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Chris Patil › Likes
Eliminate peer-review of baseline grants entirely? - http://scienceblogs.com/clock...
Mickey Kosloff, Hope Leman, Björn Brembs and 9 other people liked this
Given the costs incurred by any peer review system, economizing on them and giving the funds out on a more transparently random basis (with certain minimum requirements, of course) probably is a good idea (with some sort of post-assessment influencing eligibility for the next rounds). Is anyone aware of a major funding system where parts of the funds are being allocated in a non peer-reviewed fashion?
- Daniel Mietchen
Woah! This happened a lot sooner than I would have expected. And my impression is that Canadian peer review is held in generally higher esteem than a lot of other places.
- Cameron Neylon
I hope this gets a lot of followup.
- Michael Nielsen
They could just put more money into the universities and institutes, with a stipulation that it be used to fund research by PIs, as part of their standard funding.
- Bob O'Hara
Whatever the cost of preparation, some of it is worthwhile, though, even if the grant is not funded. Reading, planning, thinking. So that should probably be accounted for in this kind of model. That said, I of course would love to be funded without writing. If you are a billionaire reading this, I promise I will spend your money on fantastic projects!
- Steve Koch
Made contact with the authors and now have full text to read. They made the suggestion I should repeat the analysis for the UK...
- Cameron Neylon
+1 Steve. I find the grant-writing process excellent for focussing diffuse ideas into one central research plan. But if Bill Gates dropped his wallet in my office, then...
- Matthew Todd
I planted this idea in an NSF program director last year who seemed to really like such a concept. Not sure what happened to the idea at NSF after that... see also: http://bjoern.brembs.net/comment...
- Björn Brembs
Cameron - A similar analysis for the UK would be very useful, in my opinion. Seems like the kind of thing that might potentially be of interest to somewhere like Nature...
- Michael Nielsen
Additional thoughts: http://scienceblogs.com/clock...
- Bora Zivkovic
I'm confused by this para: "There are conflicts between the grant system and the patent system. Science thrives on open discourse, as each scientist’s ideas inspire new ideas for others. This is what scientific conferences are mostly about. When scientific ideas become more intellectual property than public good, mouths become closed, and scientific advancement slows. As the...
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- Ruchira S. Datta
Ruchira - I think the argument basically runs like this: Baseline grant funding would mean initial grants weren't awarded on the basis of publication record, which would free young scientists from worrying about being scooped (something they shouldn't be worrying about anyways, but they do) and they could engage more freely in open discourse, particularly with larger and more...
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- Mr. Gunn
Mr. Gunn, that's less confusing, thanks. Maybe that's what they meant.
- Ruchira S. Datta
Call for JCOM papers on participative media - http://jcom.sissa.it/call
Jodi Schneider, Claudia Koltzenburg, joergkurtwegner and 18 other people liked this
I know this has been posted a couple of times but does anyone think that it is worth trying to write a "Friendfeed for Science" paper for this (or somewhere else even)?
- Cameron Neylon
Absolutely. I'd say it's the first SM application that's truly been utilized by researchers.
- Walter Jessen
Is Cameron the lead author? Someone needs to lead and we'll all follow and jump in and try to be generally helpful.
- Bora Zivkovic
I can write an abstract by the deadline and probably an outline. I can coordinate I guess and probably write an outline but would need a reasonable number of people committed to helping writing before going too far down the road.
- Cameron Neylon
Is there an example of "citizen science" on FF? Not scientists collaborating, but non-scientists or amateur scientists pulling data about some aspect of nature together here?
- Bora Zivkovic
Count me in .. I'll commit to writing.
- Walter Jessen
Dorothea that would definitely help. My experience of the crowd sourced grant proposal as that editing and sensemaking was a big part of the headache at the end. Just pulling all the pieces together and making sense of them.
- Cameron Neylon
Bora - I'm not aware of "citizen science" per se but definitely examples of crowdsourcing (e.g. the comment categorization on PLoS ONE). Comparison with other networking sites would seem to fit with the call at some level
- Cameron Neylon
Okey dokey - wiki set up at http://ff4s-paper.wikidot.com/ I've tried to set it up so that anyone can get in reasonably easily. If you get asked for a password for access then it is the name of our most prolific blogger all lower case twice no spaces
- Cameron Neylon
Vivian Siegel and I have a manuscript in press that touches on the subject of FF in science; I started the research for it with a FF conversation http://bit.ly/1ZpfMJ Wanted to mention it so that it can be part of the discussion. Will post a link to this thread when we have a DOI URL. (If I forget and folks are interested, please remind me.)
- Chris Patil
@Cam, xlnt but looks like I'm only the first through the gate other than you. Hint to others, *first name only* of our most prolific blogger x 2 ;-)
- Graham Steel
@Chris - I just so happened to bump into Vivian over the weekend on Fb. Thanks for flagging up that other FF thread, which I don't think I'd seen before.
- Graham Steel
Cmon Graham, he's only got one name :-) Like Madonna remember...
- Cameron Neylon
Also pages are actually set to allow anonymous editing at the moment (I think) but obviously better if you do it under some name that can be credited.
- Cameron Neylon
And now with a friendly cc0 at the bottom :-)
- Cameron Neylon
Posted very quick paragraph for people to dissect as a starting point.
- Matthew Todd
If you still need people, I'm up for it, too!
- Björn Brembs
More the merrier...
- Cameron Neylon
I already made some edits on the wiki...
- Björn Brembs
Sounds like fun - I think the focus should just be on FF. Are we putting suggestions/questions in [.....] for Cameron to decide? Maybe we should tag them with our initials, like [..... -AL].
- Andrew Lang
I think we should be able to track who wrote what using the wiki functionality as long as people are logged in (see other comments for password) but tagging with initials is helpful. My thought was to let it run for a few days and then try to cut down to an abstract and save the rest of the text for the (hopefully) full paper. My experience of these things is that people don't like cutting other people's text out so we'll probably end up with lots of stuff that can then be re-used
- Cameron Neylon
mmm ok wikidot isn't quite as functional in display as one might home but its ok. Certainly got a list of contributors but if you want to make a point about some specific writing or to propose a significantly re-written version then feel free to initial it.
- Cameron Neylon
I probably cannot be an author, but I like your idea. I changed your first sentence to include "initiation" of collaboration...my first read-through it seemed to focus more on "carrying out" collaboration, which implied to me that the relationship existed prior to friendfeed.
- Steve Koch
Part of the original call that's most relevant is perhaps: "How web tools are changing and widening this way of participating in the production of scientific knowledge. Do[es] this increase in participation consist in a real shift towards democratizing science or on the contrary is merely a rhetoric which do not affect the asymmetrical relationships between citizens and institutions?" FF is a case study in wideing participation. So, yes, we should discuss initiation as well as extension of collaborations.
- Matthew Todd
Still only 183 words without the references. Perhaps need to select one or two examples. Also suggest we tone down how great FF is, and take an analytical approach - is it any good?
- Matthew Todd
I agree with Matthew and suggest embedding the toned-down FF blurb into a solid description of the social media currently available (blogs, wikis, microblogging services, social networking sites are already mentioned in the abstract), pointing out for each the pros and cons in comparison to traditional means of communication (for wikis, I have started to compile such a comparison at...
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- Daniel Mietchen
This sounds like a good plan - compare and contrast and then try to pull out what the key features are. Will try to look at this tomorrow if I can find time.
- Cameron Neylon
Ok, I'm bumping this up for another round. I think the abstract looks pretty good (less sure about the word "peripherality" but I get the idea at least). Two questions. 1) Is it time to start fleshing this out a bit more for the actual paper? 2) I am wondering about whether JCOM is the right place. No harm in putting the abstract in but what about somewhere like Nature Methods? Or both for that matter? But that involves writing two papers...
- Cameron Neylon
Actually, we have two abstracts there now since the two paragraphs are basically paraphrases of each other. 1) probably yes. 2) The purpose of the article is to describe science 2.0 through FF glasses, ideally in an updatable way, to people who do not know either, i.e. to those who prefer paper-based journals. Neither of the two options allow for both, but that could be ok for this initial shot. Alternatives? A community page at PLoS Biology perhaps?
