 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Bosco Ho › Comments
Wondering if I should finally bite the bullet and switch my blog from blogger to wordpress ...
Michael Kuhn, Lars Juhl Jensen and Deepak Singh liked this
Did this myself several months ago...... much prefer WP.
- Graham Steel
textpattern!
- Bosco Ho
well, will play around with WP but not sure when/if I will switch yet
- Jonathan Eisen
I wondered the same thing myself over two years ago, but never made the switch. http://igotgenes.blogspot.com/2008... I'm curious about your motivation. Mine was primarily a gripe with code formatting (now handled by SyntaxHighlighter http://blog.cartercole.com/2009... ) and LaTeX for math markup, which I haven't solved yet.
- Chris Lasher
Also, I only need to see things like this to decide I don't have the gumption to host my own WP instance: http://python.genedrift.org/2010...
- Chris Lasher
Chris - motivation was simply that I have been hearing lots of glory stories about WP - so I figured I should at least check it out
- Jonathan Eisen
Wordpress is nice if you are interested in plugins and themes, e.g. for reference management. I will also start work on a epub plugin.
- Martin Fenner
First moving to WP.com, then self-hosted WP, then writing custom plugins for WP, then writing custom CMS... You're starting a long journey ;)
- Pawel Szczesny
@ananelson has the ultimate geek blog: she writes her posts with vim using her dexy (http://dexy.it) language.
- Martin Fenner
4,000 new professorships for Germany? - http://bjoern.brembs.net/news...
Bjorn, you should read Science, technology and innovation reports that EU is preparing annually. The future is bright for you :).
- Pawel Szczesny
Well, I believe it when I see it :-) The future I mean :-)
- Björn Brembs
According to the Strauss-Howe theory of generational changes, this is the kind of thing that will probably kick in around 2020. Papers like these build the momentum to that point.
- Bosco Ho
OVerheard "I've got all 6 HP's. It'll be great for Hanukah". HP = Harry Potter I presume.
Or really good RPN calculators.
- Dan Gezelter
Woohoo! Winter solstice.
Mickey Kosloff and Michael Kuhn liked this
Annotatr: Post-publication peer review - http://mndoci.com/2010...
Kubke, Nir London, Mickey Kosloff and 9 other people liked this
Left a comment... it needs integration, and thus an API...
- Egon Willighagen
Bosco, Egon wants an API :).
- Deepak Singh
we need to go one more layer down.
- Bosco Ho
I finally learnt what the lambda function is good - http://www.diigo.com/item...
I finally learnt what the lambda function is good for in Python w/ @grisch. I feel I can almost call myself a legit python programmer now..
- Andrew Perry
wait till you start programming in javascript.
- Bosco Ho
What should a developer know before building a public web site? - Stack Overflow - http://stackoverflow.com/questio...
Bronwen Dekker, Andrew Lang, Nick Boucart and 8 other people liked this
I just saw a litany of mistakes that I am about to make.
- Bosco Ho
ChemWriter 2 - Better Structure Editor Deployment Through JavaScript - http://depth-first.com/article...
Bosco Ho, Rajarshi Guha and Matthew Todd liked this
Rich - it's very pretty. When are you rolling out more, like atom labels, multiple bonds etc?
- Matthew Todd
@Mat, thanks, it's a lot of fun to watch it take shape. Both of the features you mention are must-have and will be added in the near future. Those on the mailing list will be notified first when the changes go live in the preview.
- Rich Apodaca
@rich, the peeps want labels. we give them labels. the peeps want selecting, we give them selection. the peeps want color, the cup overflows. you take the colors we give you.
- Bosco Ho
Schrödinger - About - Overview - http://www.schrodinger.com/about...
Spent many years competing with them :)
- Deepak Singh
@deepak, how?
- Bosco Ho
My Accelrys days
- Deepak Singh
new journal online, which I hope will make a difference: http://www.openresearchcomputation.com/
Piotr Byzia, Just Joe, Chris Miller and 23 other people liked this
Editorial Board reads like a list of favourite bloggers. :)
- Pawel Szczesny
Man, check out the Usual Suspects lineup! Brilliant.
- Bill Hooker
Awesome! err.. Is there an RSS feed for this one? I'm not seeing it..
- Carl Boettiger
brilliant, didn't know that worked. Now in my google reader. How about an rss icon on the front page?
- Carl Boettiger
I always wondered if a social media savvy editorial board could project a journal above the rest ... I guess I will see :)
- Pedro Beltrao
Who is Keyser Sozer?
