CDD Thoughts on Data Sharing

As we enter the holidays, the season of giving and sharing, we here at CDD reflect on our commitment to broadening precompetitive collaboration and data sharing in the drug discovery ecosystem.

We see this as the necessary and sufficient condition for enabling the economics of specialization for both humanitarian and commercial drug discovery.

We are doing our small part along with a growing number of collaborators to promote a dialog on the importance of appropriate data sharing in the pharma and biotech arena. In the last few months we’ve published three articles.  The first editorial, authored by Sean Ekins and our board member Alpheus Bingham, outlines features of industrial competitive collaboration. The second paper, co-authored with Antony Williams of the Royal Society of Chemistry focuses on sharing precompetitive ADME and toxicity related data on the web, as there is the potential to learn from the errors of others and not repeat them.

CDD has also published a paper in Touch Briefings – Drug Discovery Informatics with a focus on drug discovery moving to integrated web-based sharing tools.

This of course is in addition to abstracts at Keystone, Gordon, other major conferences, and our own annual community meeting in 2009.  This year was a year of growth for CDD, from expanding our neglected disease work with the Gates Foundation, the release of CDD3, and broader pharmaceutical industry collaborations.  We’re confident that in 2010, the industry (in particular the major biopharmaceutical companies) will continue to expand precompetitive and competitive collaborations, and we will certainly do our part to help.

We would like to wish our friends and collaborators around the globe happy holidays and look forward to even more exciting developments in 2010!

Last Thursday, CDD held its 3rd Annual Community Meeting for Catalyzing Humanitarian and Commercial Research, at the J. David Gladstone Institutes at UCSF Mission Bay in San Francisco. With over 180 registrants as well as ten guest speakers and panelists, the event was an eye-opening exposé into the issues facing academics, non-profits, biotechs, and pharmas regarding data management and collaboration.

The meeting was kicked off by a training session led by Kellan Gregory, CDD’s Head of Community Interests. Kellan demonstrated new capabilities in the 3rd generation of the CDD web application (CDD3) that has just been released over the past weekend. These included mapping templates, simplification of data input, and a more elegant GUI.

Ken Duncan talks TB

After Stephanie Robertson, PhD of UCSF welcomed everyone to the meeting, the first two speakers presented, focusing their talks around Tuberculosis research. Ken Duncan, PhD, Senior Program Officer at the Bill & Melinda Gates Foundation indicated the need for a better understanding of Tuberculosis biology as well as developing novel imaging/genomic technology on the pre-clinical and clinical side. Takushi Kaneko, PhD, Senior Project Leader of Research from the TB Alliance outlined the challenges of Translational Research for a Foundation as well as how CDD was used to address these needs across multiple collaborations.

Andrea Altieri, PhD, from ASINEX highlighted novel compounds in CDD containing characteristics similar to natural products using 3D Frameworks. CDD’s own Moses Hohman, PhD, VP of Development then followed up on Kellan Gregory’s showcase of CDD3 from the development perspective, highlighting the process for implementing new features while ensuring a high level of quality by having four lines of automated tests for every one line of new code.

After a lunch break during which our poster presenters were given the opportunity to showcase their work, Sean Ekins, PhD (CDD Collaborations Director) chaired a Biotech Panel consisting of Marc Navre (Ardelyx), Ellen Berg (Bioseek), Christopher Silvia (Icagen), and Bard Geesaman (PharmSelex). The panelists stressed the importance of communication, collaboration, and blending technology and interpersonal skills in industry.

Chris Waller, PhD, gave a talk highlighting his role as Senior Director of Precompetitive Collaborations at Pfizer by speaking about the Pistoia Alliance, an initiative between the major pharmas to facilitate collaboration in precompetitive areas (such as establishing standards and partnerships as well as technology transfer). Tanya Parish, PhD, brought the audience back to TB research. Speaking as both the Acting Director of Drug Discovery for IDRI as well as a Professor of Mycobacteriology at Queen Mary’s School of Medicine in UK, she pointed out that as collaborations across the globe increased, sharing data becomes complex. As such, she discussed how CDD is helpful for tracking target validation as well as screening data.

Bringing it all together, with (L to R) Sean Ekins, Stephanie Robertson, Tanya Parish, Ken Duncan, Christopher Lipinski, and Chris Waller

Christopher Lipinski, PhD, ex-Pfizer, Scientific Advisor to Melior Discovery as well as a member of CDD’s SAB, gave a provocative talk on the need for biological and chemical collaboration, illustrated by examples where “beautiful biology is ruined by bad chemistry.” He also showcased how these instances could be prevented through a system of alerts. These alerts, provided within the CDD software framework, would warn biologists working with compounds of the presence of chemistry related problems.

Barry Bunin demoed CDD3 live and presented a roadmap for the future of the CDD Platform (CDD Vault^TM, CDD Collaborate^TM, and CDD Public^TM) – which by its nature always improves with new features, collaborators, and data. He encouraged the audience to dream about new possible technologies and collaborators.

Finally, a second panel consisting of Sean Ekins, Stephanie Robertson, Tanya Parish, Ken Duncan, Christoper Lipinski, and Chris Waller convened and talked about the “what ifs” in the future of drug discovery, namely, if they could change one thing about the industry, what would that be? It was an exciting discussion, fairly showcasing the ups and downs in the drug discovery industry.

Congratulations to Sherida Johnson from the Burnham Institute for winning the best poster drawing, and Maruti Didwania from Stanford University for winning the evaluation form drawing!

