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Chris › Comments
Should biologists study computer science? - Ars Technica - http://arstechnica.com/science...
Ricardo Vidal, Lars Juhl Jensen, novoseek and 8 other people liked this
"Science has published a pair of articles in which it's argued that biology education is shortchanging its students by not exposing them to the foundations of the computational tools they now rely on."
- Abhishek Tiwari
from Bookmarklet
fundamental issue is recognition of interdisciplinary researchers, currently not good at all.
- Abhishek Tiwari
I don't know they should study per se. Mastering your own discipline is hard enough, but they should be exposed to it, and IMO, a certain level of mathematics and statistics is a must
- Deepak Singh
it's a complicated thing: whilst it's nice to make everybody learn a bit of everything, something has to give. In my experience, the vast majority of physics graduates never learn basic statistics. I've had to learn them on the job, even at various times, consulting psych statistics first year statistics. in physics, we used to do a service course to teach quantum mechanics to engineers...
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- Bosco Ho
Should biologists study computer science? No. Should they be aware that some of the principles of computer science - i.e. how to acquire, store, process and present information - are extremely useful for any scientist? Yes. Should they strive to improve their IT skills continually, over the course of their careers, not just in a "this is what I need to pass my course" fashion? Yes. I think we need a shift in how people learn, not what they learn.
- Neil Saunders
Computational thinking perhaps? Maybe not at that scale, but the ability to think analytically as biology and other disciplines become more analytical?
- Deepak Singh
Probably one of the main generic features of a biology background is the awareness of the degree to which nature will bite you if you get too deterministic and analytical :\ That said, lots of damage is done in data analysis by biologists using stats-based analyses they don't fully understand. If we mean computer science in the sense of implementations of analysis algorithms, then I'd...
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- Chris
from twhirl
News Releases » Elsevier announces the ‘Article of the Future’ - http://www.kaizo.net/release...
Lin, Julien Sicot, Meryn Stol and 33 other people liked this
A more rich value-added editorial process? Brilliant! ;-)
- Mr. Gunn
Thanks, Alexey--fascinating.
- Hope Leman
will this change the way authors conceptualize their contributions?
- Claudia Koltzenburg
Finally! Moving to 'real' web papers. Maybe then the 'supplement' will be the printable version of it?
- Björn Brembs
hm, why still want printable versions of " 'real' web papers"? - asks an open access journal editor...
- Claudia Koltzenburg
Hopefully this is more than just corporate PR speak
- Benjamin Tseng
why still call them 'papers' at all?
- Claudia Koltzenburg
It's nice but it hardly seems ground-breaking. They've hyperlinked the references and divided the paper up into tabs, added a little bit of multimedia. But there is no marking up of terms of anything like that? Or am I missing something here.
- Cameron Neylon
Perhaps mark-up is next on the list. It is only a prototype for feedback and if you want to grab attention, dry issues like mark-up are probably not the way to start :-)
- Neil Saunders
@Cameron: agreed. Quite disappointing. Nice graphics, but nothing they should not have done 10 years ago. Where are the semantics? Where's the open API? This is *not* the article of the future; this is the (web) article of the 20th century. :(
- Egon Willighagen
Egon: agreed, absolutely. Question to the online-only journal community: Why is not even this your standard now?
- Daniel Mietchen
A similar web paper was recently published in PLoS Comp Biol: http://dx.doi.org/10... and http://www.ploscompbiol.org/article....
- Daniel Mietchen
mm, how long has hyperlinks existed......still way off the posibilites presented by the Shotton paper, I wonder how much Elsevier will charge to fake these types of journals?
- Frank
Hey, c'mon guys, the first demo of hyperlinks was in 1968 (http://www.youtube.com/watch...)! Surely, 40 years is not too long for scientists to use it in their publications? Given that some publishers (yes, some Elsevier journals among them) still want paper copies and CDs with the files by snail mail, this is a huge leap! Remember, we've started publishing in paper journals only 400 years ago, we can't change that already!
- Björn Brembs
@Claudia: because there may be times when you want to read scientific papers when you're lying in the sun on a hot tropical beach :-)
- Björn Brembs
ditto need for printable versions still and also agree that this isn't that groundbreaking (albeit much prettier than what we currently have). Need to think how #AOTF (article of the future) can be used in new ways- need for primary data, need for ability to view data with accessible programs for others to manipulate, etc.
