Its been a busy year transitioning from spending most of my time with CDD to my start-up Collaborations Pharmaceuticals, Inc etc. Along the way I found time to write a few book chapters. One of these recently published in High Throughput Screening Methods : Evolution and Refinement Editors: Joshua A Bittker, Nathan T Ross Our …
Category Archive: databases
Jul
21
Wiki, Wiki, Wiki – for chemical probes
Sorry for the cheap title (for those born after the mid 80’s its a reference to a song by a funk band called Newcleus). A very interesting commentary published today in Nature Chemical Biology by Arrowsmith et al and its all about chemical probes. Go check it out and note that it took over 50 …
Mar
22
What warrants an erratum and why the old publishing model must change
Friday AM my day started with an email which I have marked up and added links to Dear Dr. Ekins: It has come to our attention that an error was identified in your recent Perspective entitled “The parallel worlds of public and commercial bioactive chemistry data” published in the March 12, 2015 issue of the …
Feb
18
Databases and collaboration require standards for human stem cell research
Last year my then colleague at CDD, Nadia Litterman and myself put together an article on databases and collaboration around the area of human stem cell research. This built on Nadia’s extensive experience of working with stem cells. My additions were mostly around software and collaboration. It was a fun paper to write as I …
Dec
04
Chemical probes and parallel database worlds – who wants to know? More publishing fun
This post is long and a highly detailed description of the challenges involved in getting scientific work published on one level, on another it gets to the heart of discoverability of data, data analysis and just the slog of publishing something that you hope is going to interest others in your direct field. …
Oct
07
The most expensive data set I have modeled – dont blink (over $500M)
The cost of data generated in science is probably not something many people ponder. When I look back over some of the datasets I have looked at over the years its interesting to speculate on the costs of the underlying data. Working for pharmaceutical companies, data from specialist tests for toxicities (e.g. hERG) probably ran …
Apr
14
iDrug – intelligent drug discovery
I gave a little futuristic talk the other week. I made a few edits and a few more ideas to tighten its focus. Most importantly I have changed the title and scope. I think we are approaching an era I have called iDrug or intelligent drug discovery. I hope its self explanatory. I begin by …
Mar
28
Accessing gene expression-small molecule databases funded by the NIH or others
So here is a challenge which I am sure many people face. An academic does an experiment and finds a particular protein A-protein B interaction in vitro which may be important in a disease. How do you go about finding molecules to test experimentally that might up or down regulate protein B ? Fortunately there …
Jan
28
Policy: NIH plans to enhance reproducibility
I just read the commentary by Francis Collins and Lawrence Tabak in Nature re: reproducibility. As we have pointed out before, its possible the NIH should look closer to home for data quality issues. Reproducibility is important, but the databases NIH creates and funds will reach more people and have more impact on science, so …
Dec
30
Journal editors add more balance than needed – provides marketing windfall
Just when you think the year is going to end without having to get drawn into some additional discussion on publishing.. well it happens.. I get an email today that the article a (very nice) journalist, Vivien Marx had written for Nature Methods “Pouring over liquid handling” was now published. Lets get this straight at …
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