'Mummi' Thorisson › Comments

I was thinking of creating my own as a Ruby on Rails engine to hook into the lab's existing site. I don't want to reinvent the wheel though. - Michael Barton

we had started on a similar venture way back and using the Gmod tools and a rails frontend. http://rubyforge.org/project... - george

"CrossRef is pleased to announce that it will be participating in the recently launched Open Researcher and Contributor ID (ORCID) initiative to create an unambiguous identifier for scholarly and professional researchers. Our members will be aware that CrossRef has been exploring the possibility of creating an “author DOI” or “contributor ID” system. In doing so, it has become clear that the issues and use-cases involved in identifying researchers span a broad collection of stakeholders including libraries, institutions, funders, publishers and, of course researchers themselves. In short, this is not primarily “a publisher problem.” As such, we believe that the ORCID approach to creating an inclusive and open organization representing all the stakeholders in the scholarly communications process represents the best chance of creating a successful contributor identification system" - 'Mummi' Thorisson

+1 Björn, except I'm not so eager to sign up if it means letting people know that I'm an orc. :-) - Ruchira S. Datta

Sad, just sad - Deepak Singh

what is so harmful about having your research referenced by another? if it is cited, it can bring attention and acclaim to the original. if it is not properly cited, then that is itself the problem - Mike Chelen

Crud - sorry for the re-post folks, there was something in that version that shouldn't have been (and if anyone's downloaded the file and figured out what it is I'd appreciate it if you didn't spread it around - some details to be ironed out yet) - Cameron Neylon

....and its gone! - Cameron Neylon

"NASA’s Jet Propulsion Laboratory (JPL) created the first American satellite and are now using Taverna for their Web Services-based infrastructure.[..] One of the challenges faced by the research team is the integration of various models that are used to explore the science behind the JPL’s missions. These models have been developed independently and run on different platforms, so their integration is not straightforward. The JPL’s solution is to wrap each model as a Web Service and drive them with a Web Services-enabled workflow." [From the OMII-UK newsletter: http://www.omii.ac.uk/wiki...] - 'Mummi' Thorisson

?!? - Neil Swainston

Rocket Science? - Duncan Hull

"deCODE's demise leaves fate of its valuable genetic database unclear. After struggling financially for years, the genomics company deCODE, based in Reykjavik, Iceland, filed for bankruptcy on 16 November. The question now is whether other companies looking to commercialize genomics will follow the same path" - 'Mummi' Thorisson

Things looking gloomier than ever for my ex-employer back in the home country. :( - 'Mummi' Thorisson

Coverage from the Genetic Future blog: http://scienceblogs.com/genetic... - 'Mummi' Thorisson

Yeah, I think I heard about that. Isn't that what they call science? That whole thing where you observe, guess, experiment, speculate, experment again, until you can reproduce results consistently and then you tell someone else who does the same thing with your data? - Aaron Kendrick

So I've heard! :! - 'Mummi' Thorisson

No. science is where you do what you can get funded which absolutely does not include replication checking or audits. None of which generate nature papers - Cameron Neylon from Android

they should have sequenced the money tree first :) (obviously a flippant comment) - Frank

If we are going to centralize this as infrastructure we need to take a strong stance on the build quality and compatibility of these databases so we can bring down costs... - Cameron Neylon

Thorisson, G.A. Accreditation and attribution in data sharing. Nature Biotechnology 27, 984 - 985 (2009). http://dx.doi.org/10... - 'Mummi' Thorisson

+ 1 :-) - Claudia Koltzenburg

What do you want to store? Bits and bobs or lots of stuff? I use google doc for bits and prices dropbox is useful as it has an iPhone app. - Jo Badge from iPod

Mickey: flash drives are great for portability, still external hard disks are the best value for the size, for example 500gb for $100 http://www.newegg.com/Product... though online copies are important since a single drive could get lost or damaged at any time - Mike Chelen

"That's in a perfect world. The first step is to get the data out there. They we can start wondering about structure and presentation. It takes a long time to build a data infrastructure, but you should stop people who have the skills and interest from getting their hands on it. Hopefully data.gov will work with data producers to become a quality data resource, but at least there is a resource in the first place, a place to go and find material. Perhaps a model might be people starting from data.gov and then creating different views into the data for different purposes. They don't have to reside on data.gov, and personally that's what I hope the site evolves to. Making data available in reasonable formats that can then be converted into information by other people." - Deepak Singh