- Daniel Mietchen
To see existing PB community pages, run this search: http://biology.plosjournals.org/perlser... (the resulting url is horrible which is why I'm not linking directly to the result) This option might require some kind of formal community, rather than the loose affiliation of the biogang.
- Bill Hooker
I think the point of this paper is to lay down some markers in the conventional literature so I was thinking of it as as fairly conventional paper. I haven't checked the JCOM copyright arrangements but if it goes to somewhere with liberal pre-print approach then we can re-use and put up the pre-print version at least on a website for updating (OWW? Some other Wiki). I'd be inclined not to go to PLoS just because the impression could be that "of course PLoS would publish that but it's not a _real_ paper"
- Cameron Neylon
Which is NOT my view I should add - just don't want to give people any excuses...
- Cameron Neylon
the references i put there aren't really for the abstract submission - they're for later... i think we should have a new paragraph talking about what friend feed is and another maybe outlining some examples
- Christina Pikas
A good wiki place for updated versions would be near http://openwetware.org/wiki... . As for people who do not see PLoS papers as _real_, I share Camerons concerns, so we should go that extra step in their direction to pick them up near their home base. But where are suitable _real_ journals that allow reuse in a wiki? JCOM use CC-BY-NC-ND ( http://creativecommons.org/license... ) which would prohibit it.
- Daniel Mietchen
Another way to go might be to start out on-wiki directly (not at wikidot - at the "final" destination), get one version published on paper and continue updating. Nature Physics may be open to that, judging from things like http://www.nature.com/nphys... and http://www.nature.com/nphys... .
- Daniel Mietchen
Any NPG journal is ok with a pre-print and that includes writing the paper completely openly and leaving the presubmission version on a Wiki. The only license allowed for a preprint on Nature Precedings is CC-BY so for that version, re-use is perfectly allowed. It is only the peer reviewed published version that has a six month embargo on re-use.
- Cameron Neylon
I'm thinking more and more that a real practical "Web2 tools for the active and busy researcher" could be a worthwhile Nature Methods paper. We could get David Crotty to referee ;-)
- Cameron Neylon
I had a closer look at Nature Methods now and think the topic would fit (closest match I found is at http://www.nature.com/nmeth... ). However, who of the "tactile" readers are actually subscribed to the print edition of this one? I found only two Nature Methods papers in my electronic database and have never actually seen it in print.
- Daniel Mietchen
Interesting development. I would definitely agree that a submission to a NPG journal would be an excellent idea. I used to get Nature Methods in print, but no longer. It was very good last time I saw it. Something on Web 2.0 tools would be excellent. That leaves the JCOM paper. Still worth submitting an abstract, but we need to emphasise the 'democritisation' of research, rather than FF itself.
- Matthew Todd
Someone want to start a Web 2.0 tools paper on a wiki, and we can flesh out something and ask Nat Methods if they would be interested?
- Matthew Todd
15th May deadline approaches. The way the abstract currently looks includes mention of peripherality. JCOM itself is interested in participation in science of non-scientists, e.g. those at peripheral institutions (I guess) but surely more importantly those who do not have access to the hardware of science, so the public, librarians, curators, journalists. I think this is a slightly...
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- Matthew Todd
[And why is this whole thread not appearing at the top of my feed, despite my commenting on it afresh?] ugh
- Matthew Todd
Bump - 5 days left.
- Graham Steel
Two days left for this one now but I think we had agreed that Nature Methods would be a better location anyway. Still, without some sort of plan and deadlines, http://ff4s-paper.wikidot.com/ probably won't go too far but by means of http://friendfeed.com/ff-for-... we might actually get some concrete things to report about.
- Daniel Mietchen
One day left, folks.
- Graham Steel
One or two days? 15 May isn't it? I have received Nature Methods in the past, comes out monthly, got lots of good stuff in it. I agree with Mat that the focus of the current abstract is perhaps slightly off from the JCOM call but no harm in putting something in. I think we can talk about including people beyond research scientists and how that could lead to the general public. I was thinking of a NMeth paper as more of a "how to" than anything else.
- Cameron Neylon
Looking at it it is actually well under 500 words even if we combine both versions. Can add some more but does anyone have a feel for what would be optimal? I've been caught out by funny cultural things about lengths of abstracts before...
- Cameron Neylon
Chipped in a little more. Still around 400 words. Am still concerned about mentioning Friendfeed so much. Imagine in 10 years, and FF is no longer with us (I know, I know, but just imagine for a second), then this article will look terribly dated. We should mention FF, but try to also keep broadly mentioning aggregators as the central idea - the functionality is the key thing -...
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- Matthew Todd
I think the abstract is in good shape now, and with 459 words it's not too far off the mark. In case of a submission to JCOM, however, we should perhaps ask whether they agree for this article to remove the "ND" (possibly along with the "NC") from their default CC-BY-NC-ND license - otherwise there will be problems with updating the stuff the wiki way.
- Daniel Mietchen
I also need a list of all the people who feel they've contributed. Unfortunately the free settings only give us the last twenty edits and I have a feel there were more people who made some contributions at the beginning. I'm not so keen on upgrading to see whether I can recover those names...will draft up an email that says something about the ND bit - but as the license on the current piece is cc0 anyway they can't restrict our re-use anyway...
- Cameron Neylon
And the word count is now 486.... Agree with Daniel re. dropping ND and possibly NC too.
- Graham Steel
Just did another minor edit (anonymously by mistake)- 496 words! Again made FF an *example* of an aggregator, to try to make the article more general.
- Matthew Todd
The deadline has been extended to June 1st - I just got an e-mail about it. http://jcom.sissa.it/call
- Bora Zivkovic
i think it's pretty good right now. it's just an abstract and not the whole article so.. @Matthew - I like your edits making FF an example of a type of service. i'm fine with dropping the ND and NC and just keeping the by. how about we add a place for the authors on the page - with the names, e-mails and affiliation info we want to use (i use UMD for this not my place of work, btw)
- Christina Pikas
Really like the new paragraph and additions to the first one. A call again. Anyone else in this conversation made contributions that they feel should be recognized by authorship at this stage (presumably can change later anyway if accepted)? I want to interpret that generously as well. Have put up a draft submission letter at http://ff4s-paper.wikidot.com/submiss...
- Cameron Neylon
Ok so realized I can get a free upgrade for 30 days which lets me see all the revisions. So Dorothea, Graham Steel, Romney, and Walter made additions early on and aren't listed as authors currently. If you would like to be included (even if you just want to keep a hand in for potentially writing the paper) can you add your name/affiliation to the front page?
- Cameron Neylon
Am I just confused or has the deadline just shifted by two weeks in the last couple of hours? Now seems to be June 1. Still I'm pretty happy with abstract as stands and would be willing to put it in.
- Cameron Neylon
+1 Cameron. Great submission letter (BTW). I say SHOOT and let's see what happens.
- Graham Steel
If everyone is happy then I will submit it tomorrow. Speak now, or forever hold your pieces...
- Cameron Neylon
i say shoot - but do we need a catchy title first? (agree with G.S. - like the submission letter)
- Christina Pikas
Ah woops. Title. Mmmm. "Design Patterns for the Succesful Implementation of Web 2.0 Tools for Research: Does FriendFeed point the way for online tools that will enable and support widespread collaboration?" That's a bit unwieldy but it's a start...
- Cameron Neylon
"A friend in feed is a co-author indeed" was/is the working title and I say keep it at that unless anyone comes up with a better one.
- Graham Steel
+1 for Graham's -1 for Cameron's (bcs design patterns might be too hard to live up to in an article)
- Christina Pikas
Do we need something a bit more explanatory though? Or is that the right style for this kind of journal? I agree design patterns is probably too much to get into this article. Guess that one will be further down the track.