- Bosco Ho
I'm more than a little surprised Greg Wilson isn't on the board, but there are certainly a lot of recognizable names on it already. RSS feeds++.
- Chris Lasher
Nope, I can confirm there are at least three people who aren't on the list, Neil, Arfon Smith, and Peter Murray-Rust, and we're still planning to build the board up some more. I did approach Greg Wilson but he's got some other big projects on the go so understandably didn't want to take more on.
- Cameron Neylon
Should also note that the website has a lot of stock text in it still that will be being replaced with some more relevant material as soon as I get access to the ed board mailing list and we start figuring out how to get our hands into the website itself...
- Cameron Neylon
It would be nice to see people associated with the physiome project in there http://www.abi.auckland.ac.nz/uoa...
- Kubke
The plan is to expand the Ed Board reasonably organically so very happy to speak to people who would have an interest. It will take us a while to get there but always happy to talk to people.
- Cameron Neylon
I'll send them that way then. Cheers.
- Kubke
Honestly, I seem to be a bit confused - how's ORC positioned against Source Code for Biology and Medicine?
- Pawel Szczesny
Focus is a bit different and there is no disciplinary restrictions. The instructions for authors stuff on the ORC website is very generic at the moment. We're waiting for more specific stuff to go up. Basically ORC will focus more on the software quality side, with documentation and testing (including provision of test data) being an important part of the process.
- Cameron Neylon
Less Talk, More HTML - http://blog.chembark.com/2010...
Cesar Sanchez, Alex Holcombe, Laura Norvig and 10 other people liked this
"Why is it that some lab groups and managers will spend countless days travelling to schools around the globe to give talks to small audiences, but won’t devote any time to posting the same information on their Web sites that are accessible to millions of people?"
- Rich Apodaca
Because there is little or no formal credit within institutions and grant awarding bodies, unlike for conference presentations & elite seminars.
- AJCann
What AJ said: every talk I gave is one line in my resume.
- Björn Brembs
Sad but true. People seem impressed when I give a talk/sit on a panel. No-one gives a damn when a blog post gets 2500 page views (that's a lot for me...)
- Cameron Neylon
HTML is hard; let's have a meeting.
- Bosco Ho
It's sad but the scientific community reminds me of traditional media, etc. Holding on to something whose heyday was in the past
- Deepak Singh
+++ Deepak
- Bill Hooker
I agree with @Cameron, the old school metric of "authority" still value invited ( and uninvited) talks more than blog readership
- Hari
Generally true, but it depends who you are invited to talk to. Keynotes at international conferences are certainly credited in UK RAE/REF, as is media work (less so).
- AJCann
+1 Neil. Most points for publications (n x IF) then way down the list would be invited talks, then way down again would be outreach if you ever mentioned it at all. There is no metric for impact associated with the creation of web content that is highly visited. You're starting to see statements like "was one of the top ten most downloaded papers in the journal for the period March 1-April 24." Outreach counts a little in promotion decisions, but there are far fewer of these than grant proposals.
- Matthew Todd
[The original post was actually mainly about web pages, but there is a comment there about posting seminars on the web too. Becoming difficult to justify not doing this. But merits of real vs. virtual talks/lectures is a complex topic.]
- Matthew Todd
@Neil: I agree about crossing anybody's mind, but if we had the incentives in place, it would cross their minds :-) Also, I have had places where you would have to list national and international invited talks if you applied there for a job.
- Björn Brembs
Yes, terrible that ppl still using so much carbon for a few hours of face-time, but for networking, there's still nothing like a real handshake. And sadly, at least for promotions and fellowship apps in Australia, I think that although invited talks are well behind publications, they are taken as a substantial indication that one is one of the top 'experts' in a field. And perhaps the best way to get invited to more talks is to give an invited talk; audience members will later remember and recommend you.
- Alex Holcombe
Software Downsizing - http://depth-first.com/article...
Rajarshi Guha, Bosco Ho and Egon Willighagen liked this
Brilliant! I haven't made the plunge to a full unix stack yet. I still like my old textpattern.
- Bosco Ho
What advice would you give to new graduate students about creating a webpage & establishing a web presence?
GreG Durablement, Endre Sebestyen, Yaroslav Nikolaev and 17 other people liked this
For the web page, you could create a page on github like Egon did: http://egonw.github.com . Establishing a web presence: blog your research and comment the other blog, Q&A sites etc...
