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Aarthy › Comments
New Thermocyclers: We have money to buy a thermocycler(s). Any suggestions or advice?
We currently have 6 Eppendorf's which we really like but its been while since we bought anything. Any out there you prefer? I like the Eppendorf because its easy to program, stable and we never have any problems with them. The new ones will be used both for research and in a "Marine CSI" class at the Duke Marine Lab.
- Kevin Z
I would stay with Eppendorf. My wife's lab just got a couple and they are pretty good.
- Paulo Nuin
+1 on Eppendorf unless you are going for a real time instrument or a later upgrade
- Nils Reinton
We have one real time machine already. I'm doing microsat development and straight up sequencing right now and for the foreseeable future.
- Kevin Z
I like perkin -elmer, very easy to make complicated programs and run large samples, only downside, you need adaptor plates.
- Aarthy
I tried to look up perkin elmer but couldn't find thermocyclers. Do you have a model number I google?
- Kevin Z
nevermind I found it! The perkin elmer 9700, looks like an ABI 2720
- Kevin Z
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 29 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
Scientists Can Now Differentiate Between Healthy Cells And Cancer Cells - http://www.sciencedaily.com/release...
"Mick Bhatia, scientific director of the McMaster Stem Cell and Cancer Research Institute in the Michael G. DeGroote School of Medicine, and his team of investigators have demonstrated – for the first time – the difference between normal stem cells and cancer stem cells in humans. The discovery, published in the journal Nature Biotechnology January 4, could eventually help with the further customization and targeting of cancer treatments for the individual patient. It will immediately provide a model to discover drugs using robotic screening for available molecules that may have untapped potential to eradicate cancer."
- Alexey
from Bookmarklet
very cool
- Aarthy
EMBO journal introduces transparent peer-review - http://blogs.nature.com/peer-to...
Yaroslav Nikolaev, Martin Fenner, Björn Brembs and 7 other people liked this
wow! is this the first journal to do this?
- Karen James
from twhirl
no, we do it in the BMC-series, for the medical journals. see the "pre-publication history" link on the right of e.g. http://www.biomedcentral.com/1471-24...
- Joe Dunckley
and here's a brief blog post I wrote a couple of months ago on the history of open peer review: http://www.cotch.net/blog...
- Joe Dunckley
brilliant, thanks Joe
- Karen James
from twhirl
Biology Direct also publishes the referee's comments along with the paper. (http://www.biology-direct.com/)
- Pedro Beltrao
According to the same editorial they are also removing all limitations to the number of citations allowed in the article. I think this is also great news. It is really disrespectful to other authors if we are not allowed to make justice to the previous related literature.
- Pedro Beltrao
Nature has very occasionally published refs reports, author revisions and editors' deliberations online to accompany the paper ("inside the paper" feature). I personally think it is interesting and informative for readers.
- Maxine
On this blog (Peer to Peer) the Nature peer-review focus is archived - this is free access and open to comments still. We commissioned 22 articles on various aspects of peer-review. http://blogs.nature.com/peer-to... As part of that we tried to find as many types of journal peer-review in existence as we could, and we asked the people concerned to write...
more...
- Maxine
Wonderful!!
- Aarthy
ASH abstracts due today; agonizing over every word. - http://www.hematology.org/meeting...
Alexey liked this
i'm trying to submit also, hopefully will fit in last few hours :))
- Alexey
What's your favorite resource for becoming a better scientific writer?
- Donnie Berkholz
@Donnie: I follow the advice of my advisor who told me to be kind to the reader by remembering to explain/teach. For mechanics and tips, I like Elements of Style (make each word tell) http://www.amazon.com/Element...
- Maureen
Maybe we can have a FF meet-up at ASH in RL, Alexey (and others?)
- Maureen
@Donnie: one of tools for me is blogging, it's different from writing papers of course, but still very useful if english is the second language
- Alexey
@Maureen - sure! If I'll complete submission today and will get confirmation :))
- Alexey
I was originally unclear. Consequently, those ideas, while good for writing in general, aren't quite what I'm looking for. I'm an English expert, and I can write casually just fine. What I'm looking for is books/websites/etc specific to writing good scientific papers & grant proposals.
- Donnie Berkholz
I didn't read books, but i attended seminar "scientific writing", i'm actually very bad at it, so my PI do a lot for it, also many many books written about it - http://www.amazon.com/s...
- Alexey
submitted, hopefully can make FF meeting in San-Francisco on December
- Alexey
Problem with scientific writing is that we only do it when necessary and relatively infrequently; i.e. at grant time or paper submission time. So I agree that blogging can be a way to make you write more frequently and keep in practice. Best way to improve: force yourself to take on more paper/grant writing and have a successful mentor criticise your writing.
- Neil Saunders
thanks Neil, I agree
- Alexey
Would be nice if blogging could be part of scientific writing -- when it comes time to put a paper together or a conference abstract, just gather up blog posts and edit...
- Bill Hooker
Bit late now, but read FSP's latest post on science writing here: http://science-professor.blogspot.com/2008...
- Heather
The Good Paper Journal Club is a Nature Network forum on science writing. Links to many resources and examples of well-written papers: http://network.nature.com/group...
- Martin Fenner
Thank you Martin, that was a really useful site
- Aarthy
Martin & Heather, thanks for the excellent links. The comments in the blog post are quite interesting, both those who agree and disagree.
- Donnie Berkholz
hey Maureen, it's getting close, what about FF meeting in San Francisco? Somebody else would like to join?
- Alexey
@Alexey, yes, let's meet. I am arriving Thursday for Friday Am satellite. I'm just putting my schedule together now.
- Maureen
Does anyone out there have any experience with measuring research efficiency? Meaning: measuring a lab's output, quality of work, …. Or are y'all all just counting publications & citations?
Jim Hardy, sofarsoShawn and Mike Chelen liked this
publications and citations over time vs. lab size over time can give you a reasonable idea of where you're at
- Michael Kuhn
This is a huge field of study in and of itself. Try poking around in the literature regarding the UK Research Assessment Exercise, for instance, or just google "bibliometrics".
- Bill Hooker
Not "tenureology"?
- Donnie Berkholz
I just realised that" tenureology" may not mean anything!! " Bibliometrics" may be a better measure
- Aarthy
Thanks for the creative terms. I was wondering more in the direction of weekly lab output… rather than the "long term" view.
- dK
Real-time microbibliometrics?
- Mike Chelen
I think its a bad idea to think of traditional productivity metrics for most research professionals , i think the long term metrics serve their purpose and do some harm as it is
- Hari
LOL. @Hari: this may be the case for academia, at least for those planning to stay there for some years. Industry? Different game altogether.
- dK
I like the idea of meaningful actionable metrics, but is the number of papers a meaningful exercise?
- Deepak Singh
How about papers/research dollar spent?
- Björn Brembs
Including other project info like citations, word use, readership, file sizes or more can supply help to learn about and explore the research. Even if it is not a totally accurate measurement, the effort results in an improvement to the knowledge surrounding the lab or topic.
- Mike Chelen
What I'd really like to see are some large-scale studies of research outcomes: how many drugs, crops, procedures, materials, etc etc do we have in 2008 that we didn't have in 1988 (or choose your timescale) as a result of research investment? How does that break down between public and private investment?
- Bill Hooker
For the last decade, not sure we want to see the numbers (and they are available, at least for commercial investment $$$)
- Deepak Singh
Bjorn is right, whatever metrics is used, it should be normalized over research budget.
- Pawel Szczesny
Perhaps this is not what you are after, dekay, but I have been wondering for a while how to incorporate Ecological Footprint thinking in the assessment of research impact. Three papers relevant here are http://dx.doi.org/10... , http://dx.doi.org/10... and http://dx.doi.org/10... . A summary is at http://ways.org/en... . More in next comment.