- Cameron Neylon
We're talking about collaboration, rather than co-authoring necessarily, so "A collaborator in need is a friend in feed" comes to mind (though now a bit of a mouthful!), then maybe followed by ": Democritisation of Research Through New Web 2.0 Tools." ?? Agree whole things looks good, and thanks for putting together the covering letter Cameron. You happy to submit, finally? Nice that deadline is extended, but don't think we need it unless we can't decide what to call it :)
- Matthew Todd
I'll sit on it for the moment until we have had a bit more time to think about titles I think. Could benefit from a few cycles of discussion. I like Mat's but agree it is a bit more of a mouthful. My only concern with the Friend in Feed is a co-author indeed is that we probably won't write that much about authoring. Although that will be how the thing is put together so I'd be happy with it.
- Cameron Neylon
Not having seen the latest discussion here, I have just put in "The social aggregator as a tool for user-led collaborative science" as a placeholder until we have agreed on a final phrasing.
- Daniel Mietchen
How do people feel about double barreled titles. I find I do them by default but I know they irritate some. Thinking that "A friend in feed is a co-author indeed: The social aggregator as a tool for user-led collaborative science" might work?
- Cameron Neylon
Fine with me.
- Daniel Mietchen
And with me.
- Graham Steel
Fine. Really hate double-barreled titles, but feels right here.
- Matthew Todd
I would hate to impose my double-barreled tendencies on others ;-)
- Cameron Neylon
it's been proven in a seminal article by L. Puppybreath that increased titular colonicity means increased citation: I agree :)
- Christina Pikas
Ok peoples. Final draft version I propose to send off is available at http://dl.getdropbox.com/u...
- Cameron Neylon
And submission letter at http://dl.getdropbox.com/u...
- Cameron Neylon
Top man, Cameron =)
- Graham Steel
Would I be right in thinking that if I could avoid submitting it by email then email will have played no part in the preparation process?
- Cameron Neylon
Yes, absolutely.
- Graham Steel
minor edit. on the draft version, 4. Patient Advocate, Scotland 5. University of Sydney, Australia should read:- 5. Patient Advocate, Scotland 6. University of Sydney, Australia
- Graham Steel
fixed. Also minor edit to submission letter
- Cameron Neylon
Will send at end of day today
- Cameron Neylon
or tomorrow...but it's gone now... we see what happens
- Cameron Neylon
Danka very much.
- Graham Steel
just our affiliations alone are cool - what a diverse set! how exciting
- Christina Pikas
Awesome, Cameron, thanks for sending it in, and for catalysing this whole (very interesting) process.
- Matthew Todd
Well thankyou all for writing it! Now all we've got to do is turn it into a paper..
- Cameron Neylon
Can I add a paragraph about a commercial view on this? I will probably do it as free-citizen (private person), not as the employee of the company I am working for.
- joergkurtwegner
This is cool: http://tinyurl.com/l98lwp
- Bora Zivkovic
Just to keep the conversation together: Just received this back from the editor "I'm the editor of the JCOM's special issue about User-led, P2P Science. We hereby inform you that your abstract unfortunately has not been selected for publication. There was strong competition, several applicants for the limited places, and we wanted to strictly respect the topic of the call." - I guess...
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- Cameron Neylon
Yes, I think a Nature Methods paper would actually be the more interesting possibility in any case. Scope being Web 2.0 Tools for Scientific Collaboration?
- Matthew Todd
Yes, that's what I was thinking, with some use cases and examples of "how to" effectively. probably still focussing on friendfeed
- Cameron Neylon
from twhirl
Yes, "Web 2.0 Tools for Scientific Collaboration" for Nature Methods sounds good to me too.
- Daniel Mietchen
ok - best get on and write it then :-) Will try and get some sections put up over the next week
- Cameron Neylon
Was wondering what has or has not happened since the last update in June. Any clues??
- Graham Steel
Ummm not a great deal I'm afraid. It is currently No 4 on my list of papers I really must do something about...Daniel has been regularly updating the bibliography section
- Cameron Neylon
Thanks, Cameron.
- Graham Steel
The issue is out now, with quite a few interesting pieces: http://scienceblogs.com/clock... .
- Daniel Mietchen
My vote for best dressed at #sbcpa is Jason Hoyt wearing the tight v-neck white t-shirt and a black tie.
Jim Hardy, Cameron Neylon, Naomi Most and Chris Patil liked this
I dug Naomi Most's key necklace as well
- Shirley Wu
+1 to Naomi for her necklace and ninja shoes
- Mackenzie Cowell
We should also do best T-shirts. Todd's "Science: It works, bitches!"; Duncan's "Alright my luvver". Others?
- Chris Patil
Duncan's shirt was making me LOL
- Mr. Gunn
w00t! yeah i dug Jason Hoyt's hipster geek look as well.
- Naomi Most
I'm liking my new 23andMe and PLoS Hamster ball T shirts! Thanks guys!
- Jim Hardy
In all fairness, Jason's shirt was collared, so technically "not" a T-shirt http://is.gd/1uNMQ
- Jim Hardy
Data publication and openness in the scientific community - http://blogs.openaccesscentral.com/blogs...
Alexey, Richard Akerman, Chris Patil and Mike Chelen liked this
The All Results Journals - "Because all your results are good results" - http://arjournals.com/ojs...
Mike Chelen, Bruno C. Vellutini, Chris and 26 other people liked this
Just got an email from them to be on the SAB for the Biology journal. Do they typically ask people without Ph.D.s (yet)? I like the concept but have concerns about legitimacy, etc...
- Shirley Wu
If it were me, it would boil down to who else is on the SAB, and could I see myself publishing there. If it's not something I'd normally want to be associated with, then I don't think the cool title is worth it. my two cents...
- Andrew Su
Shirley: erm... no, that doesn't sound typical. looking at the few members of the board who have joined up and are displayed on the site, they look to be all prof or assoc prof level (no names i recognise, but...), which seems pretty standard...
- Joe Dunckley
It actually looks pretty good to me -- OJS, LOCKSS, CC-BY and a founding concept (publish all data) that I agree with. It's a definite plus in my book if they don't care about formal degrees and just want to get the best people. I'd like to know more about the business model/support framework, esp since there's no mention of author-side charges. I've registered as a reader/potential author/available reviewer.
- Bill Hooker
If I could double-like this, I would.
- Chris Miller
Let us know what you find out, Shirley. I'm a grad student who wouldn't mind reviewing either, if it's kosher.
- Chris Miller
I replied with some questions, we'll see what they say
- Shirley Wu
Quoting Feynman: "If you've made up your mind to test a theory, or you want to explain some idea, you should always decide to publish it whichever way it comes out. If we only publish results of a certain kind, we can make the argument look good. We must publish BOTH kinds of results." [http://wwwcdf.pd.infn.it/~loreti...]
- Eric Jain
It will be interesting to see how this plays out. My main concern is that it is a lot of work to write a paper based on failed experiments and I don't know how many researchers would be willing to do that. I don't have a problem with sharing my failed results from within my lab notebook, which I have to maintain anyway. But if scientists do contribute I think it is fantastic.
- Jean-Claude Bradley
Key questions are business model and what they are offering beyond what is already available. Also not confidence inspiring that two of the web pages provides for SAB members seem to lead to dead ends which don't have their name listed. Happy to give benefit of the doubt but presentation of these things is important.
- Cameron Neylon
@Jean-Claude: I see two kinds of papers ending up in these journals: 1, "this didn't work" papers reporting pretty much only failed expts; and 2, regular papers that simply include extra information on the stuff that failed, as well as the stuff that didn't. Even when the failed stuff is useful information, trad. journals usually tell you to leave it out. So this model seems to be a sort of compromise between ONS and normal science -- a "gateway drug" for ONS, perhaps?
- Bill Hooker
@Bill: A bit of an aside, I'm currently reviewing a paper for Neuropharmacology, a journal which is a tad out of my usual reading. Scanning the author instructions, I was struck by this line:Results. The results should be fully illustrated. Negative findings should also be noted to avoid unnecessary replication by others.
- NatBlair
Bill - I appreciate the motivation and the utility if they get submissions - I am just wondering if they can get enough people to put in the effort. It will be interesting information about the scientific community either way.