"That's in a perfect world. The first step is to get the data out there. They we can start wondering about structure and presentation. It takes a long time to build a data infrastructure, but you should stop people who have the skills and interest from getting their hands on it. Hopefully data.gov will work with data producers to become a quality data resource, but at least there is a... more... - Deepak Singh

Came across this post last week on the same subject, incidentally: Stefano Mazzocchi's Linotype blog: Data Smoke and Mirrors - http://www.betaversion.org/~stefan... "[..] By grinding all those rectangular datasets into triples, they’ve actually managed to make it *less* useful than in its original form. In the original form at least I had a little context of what this... more... - 'Mummi' Thorisson

I am planning to use WebCite for my thesis. - 'Mummi' Thorisson

not that I know of Claudia - Jean-Claude Bradley

"While invoicing is not a fun task, it’s a necessary one: by keeping clients informed of your expectations, you will get paid punctually and reinforce your professionalism. After going over some best practices for creating invoices, we’ll review some great (and not so great) online invoicing tools" - Mitchell McKenna from Mento

For OS X users - I used TimeLog very effectively for tracking time spent on projects over a period of over 2 years. Didn't use the invoicing feature though. v4 is available (http://www.mediaatelier.com/TimeLog...), though I've only used v3 in the past myself. - 'Mummi' Thorisson

I´d say it depends on whether you'll be doing a lot (or any) customization to speak of, as far as module hacking is concerned. If you only need a few additional modules + templating, it wouldn't be too bad to share a multi-site setup I'd guess, plus you wouldn't have to do maintenance yourself (security updates etc.). - 'Mummi' Thorisson

At the same time I started this thread, I sent an email off to the XC folks asking about their project a multi-site setup. They were kind enough to take the time to reply, and they said that for this particular project they didn't recommend it. - mita

"We are increasingly keeping scientific records in electronic form; it would be straightforward to wrap our notebook pages describing an orphan result with a bit of searchable text, generate a web page, and submit the whole thing to a database. The act of conducting research would thus become practically synonymous with the act of disseminating the resulting knowledge. Along the way, we would have to spend some energy improving the records that we keep in order to ensure that our notebooks were more accessible to outside readers and less like the quirky private diaries they often become." Heh. - Heather

.. and if this could result in a proper citable reference on the other end, that'd sweeten the deal :) See e.g. Jean-Claude Bradleys comment near the top of this thread, about 'dumping' data to Nature Preceding to get a reference + DOI in return: http://friendfeed.com/the-lif... - 'Mummi' Thorisson

The Research 2.0 Concept Model above is an evolution of the Academic Library 2.0 Concept Models developed for my Master's Paper (http://mchabib.com/2006... ). While the original model primarily focused on academic library services for students, the new model focuses on services for researchers. Like in the original models, the top represents communication spaces grounded in physical space, while the bottom mirrors this in the online realm. Two ends of the spectrum are informal communications and formal communications. My argument is that Research 2.0 falls somewhere between these extremes. A full presentation is located here: http://www.slideshare.net/habibmi... - Michael Habib

Interesting social status implications here, especially with the second model. The more robust both sides of the scholar2.0 identity components (UGC + trad), the "deeper" the 2.0 identity (think tag clouds as the metaphor here). Or, perhaps color combos is a better metaphor, with schol.identity2.0 being a mix of UCG (say, "yellow"), trad (say "blue") and combo being "green" -- the shade... more... - Mickey Schafer

Now that's good to know! - Cameron Neylon

Mummi - I had experimented with it a long time ago and there were some issues that led me to drop it. There are still issues - for example when they alert you to the fact that your submission is archived they don't give you all the citation information - have to remember to copy and paste all that info given on the website itself right after submission. I also don't know what happens to... more... - Jean-Claude Bradley

"A prankster in a Darth Vader suit joined the annual procession of the clergy of the Lutheran Church of Iceland. And you know what? It works." - 'Mummi' Thorisson