- Daniel Mietchen
Given that whole nations or corporations can have their ecological footprint estimated, I thought of extending this to research by looking at the resources used up for papers whose scientific impact is widely accepted to be high (one could take nobel-winning papers or highly-cited ones, for instance). I have had little encouraging feedback on this so far, and thus I have stopped working on it about two years ago but I would be glad to continue if any of you would like to join the endeavour.
- Daniel Mietchen
I report the total number of experiments on our lab wiki on my annual report :)
- Jean-Claude Bradley
You have to also remember to include your carbon footprint - as obviously - if you are a successful researcher you will be invited to lots of talks and keynotes. The larger the carbon footprint the more successful the researcher :)
- Frank
@Daniel: what a wonderful idea. Have you checked out http://www.corporate.basf.com/en... -- at least for some industrial projects the footprint that is determined actually justifies research&development!
- dK
@Jean-Claude: now, THIS is what I am talking about: what do you think, is the number of experiments performed a good indicator of research? How would you rate your experiments in terms of quality… etc?
- dK
I suspect research efficiency is inversely proportional to the amount of effort invested into measuring research efficiency at any organization...
- Eric Jain
Mathematician Stanislaw Ulam supposedly used to ask people who crowed too much about their achievements "What is this compared to E = mc^2?" When thinking about metrics, this always seems like a useful question to keep in mind - so little science is of lasting value. Not that intermediate stuff isn't valuable, too, but there are a lot of scientists out there with 300+ papers who history will rapidly forget.
- Michael Nielsen
That's usually how it's measured, even the negative one's count, so even if you produce total garbage, which people will criticize inevitably: those citations still factor in.
- sofarsoShawn
@dekay I put those experiments in my report and not all administrators weigh that contribution in the same way. I am lucky that some of my superiors do see value there.
- Jean-Claude Bradley
@dekay quantifying progress is an elusive and, frankly, a dangerous thing to take too seriously. The intent of the researchers in a collaboration cannot really be measured easily but that is the strongest factor for the advancement of knowledge, in my opinion. We have used that criterion in our evaluation of the first Submeta Open Notebook Science Challenge Award winner today: http://usefulchem.blogspot.com/2008...
- Jean-Claude Bradley
@dekay if you look at the criteria for evaluation it wasn't very quantitative but the judges reached a unanimous decision fairly quickly http://onschallenge.wikispaces.com/submeta...
- Jean-Claude Bradley
Eventually, the sweet seduction of capitalism will bring the academics into the fold. Otherwise, who ever has the biggest library wins!
- Jim Hardy
@J-C: Interesting. Nevertheless… we are on the journey to creating useful measures to improve the (meaningful results)/(€ spent)(time used). LOL.
- dK
@dekay: Thanks for the pointer. I heard of that when I was visiting their plant two years ago but hadn't seen the link.
- Daniel Mietchen
Some quote: "Hamilton [..] noticed that there were ‘people people’ and ‘things people’, classifying himself as the latter. Although these tendencies could be “disastrous socially”, he wrote, “I believe it is in essence an aberration of this kind that makes me a successful scientist”. " Source: http://www.nature.com/doifind... .
- Daniel Mietchen
@Daniel: aargh. long live non-public-access sources. ;)
- dK
Yes but the original source (quoted within the quote) was in a dead-tree book, so even less accessible. I paste it here for reference: Hamilton, W. D. in Narrow Roads of Gene Land Vol.3: Last Words. 206 (W. H. Freeman/Spektrum, 2005).
- Daniel Mietchen
Saying "When" to Literature - http://igotgenes.blogspot.com/2008...
Bora Zivkovic, Björn Brembs, Michael Nielsen and 2 other people liked this
As a very junior researcher, I shamelessly solicit your advice and experience.
- Chris Lasher
I read everything I cite to the depth necessary to ensure it supports the point I'm making with it.
- Donnie Berkholz
Don't be discouraged: reading journal articles is difficult and a skill that you acquire with practice. Read the abstract in full, several times, until the claims of the paper are clear to you. Then, ignore everything else except the figures and tables. Approach them critically and ask if they represent sufficient evidence for the claims: are the data unambiguous or has the writer presented them with a favourable spin? What are possible sources of error, alternative explanations?
- Neil Saunders
Two extreme views: Undergraduate adviser: "A month's worth of work in the lab can save you an afternoon in the library." Graduate adviser: "Would you rather spend your time reading about cool science or actually doing it?" My advice? You can make up quite a bit for not reading all that you could by talking with others (classmates, colleagues, conferences)...
- Andrew Su
Andrew hits the nail in the head, its hard to balance reading with research, unless you are off the bench. Do "smart reading", this will come with practise and more importantly with interactions.
- Aarthy
Another random suggestion - the diversity of your group sounds like some sort of journal club would be really useful in getting everyone's general comprehension up to a higher level. They may be reading different stuff - but having to communicate that to reasonably knowledgeable people can be really helpful at getting it clear in your head.
- Cameron Neylon
What kind of PCR primer design methods and programs do you use?
Alexis biochemicals, Aarthy, Richard P Grant and 6 other people liked this
Applied Biosystems Primer Express, mainly because we use a lot of MGB probes.
- Nils Reinton
from twhirl
um, I look at the sequence and count 18–21 bases?
- Richard P Grant
+1 Richard :) I was of the same mind, when I did such things. My favourite student question was "how do I design primers for gene expression?" Answer: you need one at the start and one at the end.
- Neil Saunders
Yep, by hand (hell sometimes on paper!) but then I guess I'm old fashioned. I wasn't even allowed to use PCR until the second year of my PhD and then it took us 12 months to get it working (not quite old enough to have been using multiple water baths thought)
- Cameron Neylon
NCBI has a new primer tool that uses primer3 and BLAST http://tinyurl.com/5tk67z
- Steven
I like Primer3Plus at http://www.bioinformatics.nl/cgi-bin...
- Dave Bridges
I find it odd when PhD students come into the office and don't know how to design PCR primers. Don't know what they're teaching them in the lab. I used to design mine all by eye on printouts in my wet days, and it worked just fine. Just point everyone to primer3 now.
- Daniel Swan
I used Primer3 and some obscure Mac System 7 applications. Sometimes it is easy as counting the nucleotides, but if PCR was so simplistic as that science would be much easier.
- Paulo Nuin
I'm partial to WebPrimer: http://seq.yeastgenome.org/cgi-bin... - it's not just for yeast by a long shot. Rather like Cameron, I didn't get to do a PCR until I was a postdoc. :-) But Steven's link looks good; I used to check that I would amplify something on genomic DNA by using http://genome.ucsc.edu/cgi-bin...
- Heather
Paulo, it's 2008. PCR, 90% of the time *is* that simplistic. I teach the students I have lab responsibility for to do it by eye, and to BLAST what they get to check for uniqueness. I started off by doing it on the Mac, years and years ago, but haven't used a primer design program since about 1999. And Cameron, it sounds like we started doing PCR about the same time. Worked first time for me, but took about 3 weeks to make the reagents.
- Richard P Grant
Yes, Richard, has been a while that I hadn't been to a lab doing PCR, maybe since 2001 or 2002. But depending on the availability of similar sequences the only way to go is with a program that at least gives you melting temps and some other conditions.
- Paulo Nuin
That's why I like ordering from Sigma—you get a melting temp calculation when you enter the sequences. But I only ever use that to match primers, rather than trying to differentiate between different sets.
- Richard P Grant
my primer and overall DNA experience is rather restricted to human, mouse and rat mitochondrial genome and the circular mtDNA is a different, inclusive world, I did manual design and primer3 too
- Attila Csordas
I've used a couple programs, but unless you're needing primers frequently, Richard's method is probably the best. Check for uniqueness and Tm, then order the two best looking pairs.
- Mr. Gunn
'Richard's method is probably the best'—can I put that on my CV? ;)
- Richard P Grant
I typically use vi and this primer checking tool at IDT (http://www.idtdna.com/analyze...). And WebCutter or ApE just to check my restriction sites are sensible.
