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Ntino › Likes
Would there be an audience for a Beginning Ruby for Bioinformatics blog?
Khader Shameer, Carl, george and 9 other people liked this
Perhaps it's worth finding out! I'd be interested in trying - any other volunteer authors?
- Matt Wood
I would help out, even though I am no Ruby expert.
- pn
I wonder if something along the lines of the Peepcode or Gitcast screencasts would be cool?
- Matt Wood
Gitcasts lite would be nice. Essentially a world in which the examples are about bioinformatics-related topics and not blogs and shopping carts :)
- Deepak Singh
That's the sort of thing I had in mind - teach Ruby from a bio perspective: define classes with biological relevance, using ActiveRecord in biology, show use of @jandot's Ensembl API etc. Perhaps some podcast discussions too.
- Matt Wood
Stands in front of line. I saw go for it
- Deepak Singh
I'd be interested in learning some Ruby, especially if it's bioinformatics-related.
- Walter Jessen
This is a great idea.
- Michael Barton
Yep. And I'll try to find time to contribute :-)
- Jan Aerts
That would be great - It would be great to help introduce the rest of my lab to ruby and programming. -r
- Rob Syme
I'm in a ruby bioinformatics lab - I may be able to contribute a guest post or two, and I'd definitely read the blog.
- Chris Miller
The ruby_for_bioinformatics site could be a repository on github, written in the format of Tom Preston Warners blog engine. That way everyone can contribute sections via git. The site could then be automatically hosted on github at ruby_for_bioinformatics.github.com.
- Michael Barton
Explanation of TPW's blog engine http://bit.ly/rVdl
- Michael Barton
As nice as github is, a wiki has a lower barrier to entry, which, in theory, means more contributions.
- Chris Miller
Discussion session for open science workshop
Mike Chelen, Jean-Claude Bradley, Roland Krause and 11 other people liked this
To Carole Goble (myExperiment): did you experience network effects? Carole says, a bit of seeding and curation needed at the beginning to put a foundation in place and ensure users of quality. Since trust is so important, a process for creating a safe environment is crucial, a place where people still retain some control over how much they share, etc.
- Shirley Wu
Getting users to tag things can still be a challenge. Might be because tagging was in an unnatural place in the workflow.
- Shirley Wu
Sean Mooney from Indiana University: "If you build it, they WON'T come." Note, he helped develop Laboratree, one of the other so-called "facebook for scientists". He says one thing they've emphasized is that funding institutions, grant providers etc appreciate when researchers indicate they will deposit, share, make available their data, or use these collaborative tools
- Shirley Wu
Nigam: something to talk about is the contributor to user ratio. In wikipedia, it's really low, millions of users to thousands of contributors. In science wikis, the ratio is closer to 1. You can't crowdsource effectively with a ratio like that
- Shirley Wu
Drew Endy now talking about OpenWetWare, a wiki resource that started in his lab at MIT by students. When his students started sharing protocols and resources on a lab wiki, other labs took notice and it's now pretty big, ~500 active users. But now the funding has stalled out and they want to get some data on how much impact OWW is having on research
- Shirley Wu
Showing a slide: Idea cycle --> research cycle --> publication cycle. Where are the gaps? what are the priorities? Open science not just open data, but all three cycles
- Shirley Wu
Example: current publishing cycle way too slow compared to current state of collaboration and authoring tools like Google Docs.
- Shirley Wu
Phil Bourne: there's a dichotomy. Do we just refactor things we already have, or do things completely differently? Refactoring can be inefficient but it can be effective in the short term
- Shirley Wu
Steve Brenner asks Drew Endy: what metrics could you use to measure usable outcomes for OWW? Drew answers: one metric for him could be has any user recorded all of a research progress on the wiki? How long did it take? etc.
- Shirley Wu
The problems of lack of concrete success stories is not only true for OWW but much more general for open science. It looks a bit like a chicken and egg problem of lack of identifiers/rewards that create incentives and lack of success stories to justify the changes in rewards.
- Pedro Beltrao
Heather Piwowar mentions: Information behavior issues like these are of great interest to information science field - lots of research and conferences going on so useful place to look for ideas
- Shirley Wu
Cameron mentions one example of completely open recording of the complete research cycle: Jean-Claude Bradley and UsefulChem
- Shirley Wu
Citation and credit is tricky - a lot of people might be using it but don't think to cite it. "No one cites infrastructure." "You know you've been successful when you don't get cited." Also not always clear what it is you're supposed to cite with all these new-fangled web objects
- Shirley Wu
Phil Bourne: idea of "tokens" issued for contributions. But lots of grey areas. What are the relative merits of reviewing a grant vs a paper vs writing a blog post etc. Also what makes sense in one field doesn't necessarily translate into other fields.
- Shirley Wu
One thing we could do to make science more open? Carole Goble - change whole idea of citation, and ensure persistence of identity, sustainability. Phil Bourne - needs to come from funding, funders need to be pro-active. Enormous strides already made in Open Access.
- Shirley Wu
Show of hands from those with refereed grants - how many have made comments int heir grants about data sharing and availability? Most PIs in the room raised hands. Larry Hunter mentions that many grants don't get funded if you don't mention data sharing or how you will make your research and results accessible. But there are cultural differences - genome field shares more than cancer field, e.g.
- Shirley Wu
Russ Altman notes that many studies especially clinical ones, it's not a matter of not wanting to share but it's often a lifetime of work following a very specific clinical cohort, and their entire career depends on them publishing 10-20 papers on that cohort etc so there are other considerations. Cameron says but what if instead of 10 or 20 papers they could get 40 papers out of collaborations? But that is open for debate
- Shirley Wu
Nigam Shah: One thing we could do to make science more open? Demonstrated utility and return on investment
- Shirley Wu
Heather Piwowar: One thing we could do to make science more open? Be brave. Be brave in being the change you want to see.
- Shirley Wu
Larry Hunter quotes ____ McClure: "New science out of other people's data"
- Shirley Wu
Nigam notes: openness is meaningless without context and annotation. If you don't know what the parameters are for the experiment and the data, the data is useless
- Shirley Wu
Drew Endy notes: surprising to him that he has never come across a community of people whose job it is is to make research better. Mike Wong from SFSU mentions there are some people who provide infrastructure for scientists. But problem is that previously not permanent staff, just transient students etc
- Shirley Wu
Drew Endy: Real need to combine the social support that is often there with real technological development. Audience member: problem is that these activities (developing and improving research infrastructures) not often recognized as research.
- Shirley Wu
The success of OWW comes the community, not the technology
- Graham Steel
So now Drew Endy's One Thing We Could Do: incentivize infrastructure R&D
- Shirley Wu
Phil Bourne: we may need to combine a top-down (funders, policy-makers) with a bottom-up (scientists, grassroots) approach and meet in the middle
- Shirley Wu
Dave de Roure: examples of this in the UK with funded "Virtual Science Environments"
- Shirley Wu
Phil Bourne: key component is to demonstrate that we have impacted science in specific ways.
- Shirley Wu
Dave de Roure's One Thing We Could Do: Connect and present success stories
- Shirley Wu
Larry Hunter notes: the National Centers for Biocomputing were conceived partly to accelerate scientific discovery through infrastructure and tools. 1. Driving biological problem. 2. Develop tools to solve problems. 3. Demonstrate impact of tools.
- Shirley Wu
Quo's One Thing We Could Do: Separate the camps. Open vs. non-open. We also need to reflect on our own identity and what makes a scientist. Do we define ourselves in terms of publications? citations? the data? How might this change? How do we take this into account?
- Shirley Wu
It occurs to me that a lot of people in this discussion are established PIs. Just this fact is a huge difference from some of previous discussions I have seen in real life or online where we would discuss the need to get PIs to be aware of these topics.
- Pedro Beltrao
Carole: mentions a big fear which is mis-representation. What if someone uses your open protocol for a completely inappropriate purpose and then cites you? These are important issues to address
- Shirley Wu
thank you, cameron! took the words right out of my mouth ...
- Kaitlin Thaney
Have only caught bits of this but nice wrap up Cameron
- Graham Steel
Would have loved to be there
- Deepak Singh
Ditto Deepak - looks like a very productive meeting
- Jean-Claude Bradley
Deepak Singh, "Science Big. Science Connected." High quality version, including Q&A session. (Torrent) - http://www.mininova.org/tor...
'Mummi' Thorisson, Khader Shameer, David HC Soul and 16 other people liked this
The file is about 740 MB at a length of just over an hour. H.264 encoding, MP4 container. If you can torrent, please do, even if you can't upload, as this will take weight off my server. If you can seed, thanks in advance. If you can't torrent, you can fetch the file by http from http://gotgenes.com/media...
- Chris Lasher
Also, the talk is licensed under Creative Commons By Attribution. So if you want to also provide an upload point for it, that's all the better.
- Chris Lasher
@gotgenes great work!
- tim
from Alert Thingy
I'll have divided the talk into presentation and Q&A parts tomorrow, and then I'll upload them to Vimeo, for those who would like to stream off the web. Thanks to all who have downloaded so far, to the seeders, and for the positive feedback!
- Chris Lasher
Chris ... Seeding away.
- Deepak Singh
The recording of the presentation is up at Vimeo now: http://vimeo.com/2421481 I'll upload part 2, the Q&A, a week from today (due to Vimeo upload restriction of 500 MB per week). So now that you have three ways of obtaining and watching this talk, watch this talk! =-D
- Chris Lasher
Part 2, Q&A, is now up on Vimeo! http://vimeo.com/2507911
- Chris Lasher
Deepak is turning into a Rock Star :-)
- Sally Church
Deepak was always a rock star - you need to see his old Seattle Ignite talk - serious entertainment
- Cameron Neylon
Thanks Cameron, I hadn't seen Deepak's Ignite talk before:- http://ignitenight.blip.tv/file...
- Graham Steel
That first Ignite talk was the most work I ever did on a talk in terms of preparation
- Deepak Singh
Wow, that's amazing! Well done on that talk, Deepak.
- Sally Church
If you ever get a chance to go to an Ignite event, you should
- Deepak Singh
Typealyzer - http://www.typealyzer.com/index...
Thomas Brox Røst, Morton Fox, Raoul Pop and 4 other people liked this
According to Typealyzer "The analysis indicates that the author of http://mndoci.com is of the type: INTJ - The Scientists"
- Deepak Singh
from Bookmarklet
Looks like I'm ISTP - The Mechanics. It's a fun game, but just that, I think, at the the moment: http://blog.econtech.selfip.org/2008...
- Allyson Lister
Allyson. Would explain why it worked with my blog where everything is full content. Surprising why it wouldn't work for you
- Deepak Singh
Deepak. It "works" for me - I just have no idea what my personality is according to those tests in general - not sure I've taken one recently, if at all! I did get a result, just not sure of its appropriateness :D No worries!
- Allyson Lister
Lol. Am a Duty Fulfiller: the responsible and hard-working type. I'd better tell my boss.
- Jan Aerts
I got classified as ISTJ, and from taking the MBTI tests earlier I am somewhere in-between ESTJ and ENTJ. So, I can just not believe that the socializer classified most of us as 'I'ntroverts, which means being more reserved and less outgoing. What are introverts doing here on Friendfeed?;-)
- joergkurtwegner
Oh boy, did they get me wrong! Hahahahaha
- Egon Willighagen
Introverts are "lurking" on FF
- Jim Hardy
Some librarians, myself included, played around with Typealyzer here: http://walt.lishost.org/2008...
- John Dupuis
here's one "INTP - The Thinkers",,, awesome link Deepak !
- Ntino
Another INTP "Thinker" blog here; in real life I am an ENTP so not so far off in comparison.
- Sally Church
One more "INTP - The Thinkers" for the tally
- Lars Juhl Jensen
"INTJ - The Scientists" from my blog. Cute
- Pedro Beltrao
@John: I took the genderanalyzer test and now I know that I am to 60% a woman. Mmmhhh, I got to talk to my wife about this.
- joergkurtwegner
I'm INTJ - The Scientists, my PI is INTP - The Thinkers. Pretty funny. I forget what I am in real life, I think pretty similar.
- Shirley Wu
Will Asimov’s Foundation saga be Lord of the Rings in space? - SFFMedia - http://sffmedia.com/films...
Michael Fidler, tim, Mr. Gunn and 8 other people liked this
I hope this works out. My fave scifi trilogy of all time. Of course, they better do as good as job as Peter Jackson did with LoTR.
- Deepak Singh
from Bookmarklet
double 'like' !!! thanks !! ( Actually, I plan to major in psychohistory )
- Pierre Lindenbaum
never read Asimov :( - can anyone share how Asimov compares with the creativity and spirituality of Tolkien ? thanks!
- General Kafka
Very very different. Can't really compare the two. I actually got into Asimov when I was very young (my dad's a big fan). This is classic scifi, not fantasy. Asimov is much closer to Arthur C. Clarke than to Tolkien. Philosophical, not spiritual and the source of one of my all time favorite quotes "Violence is the last refuge of the incompetent"
- Deepak Singh
I've only read Prelude to Foundation, it was awful
- Christopher Harris
woooopps changed psychology to psychohistory in my previous comment... of course....
- Pierre Lindenbaum
Christopher .. that doesn't count. The original trilogy is it!!! The rest are pretty bad. I don't think Asimov even wrote all of them (he did write Prelude some 20 years after the original series)
- Deepak Singh
oh dear, maybe i'll have to read them then.. they better be on audible
- Christopher Harris
@Christopher Harris: agree. There are many books written by Asimov with a lower quality (Foundation and Earth , ...). But 'Foundation', 'Foundation & Empire' and 'Second Foundation' are worth reading.
- Pierre Lindenbaum
does anyone know any GOOD sci-fi on neuroscience? it's always physics, space, chemistry or AI...
- Christopher Harris
thanks for the tips on Asimov. Pierre: did you read it in english or french ?
- General Kafka
French. Honestly, I read 'Foundation' when I was 14 and I still really love to re-read the trilogy but at the end, all Asimov's books seem to be the same: a big surprise at the end of each chapter ( Elijah Baley's investigations) and at the end, the bad/good guy was the less suspected (Tyrann, Second Foundation, Foundation and Empire,....) ,
- Pierre Lindenbaum
I could read either language - I guess I should just read the original -- anyone has comments on Asimov's english style ? maybe the ideas are more enjoyable than the quip/poetry/style etc ?
- General Kafka
His style isn't poetic by any standards. Actually best way to get into Asimov is to read The Last Question, which was my introduction to Asimov as a 10 year old :)
- Deepak Singh
i love Asimov as well. Read the foundation and the foundation and earth. also recommend his robot series!!
- Hayk
And lets hope they don't make a Will Smith movie out of the Foundation. It was fun, but it was not as Asimov would have intended :)
- Deepak Singh
Yeah, read the book and saw the movie... but did find only minor resemblance... the book was way better. Sorry, Will!
- Egon Willighagen
Like Pierre, I read the original trilogy at age 14. I'd grown out of SF by the time I was 15 and had read every book in the category in the library ;-) I did, however, give "prelude" a go when it came out and agree it was rubbish. Probably Asimov did not write it. Marcus Chown could tell some stories about that. But better than Peter Jackson's LOTR (extended editions)? Come off it! Not possible. ;-) Nothing could be.
- Maxine
Maxine ... it would be very very difficult. Let's start a pool on who should play the Mule
- Deepak Singh
I wasn't gonna, but now I hafta: you people who think Jackson deserves anything but being fed to weasels for what he did to LoTR are on drugs! Ugh, those movies were a travesty, a disgrace, vandalism, an abomination!
- Bill Hooker
@Deepak: for some reason I am already seeing in my head the Mule played by Kevin Spacey.
- Bill Hooker
Bill, I have to heartily disagree with you :-) I think that the LoTR trilogy are among the best movies and was pleasantly surprised how well they reflected my imagination after reading the books. I still do prefer the books, though.
- Lars Juhl Jensen
Deepak - no contest - Andy Serkis (aka Gollum and King Kong). Oh, and Einstein.
- Maxine
@Christopher: You could start with "Flowers for Algernon" by Daniel Keyes and then continue with "The IQ Merchant" by John Boyd...
- Enro
Google and the Wisdom of Clouds - http://www.businessweek.com/magazin...
Berci Mesko, MD, Ntino, Thomas Brox Røst and 2 other people liked this
Google's academic cloud initiative.
- Michael Nielsen
Starts with generic information about infrastructure, but ends by talking about "research clouds".
- Richard Akerman
Databases in Cloud Computing Environments - http://www.cs.uwaterloo.ca/~ashraf...
Ntino, Roger Chen, Deepak Singh and 4 other people liked this
Course offered at the University of Waterloo
- Michael Nielsen
Datasets for information retrieval - http://www.cs.toronto.edu/~tsap...
Ntino, Richard Akerman, Deepak Singh and Ricardo Vidal liked this
Some small datasets for running trial tasks in information retrieval.
- Michael Nielsen
How do you filter your RSS feeds from journals? Or do you at all?
Maureen, Ntino, Jere and 5 other people liked this
I have too many entries and need to declare feed reader bankruptcy. I'd like a better way to get my journal subscriptions so I don't have to do this again.
- Chris Lasher
I don't filter, but i do categorize via NetNewsReader. I'm eyeing Planet Venus: http://www.intertwingly.net/code... Plug-able filters FTW. I'm contemplating how to add feed back into the filters so that I can setup an RSS SpamAssasin filter based on what I read.
- Paul J. Davis
I'm using more and more 'saced searches' instead of firehose journal feeds. I just end up deleting a crapton of them unread.
- tim
from Alert Thingy
No filter, read them all. I am a journal junkie, have to have them all.
- pn
I use this filter http://pipes.yahoo.com/pipes... and I have a few pubmed queries set up
- Pedro Beltrao
Probably not quite what you're looking for, but I use postrank.com to filter a bunch of my RSS feeds. It does a pretty good job of taking some of the big feeds (BoingBoing, TechCrunch and similar) and extracting just the most interesting. I use the postrank Firefox plugin to integrate with Google Reader.
- Michael Nielsen
Pretty cool Pipe Pedro. Is there any reason you have done it by pulling the feeds direct from journals rather than as a series of PubMed RSS searches + filters based on your keywords ?
- Andrew Perry
Does anyone use Barf? http://barf.jcowboy.org/
- pn
Yep, but there are a couple that I use from there still.
- pn
I have a combo of ToC and search feeds in GReader. On abstract review, "Interesting" items get starred (and possibly shared) and later, theoretically, read. Starring is fairly inclusive and is analogous to an "interesting" tag, more than anything. Often reduces search space.
- Chris Cotsapas
I have a 'daily' tag in Google Reader that contains all the feeds I want to see every day, including standing PubMed searches by RSS and Scopus alerts. Various other journal tables of contents go under other tags ('structural biology', 'high impact', etc), but I only drink from the firehose in a solid session once a month, when follow up any 'must read' articles and manually filter the rest.
- Andrew Perry
@Andrew - I guess I could have filtered down the pubmed queries by journals as well but the idea is that from some journals I want everything and from others I filtered them by keywords. Plus I think yahoo pipes had just came out at the time :).
- Pedro Beltrao
I subscribe to publishers feeds from a limited number of journals, but mostly rely on targeted keyword search feeds from PubMed. for details of how to make these, see the video at: http://smallworldz.wetpaint.com/page... Using Google reader, I can scan a large amount of data very quickly, but of course the trick is choosing the right keywords (and Boolean terms).
- AJCann
Currently, I filter none of my feeds, and then feel guilty when I wake up one morning to 100+ new articles that have just been published and I just scan the titles! However, there are some interesting ideas here, which I will investigate... thanks!
- Allyson Lister
I don't filter feeds, I subscribe to the results of certain key HubMed searches. This tends to generate 20-30 articles a day, which is easily manageable. And I don't think anything important has escaped my attention, I always already have the articles people give me to read.
- Simon Cockell
I have few RSS feeds based on PubMed search queries - this goes as "high-importance" stuff, read from GReader daily. Also get a weekly digest from F1000 (configured around my research interests).
- Yaroslav Nikolaev
I think collecting a ton of feeds over at Google reader (can take them!), and then doing a keyword search to find what you looking for works best.... Also a tag to get the "daily" feeds that you always read among the mass is good..
- Ntino
SubMeta: grants for unusual research/ers. - http://www.submeta.org/index...
Mike Chelen, Sally Church, Pedro Beltrao and 12 other people liked this
thought Pawel in particular might like this
- Bill Hooker
very interesting indeed :)
- Jean-Claude Bradley
does anyone know who is behind this ?
- Pedro Beltrao
I got there from Garrett Lisi's pages so either it's his baby or he knows whose it is.
- Bill Hooker
well here's mine I would like to explore the possibility of funding for the UsefulChem project. Started in 2005, the aim of UsefulChem has been to carry out unambiguously useful work in chemistry in as transparent a manner as possible. The project currently has a strong focus on the synthesis of anti-malarial agents and supports a collaboration between Indiana University (Guha,...
more...
- Jean-Claude Bradley
part 2 Seeking to distinguish this approach from other less transparent Open Science initiatives, I have termed it "Open Notebook Science". It is an apt term since the driving force of the project is the publication of the laboratory's notebook onto a public wiki in as close to real time as possible. This provides an opportunity for anyone to participate. In fact one of the advantages of the approach is that it allows for a closer interaction between granter and grantee.
- Jean-Claude Bradley
I'll let you know if anything comes of it - thanks for the tip Bill!
- Jean-Claude Bradley
*slaps own forehead* Don't know why I didn't think of UsefulChem. I'll keep my fingers crossed for you!
- Bill Hooker
Thanks Bill! I do like it :)
- Pawel Szczesny
I'd be interested to hear how it goes. And how much money the might have available. Could do lot of things if I could get my salary paid for two years. Actually I guess all of us could probably do that :) Application from Friendfeed users perhaps?
- Cameron Neylon
so any pointers of how can a non-profit / tax-free corporation can be legally formed (how difficult would it be to found one) ? Maybe the LifeScientistsFF non-profit - hehe ... cause that's a requirement for the grant...
- Ntino
I have no idea how forming non-profit looks in other countries, but if here in Poland it is relatively straightforward, it cannot be hard anywhere else :). Non-profit can be formed by a single person, and that's a recommended way. Forming anything legal across many countries is really, really hard.
- Pawel Szczesny
Look at us, gathering like hungry vultures at the slightest whiff of potential funding! Makes my socialist-leaning heart hurt to realise that we're never going to fund the Open Science of biogang daydreams with public money.
- Bill Hooker
Public money is overrated, but then I am anything but socialist :)
- Deepak Singh
Bego from ChemistsWithoutBorders has just gone through the non-profit process - it takes time but he might have advice http://www.chemistswithoutborders.com
- Jean-Claude Bradley
Cheers!
- Egon Willighagen
Thanks Egon! FF works
- Jean-Claude Bradley
great ! congratulations :)
- Pedro Beltrao
Awesome! Congratulations, Jean-Claude.
- Bill Hooker
Collaborative Drug Discovery - http://www.collaborativedrug.com/
Aarthy, imabonehead, joergkurtwegner and 7 other people liked this
In in SF attending Collaborative Drug discovery Meeting, learning about special software now. Will keep you posted.
- Maureen
from Bookmarklet
Seems a lot like facebook model only for groups working on preclinical drug discovery. You can create groups with "read only," create new molecule records [sd file, mol files, smiles], flexible tags [pubchem CID, hyperlinks]
- Maureen
Here is the link for the conference. http://www.acteva.com/booking...
- Maureen
Me likes that they offer free access to the database for Innocentive solvers...
- Ntino
chemical structure editor, heat map for bioactivity, etc. Looks cool.
- Ricardo Vidal
The excel export is also quite impressive. Wish I was doing drug discovery work. hehe
- Ricardo Vidal
any FF or OWW folks here at the conference? Just noted a poster with Jean Claude Bradley's name. I'm wearing a name tag, all black with a fabulous silver necklace.
- Maureen
Maureen, unfortunately I had to cancel but Barry was good enough to put up my poster. Tony Williams should be there later during the poster session to talk a bit about our project's connection with CDD and ChemSpider
- Jean-Claude Bradley
@JCB, thanks. Will look for Tony and hope to see you at another mtg.
- Maureen
We've posted some falcipain-2 assay results on CDD with a public access in collaboration with the Rosenthal group at UCSF
- Jean-Claude Bradley
Here is my poster: http://www.slideshare.net/jcbradl...
- Jean-Claude Bradley
I like the focus at this meeting on industry-academic collaboration for drug discovery and that they are using web-based tools for multi-site collaborations.
- Maureen
Has anyone more information posted on this platform/topic? E.g. some case-studies, if this is really usable?
- joergkurtwegner
I'll try and round up a few and post links. Examples at the meeting focused on collaborative screening.
- Maureen
I've been curious as well. I like the concept, but there are so many other challenges here
- Deepak Singh
Why does Open Access matter to you? A blogging contest - http://scienceblogs.com/clock...
Ntino, Nils Reinton and Kevin Gamble liked this
Scripps to study lifestyle impact of gene testing - http://uk.reuters.com/article...
Thomas Lemberger, Ntino and Pawel Szczesny liked this
"LOS ANGELES (Reuters) - San Diego's Scripps Translational Science Institute said on Thursday it will conduct the first study to assess whether people undergoing genetic testing ultimately change their behaviour. Participants age 18 and older can receive a scan of their genome -- using a saliva sample -- and an analysis of their genetic risk for more than 20 health conditions that may be changed by lifestyle, including diabetes, obesity, heart attack and some forms of cancer. The study will offer Navigenics Inc scans using gene chip technology from Affymetrix Inc to up to 10,000 employees, family members and friends of the non-profit Scripps Health system. The research will assess changes in behaviours over a 20-year period."
- Attila Csordas
from Bookmarklet
We should also be studying the impact genome-wide scans have on things like mental health and life outlook. Early adopters might be comfortable with statistical nuance, but will the general population?
- Todd Harris
Agreed with Todd, it's a tough problem from a consumer recruiting point-of-view for those companies: there are a lots of geeks outside now adopting every new tech gadget in any niche but the number of biogeeks ready for a personal genetics service is only the fraction of that geeky population.
- Attila Csordas
To show or not to show data - http://blogs.nature.com/nautilu...
Ntino, Deepak Singh, Jean-Claude Bradley and 3 other people liked this
Nature Chem Biol editorial: "Given the option for including supplementary information online, the existence of public databases and the fundamental importance of a robust peer review process, we conclude that the use of 'data not shown' and other caveats that exclude relevant data from the hands of editors, referees and readers is no longer appropriate."
- Bill Hooker
Web 2.0 Is Easy -- You'll See - http://www.genome-technology.com/issues...
Deepak Singh and Ntino liked this
AJ Cann, University of Leicester
- Todd Harris
I'm wondering how many other academic settlements are doing similar initiatives.... it makes me wanna scream my lungs out, when thinking that 95 % (say even more?) of the scientists are out of the Web 2.0 loop...
- Ntino
I just set up a twitter account for my lab. Inviting all interested to follow our shenanigans. - http://twitter.com/HoatlinLab
Attila Csordas, Jean-Claude Bradley, Ntino and John Dupuis liked this
"reverse-engineering cancer", I like it!
- Bill Hooker
I have made the lab an imaginary friend here on FF; I'll be interested to see how useful microblogging turns out to be for lab bidness.
- Bill Hooker
Bill, yeah. I realized I could twitter, similar to posting in the news box on the lab wiki front page. It's an experiment.
- Maureen
Maureen - good idea -- another communication channel. I've been broadcasting news updates for WormBase (http://twitter.com/wormbase). Still a novelty at this point as we haven't been able to recruit many followers.
- Todd Harris
23andMe on Twitter! - http://pimm.wordpress.com/2008...
Deepak Singh, Ntino, Christopher Harris and 2 other people liked this
I do like the idea of a bot for news etc, but also like more human faces, e.g. Jeff Barr at AMZN, Lauren Cooney at MSFT, etc
- Deepak Singh
5 Great Science Books to Expand Your Mind - ReadWriteWeb - http://friendfeed.com/e...
Ntino and Pawel Szczesny liked this
Hmmm, read 2 out of 5. Need to try the other 3....
- Bora Zivkovic
New Pubmed feature: My Bibliography - http://www.nlm.nih.gov/pubs...
Maureen, Andrew Perry, Sally Church and 6 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
Who 'likes' my FF posts the most? - http://comments.deasil.com/2008...
Joe Dunckley, Dave Slusher, Daniel Swan and 5 other people liked this
sweet ! How'd you made it ?
- Ntino
click on the title/link and put in your nym
- Bora Zivkovic
Wow, seems like I'm liking you a lot, Bora :-)
- Björn Brembs
;-) But you need to like this one in order to stay in the lead!
- Bora Zivkovic
How can anyone not like this post?
- Bob O'Hara
Sigma-Aldrich First Official Sponsor of Open Notebook Science Challenge - http://usefulchem.blogspot.com/2008...
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Michael Nielsen, Ntino, Mr. Gunn and 10 other people liked this
A 'high 5' to ONS
- Graham Steel
thanks Graham!
- Jean-Claude Bradley
Excellent news!
- Rajarshi Guha
Looks good :)
- Ricardo Vidal
Rajarshi - we'll finally have enough numbers to make a decent solubility model I hope
- Jean-Claude Bradley
I love real data :)
- Rajarshi Guha
J-C, how much is that? I hope it's at least more than 100...
- Egon Willighagen
If you mean how many measurements we've done so far - about a dozen http://onschallenge.wikispaces.com/
- Jean-Claude Bradley
If you mean how many people involved we have currently 2 with 2 more coming on board this week and hoping that more join - with SA donating compounds hopefully that will help
- Jean-Claude Bradley
If you mean how many measurements we aim for I think Rajarshi can start working with the modeling after we have over 100
- Jean-Claude Bradley
100, that would be my minimum too...
- Egon Willighagen
note that these are actual solubility measurements, not yes/no
- Jean-Claude Bradley
"Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers" - Piwowar et al; PLoS Medicine - http://medicine.plosjournals.org/perlser...
Aarthy, Jere, Ntino and 2 other people liked this
"Sharing biomedical research and health care data is important but difficult. Recognizing this, many initiatives facilitate, fund, request, or require researchers to share their data. These initiatives address the technical aspects of data sharing, but rarely focus on incentives for key stakeholders. Academic health centers (AHCs) have a critical role in enabling, encouraging, and rewarding data sharing. The leaders of medical schools and academic-affiliated hospitals can play a unique role in supporting this transformation of the research enterprise. We propose that AHCs can and should lead the transition towards a culture of biomedical data sharing".
- Graham Steel
Big data: open-source format needed to aid wiki collaboration - http://www.nature.com/nature...
Sally Church, Graham Steel, John Dupuis and 4 other people liked this
I assume that the irony of a call for open source collaboration being published in a non-OA journal is not lost on this crowd.
- Chris Miller
Chris- Nature is open source and also open data (data reported must be publicly available). This is a different issue from the open-access business model for the articles themselves. (Maxine from Nature.)
- Maxine
"information is at risk of becoming redundant and fragmented" - I think that is the most useful form of information :)
- Jean-Claude Bradley
Thanks, Jean-Claude. Incidentally the link is to a Correspondence (Letter to the Editor), expressing an opinion on an article in Nature's recent Big Data issue. Other views are welcome, either submitted as Correspondence to the journal (email to correspondence@nature.com) or as online comment to the news story at http://www.nature.com/nature.
- Maxine
Maxine - unfortunately all I had time for is a quick FF comment on this - an example in itself of fragmented information perhaps being better than no comment at all..
- Jean-Claude Bradley
I echo Clay Shirky. It's not about information volume, it's about filter failure :)
- Deepak Singh
its also about aggregator failure as well - as Jean-Claude points out the fact that stuff is fragmented is as big a problem as the filtering
- Cameron Neylon
Maxine, I see your point, but in my mind, the biggest hurdle to open science is access. Accessible data doesn't do me any good if I can't access the article and know that the data exists. I really do applaud Nature's embrace of the web, and its requirement for open-data, but it's still not an open-access journal. I'm sure this has been argued ad nauseum elsewhere, but I feel like my point stands.
- Chris Miller
The article you have linked to is a Correspondence letter to the Editor, Chris. No data in it, it's just a couple of hundred words of someone's view. I too don't want to get into comparing publishing models, but virtually all working scientists can read nature content via site licences. And you can certainly know that the articles exist because tables of contents and abstracts are free...
more...
- Maxine
@Chris -- if you want to read the Big Data articles I saved pdfs. Pretty sure Nature won't mind. :-) @Maxine -- "virtually all working scientists can read nature content via site licences" -- have to disagree here since NPG articles are already appearing in the References Wanted room. (Was going to raise the question of developing nations but credit where due, NPG titles are available through HINARI.)
- Bill Hooker
But that's part of my problem. The current models (from funding to publication availability) really discourage the small scientific group, small company, individual software developer etc. If not discourage, they definitely make things hard
- Deepak Singh
Thanks all for the points above directed to me - I won't write more here about access to literature as there are plenty of reasoned discussions at nature.com about it if anyone wants to look. To my mind it is a side-issue to the point about wiki collaboration which is the Correspondence link at the top of this thread (eg Deepak, your point isn't about that, but a more general one about research papers and other aspects). I haven't heard about the References Wanted room, Bob.
- Maxine
Maxine, my point was definitely OT
- Deepak Singh
ot?
- Maxine
Oh, on topic, sorry. Yep, open source - open data. On topic.
- Maxine
Actually Off Topic :)
- Deepak Singh
I was thinking "out of town"? "Over the top"?......;-)
- Maxine
@Bill, "the Big Data articles I saved pdfs" thank you. I forgot to do so. too busy at work etc. can you zap 'em over please when you get a chance - no rush. cheers.
- Graham Steel
OPEN ACCESS UNDER ATTACK: - A bill that would reverse NIH open access policy goes up before House Judic Cmte on Tuesday. I'll try to get a blogpost and a DKos diary together by Mon AM, but I'm short of time. Thought others here might also want to run with this. See links I've attached as comments.
Walter Jessen, imabonehead, Björn Brembs and 3 other people liked this
PolITiGenomics: "Open access under attack" - http://www.politigenomics.com/2008...
- Chris Patil
Ars Technica: "Backlash against open access" - http://arstechnica.com/article...
- Chris Patil
That's Funny: "Open access - is there still a debate?" - http://staff.washington.edu/rec3141...
- Chris Patil
Great Beyond: "Open access: public good or publishers' evil?" - http://blogs.nature.com/news...
- Chris Patil
Chris: last I heard, the Conyers bill was shelved for the year (http://www.earlham.edu/~peters...). Is this the same language attached to another bill, or a resurrection of the original? (Either way, it's important to keep pushing back against the horrible thing!)
- Bill Hooker
Judging from this piece that I got as a facebook update - http://www.new.facebook.com/note... - it's still alive, and is going up before the Judiciary Committee on Tues. Chances are it won't pass in this Congress, but it's still important to fight. I'm in the process of verifying the Tuesday date right now.
- Chris Patil
Yes. Do it.
- Bora Zivkovic
Bora, do you know what the 9/24 deadline is about? I originally thought it was because the bill us up before the House Judiciary Committee, but now I can't find a specific reference and believe I've imagined it.
- Chris Patil
Isn't 9/24 (damn this US date order) the date that congress recesses for the break/election?
- Cameron Neylon
If that's the case then I think I won't stress myself out trying to get a major blogstorm going -- I leave for a conference tomorrow night and my poster is still not finished :-) I'll keep abreast of this situation, though, and will share important news with this group as it emerges.
- Chris Patil
At least one source says the bill is shelved but it's not well-referenced. Tracking it down now.
- Chris Patil
"With Congress set to adjourn on September 26, Rep. Howard Berman (D-CA), who chairs the subcommittee on the Courts, the Internet and Intellectual Property, which sponsored last week’s hearing, said the bill would be held until at least next year." - http://www.libraryjournal.com/info...
- Chris Patil
Thanks for doing all this Chris, esp as you are clearly v busy right now. I am also swamped but will at least blog about it as soon as I can come up for air.
- Bill Hooker
No problem. Judging from the timing of the recess I think we can safely avoid worrying about it *at least* until the lame duck session of this Congress and probably until after the new Congress is sworn in next year. But we need to spread the word and be ready in the meantime....
- Chris Patil
The goal of the W3C SWEO Linking Open Data community project is to extend the Web with a data commons by publishing various open datasets as RDF on the Web and by setting RDF links between data items from different data sources.The figure shows the datasets that have been published and interlinked by the project so far.
Deepak Singh, Pawel Szczesny, Thomas Lemberger and 3 other people liked this
More info, news etc (and full sized fig, scroll to bottom): http://esw.w3.org/topic...
- Bill Hooker
I would today count Chrome as an example of acceleration because through sheer speed (x10 for Javascript) it will redefine much what will now be possible as web application.)
Ntino and Victor Kotusenko liked this
Dear all, Nature will be publishing a "big data" special issue this week (4 Sept issue); I'm giving you a heads-up that our publisher has kindly agreed to make the content free for 2 weeks from pub date.
Sutee Dee, Ntino, Martin Fenner and 4 other people liked this
The 4 Sept issue is available online from about 7 pm local UK time on Wed 3 Sept, http://www.nature.com/nature
- Maxine
Does anyone know how I can validate RDF, OWL and/or SKOS against a schema (XML Schema/RelaxNG/whatever) locally on a Linux OS? I'm using webpages now, but that won't work on the train without web access...
Ntino and Deepak Singh liked this
Egon, I don't think this kind of RDF file can be validated with a *schema* because there are many ways to write a N3 statement, and those statements can appear at any place in any order in your file.
- Pierre Lindenbaum
Well, XML syntax would be fine too...
- Egon Willighagen
Try running the W3C RDF validator locally in Tomcat? http://www.w3.org/Status#...
- _alf
hubfeed, that's not quite what I had in mind, but will certainly do... thanx! Now, how about OWL and SKOS? :)
- Egon Willighagen
try reading your XML/rdf with the Jena API ?
- Pierre Lindenbaum
What are the "webpages" that you are using now? If you want to check for conflicting statements (rather than just RDF/XML syntax errors) you'll need to run a reasoner such as Pellet [http://pellet.owldl.com/] (OWL DL) or Jena [http://jena.sourceforge.net/inferen...] (OWL Lite)
- Eric Jain
Eric, saw Pellet mentioned earlier this week... looks quite interesting. I have not use Jena really, but Sesame (OpenRDF.org) instead as RDF storage.
- Egon Willighagen
I've used Protégé to edit and check OWL files: http://protege.stanford.edu/overvie...
- Eric Jain
I second that Protege is the best option - plus it lets you browse though OWL
- Ntino
I was actually looking for something I could integrate in build processes... e.g. with Ant or cmake...
- Egon Willighagen
Protege does have an API and can be run in headless mode, but even if you can get all of this to work (don't ask me how) it may be simpler to create an Ant task that uses e.g. Pellet+Jena (see sample code in distribution)
- Eric Jain
Cognition :: Giving Technologies New Meaning - http://www.semanticmedline.com/
Zaki Manian, Ntino and Deepak Singh liked this
Semantic medline - I haven't played around with it properly yet, but the initial results were quite good. There is also a nifty little box that shows you what terms it has identified.
- Paul Bacchus
from Bookmarklet
Neat: Terms are expanded into synonyms and also into more specific terms (based on a proprietary dictionary?). Plus you have the option of disambiguating terms with multiple meanings. But I don't quite agree with their assertion that such smart text searches remove the need for structured data, see my comment on http://blog.cognition.com/...
- Eric Jain
iPython on the iPod Touch - http://www.reddit.com/goto...
Ntino, Andrew Perry and Chris Lasher liked this
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