ScienceOnline2012 interview with Sean Ekins

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Sean Ekins. Sean Ekins is a scientist who works from Collaborations in Chemistry as well as blogs and tweets? as CollabChem. He works collaboratively with other scientists all over the world on drug discovery, computational approaches for toxicology, tools for collaboration, mobile apps for science (Green Solvents, Open Drug Discovery Teams, TB Mobile). He is adjunct faculty at 3 US universities (UNC Chapel Hill, University of Maryland and UMDNJ) and on the board of several companies and organizations such as the Pistoia Alliance. He is currently focused on neglected disease research as well as how we can do drug discovery for rare diseases openly. He is technology focused and spends most of his time writing and occasionally winning SBIR and STTR grants so that groups he works with can develop their ideas further. He appreciates a good beer with his friends and reading to his two young children.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I was born in Cleethorpes and lived nearby in Grimsby (an industrial area which is like Elizabeth, NJ..but on the east coast of the UK) until I was 18. I got interested in Biology because my uncle had left some of his high school books (when he went off to medical School) at my grandparents and I liked flipping though them. Ultimately I would study from a later edition of the very same book I read as a small child. I always remembered the picture of Crick and Watson for some reason. So I wanted to be a doctor but that was nipped in the bud. I managed to fail most of my exams (except biology) and just scrape into Nottingham Trent Polytechnic.

I then did a HND in Applied Biology and had a year in industry working at Servier (a French Pharmaceutical Company with an R&D site near Windsor) that really put me back on track. After this I went to the University of Aberdeen (Scotland) to do a masters in Clinical Pharmacology then stayed there to do a PhD. So I became a different kind of doctor. By this point I was interested in Drug Metabolism and different models for understanding how drugs behaved or interacted with each other and I was aiming for a career in the Pharmaceutical industry. In the early 90s the industry started to decline and constricted dramatically in the UK so I thought I better go to the US and do a postdoc. I landed in Indianapolis in 1996 to work at Eli Lilly and that really started me off again, kind of rebirth.

Tell us a little more about your career trajectory so far: interesting projects past and present?

So once in the USA I started doing similar work at Lilly as I had in Aberdeen, but focused on one enzyme (CYP2B6) involved in drug metabolism. This was the runt of the litter basically that no one was interested in much. Well that gave me a bit of flexibility and I started to dabble in computational software for understanding which molecules might bind to my enzyme. I basically started a new career doing computational drug metabolism or chemistry. I was having fun and realized I could do the same work with every enzyme my colleagues were working on. It was a kind of crazy time, by day I was at the bench and by night working on the computer. So in the days before a centralized database, I pulled the data they produced off the pinboard (it was all on a single sheet of paper), and used it to model every enzyme the group worked on.

I then left to work at Pfizer with my own group working on drug-drug interaction prediction while also keeping up on the computational side. Lilly then quickly hired me back to head a new group on computational ADME/Tox. Basically doing what I did as a postdoc but now the datasets were getting bigger as they started high throughput screening for lots of toxicology and metabolism related properties. I was now 100% an in silico scientist (using a computer for doing all my science) by 1999. I also started some collaborations with academics at this time which enabled me to publish research outside of the proprietary work at Lilly, this has been a continual thread to the present, each year adding more collaborators.

My next step was to join a start up in late 2001 that was using primarily computational tools to do drug discovery. I stayed with them until 2004 then joined a software company (eventually sold to Thomson Reuters in 2010) developing tools for systems biology (essentially connecting the dots between all the biology data being collected and superimposing all the genomics and proteomics data). I now focused more on integrating my models for drug-drug interactions into these tools and working on grants.

This was when I started to work from a home office which I have been doing ever since. By 2004 I had built up a nice range of publications on predicting drug interactions so I was able to obtain my DSc (science) from the University of Aberdeen in 2005. My next change of focus was getting the chance to edit a book for Wiley on Computational Applications for Pharmaceutical research and development at around the same time. This opened the door to edit a series (10 books to date) for them and coauthor 3 more books on computational aspects of toxicology, emerging technologies and collaborations.