I'd be happy to receive an invite, too :-) thanks - Claudia Koltzenburg

Mummi send me your gmail ID. - Khader Shameer

"eCAT is an electronic lab notebook (ELN) developed by Axiope Limited. It is the first online ELN, the first ELN to be developed in close collaboration with lab scientists, and the first ELN to be targeted at researchers in non-commercial institutions. eCAT was developed in response to feedback from users of a predecessor product. By late 2006 the basic concept had been clarified: a highly scalable web-based collaboration tool that possessed the basic capabilities of commercial ELNs, i.e. a permissions system, controlled sharing, an audit trail, electronic signature and search, and a front end that looked like the electronic counterpart to a paper notebook." - 'Mummi' Thorisson

Looks like a somewhat specialized wiki with support for structured data and some other useful features? But perhaps it would make more sense to treat lab notebooks as logbooks that track activities and the flow of samples etc -- in which case wikis might not be the best approach. - Eric Jain

I've been at it for years and still haven't figured it out - Deepak Singh

Yep, openID is coming. Think I'll be doing something quite simple with a Wordpress install as a starting point. - Cameron Neylon

"Our modules create RDFa annotations and – optionally – a SPARQL endpoint for any Drupal site out of the box. Likewise, we add the means to map the site data to existing ontologies on the Web with a search interface to find commonly used ontology terms." - François Dongier

"We also allow a Drupal site administrator to include existing RDF data from remote SPARQL endpoints on the Web in the site." - François Dongier

very, very cool stuff. - 'Mummi' Thorisson

Yeah. That's the way to go :) FTA: "..Thieme have actually managed to pull off quite a coup and I commend them for their efforts." second that, times two. - 'Mummi' Thorisson

DOI resolution works like a treat for the example given: http://dx.doi.org/10... - 'Mummi' Thorisson

The description looks interesting "The Science Collaboration Framework (SCF) is a software toolkit to establish web-based virtual team organizations for researchers in biomedicine ". Glad to know it is not a 'yet another scientific-social-network + web 2.0 + etc ...!'. Anyone tried this ? - Khader Shameer

These days, I'm playing a lot with Tattler (http://drupal.org/project...), which uses the OpenCalais API for topic monitoring. - François Dongier

"So, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus. The Genome Campus owes its existence to the pharmacist Henry Wellcome, pictured over on the left. When he died in 1936, his legacy founded the Wellcome Trust, set up with money from his success as a pharmaceutical manufacturer and salesman. Today, the trust is the largest charity in the UK, funding innovative biomedical research and spending over £600 million each year. A large part of this legacy is being (and has been) spent on the Wellcome Trust Genome Campus, home to the Wellcome Trust Sanger Institute (WTSI) (aka “The Sanger”) and the European Bioinformatics Institute (EBI) an outstation of the European Molecular Biology Laboratory (EMBL) based in Hinxton, Cambridgeshire. Cambridgeshire life: Good and Bad It’s a bit... more... - Duncan Hull from Bookmarklet

Continued....Hmm. I wonder if a goatee beard (bristles not shown) counts for Movember? Fav comment from folks at work today was "Mr Steel, what is that thing on your face?" You up for a Movember challenge, my good fellow ?? - Graham Steel

simple csv/tab-delimited with a README? - Rajarshi Guha

i'm testing manyeyes and factual now, but std-doi.de seems to be a good solution too, although it is for bigger data, based on the examples. - Endre Sebestyen

Great. . The journal feeds are a PITA, with all the variation in layout, in use (or rather non-use) of standard entry fields like author, etc. It's causing my colleague who aggregates these things in a our Drupal CMS no end of grief sometimes. - 'Mummi' Thorisson

Oh dear - have you commented at the blog post at the link, Mummi? Geoff answered a previous comment from Egon there. - Maxine

Maxine - I have not, but I should. - 'Mummi' Thorisson

I've neglected FriendFeed for a while now, for the same reasons you list in your post. I think the duplication of Twitter feeds was the main culprit. I'm going to remove my Twitter feed from here now and see if I can make FF work for me again. - Joss Winn

OK, paper started ;-) - Jo Badge

Liking so I can come back to this later... - Cameron Neylon from twhirl

Great article, Cameron. Instantly highlighted on the GEN2PHEN site :) http://www.gen2phen.org/syndica... - 'Mummi' Thorisson

NCBI etc use Aspera already - Deepak Singh

Any open-source alternatives to this? Just wondering - I'm not likely to use this stuff anytime soon. - 'Mummi' Thorisson

Not that I know of. Biggest users are media companies and genome centers happen to be big users as well (I think NCBI requires you to use Aspera). - Deepak Singh