- Andrew Perry
@Richard: sure you can, just credit the quote to "some d00d on teh internets" and your credibility is sure to skyrocket. :-)
- Bill Hooker
*laugh*
- Richard P Grant
Stratagene's design tools + Vector NTI
- Aarthy
Science Suffers When Getting a Grant Becomes the Goal - Chronicle.com - http://chronicle.com/free...
Pawel Szczesny, Michael Habib, imabonehead and 11 other people liked this
Only too true...
- Björn Brembs
Seconded
- Rajarshi Guha
The unfortunate truth. Getting grants has become an art and almost a full time occupation. The brains of senior scientists are lost into paperwork and time consuming tasks that in the end do little for the advancement of science
- Mounir Errami
Even junior scientists - and I'd say that the stress is even higher for them
- Rajarshi Guha
as clarification, the author was commenting on the encouragement for innovative science (or lack thereof) by the granting agencies, and not directly on the perpetual state of grant writing by many PIs. Clearly both are interesting issues. As a counterpoint to Mounir's point though, I often find that grant writing is *useful* as a reason to step out of the day-to-day management role and think about bigger picture science.
- Andrew Su
Fund raising is all I do. Because of the enormous increase in grant-writing, everything else suffers: mentoring, innovation, experiments, teaching, and discovery. University expectations are still predicated on the formula that PIs cover only 20% of their salaries. Those days are long gone, yet the obligations for teaching and other uncompensated work are increasing. It is all about the money.
- Maureen
Can t agree more, but who is going to bell the cat?
- Aarthy
Strength in numbers would bell the cat....Scientists need a union and a lobby.
- Maureen
Argh, no unions. Where there is a need there is an opportunity. That's what we should be focusing on. Disclaimer: I never think unions are a good idea
- Deepak Singh
I don't see how scientists are going to push back on the system that is happily squishing them, unless they can organize enough to lobby. (What good would a union do? Who'd care if all the scientists in the world went on strike for as long as they could last without salary -- about one pay period in most cases -- or even for a year?)
- Bill Hooker
Scientists are not alone in existing in a system that is happily squishing them (if that is what they think is happening to them), unfortunately.
- Maxine
And we all know how to get rid of oppressive regimes :-)
- Björn Brembs
Not by joining Living Marxism I trust ;-)
- Maxine
Might have to blog on this one, since Australian grant outcomes were just announced. My boss, a successful and respected scientist about as high on the career ladder as you can go uttered the words "it's really just become a lottery" the other day. Not inspiring!
- Neil Saunders
Some of you might be interested in the official Australian outcome statistics: http://www.arc.gov.au/ncgp.... The downward trend in success rates 2005-2009 is especially depressing.
- Neil Saunders
Union/lobby whatever you call it, scientists need to find a voice that the public hears. What if "Joe Scientist" talked about being squished and what that will mean to future cancer patients for example? Maybe I'm too optimistic, but I think the public would care and it would ultimately translate into better funding.
- Maureen
I'm just cranky because I'm gearing up to write grants. Haruuumph.
- Maureen
ah, the sweet smell of barricades burning in the morning :-)
- Björn Brembs
Given that the lottery aspect of grant awarding mechanism seems to have become more palpable over recent years, is anyone here aware of any serious attempts to introduce random measures into the game? That would be fairly cheap and easy to implement, and along with strict rules on abuse of the funding thus provided, could be a way to support big picture science instead of paperwork.
- Daniel Mietchen
FWIW, I have mentioned this idea to a guy from the NSF I know and he vowed to establish a grant lottery.
- Björn Brembs
How many grad schools did you apply to (if you have a graduate degree or are pursuing one)?
Kevin Z liked this
~10
- laura
~ 6 (3 east coast, 3 west coast - in the U.S.)
- Shirley Wu
None - as the UK doesn't have grad schools; you apply to work in a particular lab. I think I looked at 3.
- Neil Saunders
As Neil: I looked at one, and was offered a scholarship (which I accepted) in a second.
- Richard P Grant
Australia is (was?) like UK - I applied to three
- Cameron Neylon
Four.
- Chris Miller
Three. I might've applied to more, but I missed most of the application deadlines.
- Donnie Berkholz
Three. Geography and an infant forced the limit.
- Bora Zivkovic
~12 ... but I have already whetted groups in almost all of them. Withdrew most of those applications once I had my choices narrowed down to two.
- Deepak Singh
11 -- too many. Though it was fun to travel all over the country, it got real tiring...
- Andrew Su
Brazil, like Australia, UK. I was in the lab already for my Masters, and tried 2 or 3 for my PhD.
- Paulo Nuin
Note that all my applying was done remotely from a few 1000 miles away at a time when email and the internets were in their infancy. Was a lot of fun actually
- Deepak Singh
I applied to 7 or 8 programs four years ago.
- Chris Lasher
4
- Kevin Z
4
- Aarthy
I did my PhD in Aus as well, and only applied to one lab. (This was incredibly stupid of me. I had no specific research interests beyond "whoa, cell biology is cool", and took the position I was offered because it dropped in my lap, more or less.)
- Bill Hooker
8, in US, in 1999.
- Brian Haugen
received an email notiying an interview for a post doc doing genome analysis. This would be my first, any tips? what sort of questions will be asked? possible code debugging sessions?
Sally Church liked this
My two post-doc interviews were quite relaxed. Never in academia I was asked coding questions, even for more technical positions.
- Paulo Nuin
agreed, coding questions are unlikely. my advice is 1) know your own research inside and out, and 2) asking questions about the interviewer's research conveys interest and enthusiasm.
- Andrew Su
don't know how post-doc iv are different, but thats exactly what i've been doing in PhD interviews.
- marcin
@enigma I guess it's ok, but you would know his research interests anyway. More like his/her "current" interest.
- Jason Tsai
My lab recently interviewed for a postdoc. Our most important criteria, by the time it got as far as an interview, were enthusiasm for the project and fit into the lab culture.
- Donnie Berkholz
Understand that you'll be talking to other people in the lab, other people in the department, and maybe even giving a seminar. Don't think that just because these people aren't the PI that their opinion doesn't carry weight! Oh - and this goes for ANY interview - the interview doesn't end when you, say, go out for dinner or a beer...
- Todd Harris
Usually, a seminar, talks with everyone and the PI, lunch/ dinner. Be yourself, be curious and seem genuinely ready for responsibility. Its mostly them talking and you listening, other than the seminar. Good luck!!
- Aarthy
Don't think about getting the job, just scope out the projects and the people. If you want it for the right reasons, if you're into the work and a good fit with the lab culture, that will be obvious. "Be yourself" sounds trite but it's the best advice there is. You're better off in another job if you'd have to be someone else to get this one!
- Bill Hooker
@all thanks for all the advices; @Bill like your last sentence a lot! I'll be myself and hopefully don't laugh too loud after a few drinks...
- Jason Tsai
Good luck Jason.
- Paulo Nuin
I've only ever had one interview, so can't add much to the excellent advice above. In general though, I think interviews are more about giving the two parties a chance to check each other out, less about technical skills. You look good on paper (since you got the interview), they just want to get an impression of you as a person. Similarly, you want to get an impression of your potential new workplace. Good luck, I'm sure you'll go fine.
- Neil Saunders
New Pubmed feature: My Bibliography - http://www.nlm.nih.gov/pubs...
Maureen, Andrew Perry, Sally Church and 7 other people liked this
My NCBI was recently updated and now allows you to create a bibliography. I don't see an export function. Has this feature been around for a while and I have just missed it?
- Martin Fenner
I was hoping this would be something like the Citation Index.
- Donnie Berkholz
This is a new feature, I am still trying to understand its limits
- Aarthy
Academia.edu: A Geni For Researchers - http://www.techcrunch.com/2008...