From 2006-2008 I worked for small companies and startups getting grants and contracts working on drug discovery and pharmacoeconomics. Then my old computational chemistry mentor from Lilly recommended me to a software company in San Francisco developing a collaborative database for scientists. I have worked for them on neglected disease (Tuberculosis and malaria) work since then 3 days a week, leaving some time to carry on my academic collaborations and other consulting.

I am fortunate in that my work week rarely gets stale. I get to work on an amazing range of projects like understanding the evolution of nuclear receptors across different species from looking at the profile of bile salts that bind to them and modeling it in silico. Another day I might be building a model for a human drug transporter and predicting which other drugs may be substrates or inhibitors. I might be predicting which molecules from a drug company might interact with an ion channel called hERG, to help predict likely cardiotoxicity (something that goes back to my work at Lilly).? I might also be searching through FDA approved drugs to see if I can find new uses for them against a rare disease, or thinking of a dataset we could use as the basis of a new scientific mobile app. And that is just the 2 days of the week I set aside!

What is taking up the most of your time and passion these days? What are your goals?

Most of my time has been focused on demonstrating we can use the masses of data accumulated on compounds screened against Mycobacterium tuberculosis to build models that in turn can be used to suggest molecules to test. In this way we can dramatically focus on testing fewer compounds. All of this data is publically accessible. I would also argue that this approach can be extrapolated to other research areas. We are accumulating data but not learning from it fast enough to design the next experiment. When I am not doing this I am increasingly concerned about data quality and some of the things we take for granted like ? why would the NIH release a database with significant errors, or a list of potential drugs without structures ? I spend about 50% or more of my time either writing papers to get my observations out there or writing grants for companies or with academics. I rarely write anything on my own so it is all collaborative.

It is difficult to predict exactly what I will work on from one year to the next ??I try to move out of areas and jump into new ones because I find a project or collaborator doing something interesting which I think I can contribute too. What I find is this comes at the cost of starting from scratch, establishing your credibility with a whole new set of reviewers etc. It does not matter how many papers you have, how many citations or whatever your h-index is, because as soon as you work on something you have never published on before (e.g. green chemistry or whatever) or try to submit to a new journal I have found I spend a lot of time on these kind of transitional papers. Once you get accepted it?s a lot easier.

I like getting into new areas because you see things that are not obvious to those that focus on it for years. E.g. the green solvents app came out of me going by chance to a green chemistry conference and randomly picking a talk to listen to on green solvents. A group had worked on collating data for 2 years across pharma and then just hid it in a PDF. Being totally na?ve to the topic I asked if there was an app with all the data and tweeted the idea. Alex Clark in Montreal responded and then had the app built in a few days and on the app store. It took nearly? a year though, to get a paper written and accepted on the topic because we faced an uphill battle with established scientists not understanding the value.

So I would say that is my passion going into new areas, establishing myself and publishing and learning a lot in a short time. I am in a race against time and I feel that even more acutely in the work on rare diseases because there are ~7000 of them and few have treatments, let alone cures. I know about so few and 7000 represents a Mount Everest of sorts. I met a parent of a child with a rapidly progressive neurological disease and that really gave me pause to think how we could help using all the tools I had worked on over the years, how could we speed up and disrupt pharmaceutical R&D ? really that means just accelerate it beyond the way it has progressed for the past 50 years. Again it?s another case of adapting to change and some squeaky upstart saying lets try it this way. The great thing about each rare disease is the parents of children or the patients likely vastly outnumber the researchers so the balance of power is in their hands, they raise money and fund researchers to do what they need etc.

So my goal is to do science to help these people as much as I can while at the same time putting as much of what I do back into circulation through free apps or open papers etc..my goal for 2013 is put every paper I author primarily into open journals.