- Pierre Lindenbaum
I would suggest starting your own site. Github is a great option if you're a coder. Get on Biostar and similar sites.
- Deepak Singh
So most labs have a lab website to which a student can add their own webpage. This gives the advantage of discovery from those coming to the lab page, and both the discovery advantage and the 'professional' look of a university url, but some of that becomes a disadvantage when the student moves on. Should new graduate students be buying a lifetime url for themselves?
- Carl Boettiger
IMO anyyone interested in a professional career should. Good examples in addition to Egon's are Bosco Ho (http://boscoh.com/) and Neil/Pierre's blogs which highlight the things they are interested in.
- Deepak Singh
My advice would be to buy your own domain and get a cheap webhost. You will be moving around often enough before you get a permanent job that putting your stuff into a university system is counterproductive, especially if they have a proprietary CMS. Put Wordpress on your domain because it is easy enough to use and can be used as a CMS and/or a blogging platform. Make sure that finding...
more...
- Matt Leifer
Agree with Matt and Deepak -- potential employers search using google. It is important that either the individual has crafted what people can find OR the individual isn't there at all. Not sure what will happen as long-term use emerges, and folks find pasts they wish not so obvious present when building a professional portfolio.
- Mickey Schafer
The first advice should probably be to change their name to disassociate themselves from the drunk Facebook pictures and to pick a unique enough name...
- Eric Jain
I started my website as a graduate student in the mid-90s on a university server. Towards the end of my PhD, 1999 I got my own domain, as it was clear I'd be moving institutes for the forthcoming years. Started a blog in 2003. I think today, a student only needs a blog, as any more permanent information can be linked as separate pages from that blog.
- Björn Brembs
I had this discussion with students on the ESOF conference a while ago, here my recommendations I gave them ... Scientific presence - Never forget that it is about you - http://bit.ly/dqu84l #science #web #presence -
- joergkurtwegner
@Carl - Lab pages are certainly a good temporary solution, and they do typically not ensure long-term stability. So, I would recommend another solution, and nowadays no one has to pay for a good long-term web presence. @Eric - Agreed - Name consistency and trust building are important, it is simple, people will find you anyway, so do not try masking anything, it will not work. Be honest!
- joergkurtwegner
get your own site, most lab sites are unstable and really annoying to update. I think you have basically two options - make an online CV on steroids (link to papers/code/data/etc) or start a blog. however, starting a blog is trickier than it sounds. an abandoned half-assed blog is worse than no blog at all. honestly, it takes at least a few months before you find your voice. that said,...
more...
- Bosco Ho
I usually suggest to my students that create a FriendFeed account and start interacting with people in their field of interest. Later they can decide if it makes sense to start a blog, wiki, etc.
- Jean-Claude Bradley
Isn't friendfeed too small? Twitter will have a much larger group in any discipline, though in 2010 blogging is not arcane so anyone can set up something good if they want to maintain it; it's just finding a theme you like and not expecting a million readers a month without some effort.
- Science 2.0
This was discussed a lot at #solo10 - Its not necessarily hard to start a blog or sign up to a site like S3.0, and its not necessarily a problem if you say controversial things. Those who haven't become more aware of this new media science 2.0 approach tend to think that any time spent doing this kind of thing is time taken away from your work and so discourage it. So some people were saying that their PIs didnt understand.
- science3point0
On the 'presence' aspect: Create/obtain as many inbound links as possible (assuming visibility is desirable) and keep your CV fresh. As for general content, keep it clean and uncontroversial -- wait till you have a career path before you start stuffing it up with self-indulgences (same goes for coffee break chat). If you must vent, do it anonymously, but be aware that any complaint...
more...
- Chris
from twhirl
The reason I suggested FF is that it is an almost effortless way to follow people's collection of feeds (blogs, slideshare, linkedin, scivee, etc) and conversations are more organized. Students can also start adding their own feeds to their FF account. Twitter can't do all of that. Of course they can also use Twitter and see how useful it is for their interests.
- Jean-Claude Bradley
I'd probably recommend google sites or a wordpress site... and have that feed into your FF account of course.
- Just Joe
you could also open an Linked In account and feed updates through that or combine it with a profile on Mendeley and/or ResearchGate, and use tumblr or a similar site to create quick blog posts. I'm assuming a new grad student would have limited time and may already be using twitter or FF as a discussion tool. I would argue they would reach more people with twitter but get more useful discussion on FF.