Robert Scoble, Maureen, imabonehead and 10 other people liked this
"Whenever a new member joins the site, they are asked to identify themselves by both their department (for example, Computer Science), and then a more narrow field (example: Search Engine Algorithms). From then on, all activity submitted by this user will be added to the feeds of the fields they participate in. The site also allows users to specify certain members using a Twitter-like “Follow” system. Academia’s success will lie in its ability to build a useful news feed revolving around its professional network"
- Attila Csordas
from Bookmarklet
the website has a 500 Internal Server Error for me: http://www.academia.edu/
- Attila Csordas
I think it's pretty cool. Ben Lund who founded Connotea works there now, btw.
- Euan
Booh! It's in flash. A no-no in my book.
- Ricardo Vidal
I found the enormous CPU-guzzling Flash off-putting too.
- Neil Saunders
http://cambridge.academia.edu/Stephen... Do these guys upload everybody they find outside in advance to make them sign up? http://cambridge.academia.edu/JMEHyla...
- Attila Csordas
Its kind of cool but I don't really see what it adds to the ecosystem really. If they were prepopulating then I can see it becoming useful but if they are expecting people to add their own details I very much doubt they will get much uptake - there's other commentary at http://friendfeed.com/e... and the link in that item
- Cameron Neylon
"prepopulating" thx for the perfect term Cameron. That could work actually: are people tempted to edit their own Wikipedia entry if somebody else set it up already? Everybody is at least still an expert in 1 thing: his/her own narrative history and biographical details.
- Attila Csordas
Hi Attilla - that's precisely it, I think I got the term from somewhere else, probably a discussion with Michael Nielsen I think. See also: http://blog.openwetware.org/science... and Richard Akermans most recent blog post http://scilib.typepad.com/science...
- Cameron Neylon
Attila - Wikipedia specifically asks people not to edit their own Wikipedia entries.
- Michael Nielsen
Michael, thx, I didn't know that specific policy but obvious enough..for controversial celebrities. What I referred to with 'temptation to edit your own preinstalled profile' is that ordinary scientists probably will contribute to their Academia.edu preprofile if they check it and that's why the 'prepopulating efforts' might be successful.
- Attila Csordas
Flash turns the web into television (Glyn Moody).
- Bill Hooker
@Attila, not sure prepopulated profiles are good protocol. A scientist may not want to be associated with a specific site or service.
- Ricardo Vidal
I think Ricaardo is right about affiliations, the catchword is multiple or the more catchy "interdisciplinary" associations now. But cool project, nomnetheless.
- Aarthy
Absolutely - I do not want to be associated with Thomson ISI and want all of my information taken out right away! Seriously though, if it's publically accessible information then I can't see how they can object - worth putting in a 'this profile automatically generated' banner somewhere though
- Cameron Neylon
Ricardo, make no mistake: I didn't say that academia.edu's prepopulating concept is 'ethical', on the contrary it seems problematic to me too, but I wanted to say that even if it is 'ethical' or not, it seems like a useful business trick to attract people to the site as it could be a good bait for them. We shall see. I am not tempted at all to sign up.
- Attila Csordas
Whether or not it is ethical (prepopulating) it is illegal under terms of data protection legislation, etc. Thankfully. By the way, Noam Chomsky's on there now (academia.edu, that is). And Richard Dawkins
- Maxine
Prepopulating reduces the activation energy of contributing. But if a search hits a prepopulated entry, it should display the minimal details to make it recognizable then allow for a user to claim it as their own. That in itself raises interesting questions of identity verification. It's more like, we know you are out there, and we know some things about you, but we're not saying what until you give us approval.
- Todd Harris
I still don't see how a site could legally prepopulate with someone's details if that person had not indicated willingness to sign up. Chicken and egg?
- Maxine
Sites like this http://www.biomedexperts.com/Profile... have prepopulated with "my" public details/without my consent and though I used to be annoyed, now I just shrug. It will always be out of date but may suffice as a search result for some.
- Heather
It depends on what details they use - I've always been thinking about sites using information from abstracts, which is all I think that BioMedExperts uses, for instance. Technically speaking I guess Medline, Thomson etc are in violation of the UK data protection act. Thinking about it - most journals would be as well for holding email and work addresses. But my view is that if its on a public website it is in the public domain - the question is who allowed it to go on the website in the first place.
- Cameron Neylon
A&I services like Thomson et al. are not in violation because what they are publishing are abstracts (content) of journals. Any site that prepopulates with personal data is in breach of not only UK but international data protection and data privacy legislation - legally, a website is "published" anywhere it can be downloaded or accessed, so you can sue a website from anywhere you can...
more...
- Maxine
Cameron, it is not correct that journals are in violation. Authors and referees provide data but this data are used only for that one set of transactions (concerning that one mansucript). The data are not used for any other purpose. At nature, you can be an author/referee but if you want to subscribe or register for any content it is an independent technical system (with opt-in and out...
more...
- Maxine
Hmm not sure how this is going to deal with the ambiguity of Newcastle Univesity, UK and Newcastle University, Australia
- Daniel Swan
Maxine, I was thinking of the address and email that is printed in the journal copy itself. It's a database and its personal information I would have thought (and the reason my laptop has to be encrypted is because I _might_ have email addresses on it!) I don't recall any copyright clearance ever including the standard data protection act boilerplate - or is it isomewhere else? I'd always assumed it was some sort of 'presumed public knowledge' but hadn't really thought about it.
- Cameron Neylon
[...cont] But surely e.g. Thomson with whom I have no contractual arrangment have no right to hold personal informatio on me? Or is that covered somewhere else? As I said none of this really bothers me that much personally (but I never give out my home address) but I wonder where the legalities are actually handled
- Cameron Neylon
The email address in a journal article is on the proof so if an author does not want it there he/she can strike it out so it does not appear in the journal. I was once concerned about spamming, etc, as a result of publishing email addresses but authors strongly like it there, and we (journals) also like it as it is an initial easy contact point for materials requests, "matters arising" etc.
- Maxine
And to the question about A&I services, so far as I am aware these services simply reproduce the abstract, title and author list of the paper itself, which the journal supplies.
- Maxine
Do you think someone has been spending too much time on FriendFeed? - http://img301.imageshack.us/my...
Aarthy, Andrew Perry, Chris Lasher and 12 other people liked this
Who could that be :)?
- Deepak Singh
lol!
- Björn Brembs
haha! how did that happen?
- _alf
It's been like that for a while. At least a couple of months, perhaps more
- Deepak Singh
The link is (now?) broken so I am missing the joke.
- Maxine
ditto - crashed my browser in fact but I think that's a problem at my end not the other
- Cameron Neylon
Broken for me too. If it's what I think it is, just Google "friendfeed" and look for a familiar name in the top hit.
- Neil Saunders
it's a screenshot of http://www.google.com/search... (but I'm not saying what you'll find)
- Michael Kuhn
Thanks Michael. Nice one, Deepak. Got shares? Beats Wall St ;-)
- Maxine
Coincidentally, drove by their offices today and had lunch with a buddy who used to share office space with them till recently
- Deepak Singh
Hilarious! I love the byline - small typo that I almost read as "...build a customized feed of made up content of your friends..."
- Todd Harris
I'm getting some odd sideways glances from lab mates as I LOL lots ...
- Andrew Perry
LOL
- Aarthy
I'm doing a head count: Please say "hey!" if you are a biologist or a biological engineer. Thanks :)
What do those of us who are neither say? :)
- Deepak Singh
hey
- Paulo Nuin
forgot the !
- Paulo Nuin
he said biologist, that's pretty wide definition!
- Paulo Nuin
structural/computational biologist here
- Donnie Berkholz
compbio
- Ian Holmes
Computational Structural Bio (using a broad definition) ... hey!
- Deepak Singh
bioinformatics? hey?
- Shirley Wu
I assume bioinformatics counts. Hey.
- Chris Miller
'hey!'
- Richard P Grant
hey!
- Yann Abraham
hey!
- Pawel Szczesny
Computational biologist. Hey?
