Nicolas Bertrand › Likes

Ontogenesis (22 January 2010) In OntoGenesis we intend to provide biologists and bioinformaticians with the means to understand ontologies within the context of biological data; their nature; use; how they are built; and some of those bio-ontologies that exist. All of this is based upon knowing what an ontology is. This can then lead on to the motivation for their use in biology; how they are used; and so on. The definition of ontology is disputed and this is confounded by computer scientists having re-used and re-defined a discipline of philosophy. The definition here will not suit a lot of people and upset many (especially use of the word “concept”); We make no apology for this situation, only noting that the argument can take up resources better used in helping biologists describe and use their data more effectively. Robert Stevens, Alan Rector, Duncan Hull - Allyson Lister

there is also http://www.daml.org/ontolog... that has many different ontologies that can be used - mariana

I think its more like the Perl culture "There is more than one way to do it !!" Best practices in bioinformatics is currently in an ad-hoc state of practice.Just like Damian Conways's Perl Best Practices is one of the best guide for good coding practices for Perl - hope we will also have a book on "Best Practices in Bioinformatics" soon, may be by a group of authors from LifeScientists room - what say ? - Khader Shameer

@Frank I've been reading sequence assembly papers recently. I should start reading annotation papers though as that's the next step for me. - Michael Barton

...and not how you store it - Cameron Neylon

Can anyone point me to the post of neilfs on soundbite and any other references, which might be of interest? Fight information fragmentation ;-) - joergkurtwegner

Thank you to everyone who helped and encouraged on this and offered future support! Among many things, one thing I'm a bit embarrassed about is the lack of details in the "broader impacts" and open science parts of the proposal. Definitely it needs more planning and better writing, and the panelists are going to point that out. Hopefully you all understand that it's a product of spending all my time trying to make the research parts as good as I could. - Steve Koch

Thanks, Bill! - Steve Koch

Given the UI flexibility of the iPhone, why recreate older, less intuitive HP calculator interfaces? - Steve Levin

Older?...yes. Less intuitive? You've obviously never used the HP-12c. It has the best interface around for time value of money (TVM) calculations. Also, if you can't wrap your head around RPN logic, you could always turn that feature off. Best of all, with an app like this I can leave my HP-12c at home. - Edwin Webster

Back in March, I wrote a blog post about my experiences trying to find out a) if ontologies should be licensed, b) if ontologies could be licensed, and c) what sort of license would be appropriate. After all, it isn’t clear what sort of thing an ontology is: is it software, or is it a [...] - Allyson Lister

I wrote previously about the fact that without a high relational density, having a dataset in RDF doesn’t give any practical advantage over having it in its original format. Yet, from a marketing/political point of view, the simple act of “triplifying” a dataset and make it available on the web as linked dataseems to make it appear all more powerful, all more useful and it’s being used a lot as a way to promote the idea that the web of data is finally getting traction. Today, I stumbled upon this page which contains all the datasets made available by data.gov triplified as RDF. The result yields an eyebrowse-raising 5 billion triples, more than the entire LOD effort today. Having tried to import some of that data in Freebase myself, I looked a little deeper to see if I could build on their effort and make my import a little easier… what I found didn’t please me. - Roderic Page

The image is "constructed from 21,625 unique images of yeast spots growing on agar" :) - Simon Cockell

too cool - thanks to conor :) (and darren for pointing it out!) - Allyson Lister

"Finally, universities and individual disciplines need to undertake a vigorous programme of education and outreach about data. Consider, for example, that most university science students get a reasonably good grounding in statistics. But their studies rarely include anything about information management — a discipline that encompasses the entire life cycle of data, from how they are acquired and stored to how they are organized, retrieved and maintained over time. That needs to change: data management should be woven into every course in science, as one of the foundations of knowledge". - Graham Steel

Also see the replated report, link contained here:- http://www.nature.com/nature... - Graham Steel

So a couple of questions arise in my mind. Is it a failure of EOL to optimize their Web presence (SEO) OR is it a failure of EOL to properly market themselves to the user base OR is it a failure of the user to properly evaluate sources? For that matter, I'm not sure who the user in this instance is supposed to be. Is it someone searching out of idle curiosity or is it a professional,... more... - Jill O'Neill

"Who is the user?" is probably one of the questions EOL has failed to get to grips with. My experiments with Wikipedia assume that the "user" is anybody faced with a taxonomic name who wants to know "what is this thing?" In my case, I'd like a picture, a summary of what it does and where it lives, some links (to web sites and primary literature), and ideally a link to the original description. - Roderic Page

As Roderic says in the post it would be valuable if WP linked out to EOL and if a trail of people following those links looking for more detailed and "scientific" information could be demonstrated (and if it can't then EOL is certainly in trouble as a central resource) - Cameron Neylon

nice to see you still have a passion for looking on the bright side of life... - Frank

Maybe you're just better suited to the North. Wearing wet weather gear 9 mo/year is a small price to pay. - Helen Parkinson from email

Change your perspective: instead of trying to sell yourself, try to help people. Write publicly and give presentations. Follow-up when you offer help. Make it easy for people to find you. - Daniel Lemire

"One plugin to rule them all". Great generic DokuWiki plugin that makes a lot of tiny special plugins obsolete. - Andreas Gohr from Bookmarklet

"we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation. In all cases resolution exceeded that necessary to detect blood cell and microorganism morphology, and with the tuberculosis... more... - Daniel Mietchen

45+ Excellent Code Snippet Resources and Repositories from the diverse 'Smashing Magazine'. Good to see Stackoverflow at the top of the list! - Daniel Swan

Jay, after more then a year of using a Twitter, with only aim mindcasting and conversation, I don't see any advantage of this tool compare to blogging and FF - Alexey from iPhone

I agree with Jay and Greg, ideas like sciencepond.com are great and make me feel like it is a must to attract more analytical people that can connect the dots on making interesting contributions. - Ben Friedle

Sounds good for a start: "Typically, projects will be 6 - 12 months in length and involve up to 24 person months of effort. Funding will be made under EPSRC terms and conditions, i.e. 80% of total project cost under fEC. The closing date for this call is 14/8/09 with funding decisions being made by mid September and projects starting from October 2009. All projects must be completed by the end of November 2010." - Daniel Mietchen

If they indeed open source everything, the question only will be how to best merge the functionalities to have a tool that serves scientists best. I personally don't care what this tool will be called in the end. blog3 surely provides way more scientifically valuable functionality than Wave, but conversely, Wave has a lot of functionality I wouldn't want to miss for using blog3, if that makes any sense. - Björn Brembs

Essay based on a talk I gave on June 11, 2009, at the American Physical Society Editorial Offices. - Michael Nielsen

Sorry about that, Matthew. Not sure how to stop FF creating two separate conversations for items that come through on my blog feed and are then reshared. - Michael Nielsen

Thanks @Reinhard and everyone who helped! - Allyson Lister

<taps the mic> - Oliver Hofmann

you seem to be back folks... - Cameron Neylon

Could have been anticipated. I guess next year in Boston it is going to be Google Wave anyway. - Daniel Jurczak

Well I guess that answers the concern that without some of last year's ring leaders it wouldn't take off huh? - Cameron Neylon

Nice pics Dan. I see you're making good use of your dslr :-) - Nicolas Bertrand

Calling Nils... :-) - Bill Hooker

Maybe we should peer review the blog post :-) - Cameron Neylon