- KMS
the prototype, at least, is just repackaged text. with an extra graphic and an author interview. good material, that, but it hardly makes a dent in The Future (at least as I see it, anyway).
- tim
I agree with tim. I don't think links and tabs are something one can qualify as being from the future. However, it's good that an attempt is being made and giving way to this discussion.
- Ricardo Vidal
From a readability standpoint, I liked it. Easy to navigate, more user control of what is on the screen at any time -- if we're heading toward an all-digital reading future, then readability in addition to usability must be considered, too. I would add my two cents in with Daniel Mietchen -- why isn't this the current standard? What kind of work does it take to make the article like this?
- Mickey Schafer
It's interesting that people are saying "but this is nothing special because this is how things should be." When the fact is, this is not how things are. In effect, you're saying that you like it, despite yourself :-) I agree that it's not especially "futuristic", but I think it's a huge improvement on the way articles are currently presented on the web.
- Neil Saunders
@Neil, I agree and you are right. However, stating it to be an article of the future is rather misleading. I was expecting something more innovative. I'd call it more of something like "alternate web articles" or something of the sorts. As I also said, it's great this is being done because it will most probably shape how articles are presented online "in the future" to come :-)
- Ricardo Vidal
It is something of an overstatement to call this 'the article of the future', which implies some sort of revolutionary rupture. More like 'improvements to the article of today'.
- Andrew Spong
I guess my major dissappointment is that fundamentally this kind of re-presentation should be trivial (aside from the additional visuals) if the back end representation of the article was done properly. In fact much more (including some semantic markup) should be trivial. As Neil says, its nice and its an improvement, but the fact that it is being trumpeted as a big thing is indicative of just how bad the infrastructure is.
- Cameron Neylon
The disparity between the capabilities of an architecture designed to support a platform over a decade ago and the 'revolutionary' potential of what amounts to a pretty reskinning is significant, although I can hear cries of 'damned if you do, damned if you don't'. Fair enough. However, what I will watch with interest is whether this is a sop of innovation to appease critics and promote...
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- Andrew Spong
Yeah I'm also wondering at what point other journals will at least catch up with (for example) the RoySoc Chemistry in tagging a la Shotton. As stated then layout becomes less of an issue and in fact getting the full-blown webby loveliness or the linear paper-printable version (and I want that too) should just be a rendering. Incidentally, could the Talk Science @ BL thing be so significant as to affect the timing of this ;)
- Chris
from twhirl
yes. changes like this are definately welcome and should be encourage, maybe the branding should not have been "article of the future" but "article catching up with last years technology" - which is still somewhat an improvement on a pdf.
- Frank
And where is the drill down to the data?
- Jim Hardy
I also somehow expected a "fundamentally different" way of presenting data / information / discussion. It is neat, though, and I agree that it is very readable on the screen.
- Bronwen Dekker
PLoS ONE: Does Publication in Top-Tier Journals Affect Reviewer Behavior? - http://www.plosone.org/article...
Brian Krueger - LabSpaces, Daniel Mietchen, Allyson Lister and 7 other people liked this
Cool!
- Björn Brembs
Letter to the editor in Science - http://www.michaeleisen.org/blog...
Dirk Derom, Graham Steel, Chris and 5 other people liked this
New Nature editorial: How to stop blogging - "Organizers have only two options for their meetings: open or closed." - http://www.nature.com/nature...
Alexey, 'Mummi' Thorisson, Lars Juhl Jensen and 14 other people liked this
Nice to see Nature weighing in on this. I think this is the key point: "Any meeting to which anyone can register is fair game for all available communications technologies — and any rules that cannot be policed will be ignored anyway."
- Joe Bonner
I disagree. It is easy to set up a filter to catch blogging at real time, (see the CSHL incident) so registrants can be made aware of a no-blog policy, and sanctions that will follow breaking that policy. Also, meetings are not necessarily "all closed" and "all open" -- GRC meetings for example select their attendees. IMHO: large meeting with press etc. have no expectation of privacy...
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- Iddo Friedberg
I think this is all becoming very over-stated and confused. As Iddo says if you want a closed meeting - just have one. If it's open, new technology makes no difference to whether information can flow beyond the meeting, other than speeding the process. I can make an annotated sketch of your poster with pencil and paper if I'm really intent on taking the data away. Or you could just give me an A4 copy :-) And if you're at an open meeting and paranoid about stealing and scooping - what are you doing there?