- Lars Juhl Jensen
hey! population geneticist
- Jason Tsai
Me too! (protein chemistry/mol biol/this week's buzzword)
- Cameron Neylon
hey! neurobiologist
- Björn Brembs
hey! once long ago. (physiology and then biophysics, now I'm a camp-follower)
- Maxine
hey!
- Marian Siwiak
hey! Genetics, but now mostly bioinformatics
- Todd Harris
yup
- Maureen
hey! molecular/cell biologist
- Ricardo Almeida
used to be molbio & biochem, now bioinformatics.
- tim
from Alert Thingy
Biochemist then bioinformatics
- Pedro Beltrao
hey ! :) former developmental biologist turned bioinformaticist. I'm still a biologist even if I don't set foot in a lab :p
- Daniel Swan
neither nor ;)
- dK
*raises hand* molecular biologist
- Bill Hooker
I'm a biologist.
- Chris Patil
biochem/neurosci/genetics?
- laura
I'm a biochemist
- Sally Church
All things bio folks... or almost. Most of you know what I mean. Thanks for your participation.
- Ricardo Vidal
Biochemist, now business development
- Jack H. Pincus
Genetics / Dev biology background, turned computational biologist
- Oliver Hofmann
Biochemist / Molecular biologist / Biotechnology diagnostics hey, hey, hey !
- Nils Reinton
hey!
- Paul Bacchus
hey! from here as well
- Jan Aerts
hey! Molecular/cancer biologist and bioinformatician.
- Walter Jessen
Hey! biochemist/ Mol biologist
- Aarthy
What's your pet system for organizing articles that you read?
Michael Nielsen and Alexey liked this
still connotea, is that so bad?
- Alexey
citeulike, zotero
- Paulo Nuin
What Paulo said.
- Neil Saunders
I usually put the reference on Citeulike, then on Zotero. I am trying to use Zotero Sync to synchronize the pdf attachments, but couldn't find a WebDav system to make the storage.
- Paulo Nuin
connotea
- Pierre Lindenbaum
Wow, you've just saved me 40 bucks. Papers (the mac app) is interesting but I couldn't quite justify the price in my head. Gotta check out Zotero.
- Sutee Dee
Connotea; don't like who bought CiteULike, still waiting for Zotero to move online.
- Bill Hooker
connotea + Zotero
- Pedro Beltrao
Oh wait, articles that I actually *read*? *hangs head in shame* I print 'em out and leave 'em in piles all over my desk. When I'm being really good I punch holes in a bunch of thematically related papers so that I can put them in a binder and carry it with me to read on the bus.
- Bill Hooker
I misread too. I don't actually read, but I love organising :)
- Neil Saunders
Papers for organisation and reading: fits perfectly with my workflow.
- Matt Wood
I'm not a mac user anymore, but I think even the earlier versions of Papers were definitely worth the money. As Matt said, it's very suitable for reading.
- Pawel Szczesny
I'll be less reluctant to pay for Papers when/if there are features for syncing across multiple machines, a way to mark up papers with comments and highlighting within Papers, and more advanced collaboration features. I think they've a great job so far and am looking forward to 2.0.
- Sutee Dee
Haven't used Papers much yet, but looks promising and it might stop me from printing everything. But I keep my references in CiteULike and haven't found an easy way yet to import those into Papers (including tags and stuff).
- Jan Aerts
As an alternative to Papers I somehow ended up using Yep! (to organize all kinds of pdfs) combined with a pdf viewer called "Skim". Skim is the only pdf viewer where I found a way to export the contents I have highlighted into a textfile.
- Daniel Jurczak
Mendeley. Then I don't have to organize them, I just throw them all into a folder or two (mine and others) and find them with a keyword or author. I love it, just wish I could make my bibliographies easily in the same way. (Same problem with Connotea.)
- Heather
Heather: We're expecting to have the Microsoft Word plugin prototype (for generating reference lists) ready by the end of this week - can't say how much more testing and development is needed until we can roll it out, but it's definitely on it's way :-)
- Victor / Mendeley Team
google reader + zotero, it's a 3-funnel (first selection on what comes to Google reader, 2-nd selection what gets starred, 3-rd selection what gets read and imported to zotero)
- marcin
Google Reader is a good resource for starring and selecting papers.
- Paulo Nuin
Victor - Word plugin is the killer - if you can get that working well then I want to buy shares :-)
- Cameron Neylon
citeulike. I also like the "my pubmed" option, made me keep up with all my old reading.
- Aarthy
Connotea + Papers, not entirely in synchronisation I admit :)
- Daniel Swan
G Reader, Connotea, Del.icio.us, but also have a load in Papers and Endnote from my doctoral days.
- Sally Church
Google Reader and FF to find them, citeulike to store and annotate, zotero - when I am forced to use word
- Frank
Does anyone have a theory why exactly scientist are so "under"paid vs other disciplines?
As Fox Mulder once said, I have plenty of theories :)
- Neil Saunders
I love Fox Mulder. He had his priorities right
- Deepak Singh
One theory: skills, experience, education are irrelevant. Contribution to "the economy" determines salary. It's hard to measure how scientists in academia contribute to GDP. Let's face it, many of them don't.
- Neil Saunders
Because scientists are so much passionate that you can have them work even at very low salaries... so why pay them more? (basic supply and demand stuff...)
- Enro
In addition to what Neil said, funding is wasted on the same experiments over and over again. It's not only about five groups working on the same problem today, but also about wasting resources on repeating experiments that were done 10 years ago. As far as I heard, money wasting is included in the science budgets, but that doesn't make measuring impact of science on GDP any easier.
- Pawel Szczesny
It's not just scientists. Software Engineers (read MS in Computer Science) are pain $10-20K less that they might make if they were working in industry. They are doing the same kind of work AND getting appreciated much less. You have to really like scientific research to want to enable it in that kind of environment
- Deepak Singh
What Enro and Pawel said...
- Björn Brembs
Supply and demand? Even now, with the relatively low salary, there are too many scientists (compared to the number of tenured positions).
- Michael Kuhn
Pretty much just an echo here. Society doesn't value research appropriately because it's difficult to measure its value -- you need to think and look over long timescales, decades or longer, which people aren't used to doing and political cycles actively discourage our "leaders" (ha!) from doing. The NIH puts out a feeble little pamphlet "why fund science?" every so often, but I don't know of any concerted effort to make a strong business case for research.
- Bill Hooker
There is a common belief that science is a noble profession. Society considers those who work in science to be privileged. The privilege conferred on those who can do science is supposed to compensate for lower salaries.
- Jack H. Pincus
Jack, unfortunately, I don't see too much privilege given to scientists either these days (at least in the US).
- Deepak Singh
You're not in an income-generating field. You're also not generally employed to do something that management wants to get done so they can create a product: you're there because you've got the research bug.
- Chris Cotsapas
Interesting to see how people are reading "scientists" as "scientists in academia" ;) Thanks to Chris & Bill for a different perspective…
- dK
It's because academic scientists are the ones that are the most underpaid, dekay. Industrial scientists are still underpaid relative to their education level, but nowhere near as bad as academic scientists.
- Mr. Gunn
one of my theory that it happen because society & government can not estimate value (impact) of scientific products. It's not electronics or software or food... scientists produce papers!!! No doubt some of them will be translated and find application in medicine or other technologies but most of them not. So income (money that government or other foundations invest to academic science) much more then outcome - benefits for society and highly expected products.
- Alexey
People are rewarded ('paid') based on how much 'obvious' (or relevant) contribution or product they make for their society. Scientists are not paid well because their contribution to the society is not really obvious. Their work can be presented in an important way (e.g. fight cancer) - and I think that's how scientists manage to get some money - but the problem is that for what they do, 99% of them do not generally have (or care) about an answer that is of beneficial to the society. Only 1% do.
- JWS
(agree with Enro) ...because they - like most artists, actors, musicians, comedians - love/need what they do so much, that they'd probably (and often do) do it for free.
