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May
19

How the book “Collaborative Computational Technologies for Biomedical Research” came to fruition

I think its important sometimes to try to describe how something you worked on came about – warts and all. The genesis and evolution of a project can be interesting in itself. Co-editing a book for me is one such project which I can describe as collaboration writ large. Not only between the co-editors but between the chapter authors and the publisher. So here is how our latest book project took shape and came to be released this month. Enjoy.

Always itching for a new book to edit, in May 2009 I started thinking about one on cloud computing and bounced it off my editor Jonathan Rose at Wiley, but I think the topic was too new and outside his area. Then in June 2009 I had attended a little conference called “Drug Discovery: Easing Chemistry Bottleneck”, held in Philadelphia. I saw a few talks and gave a talk myself on my work with CDD.  Attendees included Jean-Claude Bradley from Drexel University and Keith Taylor from Symyx who I specifically remember chatting with. I came away and started drafting a new proposal for a book then titled “Collaborative Technologies for Drug Discovery and Development”. which was a bit more general than the cloud computing one. By August I had recruited Maggie Hupcey as co-editor and she came up with the structure of the book following a “man- methods- machine” format  e.g. with sections on how to get people to collaborate, collaborative methods and computational tools for collaboration. Previously I had all the chapters in no particular order and had no real concept of this following any structure. We submitted to Wiley and waited for reviews.

By late October we had 6 reviews back with very good suggestions and feedback. Several reviewers pointed to our experience in the field and the need for someone else with complementary experience and visibility. At the time I had been collaborating with Antony Williams at the RSC (whom we had in the original proposal as a chapter author) and he kindly agreed to get involved and help recruit authors etc. We then worked  on an updated proposal and resubmitted as ” Collaborative Computational Technologies for the Life Sciences “. By early November we had additional feedback from 3 reviewers and they strongly supported it. By late November we had the final title for the book and the proposal ready to send out to authors in the hope of getting them to sign up. We then waited for the contract from Wiley and things slowed down around Dec. By January 2010 we had a letter ready to go out to authors on the 12th.

From then the book moved very quickly, several original authors provided some useful pointers and suggestions for other authors if they could not contribute themselves. In particular Beth Moore at the DOE suggested a white paper and Larry Smarr at UCSD suggested a chapter author.  Another key step we took was in author tracking. Antony suggested GoogleDocs so we created a spreadsheet which we could all access to collaboratively follow chapter progress etc. As chapters and figures were recieved and finalized they were uploaded to this site as a back up repository in case our computers crashed.

By June 2010 we were well underway and I attended and presented at the Second Annual Collaborative Innovation in Biomedicine: Strategies and Best Practices (and there was a follow up in 2011), held in Philadelphia. Several of the book chapter authors also presented, notably Dr’s Jackie Hunter and Shawnmarie Mayrand-Chang. From this meeting I also added Robert Porter Lynch and Sandor Szalma who both gave excellent presentations and I thought they could add topics we had not covered. So these last minute additions rounded out the book. Another presenter Bryn Williams-Jones from Pfizer kindly agreed to write some text for the backcover.

Another novel thing I tried with this book was to use a word cloud for the book cover. Originally we thought we could do a word cloud for each individual chapter but instead opted for a design for the cover. I had tried Wordle and had some fun with Tagxedo building a word cloud around interlinked hands to illustrate collaboration. Although this is not apparent in the final cover design.

We thought it would be valuable to have a foreword from a prominent individual, and the first person to mind was Dr. Alpheus Bingham, a founder and member of the board of directors at Innocentive. He surpassed our expectations and his comments set the scene very nicely for what follows.

We had set a pretty aggressive timeline to try to get the book to the publishers by the summer 2010. We pushed it back a few times and ultimately we found we had a hard deadline in October as Maggie was to have a scheduled C-section on the 12th.  The book chapters were sent the day before.

While waiting for the proofs we put a slide presentation together which Antony voiced and made into a movie. Using SlideShare, twitter, linkedIn, Amazon etc we have tried to gain visibility for the book. The proofs came back in February and the index was completed during this time. Wiley also put online a couple of sample chapters (1 and 25).

Obviously I have skimmed a lot of the nuts and bolts but our sincere thanks go out to all involved from the authors, our anonymous reviewers and of course the team at Wiley that make the finished product. Thank you!

5 comments

3 pings

  1. ChemConnector says:

    I’d write/edit another book with you anytime Sean. It was a real pleasure! But, not for at least another year! The outline you have given above is similar to the one I have running at present on four other books…a two part series on NMR of natural products, one on N15 NMR and one on COmputer Assisted Structure Elucidation. I feel like I’m juggling flaming torches and worried about what will get dropped…

    1. sean says:

      I could not imagine doing 4 at a time! I would say if anyone gets the opportunity to edit one it is fun and is like a crash course in a topic akin to doing a PhD.

  2. Maggie says:

    Where are the warts?
    How about how my (now former) company was so into collaborating, it blocks access to google docs, and I had to get a series of signatures of increasing importance and promise on my first born that I will not use my access for ill means to get the big brother block turned off?

    1. sean says:

      That is a good point. GoogleDocs was good for tracking but I could not imagine how we would have collaboratively worked on writing something with it (with or without your companies assistance with the firewall). The few times I have tried on other projects its been painfully slow. Just think if you had not had the C-section the book might not have finished so fast. Good point for future editors – a really firm deadline is very useful – and a birth works wonders in that regard. One of the amazing things was that folks contributed even if they were dealing with some amazingly difficult times (personally or professionally).

      1. sean says:

        Been thinking how I could have made this blog more compelling but compressing two years in a page is a challenge. I do think we are documenting a fresh scientific paradigm so it was important to get voices from different perspectives. It will be tough to predict how it ends up. It’s exciting to see the finished product but even then an editors role is not over as you need to let people know what you have done. This is a new experiment for me to see if a blog can help in this regard. I hope it’s more interesting than looking at someones holiday photos!

  1. Our Book on Collaborative Computational Technologies is Shipping « ChemConnector Blog says:

    […] described in the movie posted on Slideshare here and embedded below. Sean has given the story about how the book came about on his […]

  2. Why we have to redouble our efforts to increase the efficiency of drug discovery – the need to collaborate » Collaborative Chemistry says:

    […] have been pretty specific and tied into really well defined scientific issues around databases, collaboration etc, areas that only a few people are interested in (well a few hundred) and I have pulled no […]

  3. 著者が語るWiley新刊 – 第8回 創薬のための計算的手法の専門家 Sean Ekins博士による “Collaborative Computational Technologies for Biomedical Research” | ワイリー・サイエンスカフェ says:

    […] 自分にとって本書が際立っている点は、われわれのチームがソーシャルメディアを使って本書の出版を告知したことです。私は2011年にブログ(www.collabchem.com)を始めたほか、スライドをSlideShare(www.slideshare.net)にアップして、ツイート(collabchem)もしました。ブログでは編集過程について書き(http://www.collabchem.com/2011/05/19/how-the-book-collaborative-computational-technologies-for-biome…)、また本書で取り上げる主題を説明するためのスライド(http://www.slideshare.net/ekinssean/collaborative-technologies-for-biomedical-research)をまとめました。この記事を書いている現在、私はサンディエゴで開かれるアメリカ化学会に向かうところですが、そこで行う発表では、創薬をよりオープンなものとする方法を議論するために本書をベースに使う予定です(http://www.slideshare.net/ekinssean/acs-collaborative-computational-technologies-for-biomedical-research-an-enabler-of-more-open-drug-discovery)。本書の多くの章では、前競争的なイニシアチブや、欧州で助成を受けている大規模な共同研究(FrameworkやIMI)について、また科学におけるクラウドソーシングの試みについて言及しています。共同的なツール開発、インターネット上で入手可能なデータの増大、open scienceを支持する努力といった本書の論点は、今後の可能性を示唆します。しかるべき環境とデータへのアクセスおよびソフトウェアさえ提供できれば、興味のある誰もがどの国からでも共同研究に参加できるようになるでしょう。そう考えるのは若干楽観的に過ぎるかもしれませんが、そのような状況はたかが5年前には想像すらできなかったほど速いペースで実現されつつあります。私の予測では、今後の薬学の進歩は、共同的な計算ツールを使ってオンラインで実現される方向に向かうでしょう。承認済みの医薬品が可能性として持つ新しい用法を仮想的に特定する技術は、既に複数の研究グループから提示されています。 […]

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