- Elizabeth Brown
use a freelancer site and hire a freelancer for this purpose (there are plenty these days), save time
- MohanArun
Anyone aware of universities giving out short-term bioinformatics contracts? Does the grant funding process allow "outsourcing"? Wondering if it is possible to work for university research departments without actually being employed by them?
ROY, Khader Shameer, Daniel Swan and 5 other people liked this
It would be tough. But if you were set up as a company you could probably sell services. And if you're in at the grant writing stage then consultancy and services can be written in that way as long as they are justified on a value for money basis (like for instance saving on overheads...)
- Cameron Neylon
We (http://cathdb.info/) occasionally employ people on short-term or part-time contracts to work on specific projects that they have expertise in, but AFAIK they've only ever been previous postdocs or research assistants who've left but been asked back... But that does at least mean it's technically allowed
- Andrew Clegg
Interesting question. Is it technically possible in the context of a university ? Undoubtedly yes, but it would need to be an explicitly funded component of a project. Usually money is allocated to data generating services (microarrays, NGS etc.) with the analysis component usually *implied*. These services are usually provided by core labs, so in effect you're competing for their...
more...
- Greg Tyrelle
I recently found out that the NIH in Washington practically lives on outsourcing. Since employing federal employees is such a huge investment in personnel, about 40% of US government employees are actually employed by contractors who hire personnel for the government, including a huge bunch of support staff for the NIH and NIAID.
- Bosco Ho
I've just been scratching my head recently at the absurdity of numerous, separately funded projects employing bioinformaticians to do pretty much the same thing. Outsourcing these tasks would allow the 80% of common stuff to be reused, with the 20% specialised work that is specific to a given project to be performed far more cheaply.
- Neil Swainston
Greg - very good points. We (Simon Cockell) and I run a central service for bioinformatics analysis, effectively what we do is soak up these 'discrete' units of work on grants, and are fed by the sequencing/proteomics/array core facilties to some extent. Lots of projects only need us for an hour a week, or maybe just a chunk of our time. Internal competition comes from those groups...
more...
- Daniel Swan
@Neil that's partly a case of 'academia in a nutshell' isn't it? It's the same in methods development as well as data analysis. If all the people working on (say) competing structural alignment algorithms, or competing fold prediction algorithms, or competing named-entity-extraction algorithms (for example) were instead collaborating on flagship open-source projects, there'd be a lot...
more...
- Andrew Clegg
Yes. There can be a maddening nightmare of invoicing and dealing with bean counters who have no understanding of the work. But it is possible. (I'm with OpenHelix, btw)
- Mary Mangan
I use contract programmers, it wasn't a big deal to set it up. You can include these arrangements in NIH grants as well.
- John Hogenesch
I'm pretty sure the NIH has no restrictions on outsourcing or contract work. http://grants.nih.gov/grants... I think this falls under the "Consultant Services" section...
- Andrew Su
I know a local (san diego) consultant who does this from time to time.
- Benjamin Good
finding this especially funny after weeks of going back and forth with designers. or maybe it's just a monday thing. http://www.kevmo.net/2010...
Andrew Perry, Cesar Sanchez, Mickey Kosloff and 7 other people liked this
I just died laughing.
- Bosco Ho
Hilarious. Tnx - the highlight of my day (unfortunately)...
- Mickey Kosloff
Peer review highly sensitive to poor refereeing, claim researchers - physicsworld.com (seen at http://www.quantiki.org/content... ) - http://physicsworld.com/cws...
Christina Pikas, Cameron Neylon, Bosco Ho and Bill Hooker liked this
"Just a small number of bad referees can significantly undermine the ability of the peer-review system to select the best scientific papers. That is according to a pair of complex systems researchers in Austria who have modelled an academic publishing system and showed that human foibles can have a dramatic effect on the quality of published science."
- Daniel Mietchen
from Bookmarklet
This sounds like a great study - model the game theory mechanics of reviewing strategies and its relationship to output quality.
- Bosco Ho
Paper at http://arxiv.org/abs/1008.4324 .
- Daniel Mietchen
Ah Federer on song
I assume you've read the David Foster Wallace essay on Federer.
- Bosco Ho
Yep.
- Deepak Singh
Google Wave open source next step - http://googlewavedev.blogspot.com/2010...
Berci Mesko, MD, Björn Brembs and Egon Willighagen liked this
"Wave in a Box" - Google Wave resurrected as open source.
- David Bradley
Step 1, you cut a hole in the box.
- Bosco Ho
Mendeley is going to be open source - http://blindscientist.genedrift.org/2010...