- nossenigma
from fftogo
I agree with JWS, also, the idea of value is very subjective and with the govt. involved really unpredictable.
- Aarthy
Is a personal genome sequence worth $350,000? - http://scienceblogs.com/genetic...
Chris Cotsapas liked this
To summarize: No.
- Chris Miller
Nyet.
- Paulo Nuin
Definitely not
- Sally Church
Depends on how much money you have?
- Eric Jain
I'd still rather buy (another) Aston Martin or Bugatti
- Chris Cotsapas
I don't think I'd even pay $1000 for 500K typing
- Chris Cotsapas
I'd like to generalize this question: How much would you pay for sequencing 6 billion base pairs in 1 cell type of yours now relative to your current budget? I'd pay, say $2000.
- Attila Csordas
For me, it all boils down to interpretation. Since I don't know what most of it means, why should I pay anything for it? I'd rather pony up the cash (or my genotype, for that matter) to a cohort collection so we can figure out what this stuff means.
- Chris Cotsapas
I guess its $399 (for genotyping at least) now and you can download the results. IMO you are part of a big cohort and as an opt in. As long as I maintain ownership, don't mind. $350K though is too hgih
- Deepak Singh
I don't want other people's interpretations or choice of markers--I want my whole sequence (every base pair) and I'll interpret it myself. Still, I think it's worth about $20K.
- Ruchira S. Datta
I look forward to the day, perhaps some decades hence, when every student in college or even high school gets their personal genome sequence and learns in class how to find information about themselves.
- Ruchira S. Datta
@ruchira Noble thoughts - but how exactly do you interpret our probabilistic understanding of risk modulation by common variants? What does it mean, for you, to be told you have a 14% chance of diabetes compared to a population mean of 10%? For me the perennial medical advice would still hold: quit smoking, exersize, eat well, drink red wine in moderation.
- Chris Cotsapas
Not 350K, definitely not, a lesser sum may be ok.
- Aarthy
Google Chrome - http://www.google.com/chrome
Vladimir Blagojevic, Ricardo Vidal, Jason Winget and 2 other people liked this
The beta of Google's new browser is now available for Windows.
- Michael Nielsen
I installed Chrome and was impressed with how clean it looks. It seems to render very fast. I do miss my firefox plugins, mostly the delicious plugin that I rely heavily upon. I will not use it as my primary browser unless some of the plugins that make firefox work extremely well for me are available in chrome.
- Nick Boucart
Nick - the JavaScript is apparently a lot faster than IE / Firefox, which hopefully will drive those two to speed up. That could really change things.
- Michael Nielsen
I faced chrome issues last night, but when it worked , was impressed by the speed.
- Aarthy
I liked my experience with chrome, but I'd like to see a linux version
- Jason Winget
Michael, some java pages I went to just failed to work, with no information other than "no plugin available to display this content". Using Firefox you at least get told which plug-in is expected and where to find it.
- Mr. Gunn
wow, really impressed with the speed and interface. The comic book is surprisingly informative too compared to usual guff. Now just need plugins for delicious and zotero (and a linux version) ... how many days do you think?
- Alexei
ok, quick hack: 1) copy delicious bookmarklet from http://delicious.com/help... to bookmarks bar. 2) create a new search engine shortcut (right click search box) to search your delicious bookmarks (ie do a search, copy n paste the url to the url field of the search engine and replace search term with %s, give it a keyword like del) now del<space>foo will search for foo. Appears on start page too :)
- Alexei
Hard to believe it'll be more than weeks for the plugins to appear. Chrome looks to be BSD, which should make it pretty easy.
- Michael Nielsen
Wouldn't count on Zotero-in-Chrome any time soon. Zotero is built on XUL.
- D0r0th34
The javascript engine under Chrome is probably the most interesting part of Chrome. It is called V8, is developed by google in cooperation with people who made smalltalk and java hotspot vms. This new engine might mean that javascript become actually a first class citizen using modern vm technology, including decent garbage collection, etc. And since javascript is a very flexible and dynamic language, it is not hard to think that people might implement a ruby or python or so on top of javascript
- Nick Boucart
Nick - with decent (and fast!) Javascript support, browsers may begin not to suck.
- Michael Nielsen
[cont...] giving web developers the possibility to develop both client side as well as server side in say ruby. And who knows, running this engine stand alone might give rise to sort of desktop apps and online apps using very similar code, a bit like microsoft silverlight or adobe air, but web standards based... </geek talk>
- Nick Boucart
alexei, you must be far from the command line to be comfortable typing "del X" to search for X.
- Mr. Gunn
$ which del /usr/bin/which: no del in (/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/home/cgranade/bin)
- Christopher Granade
Mr Gunn, I was translating, I'm actually using 'd' :)
- Alexei
Dorothea, on the other hand Zotero has a reasonably well documented storage structure and it's interface is not that advanced ... can't imagine it would take that much to copy for a javascript wizz
- Alexei
"The kind of money generated around the industry is way out of proportion. The admiration bestowed on actors is also out of perspective. Doctors are the stars of our society" - http://www.reddit.com/goto...
Chris Cotsapas liked this
“The kind of money generated around the industry is way out of proportion. The admiration bestowed on actors is also out of perspective. “Doctors are the stars of our society - people like my grandfather who was responsible for the health care in Canada - as well as teachers, firefighters and police officers.” ~ Kiefer Sutherland on how he feels he doesn’t deserve the millions he earns for his profession.
- Paulo Nuin
Doesn't stop him cashing the cheque, of course. But the sentiment is worthwhile, I suppose...
- Chris Cotsapas
Indeed, I don't think he complains when he gets the pay stub.
- Paulo Nuin
Of course, if he split those fabled millions between all underpaid post-docs we'd all get, oh, about $0.00001.
- Chris Cotsapas
Of course, I am one of the 5 people in the world who think doctors are overpaid, especially relative to research scientists, without whom most doctors wouldn't have medicines to prescribe or understanding of disease.
- Deepak Singh
@deepak - that would suggest researchers should be paid more, rather than doctors paid less?
- Chris Cotsapas
Chris .. correct ... and researchers are also not quite appreciated as much as they should be. How many parents jump in joy when their kids tell them "I want to do research" :).
- Deepak Singh
Thanks for suggesting higher pay for researchers, Deepak, lets start with atleast postdocs!! I think the deal with docs getting high pay, is that you really need them to be happy, satisfied and alert. Anything that causes displeasure in a doc directly impacts society.
- Aarthy
Yes, but they eventually feel some pride - I think :-)
- Chris Cotsapas
Structure of the guide-strand-containing argonaute silencing complex - http://www.nature.com/nature...
Deepak Singh liked this
Beautiful
- Aarthy
Does anyone know of any drug-gene resources/databases? I've been told there are some at NCI, Duke and MIT, but don't know where to look.
laura liked this
don't forget NextBio. Lots of data around gene expression and compouds
- Deepak Singh
http://www.pharmgkb.org/ maybe?
- laura
ChemBank (or a project related to it from Broad) might provide some info
- Rajarshi Guha
PharmGKB is probably the most comprehensive (curated) resource and there's a lot of clinical data there too (but you may need an account to access that). I know the folks who work on PharmGKB so I'll see if they know of other resources as well.
- Shirley Wu
Some colleagues suggested PubChem (drugs only) and DrugBank, and also two proprietary databases, WOMBAT and MDDR
- Shirley Wu
Depends on what you want. For drug-target interactions, there are DrugBank, Matador / SuperTarget, TTD, and various binding constant dbs. Drug-gene: PharmGKB for manually curated info, things like the Connectivity Map and ChemBank for raw experimental data. There's also PubChem BioAssay. You could also try if STITCH helps you: http://stitch.embl.de or try a review (http://www.ncbi.nlm.nih.gov/pubmed...). [Disclaimer: I've been working on Matador, STITCH, and the review I linked.]
- Michael Kuhn
Try http://www.pharmgkb.org/, I have used it before
- Aarthy
Genetics: The production line : Nature News - http://www.nature.com/news...