- Jean-Claude Bradley
Haven't heard back from them yet. The morning after I sent my response with questions, however, I got a verbatim copy of their original email sent to me again by the same person. So I don't know what's going on but like Cameron said, not exactly confidence inspiring
- Shirley Wu
Does anyone have an opinion on the Journal of Negative Results?
- Mr. Gunn
@Jean-Claude - I think your concern is well founded. We get good feedback for JNR-EEB (http://www.jnr-eeb.org/index...), but few submissions.
- Bob O'Hara
I got a reply from the section editor that contacted me. They do want Ph.D. scientists, and he didn't know I was still a graduate student (not that hard to click on the "about me" page of my blog, especially if you mention that you've seen my blog and that's why you're contacting me...). Anyway, the other things he mentioned were that there are no author fees (in addition to no access fees), and everything is done in a volunteer fashion because the people involved want to improve science.
- Shirley Wu
I'd still be concerned about whether it's possible to sustain high quality without a business model but then again, that's what this open stuff is all about, right? So it would be great if it worked long enough to get something behind it to maintain it. Of course, J-C's concern is also a big one - who will write and submit papers to it?
- Shirley Wu
I'd be very worried - getting papers is a big enough problem - but to do it with no business model just isn't sustainable. The business model can be volunteer but then you've got to explicitly worry about how to support and retain your volunteers. But in general I think I'm coming to JC's point. No-one has the time to write full papers on material that isn't up to the grade for existing journals - I don't think they are going to start just because the journals are there. The barrier has to be much lower.
- Cameron Neylon
People who start writing their papers before doing the actual work and keep them in sync with the latest progress should be glad to be able to submit them somewhere (even if a few more days of effort are required to clean up the paper and answer reviewer questions etc)? This approach also seems more effective than spending weeks after the fact going through unreadable lab notebooks and...
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- Eric Jain
Which one of the two Eric? I think the latter is more common...but even with a good record the hassle of going through a peer review process is a big disincentive
- Cameron Neylon
Kind of journal of negative data. More likely to fail, or at least what people claim as "all results" will be the tip of iceberg.
- Dean Johns
"They do want Ph.D. scientists" -- that grates my cheese. Suppose you read Shirley's blog and think "smart person, want her on board my project" -- well, what has changed when you find out she's a grad student? This feeble reliance on a piece of paper is why universities are less and less focused on actual education, and more and more on certification -- a product, bought and sold. [/rant]
- Bill Hooker
I certainly agree with you, Bill, but I think there was some validity to what they said; they went on to ask me what my plans were after graduating, whether i was going to remain in the sciences. I would assume that they wouldn't be recruiting folks with Ph.D.s in mol bio that were now working as management consultants on wall street, for example. But they didn't exactly do a great job of vetting if they didn't know I was still a student.
- Shirley Wu
@Cam: I think this is basically another "journal of negative results", not so much about material that isn't up to scratch. Eric's comment about people who keep notes in sync with benchwork makes me think that journals that are willing to take negative results are likely to be a boon to anyone who keeps an open or semi-open notebook. (I disagree that peer review is a hassle or a disincentive. Sure, some reviewers are jerks, but overall the process is fun.)
- Bill Hooker
I've never looked at the journal of negative results. But it strikes me as quite weird to think about peer-reviewed negative results. I think it's sufficient to just publish your notebook and an informal summary ("we were hoping this would happen, but instead this happened and we don't feel like publishing it in a peer-reviewed journal. Hope these results are helpful!") It's tough to see what peer-review would add w/o asking the researchers to do extra experiments?
- Steve Koch
I'm also unclear on whether there is a definition of "negative result." Does the term originate from pharma stuff? I.e., drugs that didn't work? In other fields is "negative result" a synonym for "less-interesting result?" That's sort of what I was thinking and why peer review would seem weird.
- Steve Koch
Steve, I think there does need to be some degree or review, or they could end up with a bunch of "Bigfoot was not discovered in Alaska" kinds of submissions. Negative, in the sense of isn't something that will support a grant application, is how I imagine it to be used.
- Mr. Gunn
Mr. Gunn, yeah I agree with that. I was really saying I don't see the point of having a journal like that. It seems like a waste of peer-review resources. Self-publishing seems to make more sense to me...but I'm probably not thinking about the right examples of negative results.
- Steve Koch
What the journal adds over self-publishing is editing, review, and discovery. Pretty much the same as other journals. I see what you mean about a waste of resources, though. Some people consider Friendfeed to be a waste of resources, too, so there's that.
- Mr. Gunn
This is all fascinating. Mr. Gunn says, "What the journal adds over self-publishing is editing, review, and discovery. Pretty much the same as other journals..." But it is the same as other journals? This one would be specifically devoted to secondary findings—that would set it apart, wouldn’t it? If this journal were well run (which doesn’t seem to be the case, based on Shirley’s...
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- Hope Leman
Hope, my comments were directed towards Steve's question of what value publishing negative results in a journal would have over simply self-publishing them. Of course the journal would be set apart from others in terms of content.
- Mr. Gunn
I can't make much comment about how organized they are other than that they didn't know I wasn't a Ph.D. despite having been to my blog. Even if they do have a committed and organized core of people, the bigger concern is whether they can sustain a purely volunteer effort. If they can't, they need an actual business model, and the arguments here (and elsewhere: http://tinyurl.com/c2b3xm) are of the mind that a full-fledged journal of negative results isn't cost effective.
- Shirley Wu
Thank you for your patience, Mr. Gunn. Thank you for the link to Cameron's post on the topic. That is an outstanding, asute bit of analysis.
- Hope Leman
Another possible use for the open journal system model would be using it for well-done student publication -- another venue of practice before hitting the bigger journals -- individual schools/labs could put OJS to use, students learn not simply to write for publication but also how to act as reviewers -- provides a neat continuing reinforcement of how to read science (stats, design, etc) -- basically a more finished open notebook product -- also useful for initiating new people into the lab
- Mickey Schafer
Hey all -- I got an email invite from All Results Journal:Physics today for the scientific advisory board. I reread my comments above and still agree with my own skepticism. On the other hand, wouldn't mind supporting it to see if it can fly. Did any of you end up getting invovled? Jean-Claude, I see your name on the SAB for ARJ:Chem ... any opinions?
- Steve Koch
(As an aside: is this thread sufficiently public that the majority of reasonable people wouldn't mind if I linked it to the editor who sent me the invite? I think definitely yes, but given the hoopla that ensued several weeks ago, figured I'd ask first.)
- Steve Koch
I'm still skeptical - I don't see evidence of awareness of the magnitude of the job they're taking on. But then anything that starts from the assumption "publication should basically be free" sets my alarm bells ringing. Happy to see this made public but then I would be I guess :-)
- Cameron Neylon
Pity is that it's not what I thought at first, which is a journal that publishes just data sets with structured annotation (rather than a full paper being needed, shortcutting the idea of the paper-writing robot) to really get people to clear out their lockers. Just a tab-format form answering the kinds of questions listed in projects linked to by MBBI (ref....
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- Chris
from twhirl
Yeah, I agree, Chris. It'd be much better w/o need for formal paper and "rigorous peer review" as they state now. Editorial or peer review should just make sure that necessary info has been included. Wonder if SAB members can change any of these decisions before they go "live?"
- Steve Koch
$120m - will it help, and a look at the greater issues - http://sniffingthebeaker.blogspot.com/2009...
Chris Patil liked this
What about a loosely organized but thorough WolframAlpha gene/nucleotide/biology search module testing here by this community starting on the 18th May? we can send back an error/suggestion list to the Wolfram people soon. Early but strong feedback should help.
Robert Wheeler, Dave Bridges, Michael Habib and 7 other people liked this
Doing a collective, "real-time" review could be fun, regardless of whether or not anyone at Wolfram cares. Not sure what the best way to do this is: Create a separate FF room where people can post and discuss comments, screenshots and links to other reviews?
- Eric Jain
I think this could be an interesting experiment. I've only seen a couple of screenshots. I'm hoping that proper references are provided for the data presented.
- Ricardo Vidal
I'll be testing/reviewing WA as soon it's published so I'm interested in participating in such experiment. I've created a group here: http://friendfeed.com/wolfram...