Sathishk, Roderic Page, len hat and 7 other people liked this
That would be an interesting and welcome move... client and server side?
- Egon Willighagen
omigod! Is pn a sleeper mole ... for mendeley?
- Bosco Ho
This is something that I so want to be true, like the iPad Mini, more money for research, or Bill Gates turning out to be one of the good guys. Oh, wait...
- AJCann
What is the evidence for this claim? Also, this is another blog post that would be easier to read if there were a standard html markup for sarcasm.
- Matt Leifer
connotea code is open source... obviously not a magic bullet for making things better
- Benjamin Good
@Benjamin: indeed, Open Source != Good Project
- Egon Willighagen
Hari, Nina, Egon at tamarind, boston ff meetup http://twitpic.com/2i667x
 |
Michael Kuhn, Egon Willighagen, Wladimir Labeikovsky and 2 other people liked this
The food was great! #acs_boston
- Egon Willighagen
Where was Robert Scoble?
- Bosco Ho
yummy
- joergkurtwegner
If your PhD supervisor moves abroad for a few months, what web tool/application/site would you recommend him that could help him manage the workflow of the lab, schedule online talks, see how things are going at home?
Endre Sebestyen, Bill Hooker, Pedro Beltrao and 8 other people liked this
I'd recommend him to require you to keep a blog, source code repository, and be Open Notebook Science... shared Google calendar, blog planet for the lab. Group 'teams' for bookmarking services like Delicious, Mendeley/Connotea ... anything specific you are looking for?
- Egon Willighagen
The lab team is not too web-savvy or web-based so there should be one site/app through which he can manage the workflow and not the lab (schedule meetings, marking milestones of PhD projects, follow developments, etc.)
- Berci Mesko, MD
I'm sure it would be impossible to get everyone online, but he is a regular web user and is open to such things (in case I can find the right tool for this).
- Berci Mesko, MD
Yes, the one site thing is important - things need to look integrated of have a single gateway at least. A blog that brings elements from other services into a central place could work well for this. Lots of good Wordpress plugins for creating content. Pull in IM/twitter feeds and get everyone to write a brief post at least once every second day. Use the comments for communication via...
more...
- Cameron Neylon
If you want a one-stop solution... I think a wiki is the best approach.
- Egon Willighagen
You can also take the opportunity and lead the troops into the Web2.0 era, all in light of your PhD supervisor's ability to monitor things...
- Egon Willighagen
Google groups is not bad. Especially if you email through that interface. You can store documents, have a calendar, edit a wiki, as well as have threaded messages. By leveraging email, your boss doesn't have to learn no "wiki" interface.
- Bosco Ho
My supervisor uses Google Calendar for scheduling meetings (each of us will Skype him every second week) and the lab uses Google Groups for group e-mails but I wanted to centralize things somehow.
- Berci Mesko, MD
Anyway, thank you for the great suggestions!
- Berci Mesko, MD
I haven't tried it yet, but posterous has a group blog feature that might be useful for that. You just need one person to create the blog and add other collaborators' emails. With this set you (and everyone else) can send emails to a specific address to communicate and everything (including attached files) are aggregated into the blog. Might work for the not web-savvy since all you need is to write and reply emails.
- Bruno C. Vellutini
how non-public do you want the exchanges to be, Berci? I mean: gpg-style wanted/needed? or are digital postcards fine?
- Claudia Koltzenburg
Absolutely non public.
- Berci Mesko, MD
Just check the CMS list for features you need and like, integration options with other tools might be one of the corner stones - http://en.wikipedia.org/wiki... As usual there is no one size fits all solution for all needs, so happy digging and taking it from there. Depending on the possible investment options you might find more information and insights out there. P.S.: I like Drupal, but are biased and not fully informed about other options !
- joergkurtwegner
Great list, thank you for sharing!
- Berci Mesko, MD
Berci: also check out Open Atrium (http://openatrium.com), a pretty sleek intranet/collaboration-focused CMS based on Drupal. Our group is looking at this for a couple of projects in our group. Disclaimer: we're fairly Drupal-biased; we use it as a base for a production community portal site (http://www.gen2phen.org). Still, Atrium might make a great base for a group website and can be customized ad infinitum if desired.
- 'Mummi' Thorisson
Thank you, Mummi, for the suggestion!
- Berci Mesko, MD
My lab uses 37signals' Basecamp to manage and monitor most of the daily activity (ordering reagents, sending out announcements, internal communications, etc). I'd highly recommend looking into it, as it's inexpensive and the learning curve is very small for those who are not very web-savvy.
