make a living out of it, I salute you :-) - Nils Reinton

Perhaps consider not just consultancy for companies, but also undertake work for public sector agencies (major libraries or funders), charities or not-for-profit companies. - Frank Norman

Mr. Gunn - sure I think such a person would definitely be worthwhile to us! I was referring to people who do not know you: if you approach them and tell them you work for company X, my bet is that most of them will think "ah, he's a failed scientist trying to get me to use their products". Of course, this doesn't stop people from using company X's products (or sales reps would die out... more... - Björn Brembs

this is a great thread, Mr. Gunn, cheers for starting it, very interesting points, everyone; I would like to second Nils and Frank, and I think that some journals might also be interested in your advice (and community liaison work) and that this would certainly be a great service for anyone near to being an OA and linked data addict - isn't this a pretty wide range of users? we might create a list of arguments that you might wish to choose from when talking to journal publishers - test them on me ;-) - Claudia Koltzenburg

Mr Gunn...you might know me from the ChemSpider system. For almost 3 years ChemSpider was run as a "for the community" project at my cost. i.e. My wife and kids lost a lot of access to me, despite the fact that I worked from home. It did NOT pay any bills...it just about covered costs. No, I was a consultant for a number of companies and worked hard for them, traveled a lot and used my... more... - Antony Williams

OT b/c it's blog not job related *but* I would cite this FF thread at some stage in this one. http://ff.im/YB4p from Feb '09. - Graham Steel

Nils, thanks! Frank - that's a great idea. Can anyone put me in touch with someone at one of those agencies/companies? Björn - I see what you mean. Online rep doesn't translate offline automatically. Claudia - I've got a series of arguments, gleaned over the years from participation here and elsewhere. Can I send you an email? Antony - yes, I'm familiar with your work, and I have a... more... - Mr. Gunn

Daniel Mietchen to Daniel's feed, Science 2.0, Science Online, Science in the long run

Fwd: Should you be tweeting? - http://www.hubmed.org/display... (via http://friendfeed.com/ff-for-...)

18 hours ago - Comment - Like - Share

Alexey, Pawel Szczesny and Claudia Koltzenburg liked this

No mention of friendfeed, so what about writing a correspondence piece on this? It could be based on http://ff4s-paper.wikidot.com/start and perhaps also put the recent NIH grant for a "Facebook for Scientists" ( http://ff.im/beKk7 ) in perspective by providing an overview over existing tools along these lines and why they are not widely used. - Daniel Mietchen

http://www.cell.com/authors... / Correspondence: "The Correspondence format provides our readers with the opportunity to respond to an article in Cell—either a research article or Leading Edge article—that has been published within the last 2 months. Correspondence should be no more than 900 words in length with up to five references and should be of interest to the broad... more... - Daniel Mietchen

Now that sounds like a good idea! I'm all for it - especially mention the gazillion "facbook for scientists" already out there. - Björn Brembs

Pedro Beltrao

Nature Cell Biology joins call for microattribution of datasets - http://blogs.nature.com/nautilu...

19 hours ago from Google Reader - Comment - Like - Share

Mr. Gunn, Jean-Claude Bradley, Peter Miller and 3 other people liked this

Earlier similar calls: http://ff.im/5s2Dc and http://ff.im/9hscn . - Daniel Mietchen

Roland Krause

PLoS Computational Biology: A Collection of Education Articles in PLoS Computational Biology - http://collections.plos.org/ploscom...

20 hours ago from Google Reader - Comment - Like - Share

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Neil Saunders

STITCH 2: an interaction network database for small molecules and proteins - http://www.citeulike.org/user...

Sunday from CiteULike: neils's library - Comment - Like - Share

Pawel Szczesny, Yann Abraham, Pedro Beltrao and 3 other people liked this

Nucl. Acids Res. (6 November 2009), gkp937. Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. 10.1093/nar/gkp937 Michael Kuhn, Damian Szklarczyk, Andrea Franceschini,... - Neil Saunders

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I didn't expect the paper to come out this quickly, I was quite surprised to see it in my feed reader on the weekend. I have now activated STITCH 2 as public website ... hope it's not too buggy :) - Michael Kuhn

this looks like it could be quite useful for our cheminfo retrieval class - I added it to our resources and will let you know if any students make use of it for their term projects http://getcheminfo.wikispaces.com/resourc... - Jean-Claude Bradley

umm .. you are going to make me re-do some work :p - Pedro Beltrao

@Michael - quick questions: I don't think I ever saw homology evidences in the drug-gene interactions. Do you guys avoid doing this or it is just not reported in the evidence info ? - Pedro Beltrao

Congrats Michael! - Ruchira S. Datta

@Pedro: going from STITCH 1 to 2 will change the identifiers of proteins and chemicals, so check first if you run into trouble there - Michael Kuhn

re transfer: if you are in human or mouse, you probably won't see so much transfer. but if you go to e.g. chimp, you'll see a lot of transferred evidence - Michael Kuhn

Michael Nielsen

An interview with Alain Connes (pdf) - http://ipm.ac.ir/news...

yesterday from delicious - Comment - Like - Share

Pawel Szczesny and Daniel Mietchen liked this

Connes on the future of mathematics, the value of freedom in mathematical research, and much else. - Michael Nielsen

Science 2.0: Steve Koch

Meeting with two Media Arts majors at UNM, discussing ideas for collaborations on science outreach. Thinking that a video explaining Open Science to the general public may be a good idea?

May 29 - Comment - Like - Share

Daniel Mietchen, Lisa Green, Pawel Szczesny and 6 other people liked this

Definitely! - Mr. Gunn

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We were mulling over a few ideas: (1) Like I mentioned in the title of this post: A combined video / screencast to explain what scientists are doing nowadays to make progress towards open science. Audience would be general public and scientists. Could use friendfeed as a starting point and then show things like open notebook science, etc... - Steve Koch

(2) Making a 5 minute video explaining the Open Notebook Science we're doing in Junior physics lab here. Target audience: other science instructors around the globe who'd be interested in using our experience to add open notebook science to their own courses. - Steve Koch

(3) (This what inspired our meeting, but then we thought up 1 and 2 above while talking) Making science videos explaining the research in our lab. Target audience: general public. - Steve Koch

(4) (This just occurred to me, we didn't talk about it): We could collaborate on making high-quality protocols videos. Something like in JoVE, but produced locally. I like all of these ideas and glad I met these students! - Steve Koch

Very cool, Steve. What can I do to help? - Mr. Gunn

Why don't you make a similar video explaining Open Science to scientists? I bet you will find a larger (or smaller) audience. - Paulo Nuin

I agree it would be larger or smaller :). @Mr. Gunn, thanks! I don't know what help -- the barrier now is to know what to do. Which of those #1-4 seem most worthwhile to you and most in need of digital media experts? #4 is the easiest for me to imagine, since I actually know what I'm trying to convey. #1 is the hardest, since I'm not sure how to coherently explain that. - Steve Koch

I am going to put a bit in my NSF CAREER budget for these projects. Talking with the students today, it seems like they could get academic credit for the project in the Media Arts programs, and also get access to the equipment. So, even there, I'm not sure what I'd need to budget for. - Steve Koch

And BTW: Both of these students took my Physics 102 "Conceptual Physics" course and did very well. So, this is cool validation for the whole teaching/research synergy idea. - Steve Koch

What is Open Science? - Paulo Nuin

I'll give this some thought, Steve. I've got my hands busy right now in terms of developing a presentation, but of course you're welcome to reuse any of my or Mary Canady's slides. - Mr. Gunn

@Paulo: what I mean by the term is the application of the free-as-in-speech principles of Free/Open Source Software to the entire enterprise of science. The Blue Obelisk folks refer to ODOSOS (http://blueobelisk.sourceforge.net/wiki... Open Data, Open Source, and Open Standards); to this I would add Open Access (publishing) and Open Licensing, to give the "five pillars" of Open Science. - Bill Hooker

Hmm. Open Data, Open Source, Open Access, and Open Standards are all forms of open licensing, aren't they? Or is there something specifically called Open Licensing that I'm not aware of? - Michael R. Bernstein

What I mean by Open Licensing is CC-style explicit permissions for re-use in copyright, and things like Science Commons' MTA or CAMBIA's BiOS licenses for stuff that's covered by patents. So yes, that's all part of Open Foo, but I think there's more to Foo than just the licensing and more to licensing than Data/Source/Access/Standards. - Bill Hooker

Ah. Open Content covers CC licenses, I'm not sure what to call MTA and CAMBIA BiOS. - Michael R. Bernstein

Other possibilities might be to include a citizen science project as an example of what can be done with greater collaboration -- such projects are good entryways into outreach since they seem to make science "closer" to a non- or emerging scientist. You could even go so far as to tailor portions of your own projects to younger audiences (K-12) -- and by doing so entice classrooms of... more... - Mickey Schafer

Sounds like a great idea and one I'm all in favour of. An idea, Steve. You might want to alert SciVee's Prof Phil Bourne http://www.scivee.tv/user/phil as I'm pretty sure he'd be [1] interested and [2] willing to lend a hand in hosting/promoting this type of project. - Graham Steel

Hey Mickey, Thanks for those ideas! Definitely interesting to me and will think about it. @Graham -- thanks for that link, I will definitely contact him when we have a clearer idea of what we're wanting to do. - Steve Koch

If you're looking for additional inspiration, try googling "digital ethnography" -- you should get to the Kansas State stuff (both their blog/web pages and youtube videos) -- you may or may not like the science-y part (anthropology -- the first video ever produced in the series was fairly annoying to me, though the subsequent ones are quite interesting), but they have some great teaching experiments using web re/sources that you might find useful. - Mickey Schafer

Second Mickey's recommendation. Very interesting stuff - e.g., a short presentation at: http://www.youtube.com/watch.... I really like the idea of doing something of similar impact for open science. The longer 55 minute Library of Congress talk from the same channel is well worth watching, IMO. - Michael Nielsen

That's spectacular! - Steve Koch

STeve - It'd be really nice to have something similar for open science. Some visual ideas I like are to make a movie of the version history on, e.g., OWW, or the Polymath wiki; visualizations of the evolving network of relationships from, e.g., GeneWiki... I'll bet things like diseases gradually being understood are actually visible in the network of links on Wikipedia. - Michael Nielsen

Steve - Jon Udell does an awesome Wikipedia movie at http://jonudell.net/umlaut.swf Things get really fun a couple of minutes in... - Michael Nielsen

Hey Michael, that too is very cool. And I really like your idea of adapting that for OWW or the other sites. I don't know if the students I talked with are good at that or not. Looking at the things you linked me made me realize that if I'm going to be heavily involved (say as "producer" with the $), then I think I'm missing some talents to lead those kinds of things. So, maybe I'm not... more... - Steve Koch

Demonstration is a more effective way of explaining a concept than just explanation is anyway! Hmm. That could've been more elegantly expressed. In any case, Demo of what you are doing with some discussion of implications (pedagogical to philosophical) also sounds like a great project. - Mickey Schafer

Hi All -- Met again with Noel and Leslie (the Media Arts peeps), and we've planned to start making the video on November 23. We're planning on short video showing what we're doing in Junior Lab with Open Notebook Science. General plan can be seen here: http://docs.google.com/Doc... and a list of potential interview questions is being generated here: http://docs.google.com/Doc... - Steve Koch

Muchas excellentos - Graham Steel

Lars Juhl Jensen

Predicting new molecular targets for known drugs - http://www.nature.com/nature...

November 1 from Google Reader - Comment - Like - Share

Ed Millard, Khader Shameer, Matthew Todd and 10 other people liked this

The title is a bit generic, isn't this what Phil Bourne's been doing? - Ruchira S. Datta

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I think this is an extension of their (Kieser et al) previous work with SEA - Rajarshi Guha

Nature has a story on this in their news section: http://www.nature.com/news... - Michael Kuhn

Is this using Lasso or similar program? Interesting appearance of DMT as a molecule of interest - I have a student doing a report on it this term http://getcheminfo.wikispaces.com/Adam+My... - Jean-Claude Bradley

Uses SEA http://sea.bkslab.org/ - Rajarshi Guha

Thanks Rajarshi - looks like another cool online resource to explore - Jean-Claude Bradley

That's cool. How likely is the top match to be a real inhibitor? - Andrew Lang

We're trying to run our virtual library of Ugi products we can make in my lab http://usefulchem.wikispaces.com/UClib00... I hope that isn't too large a task - Jean-Claude Bradley

We did some of this validated cross-target prediction also http://www.nature.com/doifind... - Matthew Todd

That's awesome Mat! What would be the next step to processing our Ugi product library on the TDI kernel? - Jean-Claude Bradley

Michael Habib to Michael's feed, scienceapps, Science 2.0, The Life Scientists

Fwd: Research 2.0 Concept Model - http://www.flickr.com/photos... (via http://friendfeed.com/habib...)

November 4 - Comment - Like - Share

Heather, io2a, Thomas Brox Røst and 11 other people liked this

The Research 2.0 Concept Model above is an evolution of the Academic Library 2.0 Concept Models developed for my Master's Paper (http://mchabib.com/2006... ). While the original model primarily focused on academic library services for students, the new model focuses on services for researchers. Like in the original models, the top represents communication spaces grounded in physical space, while the bottom mirrors this in the online realm. Two ends of the spectrum are informal communications and formal communications. My argument is that Research 2.0 falls somewhere between these extremes. A full presentation is located here: http://www.slideshare.net/habibmi... - Michael Habib

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The above Scholarly Identity 2.0 Concept Model takes the series of concept models one step farther, but with a slightly different twist. The divide between online and offline scholarly communication is largely meaningless, so has been discarded. The spectrum in this case is more specific with one end being entirely user-generated content and the other traditional scholarly... more... - Michael Habib

Michael - interesting stuff. Do you have that paper you mentioned published by now (blog post is dated mid-2006). I would like to mention some of this in my thesis and cite your publication of course. - 'Mummi' Thorisson

some comments here http://ff.im/aXOKZ, - so what's your thesis about, 'Mummi' Thorisson? - Claudia Koltzenburg

Thesis located here: http://hdl.handle.net/1901/356 and the title is "Toward Academic Library 2.0: Development and Application of a Library 2.0 Methodology" - Michael Habib

Claudia - the overall theme is data publication and the role of data standards, federated database networks and digital identity in facilitating/encouraging data sharing. The context is research into correlation between genotype and phenotype, or medical genetics/genomics more generally. Have a look at this review published last year that i co-authored with my supervisor: "Genotype-phenotype databases: challenges and solutions for the post-genomic era" - http://dx.doi.org/10... - 'Mummi' Thorisson

Nice. Thanks Michael!! - 'Mummi' Thorisson

The second (right) model above on identity is the more interesting of the two. If you are going to look at just one.... - Michael Habib

Interesting social status implications here, especially with the second model. The more robust both sides of the scholar2.0 identity components (UGC + trad), the "deeper" the 2.0 identity (think tag clouds as the metaphor here). Or, perhaps color combos is a better metaphor, with schol.identity2.0 being a mix of UCG (say, "yellow"), trad (say "blue") and combo being "green" -- the shade... more... - Mickey Schafer

Walter Jessen

DeepDyve Offers Scholarly Literature Rental Service [NGS] - http://www.nextgenerationscience.com/science...

November 4 from Next Generation Science - Comment - Like - Share

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Björn Brembs

Science favoured by German coalition : Nature News - http://www.nature.com/news...

November 5 from Bookmarklet - Comment - Like - Share

Pawel Szczesny liked this

"The generous funding agreements for universities and research agreed by the previous government last June will be maintained. So the budgets of major research organizations, including the Max Planck Society and the DFG, Germany's main research granting agency, will rise by 5% a year until 2015. Universities will receive a €5-billion (US$7.4-billion) supplement between 2011 and 2015 to improve teaching and research." - Björn Brembs from Bookmarklet

Kevin Emamy to Kevin's feed, Science 2.0, The Life Scientists

Early data from citeulike's automated article recommender http://blog.citeulike.org/...

November 4 - Comment - Like - Share

Yann Abraham, Martin Fenner, Mr. Gunn and 16 other people liked this

"It’s really gratifying to see the social discovery of science generated by the simple act of keeping your references public on a Web page." - Duncan Hull

Thomas Sharpton

HMMER3 is quickly becoming my primary homology detection and alignment tool, especially for metagenomic analysis: http://hmmer.janelia.org/

November 3 from Twitter - Comment - Like - Share

Michael Barton, Paul Gardner, Pawel Szczesny and 7 other people liked this

HMMs FTW! - Ruchira S. Datta

No doubt, especially now that HMMER is blazing fast! Hats off to Sean Eddy. - Thomas Sharpton

We'll be using this quite a bit locally, enough that we have people interested in getting BioPerl up-to-speed with parsing this. - Christopher Fields

Pedro Beltrao

DRYGIN: a database of quantitative genetic interaction networks in yeast. - http://www.ncbi.nlm.nih.gov/entrez...

November 3 from Google Reader - Comment - Like - Share

Pawel Szczesny and Ruchira S. Datta liked this

umm .. everything is password protected. Not a very useful database if you cant actually use it. - Pedro Beltrao

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they might have been aiming for January 2010, when the NAR db issue officially comes out - Michael Kuhn

It makes sense, since the data they have on this database is part of paper that Boone talked about and that I assume is currently under review. Still .. annoying :) - Pedro Beltrao

yep, I just got the email response back. They will remove the password protection when the other paper describing the data is published. Bummer :) - Pedro Beltrao

Lars Juhl Jensen

Analysis: Limited agreement among lists of Cdc28p substrates - http://larsjuhljensen.wordpress.com/2009...

November 3 from Buried Treasure - Comment - Like - Share

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Bora Zivkovic

The beginning of the end for impact factors and journals http://blogs.bmj.com/bmj... via @doctorblogs @richard56

November 2 from Twitter - Comment - Like - Share

Graham Steel, Jean-Claude Bradley, Pawel Szczesny and 9 other people liked this

I'm looking forward to the end of the end...! - Bill Hooker

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I wish he's right! - Björn Brembs

To me, the paper based stats only reenforce the idea that 'a' impact factor is actually good... - Egon Willighagen

Couldn't that section not better say: the results in this paper are refuted by this and this paper, and confirmed but this and that paper... - Egon Willighagen

Yes, Egon, and they could do it easier and in a more open way than some proprietary algorithm. - Mr. Gunn

AJCann to AJCann's feed, Science 2.0

PLoS ONE Impact Factor and Page Rank - http://www.sciencebase.com/science...

November 3 from Bookmarklet - Comment - Like - Share

io2a, Björn Brembs, Jean-Claude Bradley and 5 other people liked this

David Bradley on the impact factor game. - AJCann from Bookmarklet

The IF is now an anachronism. - Mr. Gunn

Deepak Singh

That Didn't Take Very Long - http://pipeline.corante.com/archive...

November 3 from Google Reader - Comment - Like - Share

Björn Brembs, 'Mummi' Thorisson, Michael Kuhn and Pawel Szczesny liked this

I have a lot of sympathy for people who are willing to be spectacularly wrong, but that starts to evaporate when they don't realize that they've been spectacularly wrong. Williamson appears to have had a fair hearing for his ideas, and as far as I can tell, they've come up well short. And while we need brave renegades, cranks are already in long supply. - Deepak Singh

Daniel Mietchen

Morpho-tools - a repository of morphometric tools and online morphometric workbenches - http://www.morpho-tools.net/

November 3 from Bookmarklet - Comment - Like - Share

Sebastian Wain and Pawel Szczesny liked this

"The purpose of this site is to provide tools to make morphometric analysis more widely accessible and quicker. All of these tools are open source, written for Mathematica. Many of the analyses can be run for free through this server. Notebooks may also be downloaded and further developed (see contributing)." - Daniel Mietchen from Bookmarklet

Deepak Singh

The main product of academia is not knowledge but the reproduction of academia. - http://news.ycombinator.com/item...

November 2 from Backtype - Comment - Like - Share

'Mummi' Thorisson, Benjamin Tseng, Claudia Koltzenburg and 6 other people liked this

"In fact, in the life sciences, the back and forth is getting more common, and will increasingly get so as the models for research, esp in large scale biology change. On the CS side there are any number of examples as well." - Deepak Singh

To paraphrase Ken Robinson: the purpose of academia is to produce university professors. - Pawel Szczesny

It's kinda like law ;) - Benjamin Tseng

Pierre Lindenbaum

RT @pansapiens Nodalpoint is dead !! http://www.nodalpoint.org/ ... Long live NodalPoint !! http://archive.nodalpoint.org/

November 2 from Twitter - Comment - Like - Share

Euan, Konrad Förstner, Chris Lasher and 4 other people liked this

but what is the "something new" :-) - Neil Saunders

I am glad it was archived :) ahh the good old days - Pedro Beltrao

Where many of us started, really. And then to personal blogs and now, microblogs ;-) - Neil Saunders

The Life Scientists: Deepak Singh

Zachary Voase’s Blog — Bioinformatics and the Semantic Web - http://blog.zacharyvoase.com/post...

November 2 from Bookmarklet - Comment - Like - Share

Khader Shameer, Donnie Berkholz, Pawel Szczesny and 2 other people liked this

Also check out his other post: http://blog.zacharyvoase.com/post... Awesome awesome stuff. Also, I'm more than a little relieved to find out I'm not crazy. Or at least that I have company in crazy town depending on the interpretation. - Paul J. Davis

Nice post, but I don't think it would sell me on using RDF. It's not like you can't agree on syntax and meaning (or even use ontologies) without RDF. Better to show how RDF helps deal with the fact that not all databases are ever going to agree on a single set of non-overlapping concepts for describing their data, and -- more important -- with more fundamental disagreements (such as what an organism even is). - Eric Jain

Björn Brembs

When even Impact Factors don't help any more - http://bjoern.brembs.net/news...

October 30 from bjoern.brembs.blog : a... - Comment - Like - Share

Claudia Koltzenburg, Jean-Claude Bradley, Graham Steel and 5 other people liked this

Some of us do actually know that IFs are crap. :) Nor are they what we uniquely rely on when considering cancellations. Cost-per-use is a big one, and I don't wonder that the heinously expensive journals fall down. Ask your library about document delivery for the articles you need. - D0r0th34

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Document delivery is actually far inferior to the references wanted room here. I've kept a list of papers I need, because I thought it was a temporary glitch (I still sort of hope it is). I guess I need to post that list to the Refs Wanted room soon... - Björn Brembs

impact factor is way down on the list, but i'm surprised there would be a lapse in their cell subscription. maybe there's just a technical glitch - that happens all the time. - Christina Pikas

yup, also possible... I have heard mild-mannered librarians swear sulfurously about service outages - D0r0th34

FWIW, I talked to 5 librarians at Caltech recently and just got nods of agreement when I maligned the IF, and they even knew about the alternatives, h-index, eigenfactor, etc. - Mr. Gunn

Just got a response from our library: Cell access only after 12 months embargo and Neuron access was canceled in 2007. Apparently, we only had access through other, departmental channels and something happened there. Obviously, our university has never had regular access to these journals, how pathetic! - Björn Brembs

Do you know what Cell costs? There is patheticness here, but it's not at your library or your institution. - D0r0th34

What I recall from conversations involving our Med Library colleagues is that Cell Press titles are always under "separate arrangement" as opposed to grouped with the rest of Elsevier's titles when license negotiations are made. Typical of the large publishers to know which titles are their gems. - carolh

@D0r0th34: Subscription prices: see original post :-) The patheticness lies in the title "Excellence University" which our university likes to use a lot and then not having enough sense to fund the library to be able to afford the 'excellent' journals. - Björn Brembs

@D: no one knows what Cell costs! That's half the problem right there -- a different, secret deal for every different subscriber. - Bill Hooker

Bjorn, the problem has gotten so out of hand that "funding the library" is no longer the right answer. I'm all for library funding, but I'm *not* all for pouring yet more money into big-pig publishers. We have thirty years of evidence that do what you will, their prices will expand to mop up the budget available. - D0r0th34

@D: I so agree with you - I tried to hit two birds with the same stone: one was to mock the 'excellence' of our university, because the 'excellent' journals would be the last to go if the university actually were that excellent (hence the title). The other was that this just had to happen at some point, because of the hyperinflation (see graph). I'll update the post with something to make that clearer. - Björn Brembs

This month's SOAN is remarkably apropos: http://www.earlham.edu/~peters... - D0r0th34

Jean-Claude Bradley

Fwd: http://openwetware.org/images... I think you'll like this. (via http://friendfeed.com/anthony...)

November 1 - Comment - Like - Share

Anthony Salvagno, Pawel Szczesny, Steve Koch and 2 other people liked this

It's great Anthony! I put it up on the ONSclaims page as the first animated gif http://onsclaims.wikispaces.com/ (for some reason I image Andy's orac (or a Dalek) speaking the words as they pop up) - Jean-Claude Bradley

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NICE - @J-C thanks to this http://supportpcs.co.uk/index... I've been experimenting in Dalek-ian terms. http://www.divshare.com/downloa... or http://www.divshare.com/downloa... - Graham Steel

thanks Graham - that was pretty spooky! - Jean-Claude Bradley

I think it should be autotuned, where is T-Pain or an iPhone when you need one? - Anthony Salvagno

Bill Hooker

Matrix Analysis (SPARC) - http://www.arl.org/sparc...

October 25 from Cwhooker's Favorite Links... - Comment - Like - Share

Pawel Szczesny and Claudia Koltzenburg liked this

Tags: oa.waivers oa.money Posted by: cwhooker - Bill Hooker

Duncan Hull

Can literature analysis identify innovation drivers in drug discovery? - http://www.citeulike.org/user...

November 1 from CiteULike: dullhunk's library - Comment - Like - Share

Michael Habib, Pawel Szczesny and Mr. Gunn liked this

Drug discovery must be guided not only by medical need and commercial potential, but also by the areas in which new science is creating therapeutic opportunities, such as target identification and the understanding of disease mechanisms. To systematically identify such areas of high scientific activity, we use bibliometrics and related data-mining methods to analyse over half a terabyte of data, including PubMed abstracts, literature citation data and patent filings. These analyses reveal trends in scientific activity related to disease studied at varying levels, down to individual genes and pathways, and provide methods to monitor areas in which scientific advances are likely to create new therapeutic opportunities. - Duncan Hull

via rajarshi guha http://blog.rguha.net/?p=428 - Duncan Hull

Deepak Singh

Data driven science revisited - http://mndoci.com/2009...

October 31 from business|bytes|genes|molecules - Comment - Like - Share

Pawel Szczesny, Abhishek Tiwari, Ruchira S. Datta and 3 other people liked this

Indeed this is essentially the Baconian approach. Make a large list of facts of nature and Bacon expected the principles would ultimately become obvious. In some senses theory driven research has just given us the opportunity to become much better at designing those laundry lists so as to maximise the potential for principles to emerge - or at least make it easy to test models against the data. - Cameron Neylon

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What it comes down to is that regardless of data volume, science is about asking questions. In the past we posed questions, then collected the data. Now we generate data then ask "what can I do with this?" Data without interesting, sensible questions is just that - a pile of data. - Neil Saunders

What it comes down to for me is once again that humans ask questions. If we have fully data driven science in the Andersen vein then there will be no place left for us. I think we'll notice when that happens, not least because our publication records will be massacred by computers :-) - Cameron Neylon

Right. Science is a human activity, regardless of data volume. The day a computer says "I wonder if...", I'll quit :-) - Neil Saunders

We all will, and submit ourselves in servitude to our robot overlords - Deepak Singh

Noah Gray to Noah's feed, The Life Scientists, Science Online, Science 2.0

*Cell* wonders out loud... Scientists, Should You Be Tweeting? - http://www.cell.com/fulltex...

October 29 from Bookmarklet - Comment - Like - Share

sanju ashraf, Richard Akerman, 'Mummi' Thorisson and 10 other people liked this

With mentions of @phylogenomics, @girlscientist, @sciencebase and @dgmacarthur - Noah Gray from Bookmarklet

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I really hope David Crotty tells us his opinion on this. - Mr. Gunn

*snerk* - D0r0th34

*fluff* - Graham Steel

too bad they did not mention friendfeed - Pedro Beltrao

You mean Facefeed, don't you? - Noah Gray

Mr Gunn wins the thread. - Bill Hooker

No, it's Friendface: http://www.youtube.com/watch... - The Neurocritic

He's written about social networks, anyway, http://www.cshblogs.org/cshprot... - Maxine

Yes, Maxine, he certainly has. He didn't link to the earlier posts, but he used to be quite firmly in the "blogging is a waste of time, now get back to the bench" camp. - Mr. Gunn

Bill Hooker

"Guerrilla OA" done right. - http://www.sennoma.net/main...

