Books and Papers - 1 - Walter Sneader

Some of the best books on the history of drug discovery have been written by Walter Sneader of University of Strathclyde. Recently I came across a copy The Evolution of Modern Medicine for only $1 in the excellent Strand Books on Broadway, NYC. Of particular interest is the phylogeny of key drug series.

Here are the references in the old-school refer format.

%D 1985
%A Walter Sneader
%B The Evolution of Modern Medicines
%I John Wiley & Sons
%O ISBN 978-0471904717

%D 1986
%A Walter Sneader
%B Drug Development: From Laboratory to Clinic
%A John Wiley & Sons
%O ISBN 471-91116X

%D 1996 
%A Walter Sneader 
%B Drug Prototypes And Their Exploitation
%I John Wiley & Sons
%O ISBN 978-0471948476

%D 2005 
%A Walter Sneader
%B Drug Discovery: A History 
%I WileyBlackwell
%O ISBN 978-0471899808

Details for recruitment of ChEMBL positions available online

Some job adverts are available on the EMBL website. I will expand this post a little more later with links to each of the individual ChEMBL positions.

Group Coordinator

Senior Data Integration and Development Officer

Scientific Application Developer

Chemical Content Curator

2 Web Application Developers

Closing dates for application are in the links above.

StARlite: Compounds, Targets and Publications over time

Given that StARlite lives, I should update my general slides, put together some new views, and so on. And so here are a couple of views on the publication rate of compounds. We started to abstract data from 'core' journals published in 1980 and onwards, and then added ten additional journals from 2007 onwards, hence the spike. Click images below for a usable view.

Firstly, compound records per year.

The SQL for this is trivial....

select year, count(distinct act.record_id ) as comp_record from docs d, activities act where act.doc_id = d.doc_id group by year;

Secondly, cumulative number of compound records.

Thirdly, targets per year. However, note that this is not new targets per year, just the number of distinct targets that were published within a given year.

Fourthly, cumulative targets covered over time. This of course, is unique targets.

Finally, the papers abstracted per year.

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.