- Ben Ferguson
from iPhone
You can make posterous non-public and it's pretty easy to just email things into posterous and let it handle it. Basecamp is another solution, but you'll have to pay for it for your level of use and it's not brain-dead easy like posterous (of course, you can do a lot more, like manage projects, with Basecamp but hey, a lesser tool people use is better a great one people don't, right?)...
more...
- Mr. Gunn
+1 Basecamp
- John Hogenesch
Kurzweil Responds - http://pipeline.corante.com/archive...
Chad Orzel and John Dupuis liked this
What about neuroscience get's people to get all scifi about it? I like that it's a hard problem, but the Kurzweil-ian gobbledegook only muddies the waters
- Deepak Singh
@Deepak: I think it's a wider application of Clarke's 3rd Law: any sufficiently difficult problem attracts magical thinking.
- Bill Hooker
honestly though, scientists can write compelling fiction about as well as they can dance.
- Bosco Ho
lol. You haven't seen me dance have you :)
- Deepak Singh
from IM
Oh fuck, hard drive failure on laptop.
I almost don't dare to ask: when did you last do backup?
- Lars Juhl Jensen
A mixed story - dropbox has the most important code. most simulation data on linux servers. copying from drive in target disk mode, very slowly, photos/music and a handful of scripts/images
- Bosco Ho
I Hate Your Paper - The Scientist - Many say the peer review system is broken. Here’s how some journals are trying to fix it - http://www.the-scientist.com/2010...
Steve Koch, 'Mummi' Thorisson, Lit and 26 other people liked this
“When it comes to journals and publications, I’m highly skeptical that [the peer review] process adds much value at all,” adds Richard Smith, former editor of the British Medical Journal, who has written extensively about peer review. “In fact, it detracts value because it wastes a lot of time of a lot of people,” he says. “There’s lots of evidence of the downside of peer review, and very limited evidence of the upside.
- Alexey
from Bookmarklet
Wonder about studies that have measured the relative quality of various review processes?
- Mike Chelen
"The full podcast, originally created for the Journal of Participatory Medicine, is hosted here." http://www.patientpower.info/JoPM... (Podcast with transcripts) -- Peer Review and Reputation Systems: A Discussion -- 1. Defining the Problems and Issues with Peer Review Today -- 2. Light Versus Heavy Peer Review -- 3. Transparency in Peer Review -- 4. Wikipedia-Style Peer Review…and Rating/Reputation Systems -- 5. Crowdsourcing Research/Peer Review -- 6. Building a Community
- Claudia Koltzenburg
Hmm, I don't know if peer-review improves papers but it has so far often improved *my*papers...
- Björn Brembs
what's your take, Björn, does review quality depend on anonymity? should we say blind or non-blind should be up to the reviewer?
- Claudia Koltzenburg
btw, have not seen this idea voiced before ;-)
- Claudia Koltzenburg
I am with Bjoern here, I see improvement of papers on peer review (mine and others'). Both on substantial issues as much as smaller things. But i also don't think that peer review is a bulletproof system.
- Kubke
I think the point of peer review is not to improve papers but to prevent the publication of truly shitty ones. We really should judge the system on the true negatives. Kind of like democracy - democracy is great, not because it helps you choose great leaders, but because it helps you get rid of shitty ones.
- Bosco Ho
if publications were wiki documents then... +1
- Claudia Koltzenburg
Yes, like Kevin Kelly proposed (wikiscience): http://www.edge.org/3rd_cul... Additionally micro-contributions like comments and corrections should be measured and added to the overall reputation of a person.
- Konrad Förstner
I'm going to offer counter examples. I've had several papers that were damaged by peer review in my opinion and several more which were severely delayed to publication and not significantly improved by the process, leading to potential opportunity costs (one paper which took nearly two years to get published subsequently has got around 50-80 citations depending on what you count). but...
more...
- Cameron Neylon
Bosco, I disagree. Firstly the evidence suggests that most of the shitty papers get published anyway eventually and secondly, like I argued here (http://cameronneylon.net/blog...) actually the more rubbish is out there, the easier it will be to find what you want.
- Cameron Neylon
Bosco. While Cameron may be right on arguing against the papers part of your argument, I think the democracy part is a true gem......
- Nils Reinton
Yep Nils, I don't think search is going to do much to improve our parliamentarians unfortunately...
- Cameron Neylon
In both cases, though, bringing in transparency has lots of potential to improve the system. By the way, I listened to the podcast last night (not knowing about this thread then) and took my notes at http://ff.im/oVHcb .