- Pawel Szczesny
good job, Pawel, I wanted to create a room for this purpose yesterday but was unable to figure out a good name in <26 chars :) let's test!
- Attila Csordas
There's a longer demo here: http://www.wolframalpha.com/screenc...
- Sally Church
As far as i can tell from my preview account, W|A only has human genome, nucleotide sequences, only protein coding sequences, and only exact matches (on DNA level) come up. Not a lot to work with unless they change it.
- Iddo Friedberg
A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species - http://www.pubmedcentral.nih.gov/article...
Chris Patil liked this
"We have mapped a protein interaction network of human homologs of proteins that modify longevity in invertebrate species. This network is derived from a proteome-scale human protein interaction Core Network generated through unbiased high-throughput yeast two-hybrid searches. The longevity network is composed of 175 human homologs of proteins known to confer increased longevity through loss of function in yeast, nematode, or fly, and 2,163 additional human proteins that interact with these homologs. Overall, the network consists of 3,271 binary interactions among 2,338 unique proteins. A comparison of the average node degree of the human longevity homologs with random sets of proteins in the Core Network indicates that human homologs of longevity proteins are highly connected hubs with a mean node degree of 18.8 partners. Shortest path length analysis shows that proteins in this network are significantly more connected than would be expected by chance. To examine the relationship of...
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- A Roy
from Bookmarklet
A bit of analysis at Ouroboros: http://ouroboros.wordpress.com/2009...
- Chris Patil
@ Chris Patil, I should have read your analysis first, nice work.
- A Roy
Scale-free flow of life: on the biology, economics, and physics of the cell - http://www.tbiomed.com/content...
ROY, Abhishek Tiwari, Fossil Huntress and 4 other people liked this
Wow: paradoxes, controversies, and contradictions accumulated in molecular and cell biology over many years of research can be readily resolved if the cell and living systems in general are re-interpreted within an alternative paradigm of biological organization that is based on the concepts and empirical laws of nonequilibrium thermodynamics.
- Jim Hardy
from Bookmarklet
"One of the basic assumptions that make proteomics data appear surprising is the conventional deterministic image of the cell. The cell is commonly perceived and traditionally presented in textbooks and research publications as a pre-defined molecular system organized and functioning in accord with the mechanisms and programs perfected by billions years of biological evolution, where...
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- Jim Hardy
Sounds like someone's been reading Stuart Kaufmann again. Sadly, i can't tell whether that's a good or a bad thing ;)
- Wladimir Labeikovsky
Have a look on this related video http://science.videosift.com/video...
- Abhishek Tiwari
PLoS ONE: Mesenchymal Stem Cell Transition to Tumor-Associated Fibroblasts Contributes to Fibrovascular Network Expansion and Tumor Progression - http://www.plosone.org/article...
Mr. Gunn, Chris Patil and Alexey liked this
Our results suggest the dependence of in vitro Skov-3 tumor cell proliferation is due to the presence of tumor-stimulated MSC secreted IL6. The subsequent TAF phenotype arises from the MSC which ultimately promotes tumor growth through the contribution of microvascularization, stromal networks, and the production of tumor-stimulating paracrine factors.
- Jim Hardy
from Bookmarklet
Snowdrift game dynamics and facultative cheating in yeast - http://www.nature.com/nature...
Ruchira S. Datta and Chris Patil liked this
SciBarCamp Palo Alto, July 8-9, 2009 http://www.scimatic.com/node...
Jim Hardy, Shirley Wu, Pedro Beltrao and 5 other people liked this
Gonna see if I can make it!
- Mr. Gunn
Other than an extremely questionable choice of co-organizers, I heartily approve! :-)
- Chris Patil
"scientists of all disciples"? Otherwise, I too heartily approve.
- Michael Nielsen
funny, I knew that would get a comment... of course everyone is more than welcome to come. I'm not scientist and I organized the event.
- Jamie McQuay
Jamie: "disciples" != "disciplines". The former makes me think it would be a cross between a scientific conference, and a religious revival...
- Michael Nielsen
oh my, its be a long day... cheers Michael
- Jamie McQuay
I can almost walk there so count me in :)
- Pedro Beltrao
Duncan, can you please update the yahoo event when the tickets are released in may? I will update the scibarcamp page with the link for May 1st.
- Jamie McQuay
@Duncan, no idea... I have to go to New York on the 1st so likely very early that morning.
- Jamie McQuay
Jmol as a 3D solubility data visualization tool.
Bill Hooker, Jesper Lind, Chris Patil and 2 other people liked this
Descriptor chemical space for methanol solubility data rendered in Jmol.
- Andrew Lang
Nice!
- Jean-Claude Bradley
I'm thinking of how social networking fits into scientists daily activities. What research-related activity have you engaged in using a social network this week?
Patricia F. Anderson, Chris Patil, novoseek and 2 other people liked this
I actually use social networking as a distraction from research. That being said, FF is a great resource for "file for later" information relevant to what I'm doing
- Iddo Friedberg
Certainly fitting into our working day at BioSysBio, even talking to people on the podium during the panel session via Twitter!
- Daniel Swan
In the past couple of days .. I had a discussion on facebook about ratio of positive to negatives in machine learning and I learned here on FF that Reactome now has reactions for Drosophila and this is immediately applicable to what I am doing right now. More generally it is a good source of science news and articles. It is still not a good source of collaborations but I think it is a matter of time.
- Pedro Beltrao
Daniel, I'm following the BioSysBio stuff on twitter. One of the really compelling applications is real-time conference reporting, as we've seen.
- Mr. Gunn
I use the Regenerative Medicine room posts to use other people to find interesting research/reading material. LinkedIn has provided me a number a valuable business and research collaborators this week alone.
- Jim Hardy
Sure, Jim. If it wasn't for you and Sally Church and Alexey, I'd probably miss a lot of good stuff!
- Mr. Gunn
I was planning on contacting Maureen via Facebook to continue conversations about collaborating. But via Maureen's facebook status updates, I know that her granddaughter is sick, so I'm holding off. BTW: I met Maureen via OpenWetWare and communicated primarily via facebook and friendfeed before actually meeting in person a couple weeks ago.
- Steve Koch
I definitely use facebook and friendfeed as a distraction sometimes. On the otherhand, there's no doubt that I've learned a tremendous amount from people I've met on friendfeed. Much of that feeds into the background information that feeds our research ideas. And sometimes information is directly helpful. Basically I'd expect good and helpful answers anytime I'd post a question on here.
- Steve Koch
And while I was writing this, a former summer research student facebook instant messaged me to update me on the wonderful grad schools he's gotten into!
- Steve Koch
I use Evernote and G reader daily t o track my science pubs and notes etc for blog research and science articles
- Sally Church
This is a little bit meta, but -- last week I used FriendFeed to research an article about how social networking is used in scientific research: http://bit.ly/1ZpfMJ Lots of great stuff from the commenters.
- Chris Patil
just links exchange on Twitter and some links and minds exchange on FF, not much, not enough, really missing ideas exchange and real collaboration. Also use social networking to meet new people offline, how we did with Sally and Maureen in San-Francisco trough FF
- Alexey
Copynorms: Copyright and Social Norms - http://papers.ssrn.com/sol3...
Chris Patil, Chris Granade, Cameron Neylon and Michael Nielsen liked this
Ah! I didn't know you could RSS feed from Connotea! There's probably a giant icon on the Connotea page, but still. Sometimes the intertubes are too complicated for me.
- Chris Patil
"Know Your Rights: Who Really Owns Your Scholarly Works?" - panel hosted by Columbia University on April 8 - http://network.nature.com/hubs...
Michael Nielsen, Chris Patil and Jean-Claude Bradley liked this
Some heavy-hitters on the Upper West-Side for sure.
- Garret McMahon
Pharyngula: Where do Satan et al. publish, anyway? - http://scienceblogs.com/pharyng...
Anil Thomas, Rick, Daniel Jurczak and 4 other people liked this
God's publication record isn't all that great, either: http://www.gettingintogradschool.com/book...
