Duncan Hull › Likes

I was thinking "nah, it's probably about as bad as I thought" - but you're right! - Neil Saunders

Thanks Iddo. I lost count of how many times annotation errors came up in my discussion with experimentalists who lack experience with such databases. (Not surprisingly, they usually think these errors are negligible, especially when it comes to THEIR proteins.) Now I'll just send them a link to your post... - Mickey Kosloff

My review of "The Fourth Paradigm: Data-Intensive Scientific Discovery" - Michael Nielsen

I changed the title a couple of months back - I like this one more, although it's still a working title. The timeline is tentative. - Michael Nielsen

"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races." - Itachi from Bookmarklet

Certainly, one could never use knowledge of how drugs work differently in different genetic backgrounds to help cure disease, right? - Mr. Gunn

(via pedrobeltrao) A proposed author ID system is gaining widespread support, and could help lay the foundation for an academic-reward system less heavily tied to publications and citations. - Pierre Lindenbaum

Fantastic article! Finally: "But perhaps the largest challenge will be cultural. Whether ORCID or some other author ID system becomes the accepted standard, the new metrics made possible will need to be taken seriously by everyone involved in the academic-reward system — funding agencies, university administrations, and promotion and tenure committees. Every role in science should be recognized and rewarded, not just those that produce high-profile publications." - Björn Brembs

"“Pdfs paralyse the proper and efficient use of scientific knowledge. By burying information in static, unconnected journal articles, scientists waste countless hours either repeating experiments that they didn't know had been performed before, or worse, trying to verify facts that they didn't know had been shown to be false.”" - Mr. Gunn from Bookmarklet

OT - For the record, I started off as a New Romantic, drifted into Old Schematics and ended up being a New Semanticism-ist. - Graham Steel

"A proposed author ID system is gaining widespread support, and could help lay the foundation for an academic-reward system less heavily tied to publications and citations." - Pedro Beltrao from Bookmarklet

This looks closer to reality than ever. 23 organizations supporting the idea with plans to have working code within 6 months based on Thomson Reuters' ResearcherID. - Pedro Beltrao

"thanks to the new HTML5's Audio element and rel="noreferrer", the service may be utilized by client-side web applications" - _alf

good luck, and enjoy it - Frank

Thanks for the nice comments everyone. - Michael Barton

Had the pleasure of visiting the exhibit a couple of months ago. Highly recommend the Wellcome Collection, if you find yourself in Euston with some time to kill. - Neil Saunders

Thanks, Neil, that sounds like a great idea! - Cesar Sanchez

@Neil aye: see http://www.wellcomecollection.org/ - Duncan Hull

"Don't rely on your host or anyone else to back up your important data. Do it yourself. If you aren't personally responsible for your own backups, they are effectively not happening." - Duncan Hull

"One thing to look forward to in 2010 is a very strong probably that the world's largest scholarly journal will be an open access journal, the award-winning PLoS One. OA mandate mania is sure to continue ~ not only are discussions underway at many a university and department, but now that we have a substantial and growing set of role models the benefits of an OA mandate ~ such as increased impact and web presence ~ will become that much more obvious, inspiring yet more mandates". - Graham Steel

BMC Systems Biology, Vol. 3, No. 1. (2009), 109. BACKGROUND:DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources.RESULTS:We developed DASMiner, a Matlab toolkit for querying DAS data sources that enables creation of integrated biological models using the information available in DAS-compliant repositories. DASMiner is composed by a browser application and an API that work together to facilitate gathering of data from different DAS sources, which can be used for creating enriched datasets from multiple sources.The browser is used to formulate queries and navigate data contained in... - Daniel Swan

Nice article. Not sure about "Exaflood"?! Add that to "the metaphors of doom used to describe the phenomenal pace of data acquisition (from data floods, deluges, surging oceans and tsunamis, to icebergs, avalanches, earthquakes and explosions)"... http://pubmed.gov/19929850 - Duncan Hull

Now I have scenes from a disaster movie in my head, as scientists race to save the world from the data deluge... - Neil Saunders

Did you have a look at Law's Laws? (from Andy Law, my ex-boss) http://bioinformatics.roslin.ac.uk/lawslaw... - Jan Aerts

Yeah, good stuff and familiar to us all :-) - Neil Saunders

Usually the inventor, and on first release... - Chris Rusbridge

FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields - Jean-Claude Bradley

Deepak, I think I was just using terminology incorrectly. I was assuming Facebook = social networking. - Steve Koch

Wondering if any seriously large database has experience with making it an open project? - Egon Willighagen

For example, by crowd sourcing curation, allowing replications, streamlining sending around updates, etc... - Egon Willighagen

Has there been much research into this (i.e. quantified "hardly ever")? - Sarah Kendrew

In astronomy data are re-used all the time - scientists often re-use archival data, although there is a certain etiquette to doing this. It's led to new discoveries years after the data were taken, e.g. reprocessing of Hubble images from 1998 led to the retroactive discovery of an exoplanet, see this paper by Lafreniere et al '09 on arxiv http://arxiv.org/abs/0902.3247. Many publicly... more... - Sarah Kendrew

It's unfortunate that you can't delete an uploaded file when editing. OK, this is the version with correct counts for each date - as opposed to the previous, which used the count for the first occurrence of the (multiple, same) date in the file (oops!) - Neil Saunders

Per user stats would be interesting. I'm not sure if the API returns "date user joined" - will look into that. - Neil Saunders

what do you think of this? "By contrast, early bioinformatics work was almost invariably founded on biological concepts from the onset. A biological issue was raised and then a technique to address that issue was presented. That is, theoretical biology was the foundation on which [early] bioinformatics was built. I fear this is being lost in the mass-data and technology-hype driven bioinformatics. It seems to me that unless companies and research groups are careful many will waste time and money “stamp collecting and cataloging”. Certainly the organized data is useful, but only if it is applied with biological principles." - Attila Csordas from Bookmarklet

Grant: it's really good to see you here, every time I cite somebody living here I have the hidden motive to draw the author into this community, get her/him involved, make him/her part of a 'community of equals'. The paragraph cited is itself a good source to initiate a standalone conversation here w/o reflecting to everything in your article. That sad, I encourage people to continue this conversation here. :) - Attila Csordas

I'm not normally "creeped out"...but this time... - Neil Saunders

that's new york... - Rafael Sidi

it's obviously fake, but kind of fun :-) - Neil Saunders

A senior scientist once told me "We all work in public relations"... - Duncan Hull

I think they were right. - f1000

A few weeks ago I had the chance to present the PLoS Article Level Metrics program to audiences at both Berkeley and UCSF (via a simulcast). The organisers allowed me to devote a full hour to our program, and as a result this is the ...

Absolutely: production + consumption, equally important, equally challenging. For me, the practical challenge is how best to do both. I know from experience that working alone on both aspects doesn't work too well sometimes - inevitably you gravitate to one or the other. Somehow we need to build teams, where all contributions are valued and data flows smoothly from production through storage to consumption. - Neil Saunders

At the rate of production, the variety of data types, and all the other crap you have to deal with, IMO it's just not possible, even if you have the skills and knowledge. Has to be a team effort and yes, you have to value the "operational aspect" - Deepak Singh

show us the data! - Jason Stajich

OK, spent a little time playing with Exhibit and I am now officially really impressed. Giving me lots of ideas. But I'm wondering how large a JSON file can be? Hundreds, thousands, millions of items? - Neil Saunders