- Daniel Mietchen
Not sure I've done this before, but -- I disagree with Cameron here. The assumption that more data = better search just doesn't convince me at all. I've seen a lot of papers that were basically trash, but that would appear as hits in any search that would also find good work on the same topic. I think the figure that gets bandied about is that only 30% of papers fail to find a home...
more...
- Bill Hooker
There's a step missing there. My argument was more that we need more data to build better search systems to enable better search. Putting out more stuff with today's Google won't help but it could help build tomorrows was the idea. In terms of the 70/30 figure the thing we don't have any real data on whether papers are improved, delayed, or made worse - most scientists say it improves...
more...
- Cameron Neylon
Well, we've had this part of the conversation too -- if reviewing were seen as part of a researcher's job and being good at it were properly rewarded, then studies like the BMJ one might not find such rampant slack-arsery. I guess part of this is failure of imagination compounded by lack of knowledge on my part -- I don't see how any search algorithm is going to be able to distinguish...
more...
- Bill Hooker
Imagine two papers, reporting the same experiments but in paper A the obvious control was omitted in each case, whereas paper B included proper controls. A and B may even draw the same conclusions! Both are going to be hits on any search I can imagine, and then you have to read 'em to know that A is rubbish. Scale that up, and you pretty quickly get beyond the point where you can read...
more...
- Bill Hooker
I begin to think that what we need most is more data...
- Bill Hooker
I don't really buy the opening crystallography example as an argument that peer review is broken. Okay, one reviewer suggested something unnecessary. There should have been more than one reviewer, and the editor (or his/her minions) should have reviewed the reviewer's comments, either omitting any blatantly ridiculous ones in correspondence back to the author or easily accepting the author's note that it did not need to be addressed.
- Rachel Walden
Bill, agree that more data is required to draw any sensible conclusions but in response to your point about paper A and B, as far as I'm aware we have absolutely no credible evidence that this is _not_ the case and some examples of dreadful peer review at the top of the pile. So should we be spending billions a year on something we have no evidence does any good?
- Cameron Neylon
In any case, my argument would be that unless you have both papers A and B then there is no way anyone can develop tools to distinguish between them, whether they be social or technical. Also surely the argument must be that both support the same conclusion and it is only by reading them together that you get the fullest possible picture...even without the control paper A strengthens paper B's case.
- Cameron Neylon
Bill: Why should the concept of search be limited to keywords? Consider Friendfeed for example, where results are highlighted by number of Likes. If anyone considers one paper better than the other, it would appear higher in the search results.
- Mike Chelen
Mike, may be a matter of semantics but when you get into "likes" etc, to me that's post-publication review -- in other words, a filter. I love the idea, but a glance at PLoS journals (and other experiments) will show that it hasn't taken off: people just don't interact with the research literature (yet?) in a way that makes social filtering effective.
- Bill Hooker
Cam, if A really is going to get published without the controls (70% of the time), then I'd have to conclude that peer review is a waste of time and money. I'm finding that hard to believe, but as you point out -- I have no evidence. I've made fun of other people for falling into the trap where "I can't imagine it" == "it's not possible", and now it seems I am hoist on my own petard......
more...
- Bill Hooker
A different way to consider peer review: it's as much a psychological barrier as a real one. So, consider paper A -- it may be shite but the authors thought it was good enough to pass peer review. If they didn't even have to consider that hurdle, what might they be pushing out? Is there a mountain of substandard work that would be dumped into the knowledge base but for fear of the Peer...
more...
- Bill Hooker
That argument I'd agree with more. One of the things I've not seen a discussion of is the extent to which the citation advantage in high IF journals is a result of author selection bias (i.e. authors are probably pretty well placed to say which of their papers will be most successful and send them to 'appropriate' journals on the basis of that). There's a flip side to this tho. What...
more...
- Cameron Neylon
from twhirl
see also http://journalology.blogspot.com/2010... (e.g., "CNS" disease explained) thx to http://ff.im/oZdka
- Claudia Koltzenburg
Running Your Fingers Over A Single Molecule - http://pipeline.corante.com/archive...
Cameron Neylon, Mickey Kosloff and joergkurtwegner liked this
I'll thai massage your molecule, if you know what I mean.
- Bosco Ho
Bosco, just make sure the cops don't catch you
- Deepak Singh
Help, my GitHub account is now in Spanish. I didn't do it, honest! How do I change the setting to English?
