• StARlite Schema

    The StARlite database has a very simple schema, and should be easy to integrate other resources against. I have had a couple of requests for the schema, so here it is, in its current form. It may change a little, but not much, as we align it against other EMBL-EBI resources.

    We will also arrange a web meeting, probably at 8pm GMT on Thursday 5th Feb to talk through the data model and schema, describe some sample queries, etc., for those interested, mail me to get further details.

  • Hit the sack - Pt. VI - Sheraton University, Philadelphia

    A convenient hotel, booked for accommodation for a TDR targets meeting. Overall an MOR score of 48%. Located in the academic part of Philadelphia. Close to a really good academic bookstore, with lots of second-hand books, University clothing, etc.

    Hotel Web Site

  • Room Quality - 3/10 OK room, noisy air-conditioning, a nice view from the window. The staff did not seem too happy, and were not that helpful, and service was slow.
  • Getting There - 7/10 About a 20 minute cab ride from the airport (ca. $30), but conveniently located. Close to the University (I guess the name is appropriate then), and also close to a good University beek store.
  • Cost - 5/10 - ca. $200 a night.
  • Phone reception - 7/10 - Good reliable signal, but it is a city center location....
  • Internet - 6/10 - Wireless in the rooms, but a convoluted security key mechanism. But there is a PC with a web browser in the room.
  • Conference facilities - n/a. Typical hotel meeting room setup - did not try them out.
  • Mushroom factor - 1/10 - looks like a pretty bleak place nearby, but I didn't have the time to fully check.

  • Hit the sack - Pt. V - ISG Hotel, Heidelberg

    It's been snowing, and I'm just here on an overnight stopover - but it is a really nice place, looks very pretty, clean efficient and friendly. Haven't been here for about 20 years, but it hasn't changed. As the picture above shows, it has a Bauhaus inspired design, and there's quite a lot of period posters and explanation of the style around the building, but the rooms (at least the one I had) have a more conventional decor. And it is close to the EMBL Heidelberg campus. As expected due to its location, there are special links to EMBL itself.

    The hotel website (German and English) makes clear the special benefits. This is the best 'visiting scientist hotel' so far with a stonking 66% score. And a visit in September/October with little wrinkles sorted out on internet access, it could be even higher.

  • Getting There - 4/10 Why, Oh Why, is there not a Heidelberg airport ? - about 45 minutes to get here from Karlsruhe. So make sure you have some cash for a cab (60Euro will be sufficient).
  • Cost - 8/10 ca. Euro70 a night including breakfast, with a discount for EMBL staff. Now if only the pound wasn't so weak against the Euro.
  • Internet - 8/10 Free! (to EMBL staff anyway) fast and didn't find any port oddities. This would have been a 10 but the first password I had had expired, and there were a few problems with my DNS that meant I couldn't get to certain domains - no real pattern to these, but the essentials all worked.
  • Conference facilities - 7/10 - Looks very good indeed.
  • Mushroom factor - 6/10 Snow on the ground, but looks really promising. All I need to do is to get a meeting here in September.

  • Conference - 7th Annual Pharmaceutical Technology IT Summit

    We are going to be at, and present at the 7th Annual Pharmaceutical Technology IT Summit, held on the 15-16 June 2009, Le Montreux Palace, Switzerland. A link to the conference is here.

  • Books and Papers - 4 - The Cathedral And The Bazaar

    All this travelling is making me read. This was a book I picked up over the summer, but have only recently properly read. It is a classic in the open source field, and is a very lucid discussion of the culture of open source projects. It is excellent in quite a few places, and my copy is now dog-eared where I thought at the time that I must remember some point or other. Many things I simply had not though of before, in particular the multifaceted discussions of 'free' vs commercial were particularly interesting. One definite down side was that I felt like I was 'l33t' after I had finished it, and tried to bore my kids with my new insights - I guess this is may be the modern equivalent of you dad dancing at a disco. 

    %T The Cathedral And The Bazaar
%A Eric Raymond
%I O'Reilly Media, Inc.
%D 2001
%O ISBN 978-0596001087

  • Calling SMEs and consultants

    One of the anticipated user groups for the ChEMBL data are for SMEs and 'sole trader' type consultants (i.e. very small consultancy businesses, one-person-bands, etc.). So, as a general question, what sort of access and query tools would be most useful for this type of user. We have contacts with quite a lot of large pharma, non-profits, universities and larger biotech, especially in Europe and the USA, but could do with more diverse contacts to make sure we align our services with a broader community.

    I guess there are a number of obvious options for delivery.

  • Locally installable databases - what sort of technical environment would be wanted for this (Oracle, mySQL, ....)
  • Hosted web server access - what sort of queries would people want to do, how would they like the results?

    Where should our priorities lie?

    So, please, mail me (jpo (at) ebi.ac.uk) if you have some thoughts, or would consider yourself to be one of these types of users. Contact and input from developing economies is especially welcome.

  • There's A Party Going On Around Here...

    So, we have appointed the first ChEMBL group member! It is for the Biological Curator role, and she starts on January 19th. The trailer will be less empty, and we can start getting some actual work done now. I'll let her introduce herself when she starts....

  • Books and Papers - 3 - The Long Tail

    The power law is everywhere - in choice of food, types of music, species distributions, etc. Over the holiday season I read The Long Tail by Chris Anderson. The subtitle of the book is How Endless Choice is Creating Unlimited Demand, and there is a provocative mix of economics alongside the reality of the power law frequency distribution of assets. The discussion of physical vs virtual assets is nice and balanced, as also is the discussion of the strategies for economic exploitation on various portions of the demand curve. I guess on-line resources, specifically scientific data sources, (both free and commercial) are a lot like this as well - the vast majority of the data is never accessed, whilst a small fraction makes up the majority of the interest. It does make you think about the 'long tail of scientific data', and the best approaches to archive, preserve and distribute it.

    As an aside, when the book first came out, it seemed highly lauded, as a refreshing boost to business models built around the internet, diversity and revenue generation. However, it seems, even on the internet the 80:20 rule rules. Don't get me wrong, I think this is a really excellent though provoking book. Buy it! 

    %D 2007
%A Chris Anderson
%T The Long Tail: How Endless Choice is Creating Unlimited Demand
%I Random House Business Books
%O ISBN 978-1844138517