What aspect of science communication and/or particular use of the Web in science interests you the most?

I like the speed of putting ideas out there immediately on the web compared with the process of write a paper, get it reviewed and maybe many months later see it in print. I also like the ability to give a talk or poster and put my slides on slideshare, figshare etc so anyone can find them.

I am fascinated by the creative part of science. I have rarely had the vision (or aha moment) of the final paper idea before doing the research that led to it. But I can see how using the web and other tools may speed up the science to the point where the write up has to be automated or sped up too.? What tools could help with ideation? I do all my science on a computer,? all my papers are written on a computer..why not have all my ideas provided by it too.? Writing on a beermat or back of a napkin is one thing but is the iPad a good substitute? I have blogged by phone (painful), by iPad in a moving car (very slow) so I cannot see it as actually being ?science communication anytime by any device?. A stationary position helps and some paper to draft ideas is handy. I say that as I stand typing this on a laptop surrounded by piles of papers and notes.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I blog frequently about anything I see scientifically, perhaps the science I or others publish. I have an interest in collaborative elements and that may be what sets my topics apart, the collaborative angle.

I have found that I do get a sense of instant gratification from blogging by putting what I am thinking (for good or bad) out there on the web. My blogs have started collaborations, they have led to numerous papers. I even had a person quite high up at the NIH, send a rant by email to me and about 70 other scientists after one of my blogs caught their attention. It would have been better if they had posted it on my blog because the whole world could see what they were thinking too rather than just a select audience.? I have also had other experienced scientists support my views on my blog.

I tweet (I was slow to come to it) more at conferences which I in turn use for ideation and as a persistent memory device. For me it is just an extension of technology development and the marketing ideas as I tweet a link to blogs, slides, posters, papers etc? I have websites, linkedin etc which help bring in business but my science collaborations happen primarily through who I know, their connections and personal interactions. I have found that email blasts and blogs and tweets occasionally bring in collaborations too. The web represents another tool for reaching people as far as I see it. I do not live in it. I live with it.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I had been reading my friend Antony Williams blog as ?ChemConnector? for a long time.? A few years ago my wife pointed me to ?In the Pipeline? and I like that a lot because of the topics relevant to pharma, the comments are usually funny too. Since ScienceOnline I have been following lots of attendees and they point to good blogs so my eyes have been opened. I have to ration my time using Twitter and Flipboard, but I would point to David Kroll who writes very clearly.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference ? a session, something someone said or did or wrote ? that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

The sessions on ?information overload? and ?open science? were highlights for me. The former made me think up an app that would bring all the information from the web and Twitter together. I got chance to work with Alex Clark again on this and we launched it early in 2012 called Open Drug Discovery Teams (a flipboard for science). We focused it on rare disease topics so we could help people share ideas, molecules and data and it inspired an IndieGoGo fundraising effort, numerous posters, a paper, a Youtube video etc..I think it?s still taking off and has potential to be developed for other uses. Over the year I have tweeted molecules and data into it so I can see the potential. If I had not attended the conference I doubt the app would have been developed. I would be keen to see what ideas people come up with that relate directly to the conference ? perhaps it could expand my theory that conferences now are useful idea generators as much as for social networking.

The standard of the other blogs from the community have made me step up the quality of what I put out, I still have a way to go but if what I write gets someone in the mood to try some computational tools or connect to collaborate, I will have achieved something. So if there are folks at the next meeting who need a guest blogger or someone to throw their data at to model, then please get in touch. If you have ideas to improve what I put out I want to hear that too.

Antony Williams made me realize that blogging and everything we put on the web is as important as all the papers and patents because this can be used for altmetrics too. Being at ScienceOnline2012 made me realize that there were hundreds of other scientists on the same wavelength. Science communication is important and there are many ways to do it, even Twitter is useful as a tool for science.

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Source: http://rss.sciam.com/click.phdo?i=cbc6741013eac1032b0d191aecd9786c

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