- Neil Saunders
"And if you're at an open meeting and paranoid about stealing and scooping - what are you doing there?" Exactly.
- Neil Swainston
Just had a similar conversation about phud theses -- you could technically always get them but really they were not listed and difficult to get copies of, so there was this sort of limbo let's-not-think-too-hard-about-this approach. Afaik very few meetings ever feature anything really new -- it's more 'what we were doing last year'. Any electronic restrictions seem entirely circumventable through the use of pencil and paper anyway..?
- Chris
from twhirl
@Neil Saunders - agreed!
- Allyson Lister
I lost track of what was being debated here. It seems that we are all in agreement RE: meetings should just be "Open or Closed". Which is what the editorial is saying. The real debate is whether they *should* be open or closed. And this will differ from field to field. An interesting caveat suggesting how openness (although theoretically a good thing) can lead to an easy infiltration of the wrong kind of influence is being made here: http://ff.im/50myz
- Noah Gray
There's also a conversation going on at FF Science Online room about this same editorial.http://ff.im/4Y5Ts I was just going to make Noah's point when his response came in while I was writing - seems to me that Iddo and Neil's comments are along same lines as what the editorial is saying.
- Maxine
The Dataverse Network Project - http://thedata.org/
Mike Chelen, Konrad Förstner, Andrés David Aparicio and 4 other people liked this
"Via web application software, data citation standards, and statistical methods, the Dataverse Network project increases scholarly recognition and distributed control for authors, journals, archives, teachers, and others who produce or organize data; facilitates data access and analysis for researchers and students; and ensures long-term preservation whether or not the data are in the public domain."
- Bill Hooker
from Bookmarklet
More of a checksum though (just thinking lots of very nig data sets coming)? And wouldn't it be better to piggyback on a DOI at least (e.g., http://DOI_stem/your_extension)?
- Chris
from twhirl
Regarding DOIs: any connection here to the STD-DOI project for archiving primary datasets and assigning DOIs to them to make them citable? Example dataset citation: Kamm,H; Machon, L; Donner, S (2004): Gas Chromatography (KTB Field Lab), GFZ Potsdam. doi:10.1594/GFZ/ICDP/KTB/ktb-geoch-gaschr-p (from http://www.std-doi.de)
- 'Mummi' Thorisson
Absolutely I'm campaiging for it myself (not this specifically though I was very pleased to stumble on it) -- just gave this (http://tinyurl.com/nvyb57) talk at ISMB on Thursday (just the last couple of slides are the relevant ones). So I'm all for it and liked the mention of standards, just that DOIs are so close to being widely-enough used already that it seems a shame not to build on that.
- Chris
from twhirl
Meeting peopl efrom the British Library on Monday to talk about this very kind of thing and amongst the (MI) standards people and at www.rin.ac.uk we've been talking about it quite a bit -- the principle more than the exact mechanism, which for easy-bridging reasons seems to make sense as a kind of vestigial journal as a vehicle...
- Chris
from twhirl
@ Mummi, good lord that's rather interesting isn't it -- no relation to me at all no. The BL group I'm meeting also have a guy that's a big DOI advocate and his talk mentions some kind of euro registry? http://tinyurl.com/mkuhvq slides 6+ (DOIs) and 12+ (JRA)
- Chris
from twhirl
@Chris, sorry my bad, I was being unclear which didn't help! I meant to say earlier whether there was any relation between the Dataverse thing and the German (based/funded..?) international TIB project.
- 'Mummi' Thorisson
@Chris Thanks for the PDF, very helpful to know about this JRA initiative which I don't know yet if is an extension/expansion of the TIB thing, or modelled after it. Will read property around this in PDF + elsewhere ! BTW I'm tangentially interested in this topic, from the perspective of genome-wide association study datasets and ways to archive them and cite them.
- 'Mummi' Thorisson
Okay. I'll try to give a bit more info about the JRA thing once I have it. Incidentally, on association studies (QTLs too?) I ought to mention one of the projects we have registered at MIBBI for reporting QTLs and association studies: http://mibbi.org/index...
- Chris
from twhirl
The All Results Journals - "Because all your results are good results" - http://arjournals.com/ojs...
Mike Chelen, Bruno C. Vellutini, Chris and 28 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
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