Chris Miller, Sally Church, Pawel Szczesny and Björn Brembs liked this
Fantastic summary/review article!
- Björn Brembs
Excellent article
- Aarthy
PNAS: Read It, or Not? - http://pipeline.corante.com/archive...
Duncan Hull, tim, Martin Fenner and Björn Brembs liked this
Since we love journal bashing around here :)
- Deepak Singh
Haha. That's okay, I dig on skepticism for science.
- Chris Lasher
Journal bashing? Who?
- Paulo Nuin
At least they're open about how it was reviewed. For instance, with PLoS One papers, nobody knows if the AE just waved it through without even reading it or if it went through 5 revisions by 4 reviewers.
- Björn Brembs
I hear a good deal of naysaying of the PNAS submissions process, but not so much against the quality of the actual research they publish.
- tim
from Alert Thingy
Yes, they have some good cancer articles by some top researchers
- Sally Church
I've actually kinda always liked PNAS quality and papers are free after a while. My group always considered it one of the top 3 journals to publish in and I proudly wear a PNAS "We are number E/MC^2" shirt
- Deepak Singh
Good read, especially when I have just sent a paper to PNAS. The initial screening and review process is painfully slow, but who dares say anything against our esteemed academy!! I remember what Feynman said about the academy, while waiting for the review process to end.
- Aarthy
Richard Feynman explains the feeling of confusion - http://www.youtube.com/watch...
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Amira, Jo Vermeulen, Jorge and 37 other people liked this
I've been thinking a lot lately about confusion and how much information we humans throw away all the time. I think there is also a comforting side of confusion if you don't push too hard on it.
- Clare Dibble
great comment
- j1m
I think many of us avoid confusion the same way we avoid physical and emotional pain. Confusion is intellectual pain. And if you are highly intelligent, confusion can crush your self-concept/ego because it reveals your limitations. But there is no real logical reason to avoid confusion. It is a result of attempting to understand.
- Steve Olson
I think confusion in a intellectual flowers into important thoughts and benefits everyone
- Aarthy
I agree with Steve. Many people (including yours truly) go as far as trying to avoid confusion altogether by not thinking, because, yes, it's painful and it's crushing to know that you don't know all that much. But it's the realization of your own intellectual limitations that's important in fueling that desire to learn, imho. I find that intelligence is more about knowing you don't really know all that much and being open to learning.
- April Buchheit
@Aarthy: I'm confused _all_ the time. I don't see how my particular brand of confusion is beneficial to anyone. I'm confused by my own confusion.
- April Buchheit
April, When I was a student I was afraid of being wrong so I avoided confusion. It seems as though I was taught that not knowing was a bad thing, so I stuck with safety, what was known. Now I love confusion, because I realized later in life that feelings like confusion and anxiety mean I am approaching something worth doing or knowing.
- Steve Olson
I feel that it is important to feel and not to think to much about something because that can lead to rationing your thoughts onto something and finding it hard to let go, I think that if I feel that I'm thinking then it takes you down roads which become harder because you are no longer feeling the thing you are thinking and so make decisions which mean that you plan and thus time of doing becomes a time about thinking of doing and not much gets done. Anyway I feel that I'm hungry and foodstomp time.
- Jason
Feynman's writing shows a guy who had thought a lot about confusion and ignorance, and had many strategies for dealing with it. Basically, he had a theory of his own ignorance. Seems like a useful model to emulate.
- Michael Nielsen
Happy Accidents: A Must-Read for Open Scientists - http://drexel-coas-elearning.b...
Michael Kuhn, Bill Hooker, Pawel Szczesny and 7 other people liked this
Some excellent views. It's always been frustrating to me to write a grant in such a manner that I'm supposed to have done the (the bulk of) work I'm trying to get money to do.
- Rajarshi Guha
Very accurate assessment. I have had grants denied due to " unexplainable developments" which is an other term for accidental discoveries. Recognition of these points will make science more exciting and young scientists more comfortable.
- Aarthy
Thanks for the comments Rajarshi & Aarthy. The current system does reward data hoarding - there is little risk in proposing to do work that you have done but not yet published.
- Jean-Claude Bradley
It's way past time we stopped pretending science is some godlike activity carried out in perfect objectivity, blahblahblah like they feed you in grade school. I always see people cherrypicking their results when the whole dataset, taken together, supports the same conclusions -- but $deity forbid we ever show our mistakes or our less-than-perfect gels! It's one thing to structure a paper so as to facilitate information transfer, but quite another to pretend that you actually did those expts in that order
- Bill Hooker
[cont'd] for those reasons! If everyone knows that science moves forwards in bits and pieces, as much by luck as judgement, why do we have to keep pretending otherwise?
- Bill Hooker
Bill I hope many people read this book to get an idea of how things really happened. Chemists used to test compounds on themselves apparently a lot. One guy and his buddy thought a compound that was shown to kill intestinal worms in rabbits might cure scabies so they started swallowing it to prove it was safe in humans! Then every time they drank a beer they got sick - thus disulfiram (Antabuse) was born.
- Jean-Claude Bradley
Wikifying Peer Review - http://mndoci.com/blog...
Thomas Brox Røst, Amund Tveit, John Duff and 6 other people liked this
I'm not sure this qualifies as "peer review" - there are no conclusions derived from data - just a summary of the available services. The fact that people can add new information is helpful - though it will be interesting to see what the editors will accept. The one thing I disagree is the the requirement to register (even if free) to just read the article
- Jean-Claude Bradley
Euan tells me the wiki will be (peer?) reviewed by Lincoln Stein and the journal editors, we're also drafting a response to the original article on the wiki http://nrgwiki.nature.com/cyberin...
- Duncan Hull
I am not sure the Wiki should be peer reviewed either, but it take off from a peer reviewed article, hence the title. Duncan, looking forward to the response
- Deepak Singh
The wiki does need some kind of review, maybe not full peer-review, its already been spammed with annoying comments http://nrgwiki.nature.com/cyberin...
- Duncan Hull
Moderation is fine. Question is, who should own that part. The publisher or the author?
- Deepak Singh
Is this really peer review? In any case, along the conclusions of this post, in the present system, most scientists survive by publishing incremental results. If prestigious publishers take charge of the Wiki, it may take off in some way. Otherwise, I see authors resisting this type of publishing.
- Aarthy
IMO, publishing incremental results is a function of the need to publish in volume, when the follow up paper really doesn't merit being a paper on its own. I definitely acknowledge that publishers owning the wiki platform reduces friction
- Deepak Singh
we are having a serious think about Connotea. What would it need to do to be a killer app for helping scientists?
Ana Ivkovic, Björn Brembs, Pierre Lindenbaum and 20 other people liked this
Liking it cause I think many will have opinions
- Deepak Singh
I'm developing a tentative set of user needs right now, I'll post them for review at the end of the week, I hope.
- Ian Mulvany
Mining features... take advantage of citation trees. Say, we have paper X, this is cited by a number of papers, which are cited by etc. On each depth, the citing papers form a cloud based on the user tags, describing the literature that it citing paper X. This gives a quick overview of the types of literature citing the original; effectively, giving an overview of the research lines that refer to paper X. Possibly, this can be extended to start with the papers {X1, X2, ..., Xn}.
- Egon Willighagen
Yup, prepare for a barrage of blog posts and opinions :) (assuming I can make time)
- Cameron Neylon
Egon, the analysis is known as Main Path analysis, I've been reading up on it. It's pretty cool. It could be also useful for filling in a users personal bibliography
- Ian Mulvany
Tell me which papers I should read based on the ones in my collection. Facebook has a "people you may know" suggestion thingy.
- Michael Barton
Off the top of my head, I would mostly like to see more integration like with Google Docs, Zotero, Open Office, MS Word. For me to be able to show that kind of integration to students would be a killer app.
- John Dupuis
i'd like to see search by 2 or more tags together, sometimes tags edit doesn't work
- Alexey
John makes an excellent point. The biggest problem with so many of these Web-based apps is that they aren't readily integrated. As a knowledge worker, I should be able to move between Nature's applications, Google's applications, and other third-party tools without having the system stall out on me. No one has (to my knowledge) really managed to deliver this. It's lots of cut-and-paste, or emailing of content, and other work-arounds. Fix that problem and, as John says, that would be a killer app.
- Jill O'Neill
Aim to be the Nielsen of science ? ;) Get the users to add a browser plugin that can track readers habits across different scientific publishers. Link that to a profile that has users scientific interest and publications (NN). The users get back recommendations based on bookmarks, reading habits, articles similar to those that he/she published, articles recommended by NN contacts,etc.
- Pedro Beltrao
Add ratings to bookmarks and let the users opt in to get a reminder once a week/month to rate articles bookmarked in the previous week/month (something like Netflix does for movies)
- Pedro Beltrao
Get a couple of really famous scientists to use connotea and promote a page with their shared feeds (something like what google is doing now for Greader)
- Pedro Beltrao
Hi Jill, John, it's a well well known problem, and I think that it's not impossible to get around on an app by app basis. Word should be OK, Google Docs is harder as there is no API yet that I know of (is there? is there?), but there might be a way to get bookmarks to sync with google bookmarks, and that would work. Ah, idea.
- Ian Mulvany
Focus on literature bookmarks again, not any bookmark.
- Egon Willighagen
Oh, if you keep any bookmark in, make sure to use it to contribute to a researcher impact factor, based on link counts, ala Google Page Rank, but counting not just papers, but software projects, databases, etc too.
- Egon Willighagen
integration would be the key, but simple things like tab-completion of tags would be a good start
- Paulo Nuin
What Deepak said. Does FF need a "bookmark" as well as a "like"?
- Bill Hooker
Would love to see Connotea include a pdf upload like CiteULike's.
- Bill Hooker
I was actually thinking about this the other day. Activity feeds - bookmarked, "starred", commented. Ability to link to local and network storage of PDFs (whatever system user chooses - Amazon S3, C: drive, Google Docs, whatever). Tag recommendations, article recommendations, open Recommender API, private groups, social network sharing, how's that for a start?
- Richard Akerman
Must use citation tree, have a serious cite and write option compatible with existing word processors.
- Aarthy
don't say I didn't warn you :) http://blog.openwetware.org/science...
- Cameron Neylon
@CameronNeylon I'm liking prepopulate a lot in other contexts - it's a great way to kickstart IRs.
- Richard Akerman
@Richard - I think its crucial to get people to understand what would be possible if they bring more people in. The benefits kick in when you have a whole research group for instance but until people see that this might be a good thing they are not going to expend the effort on bringing the rest of the group in.
- Cameron Neylon
everything that http://www.citeulike.org does but better, pdf upload, download RIS/Bibtex per tag or per paper (rather than just one big batch), fix what is left of buggotea (thats a tricky one) http://www.nodalpoint.org/2006... and ditto what everyone has said above...
- Duncan Hull
Integration with Nature Network. Direct PubMed queries. Private shared reference lists. And what Cameron says in his blog post...
- Martin Fenner
Also, Connotea and CiteULike and 2collab and Mendeley need to get together and decide what fields in the RIS they're going to export and import as what data, so you don't end up losing data such as tags and comments when exporting and importing to another service. Citation tree, search/sort by date/author/journal, and easy integration with Word would be on my list
- Mr. Gunn
I just wish it were better at what it's supposed to do, never mind the killer app. Fix the bugs, fix the speed/scalability and make it less ugly :) However, FWIW, the "killer app" in online reference management is not social; it's Endnote-like integration into word processors - of any kind.
- Neil Saunders
Incidentally, there are already ~ 30 comments here, versus 3 at Nature Network; speaks volumes.
- Neil Saunders
From my perspective, integration into word processors and easy IO would be the necessary requirement. The next would be good search engines that take into account relevance based on your "graph" as it were. That same engine can be used to drive a recommendation engine. If I had all of those, with a good API that could be used to drive mashups, and of course appropriate scalability and availability, then at least one person would be happy :)
- Deepak Singh
make it easy to monitor PubMed alerts, TOC alerts, citation alerts, ... http://blog.mckuhn.de/2008...
- Michael Kuhn
I'm pretty overwhelmed by the feedback, in a good way of course. Thanks so much for all of the suggestions. I'll now go and take them on board and try to beat them into some coherent shape.
- Ian Mulvany
Have a citation tree (this article cites these articles) and pre-load with entire network of Nature citations (that is, articles cited by papers in Nature), highlighting some famous papers.
- Richard Akerman
The ability to embed all or a portion of the library (i.e your own papers) in other sites, exactly the same way you would embed video in a blog. Would save me repeating my library across multiple sites and keep them sync-ed, rather than just including a link. Have a tag cloud, not a tag list. Present tags that other people have used to tag the same resource. Normalise your tags, for example use all lower case, TAGX and tagX can end up not pointing to the same document.
- Frank
what everyone else said - plus, if you upload pdfs, why not do some nlp analysis and then map similarities? so extract key entitites and relationships and do analysis on those
- Christina Pikas
oh - plus - if you get it down where you can integrate with Word or LaTeX or open office or what have you - you should also have an option to "work offline"
- Christina Pikas
One thing that I absolutely *love* about Zotero is how it can pick up bibliographic information for books directly from library catalogue screens or when you're looking at a book in Amazon or whatever. When you're looking at a list of books in our catalogue, Zotero will show all the books in a list and let you choose the ones you want for your list of references. So cool.
- John Dupuis
Take a close look at Zotero from a feature perspective. It's a great app. It's limited to FireFox but represents a hybrid desktop/web app that resembles what we'll be seeing. The community built around Connotea (i.e., the people willing to park and comment on citations, build good tags, etc.) may be the real value. Will that community persist once some people can do things others cannot do as Pro users?
- Bill Flanagan
Hi Bill, that's a good point. If you look at flickr (my favorite freemium example), they have maintained their community with a two tier product. I'm interested in knowing what features we could add to Connotea that we could charge for that would retain the community. I have some ideas, but want to hear yours!
- Ian Mulvany
Well, I am glad about the support in favor of word processor integration (Ian surely knows why). I would say that anything that can help scientists write papers will make Connotea more interesting over its competitors. Word processors integration would do. Other possible functions: 1) My articles feature with a warning if anyone bookmarks one of my works, with a mapping users/urls it may not be that hard to do. 2) See next post.
- Mounir Errami
2) If we take two users randomly what are the chances that they share any bookmarks? the point is that a stat study can show when to introduce users to each other for collaboration, or simply because they share a similar interest (competition?). I would also dig around the time consuming paper submission process. For instance identifying reviewers, that's where suggestion 1 would pay. I have to think more about this one.
- Mounir Errami
Ian, sorry for this late response (sorry all, no time to read all your 39 answers...). What I expect from connotea: 1) more reliable, faster. 2) an option for hiding my tags in my page and in the popup windon (takes hours to load !) 3) seeing my group just like delicious networks: hide my entries. 4) complete the profiles (geo-position: what is the closest person interested in NFkB ?).
- Pierre Lindenbaum
my talk about ONS tomorrow at 9:55 at ACS - I'll discuss some interesting correlations between falcipain-2 docking and anti-malarial assays - http://oasys2.confex.com/acs...
Cameron Neylon and Rajarshi Guha liked this
Cool, the achedule looks very interesting. Best of luck!!
- Aarthy
Organelles in Blastocystis that Blur the Distinction between Mitochondria and Hydrogenosomes - http://www.sciencedirect.com/science...
Aarthy, Ricardo Vidal and Neil Saunders liked this
a couple of months old now, but shared because it's a cool paper nonetheless
- Andrew Perry
Wow, thanks for sharing this.
- Ricardo Vidal
Very cool, thanks
- Aarthy
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