- Eric Jain
Good one, Eric :-)
- Jim Hardy
I liked one of comments on that post: ". . . and just who is the senior author on the Satan et al. manuscript, anyway? "
- Pawel Szczesny
+1 Pawel, or at leas the commentator
- Bob O'Hara
That abstract totally slays me. AWE. SOME.
- Chris Patil
Pawel ... lol
- Deepak Singh
Is there a list somewhere of "most wanted protein (function)s"? I.e. really interesting proteins whose functions or mechanisms of function aren't really known? Or if you have your own such protein in mind, what is it? Proteins with PDB structures are ideal but list whatever you think is compelling
Khader Shameer, Steven Perez, Chris Patil and Deepak Singh liked this
I saw that there was a "10 most wanted protein structures" thing in 2001 so this would be similar, except function rather than structure. Previously, I'd been approaching protein function prediction + bio validation as "look for high-scoring predictions, then look at the proteins", but I just realized that it should be the other way around - "look for really interesting proteins, then look at their predictions"
- Shirley Wu
The following query http://tinyurl.com/bzgojc returns 736791 proteins ;-)
- Pierre Lindenbaum
how long a list can you handle? makes sense to cap protein structures at 10, but if you're talking about bioinformatics analyses, perhaps a bigger scale is reasonable... Also, what types of function would you be predicting (molecular, cellular, physiological)?
- Andrew Su
Shirley, whatever with non-standard secondary structures (previously annotated as "disordered/unstructured") will be very exciting :).
- Pawel Szczesny
@Andrew, the list can be arbitrarily long, sure. We'd be predicting function at the molecular level, so binding sites, active sites, etc.
- Shirley Wu
@Pierre, thanks ;). But I guess I should clarify - we do routinely focus on proteins with unknown function, but the problem is that the vast majority of these are proteins no one really cares about - they just came out of high-throughput pipelines. So I'm interested in applying a second filter, let's call it the "gives a sh$t" filter... ;) proteins that people are interested in for reasons other than that they exist / can be sequenced / can be crystallized
- Shirley Wu
Another great example of why we need more experimental people in FF :).
- Pedro Beltrao
Well, I'm interested in 5730508B09Rik as a hit that came out of a genetics screen. But more generally, I'm trying to think of a scenario where I have a sub-genome size list of genes, and where fantastic predictions of molecular function would filter that down to an experimentally testable list of genes. I think lists from GWAS and functional genomics satisfy the first, but not second. Probably the better use case is, I already know I care about a gene, now what's the mechanism. Just thinking aloud here..
- Andrew Su
maybe take all known drug targets, and cross with unknown molecular function. Or, use what my colleague calls the "sexy gene list". Parse gene2pubmed and sort genes by number of linked citations, cross with unknown molecular function, start at the top and work your way down... You'd even know who to go with with your predictions (past people who've published on the gene or protein...)
- Andrew Su
Thanks, Andrew, that sounds like a good place to start. Unfortunately, 5730508B09Rik doesn't have a protein structure, otherwise I would immediately go see what our method comes up with!
- Shirley Wu
I'm currently looking for a function for the Radish protein in Drosophila, does that qualify? See this thread: http://friendfeed.com/e...
- Björn Brembs
if protein structure is a primary starting point, then don't most (all?) structures pass the "gives a sh$t" filter? solving a structure is no small task, so minus the structural genomics efforts, I'd think all would be pretty relevant to someone, right? One other possible filter, you could mine the PDB-related wikis (PDBwiki, topsan, proteopedia) for structures that have been edited...
- Andrew Su
@Bjorn, it doesn't appear to have a structure solved which makes my method inapplicable, unfortunately. @Andrew, that's true, but most of the "unknown function" comes from structural genomics, so it can be hard to find the diamonds in the rough, so to speak. Obviously we think they're all diamonds. ;) Good idea with the PDB wikis.
- Shirley Wu
May be you can try a combination of function specific search in Uniprot and try to get the structure from ModBase ? :)
- Khader Shameer
Here are the (~300) proteins that have a known structure (PDB) and that have been deemed important enough to be annotated in UniProt, but that have neither a function described there, nor a (confident) GO term: http://www.uniprot.org/uniprot...
- Eric Jain
Should perhaps check what criteria Swiss-Prot's new CALIPHO project uses to prioritize proteins that would benefit most from getting some attention in the lab.
- Eric Jain
If bioinformatics is a profession on its own it should have some core basics. Would you help me to delineate the current core IT/programming knowledge and skillset that is needed for any bioinformatician wannabe? Just concentrate on the basics and don't talk about the biology side this time.
Sung W. Lim, Konrad Förstner, Allyson Lister and 5 other people liked this
I'm teaching programming to bioinformatics MSc students at the moment and I wish it was that easy to define :-) I'm starting to think that the 'core' skills are things like version control, IDEs, unit testing, debuggers, and design principles, and not any one language -- because there are so many languages in use (often within just one lab). SQL and XML are always helpful though.
- Andrew Clegg
Add to that, R + some basic stats and modelling skills, and an understanding of some of the fundamental algorithms like dynamic programming.
- Andrew Clegg
in case of programming languages we may use the and/or logical disjunction form: Perl or Python or Java or Ruby or....
- Attila Csordas
Not all bioinformaticians are programming, and not all should. Are you asking about programming or non-programming type?
- Pawel Szczesny
Learn a scripted language and a compiled language (whatever languages as long as your job is done). Learn them, master them. Learn about a database engine. And write a LOT of code.
- Pierre Lindenbaum
@Pierre, yeah, I like that. We currently teach them Perl and Java. Not sure what I'd pick with a blank slate though.
- Andrew Clegg
@Pawel, if a bioinformatician doesn't (can't??) code, what's the difference between him and a biologist who learned how to press the buttons in some tool after reading the manual? In other words, if a bioinformatician can't create a new solution, what';s the value add?
- Rajarshi Guha
@Rajarshi. I know a few "bioinformaticians" spending their days in front of the screen , looking for SNP in the traces, or surrounding some spots. They use accurately some tools developed by some others.
- Pierre Lindenbaum
@Andrew: today I would recommend to learn python and C. But if your students are not certain to find a job in science, then without any doubt.: java.
- Pierre Lindenbaum
Rajarshi, what's the value added of programming bioinformatician that is using his skills to reinvent the wheel/redo the solutions available for years in new programming language (bioinformatics journals are full of examples of re-developed tools)? I'm being tongue-in-cheek here, but I think "bioinformatician=programmer" is extremely skewed view of the field.
- Pawel Szczesny
@Pierre There has been talk of dropping Java but apparently they like having a Java course on their CVs. For that reason I guess. (Also I teach that one so I'm happy for it to stay :-)) @everyone-else Maybe there's a useful distinction between bioinformatician (hate that word) and computational biologist?
- Andrew Clegg
We had similar discussion couple of months ago and I was advocating the same thing as Neil right now - all courses should prepare people to learn new things quickly when they need them. Depending on the preferences there should be more or less programming involved, but I don't think putting everybody into one basket is a good idea.
- Pawel Szczesny
@Pawel, re reinvention, fully agree. That's pointless. But why have a degree in bioinformatics if you're just going to look at SNP's using somebody elses tools? I also agree that if bioinformatics == programmer and nothing else, that's a waste. Anybody can program. The value add is bioinformatics = programming + biology. I still think 'computational thinking' and its realizations is what will differentiate a bioinformatics person from a programmer or biologist biologist, in the ability to whip up ...
- Rajarshi Guha
@Pawel it's a little bit hard for me to imagine a bioinformatician who has never done a little bit of coding, it's like a molecular biologist who has never run a gel before. (also would you give me the link of that similar discussion?)
- Attila Csordas
...computational solutions (hopefully new) to new problems.
- Rajarshi Guha
@Rajarshi "computational thinking"++ I spent a while working in medical informatics with people from librarian/information-management backgrounds, it was a nightmare, they would keep doing repetetive scriptable tasks by hand cos they didn't stop to think "I can automate this". Teaching people programming gives them a more productive mindset.
- Andrew Clegg
++Andrew: I've heard people use the phrase "computational thinking" a lot, but usually in too vague a way for it to really be all that helpful. I'm guilty of this. "Automate everything" is nice and precise.
- Michael Nielsen
Of course I'm sure many of us have been guilty of spending a day writing some code to automate an interesting task that we could have done by hand in a morning ;-)
- Andrew Clegg
Attila, I didn't say that bioinformaticians don't code, but only that not all of them should do that full time. Automation is one thing, producing applications is the other. (I cannot find the respective discussion right now, will look for that it later.)
- Pawel Szczesny
Rajarshi, my distinction between programming and non-programming bioinformatician is about people who build tools and people who do mashups of these tools. I'm lousy coder in any language, but at least I can glue things together. There's some coding background needed for, as you say, "computational thinking", but it's different for different groups. So, my first question in this thread was about which group we're talking about.
- Pawel Szczesny
@Pawel I'm only talking about "the current core IT/programming knowledge and skillset that is needed for any bioinformatician wannabe" isn't that clear enough? It's an educational/practical question for the starters.
- Attila Csordas
@Michael - re vagueness of 'comp thinking' - I was puzzled by that the first few times I heard it. But after reading http://www.cs.cmu.edu/afs... it got a little clearer
- Rajarshi Guha
@Andrew, yes 'automate everything' is a good summary. But like Neil wrote, the ability to map natural (physical?) objects into a comp framework is a very desirable skill for anybody working with comp tools
- Rajarshi Guha
@Pawel, aah, yes, I agree with the distinction. But given the development of pipelining tools etc - the ability to do mashups slowly becomes available to everybody with a modicum of programmin skills. If one wants to be considered a 'bioinformatician' - I think it'd require more than just the ability to mash things up (in addition to biological knowledge). I can manipulate sequences etc - but I'm certainly not going to pass myself of as a bioinformatician :)
- Rajarshi Guha
Attila, I was going to suggest something along the lines of posts Paulo has linked, but then you've mentioned Java, and I wasn't that sure anymore. For me Java doesn't really fit core skill set "any bioinformatician wannabe" (that's just my opinion, Pierre would disagree :) ).
- Pawel Szczesny
If it helps bring it back onto more concrete ground, this is what we give em: http://mscb.cryst.bbk.ac.uk/modules... Not saying this list is perfect by any stretch though. But it is one of the longest-running bioinf courses in the UK (I did myself 6-7 years ago)
- Andrew Clegg
@Neil this is not an introspection on my part because I am a traditionally trained (wet lab) molecular biologist (with an extended software testing experience) who has the ambition to work as a bioinformatician in the near future so I am asking all practicing bioinformatician/computational biologists here to help delineate the necessary core skillset. That's all.
- Attila Csordas
wrt language, I think any competent computational scientist should be expert in one language and be able to pick up any other language (of the same type) in a week or two. Python FTW :)
- Rajarshi Guha
I would define a bioinformatician as someone who applies quantitative methods to understand and simplify biological data. Therefore the core skills would consist of statistics( lots and lots of it) , computer science and information theory ( lots of it ) and some language or platform as a glue to hold it all together . The programming language is necessary as a glue, but should never ever be the focus of learning the approaches. The bioinformatician should be able to abstract the process from the tools!
- Hari
@Pawel Hey ! read my comment ! :-) I didn't say that java should be teached ! :-)
- Pierre Lindenbaum
I tend to think that there are two types of bioinformaticians: Programmers and Biologists. Other than that, I think the key for bioinformatics is not a specific toolset (languages or otherwise) but a great deal of knowledge.
- Paul J. Davis
There are many ways to divide what I think many of us perceive to be two camps under the "bioinformatics" umbrella. My take: people who write code for others to use/reuse, and people who write code to get their own stuff done...
- Andrew Su
If I took a bioinformatics course and a lot of time was spent teaching programming I'd want my money back :-) I'd expect to learn about different sequence search and alignment algorithms -- up to the point of being able to choose the most appropriate implementation for a task (or even write my own). To keep such a course practical it may be a good idea to use e.g. pseudo-code level Python (which can be taught in an optional introduction course).
- Eric Jain
@Eric It's pretty hard teaching people to evaluate or design/implement algorithms if they don't already know how to program a bit, and have the faculty of computational thinking as discussed above... Just like it's hard to choose the most appropriate statistical test if you don't have a bit of a stats background.
- Andrew Clegg
Ruby | Python, R, Databases, makefiles, testing, linux, latex, classical statistics, machine learning + data mining.
- Michael Barton
just to add to Michael's list: some kind of version control system.
- pn
Doh! How could I forget git...
- Michael Barton
I didn't mention git. Anyone would be fine :-)
- pn
I totally agree with what Neil Saunders and Eric Jain say. Its sad when people think Bioinformatics is just programming. I think programming is a distant third as a Bioinformatics skill. Its got to be more about statistics and algorithms . The only way to learn programming is well to write programs , and what better way to learn programming than understanding and implementing algorithms and applying statistical methods to data. Bioinformatics is more Computer Science than IT ( information technology ) .
- Hari
@Hari, nicely put and agree with bioinformatics being CS ratehr than IT
- Rajarshi Guha
or perhaps rather IS than CS?
- Adam Kraut
Second the programming concerns. Yes, scripting is useful, no doubt, but I tend to distinguish between the tool builders and the users. A good bioinformatician has an overview of several fields, knows and understands the tools at his disposal (including parameters), when to apply which solution, what standards are out there etc. I pay very little attention to code background when hiring a bioinformatics analyst. Different story when hiring a developer.
- Oliver Hofmann
Knowing more about version control and such topics would no doubt be beneficial to a lot of bioinformaticians. But I don't see much that would be bio-specific about a course teaching such topics? Unless of course branding it as such gets the course more interest and funding (and this way you don't need to compete with programming courses offered by other departments)...
- Eric Jain
great topic! I agree with the suggestion of one scripted, and one compiled language (perl or python work admirably here), and java is a good choice. IMO- as essential as languages, are being able to handle often massive datasets. For this, familiarity with a real RDBMS (Oracle, Postgres, or i guess mySQL) is *essential*. Add some R and stats for good measure.
- John Major
John (Mr. Prime Minister?) I would extend that to a general understanding of data structures and data models, especially in an age where you might not always need to go with RDBMS for everything.
- Deepak Singh
Just got an interesting email via University of Melbourne "Knowledge Transfer", requesting catalogues of "Grey literature" .. eg annual reports, green or white papers, written or electronic versions of internal or public presentations (including pod/vodcasts), newsletters/guides/manuals etc.
Chris Patil liked this
"They also represent hours of work by university staff which may not be currently “valued” as they should.". I'd say this includes blogs too. Nice to see they are working toward recognizing these contributions (just after I've left the University of Melbourne, that would be right :) ). Any other Institutions doing this ? I wonder how this type of "Knowledge Transfer" will actually be rewarded by the Institution ?
- Andrew Perry
The problem with CVs etc is that they focus too much on the work that went into something instead of the impact it had, which is the important part. Why isn't a citation count a mandatory part of any reference to your own papers, and an overall H-index for the whole CV? As Andrew suggests, a lot of the impact isn't on CVs at all. But how do you measure the impact of a presentation, or a blog post?
- Donnie Berkholz
Along these lines: Vivian Siegel has a recent piece in DMM entitled "Where Credit is Due" http://dx.doi.org/10... ... "Scholarship builds not only from published results, but also from the unpublished work, ideas, reagents and goodwill of others. We need to acknowledge this – to celebrate this – every chance we get."
- Chris Patil
Chris - that doi doesn't resolve.
- Michael Nielsen
'Immortal' jellyfish swarming across the world - Telegraph - http://www.telegraph.co.uk/earth...
Mr. Gunn, Chris Patil, David Adam and Khader Shameer liked this
The world will not end because of a black hole from the LHC, but because of immortal jellyfish taking it over
- Benjamin Tseng
from Bookmarklet
We're gathering examples of the use of FriendFeed for concrete accomplishments in science for an article due in a few weeks. Please add examples as you think of them to this GoogleSpreadsheet. - http://spreadsheets.google.com/ccc...