!Ai caramba!
- Noel O'Boyle
lol Noel.
- Andrew Lang
Ask Elano!
- Bosco Ho
Logged out then back in and that fixed it. No language setting that I could see. Strange.
- Rich Apodaca
Tip: don't use relative paths in your automated scripts. Will screw you. Have to rerun day-long analysis because I saved in subdir.
imabonehead, Dan Hagon, Deepak Singh and Chris Miller liked this
Been there. Done that. Wasn't fun.
- Chris Miller
Until you move from one machine to another... than relative paths save your day :)
- Egon Willighagen
join the club.
- Bosco Ho
Had a case once where not only were they using relative paths but they were also wholesale modifying files based on globs. When the base directory change it screwed up a huge number of things before it was tracked down. Goodness knows what might have happened if they had been using rm.
- Dan Hagon
I'm with Egon. I keep my research directories synchronized between laptop and workstation. Relative paths help tremendously here. More importantly, I can publish my data, one-off support scripts, and all documentation on how I ran everything, contained in README.rst files; keeping all these paths relative to some well-defined top-level directory keeps my research reproducible by other members of our group, reviewers, and any other interested parties.
- Chris Lasher
All that said, I just noticed Jan wrote *automated* scripts. Maybe these are separate cases.
- Chris Lasher
And I suppose, somewhat related: http://biostar.stackexchange.com/questio... [Found via Coast-to-Coast Bio Podcast]
- Chris Lasher
Of course, had you used #Taverna, # Bioclipse, or ..., you'd have used unique identifiers to pull in data, not file names, and the problem was solved (better, traded for other problems ;)
- Egon Willighagen
Probably the best compromise between completely relative paths and full absolute paths is to have a configuration file specific to each deployed instance of a script (i.e. so you don't need to change the source of the script itself) which contains a parameter which is the base directory. Within your script you then use this to construct the full absolute path and ensure that you only...
more...
- Dan Hagon
@Dan That looks a lot like what I did. But with just one path somewhere not following this approach and that's what got me.
- Jan Aerts
Sad as I've handed over my resignation at Sanger. But for a good cause: will be starting a tenure-track in Belgium in October.
Christopher Fields, Egon Willighagen, Martin Fenner and 20 other people liked this
congrats Jan !
- Pierre Lindenbaum
Congratulations Jan!
- Lars Juhl Jensen
congrats Jan!!!!
- Abhishek Tiwari
congratulations Jan !!
- Mitsuteru N
Congratulations!
- Chris Lasher
Oufti! I assume it's in Vlams?
- Bosco Ho
Congrats and good luck
- Deepak Singh
Good luck!
- Paul Gardner
Congratulations and good luck!
- Michael Barton
@Bosco Ah! You're the Trapped in the USA-guy... Leuven is only a short drive from Brussels, so I might get a Manneken :-)
- Jan Aerts
congrats! I guess you might be too busy to do PFB this year?
- Jeremy Leipzig
@Jeremy. Indeed. And I haven't been asked anyway :-( But I'll probably be teaching databases from next year on, which might be useful for the course :-) (Does Simon read FF?)
- Jan Aerts
Congratulations Jan.
- Khader Shameer
Congrats Jan!
- Christopher Fields
I feel like butter being spread over a bigger slice of bread
Butter as in "Last Tango in Paris"
- Bosco Ho
Metrics: don't dismiss journals with a low impact factor : Nature : Nature Publishing Group - http://www.nature.com.ezproxy....
Claudia Koltzenburg, Jason Priem, Ruchira S. Datta and Björn Brembs liked this
"Researchers do not want their worth to be assessed on the basis of a single metric because metrics can be misleading and manipulated (Nature 465, 860–862; 2010). The same logic applies to journals."
- Kubke
from Bookmarklet
Oh yes they do. In my last lab, I know one postdoc who was furious at the UCSF proposed ban for Nature journals because that might have prevented him from publishing a Nature article, and thus stymie his chances for a faculty position. Shortsighted but understandable.
- Bosco Ho
@Bosco but being realistic that those are the metrics that are used is not contradictory with not wanting it to be so. The question for the postdoc would be whether he is happy that he has to consider that.
- Kubke
@Kubke, my feeling is that this postdoc has never thought beyond his own process.
- Bosco Ho
@Bosco I wouldn't be surprised and that is probably why the system continues to exist
- Kubke
But it wouldn't have a big an effect on his position at a UC university, right?
- Mr. Gunn
Other ways to read this feed:
