• Hit the sack - Pt. IV - Days Hotel, Newark Airport, NJ

    Hey, it's lucky that I love the smell of kerosene in the morning. My travel plans had been disrupted by snow storms, so I had a bonus night with a bed (as opposed to a red-eye seat) at Newark Airport. There aren't many places you can watch a monorail directly from your bed - and probably even fewer where people on the monorail can watch you - this may not be to everyone's taste.

    Hotel Web Site

    However, overall, on the scored features, a solid 47% score.

  • Room Quality - 5/10 'Functional', you get the idea.
  • Getting There - 5/10 A quick courtesy bus ride from P4 terminal on the monorail. However, I had to call the bus after being out in the cold.
  • Cost - 8/10 ca. $70 a night, can't be faulted, excellent service from staff.
  • Phone reception - 7/10 good solid four bars.
  • Internet - 3/10 I found the wireless intermittent, and slow.
  • Conference facilities - n/a - Not part of their offering.
  • Mushroom factor - 0/10 not a hope of a fruiting body with ten miles of here, I fear.

  • Celebrate good times, Come on!

    Well, we have a fully functioning Starlite (release 31) up and running on RoyalOak (our internal development database server), with preliminary testing all looking good. Current configuration is with the Symyx MDL Direct cartridge 5.2 under Oracle 11.1.0.6. RoyalOak is a SPARC Enterprise 5220 with 64GB RAM and 64 cores, so this should be sufficient ;). We'll do some further tests over the next few days, but it is very good to be properly up and running again, and also have rolled forward a few versions of the cartridge and Oracle. We'll also get some exports knocked out, reimport, etc; just to make sure. In addition, Kinase SARfari is up and working with the chemical content live.

    Here are some summary counts from StARlite release 31.

  • Number of compound records: 521,237
  • Number of unique compounds: 440,055
  • Number of assay data points: 1,936,969
  • Number of papers: 26,299
  • Number of targets: 5,439
  • Number of protein targets: 3,512
  • Number of human protein targets: 1,644
  • Tablespace size: 8GB (actual used, 20GB tablespace recommended)

    There are also an additional 19,719 compound records, which will be loaded into StARlite 34 (probably the next viable release). As a brief note of explanation on the numbers, the unique compound number is lower than the compound record number due to 1) some compounds (assay standards, competitor compounds, drugs, etc.) are reported in multiple publications, and 2) stripping of salts, etc..

    Despite this excellent progress "back at the ranch", I on the other hand, have cancelled a trip out to New Mexico, as bad weather disrupts flights.

  • Hit the sack - Pt. III - Hyatt Regency, Cambridge MA

    Well, I'm travelling a lot at the moment, and this particular place is like returning home - if your home is a stylish 70's themed hotel that is.

    Hotel Web Site

    Overall a rib-rattling score of 58%.

  • Room Quality - 7/10 Only one sachet of regular coffee, and few power points in the room, so I had to get down on all fours to charge my laptop. However, the staff are truly excellent and very helpful.
  • Getting There - 6/10 About a 20 minute cab ride from the airport (ca. $40), but conveniently located, and there is a cool PC hardware store down the road.
  • Cost - 6/10 - Cheaper rooms around the back of the hotel, nice to have the choice.
  • Phone reception - 7/10 - Good reliable signal.
  • Internet - 7/10 - Wireless in the rooms, $10 for a day, not too zippy though, need to pay another five bucks to get the fast service.
  • Conference facilities - n/a. But they do look pretty good.
  • Mushroom factor - 0/10 - city centre location, nothing nearby

  • Hit the sack - Pt. II - Marriott Bethesda, MD

    A new hotel for me. Near to the NIH in Bethesda, and overall a 40% score.

    Hotel Web Site

  • Room quality - 4/10 not much coffee supplied for the machine in the room, no toilet roll!, and too close to the lifts. But a good sized bed.
  • Getting there - 3/10 - a half hour cab ride from Dulles, about 50 bucks, I needed to tell the driver where it was though.
  • Cost - 5/10 - $219 for the night.
  • Phone reception - 7/10, excellent cell phone coverage, but if only I could afford data roaming while in the US.
  • Internet - 5/10 only wired access in room, and about $13 for a days access - it is fast though, and no need to fiddle with smtp ports.
  • Conference facilities - n/a did not use them
  • Mushroom factor - 0/10 seems miles away from any woods, but wrong time of year to judge anyway.

  • One More Thing...

    I forgot to add one additional postdoctoral position in the list of ChEMBL posts recently.

    There is a research position investigating the selection and prioritisation processes applied in lead optimisation, based on analysis of the large scale SAR database within ChEMBL (~500,000 compounds). The project will be highly multidisciplinary and involve a mix of KDD and visualisation technologies. Mail me directly (jpo (at) ebi dot ac dot uk) if you want more details.

    The image above is from Scientific American, November 1992.

  • Conference - Slides from RSC meeting

    Here is a pdf of the slides from the joint Biochem. Soc./RSC meeting on integration of biological and chemical data.

    Wooo! - the link to the presentation is now there. Thanks for all of those that mailed in.

  • Positions within ChEMBL

    Here is an outline of the positions we have available within the ChEMBL group at the EMBL-EBI. They are:

    Wellcome Trust Grant

    • Group co-ordinator
    • Biochemical/Pharmacological content curator
    • Chemical content curator
    • Web developer (ChEMBL)
    • Scientific application developer
    • Senior developer - systems integration
    EMBL-EBI Funding
    • Web developer (Druggability Portal)
    These positions should shortly be advertised on the EMBL-EBI web site......

  • Just how does ChEMBL fit in?

    A classic image, showing the relationship of scientific paradigms. Note the distance between chemistry and biology, and just look at the distance between therapeutic research and chemistry. This must change! Click for larger image, and here for more details on the work.