Chris Patil, Mr. Gunn, Gideon Burton and 27 other people liked this
So does the spreadsheet aggregation itself count?
- Cameron Neylon
@Cameron yes I suppose - if we get enough entries :)
- Jean-Claude Bradley
@Cameron your proposal writing using FF is a classic
- Jean-Claude Bradley
You could add further examples to the "expanding the reach of conferences" one -- there has been lots of excellent liveblog coverage of conferences. (In a little over a week, Science Online 09 will no doubt join the list.)
- Bill Hooker
@Bill yes we can add a few more examples (there are so many now) of conferences - note that this is a chemistry journal so the reporter will probably focus on those if possible
- Jean-Claude Bradley
Well the on the fly CID to CAS lookup by Rajarshi is a clicher..the chem journal should really like that kind of stuff
- Hari
Added Survey of the protein in WP: http://friendfeed.com/e...
- Pierre Lindenbaum
Added sorting papers on impact factors: http://tinyurl.com/5qtu9h
- Pierre Lindenbaum
I could add: FF motivated me to learn new things (isn't it concrete ?) e.g. learning SPARQL.
- Pierre Lindenbaum
@Pierre - those are great examples. The longer conversations really highlight the strengths of the platform. Yes the article will cover things more broadly but I thought it would be nice to have a table with some nice examples
- Jean-Claude Bradley
@Hari - yes good example, although I wonder if everyone will be happy with the way it started on Twitter (I can't repeat the comments here :)
- Jean-Claude Bradley
Thanks for your help, everyone. I'm the science reporter working with Jean-Claude. I'm also trying to brainstorm ways how one might represent a FriendFeed conversation to someone who only uses the web for very routine things, and may not be familiar with social networking tools.
- Carmen Drahl
@jean-claude - added my one. @Carmen - Friendfeed has been described as the Higgs boson of the web2 world. No-one can quite describe what it does...
- Cameron Neylon
@Cam - thanks I like that example
- Jean-Claude Bradley
I learnt so much from friendfeed, a great way to keep abreast of development, since it is not possible for everyone to read everything.
- Aarthy
@Cam&@JC The 'Invisible' Higgs Boson may not exist, though it would be cool if it did. We'll hopefully find out when they get the LHC online, but don't hold your breath. :)
- Andrew Lang
So, do we need to build a Web2.0 LHC to figure out what FF does? :)I'm still getting used to all these layers- I was going to ask Hari what his abbrev's meant and then I clicked on the spreadsheet.
- Carmen Drahl
@Carmen this post is turning out to reveal what happens when over a dozen human particles collide on FF - for constructive purposes :)
- Jean-Claude Bradley
@Cam - this comment stream is itself an example of what a FFeed conversation can provide. While I think the analogy to the Higgs boson is generative; it's not because we don't know what FFeed does. We're demonstrating and documenting it right now!
- Bill Anderson
@Bill - that's fair and I think I mangled the original quote anyway - here is the link http://scienceoftheinvisible.b...
- Cameron Neylon
@everyone Thanks for your contributions! We've got 12 examples showing both individual conversations and FF rooms. I separated the multiple links into their own columns so that you can click on the top left corner of the cells and to right to the web page.
- Jean-Claude Bradley
Seconded. I very much appreciate everyone's help.
- Carmen Drahl
The Niche: Pfizer launches regenerative medicine unit - http://blogs.nature.com/reports...
Chris Patil liked this
as some other BigPharma giants "suddenly" got an interest in Regen Med - other examples - GSK, Johnson & Johnson, read more here - http://hematopoiesis.info/2008...
- Alexey
and here - http://www.nature.com/stemcel...
- Alexey
One scientist's Wikipedia "CV"... - http://en.wikipedia.org/wiki...
Michael Nielsen, Chris Patil, Richard Akerman and 2 other people liked this
Thought this was interesting in light of the frequent comments that contributions to Wikipedia do not earn any "credit" in academic circles.
- Hilary
People also fill their profiles in OWW. e.g.: Cameron's page http://openwetware.org/wiki...
- Pierre Lindenbaum
it is making me think about adding the wikipedia ons page to my publication list. Not perhaps the oww pages that i have put up because they are less 'peer reviewed' as it were
- Cameron Neylon
from fftogo
Deep Dyve: Search Engine With Roots in Genomics Unlocks Deep Web - http://blog.wired.com/busines...
Hilary, Paul Bacchus, Paul J. Davis and 3 other people liked this
"The company's technology uses an algorithm called “KeyPhrases” which indexes passages up to 20 words in length -- not just single key words. Since the technology was conceptualized to identify long, complex strings of DNA, there was no need for semantics, just character recognition to sequence the human genome. “It’s really doing pattern matching; it’s not at all language dependent,”...
more...
- Attila Csordas
Circulating mutant DNA to assess tumor dynamics. [Nat Med. 2008] - PubMed Result - http://www.ncbi.nlm.nih.gov/pubmed...
Aarthy, Sutee Dee, Chris Patil and Maureen liked this
"DNA containing somatic mutations is highly tumor specific and thus, in theory, can provide optimum markers. However, the number of circulating mutant gene fragments is small compared to the number of normal circulating DNA fragments, making it difficult to detect and quantify them with the sensitivity required for meaningful clinical use. In this study, we applied a highly sensitive approach to quantify circulating tumor DNA (ctDNA) in 162 plasma samples from 18 subjects undergoing multimodality therapy for colorectal cancer. We found that ctDNA measurements could be used to reliably monitor tumor dynamics in subjects with cancer who were undergoing surgery or chemotherapy. We suggest that this personalized genetic approach could be generally applied to individuals with other types of cancer."
- Attila Csordas
from Bookmarklet
The Beagle Project Blog - http://thebeagleproject.blogspot.com/
Chris Patil and Kevin Z liked this
Quote: "The HMS Beagle Trust are now the very proud owners of signed NASA Space Act Agreement. Yes, you heard that right: The Beagle Project and NASA are an item."
- Maxine
from Bookmarklet
Comparison of academic salaries - http://scienceblogs.com/evolvin...
Alexey and Chris Patil liked this
(via Pharyngula)
- Shirley Wu
When his grant ran out, this man selflessly gave his colleagues his work to continue. *They* just won the Nobel Prize with it. This is the very best of science and of humanity - http://www.reddit.com/r...
Michael Kuhn, Chris Patil, joergkurtwegner and 3 other people liked this
"You have to put aside any sort of personal desires to be better than everyone else because if your grant isn't funded, you're in trouble,"
- pn
really quite amazing
- Jonathan Eisen
Indeed.
- Deepak Singh
The open science society will not forget this, http://en.wikipedia.org/wiki...
- joergkurtwegner
He did what a scientist should do. That we find such an act extraordinary and single it out for praise because of its rarity is what's fucked up here. We know about Prasher because his work set others up to win a prize that everyone gets all bent out of shape about. How many other scientists are in a similar position, minus the five-minute spotlight from our celebrity-addled media?
- Bill Hooker
I do not think it was his sharing that impressed me. It was that now that he did not get the prize, he said that it was his responsibility to share. In the end, it seems like they could have given him the Nobel Prize though.
- Jonathan Eisen
Yeah, I think he should have been included too. I don't mean for my more general grumpiness to imply that Prasher doesn't deserve the praise, he certainly does. The rule about "only three recipients" is absurd.
- Bill Hooker
Yes the three only rule is lame. However, I have a solution and am going to post about it later. I think any group that thinks their field might win a Nobel but for which there are too many people, they should form a "Committee" or "Consortium" --- they give Peace Prizes to these groups all the time ...
- Jonathan Eisen
Or they could just announce that they're boycotting the Prize until such time as the arbitrary rule -- which hasn't evolved along with the way science is done -- is revoked. "If nominated I will not run; if elected I will not serve." :-)
- Chris Patil
http://www2.b3ta.com/host... see what makes this LOL?
Rachel Lea Fox and Chris Patil liked this
At least it's blue.
- Kevin Fox
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