October 19 from Open Reading Frame - Comment - Like - Share

Steve Koch, Nils Reinton, Björn Brembs and 7 other people liked this

"Elsevier: just another greedy bottom-feeder, or SPAWN OF SATAN????" - Bill Hooker

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Comment left on Bill's blog... - Graham Steel

Bill, did I ever tell you that your "I wouldn't give them the steam off my ****" comment made it into a strategy discussion session as a conversation point at the big E? - Cameron Neylon

Bill: SPARC has some of the items you mention -- certainly the cards -- and I just bet if you presented this idea to them, they'd bite. I hereby volunteer to staff the OA booth at any conference I'm going to! - D0r0th34

for what it is worth - I still wear my PLoS ONE T-shirt once a week :) - Jean-Claude Bradley

This subject came during an interview I gave a month afterwards, blog post here with the MP3 http://mcblawg.blogspot.com/2008... (section 18:38 to 25:45) SPARC comes up at the end of that section and thanks to this post & discussion, I must contact them again ! - Graham Steel

Cameron -- no, you never mentioned that... do I need to go into witness protection now? :-) - Bill Hooker

*imagines the Elseviley Verlag mafia* *shudders* - D0r0th34

Hmmm. After many years of avoiding the damn things, I'm being sent to a discipline-specific conference next March... will have to clear the OA activism with the boss though since I'm on the company dime. - Bill Hooker

Based upon my own experience, def. worth clearing with "the boss" beforehand, Bill. That was the *only* lesson that I learned from this. In my case, I got a 'mild-slap' for not announcing what I intended to do but that said, I didn't know what I was going to do but "I'll certainly do this again". - Graham Steel

I am very tempted by a new excuse to wear t-shirts more of the time. - Steve Koch

Steve the ScienceOnline2010 conference usually has some pretty decent swag - including t-shirts from the OA crowd - Jean-Claude Bradley

Daniel Mietchen to Daniel's feed, Science 2.0, Brain morphometry, Primate brain MRI, Evolutionary MRI

How to incorporate Open Science into a grant proposal on primate brain morphometry? - http://etherpad.com/Open-Sc...

October 22 from Bookmarklet - Comment - Like - Share

Pawel Szczesny, Steve Koch and Claudia Koltzenburg liked this

I plan to submit the proposal by the end of the month and naturally want it to be as strong as possible but still able to pass the review. - Daniel Mietchen from Bookmarklet

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No idea what discipline they will assign the project to but the focus is on adapting a set of computational morphometric tools (so far basically only used in clinical settings) to comparative evolutionary studies of brain structure across species, starting with primates. - Daniel Mietchen

If you do not like TeX, a pdf of that section is at http://dl.getdropbox.com/u... . For the moment, I cannot put the whole proposal online but would be happy to make it accessible in private to anyone interested. - Daniel Mietchen

Background on the methodology: http://dx.doi.org/10... and http://en.citizendium.org/wiki... . - Daniel Mietchen

Would it be useful to add to the "Hypotheses" section one of the sort "Many can solve problems better than the few" (quote from http://jopm.org/index... )? How should that be phrased out, knowing that one research project will be just one data point in the assessment of this hypothesis? - Daniel Mietchen

I have now added one such hypothesis to the brain morphometric ones: "Research requiring distributed expertise and/ or instrumentation~-- like this project~-- benefits from being conducted in the open \citep{Patil:2009p56609,Gowers:2009p60590}." It is clear though, that this project cannot be more than just one data point in the comparison between research conducted in the open or in the traditional way. Still thinking about how to phrase this. - Daniel Mietchen

Had to remove the latter hypothesis during in-house pre-submission peer review - "don't be too innovative if you want to get funded". - Daniel Mietchen

which IMHO indicates that scientists who want to get innnovtaive stuff funded should help innovative thinkers get into good funder positions, doesn't it ;-) - Claudia Koltzenburg

Pawel Szczesny › Likes