At the end of the day, it truly was an honor for CDD to have such talented guests from every part of the drug discovery ecosystem. It was also great to have so many interested attendees share in this wonderful experience. We’ve enjoyed hosting these meetings immensely, and we plan on doing it again. See below for uploaded PDFs of approved slides from our speakers.

Sherida Johnson celebrates her best poster win with Christopher Lipinski. Rule of What?

Here are links to approved PDF versions of the talks (they are large files, so don’t worry if it takes some time to open):

Barry Bunin, PhD (CDD)
Ken Duncan, PhD (BMGF)
Christopher Lipinski, PhD (ex-Pfizer, Melior Discovery)
Chris Waller, PhD (Pfizer)
Andrea Altieri, PhD (ASINEX) – to obtain the presentation made by Dr. Altieri, please e-mail him or his colleague Mark Parisi for details.

Below are links to two blogs to give additional perspectives on the meeting:

http://researchscorecard.com/blog/archives/262

http://leverageinnovation.com/wordpress/?p=14

We are excited to announce that the CDD database platform is getting a new moniker! In fact, there are three new names to look out for.

Why does it matter, why should you care?

Good branding, like good product design, is about defining and communicating the essence of a product and its function. Our goal is to have the names reflect the capabilities, the benefits, and the value of CDD for all of you clearly and succinctly.

To emphasize security and privacy, the core of our business, we’ve named the aspect of the platform in which customers archive and mine private data securely “CDD Vault™.” With a CDD Vault, only those with designated access have the ability to interact with the research contained inside. A customer’s secure login and password act as the combination to the valuable data inside. While CDD Vault focuses on the private nature of storing and managing molecular drug discovery data, we want to also highlight the spirit of teamwork involved in drug discovery.

In addition to the CDD Vault™, we are also introducing CDD Collaborate™ and CDD Public™.

CDD was founded on the principle that collaboration (private-to-private, pre-competitive, private-to-public, etc) is the key to streamlining drug discovery in the future. In the spirit of this collaboration, the ability to selectively and securely share data between peers and private databases has been named “CDD Collaborate™.” This is particularly useful for screening centers working with outside collaborators, big companies working with many parties, and virtual companies that outsource significant work. There are two modes for using CDD Collaborate™ – both are unique to CDD and cutting edge capabilities not currently in other technologies.

Finally, to acknowledge the contributions to our Public Access site and emphasize the community spirit fueling collaborations, the portion of the application focused on Public data sets has been aptly named “CDD Public™.” Read-only access is free-of-charge, read and write (with the ability to import/export and combine datasets) content access is available via the CDD Vault. Public Access registration allows a user to browse and mine a constantly growing body of drug discovery data contributed by top researchers and vendors around the globe.

Give us feedback on whether or not CDD Vault, CDD Collaborate, and CDD Public are clear – given the CDD business model, we strive to improve these offerings constantly, making them more valuable to our customers with increased use.

With these new brands, we hope to both qualify the primary functions of our database platform as well as strengthen the messaging behind our mission to catalyze humanitarian and commercial research.

CDD is pleased to announce that the “3rd Annual Collaborative Drug Discovery – UCSF Community Meeting for Catalyzing Humanitarian and Commercial Research” will take place on October 1st 2009 at the J. David Gladstone Institutes in San Francisco CA.

This prestigious (yet informal) single day meeting is open to the public for registration now and will feature leading researchers from academia, industry and foundations.  We are pleased to welcome back Dr. Lipinski and other dynamic speakers who we believe broadly will be of interest including our first presenters from Pfizer, the Bill & Melinda Gates Foundation, and our first biotech panel.  We are also currently accepting poster submissions.

In previous years, the meeting has been a special opportunity for researchers to share their work with members of the CDD community and the public at large.  This year, we continue this grand tradition with a much larger, growing, and increasingly mainstream drug discovery researcher community!

We are delighted to announce that so far the following stellar speakers are already confirmed:

• Christopher Lipinski, PhD, Adjunct Senior Research Fellow (ret.), Pfizer
• Ken Duncan, PhD, Senior Program Officer, Bill & Melinda Gates Foundation
• Chris Waller, PhD, Senior Director of Precompetitive Collaborations, Pfizer
• Tanya Parish, PhD, Acting Director of Drug Discovery, IDRI; Professor of Mycobacteriology, Queen Mary’s School of Medicine
• Clifton Barry, PhD, Senior Investigator, NIAID/NIH

We also have two panels lined up: one is focused on the advantages of data collaboration for commercial biotech companies.  In contrast, the second panel is on our original area of focus on more neglected disease research.

Whether you are a basic or applied research scientist, a business person networking, a student or postdoc interested in collaborative drug discovery, a member of the CDD community curious about what other members are doing or where the technology is going, or anyone who just wants to learn more about molecular drug discovery, we encourage you to register.

We hope to see you there!

CDD has joined the fray of Web 2.0 on-the-go!

Last week, Barry Bunin, PhD (our CDD CEO) gave a presentation at the Bio-IT conference in Boston. Les Jordan of the Microsoft Life Sciences division, while sitting in the audience, posted a tweet about Barry’s talk, even providing a link to our website.

With the Twitter craze in full force, it’s great to see CDD getting exposure.  Hopefully we continue to inspire more tweets!

The following is a rare note from the CEO’s desk:

Congratulations CDD – now you are 5!

April  1 of 2009 commemorates the fifth year since CDD was incorporated and spun out of Eli Lilly.  First and foremost, we thank our customers and the CDD community for all of their contributions that have allowed CDD to become an exciting and valuable tool for the drug discovery industry.  It is gratifying to see the market confirm that CDD has addressed researchers’ real needs.  We have new collaborators logging on daily and thousands of researchers consistently visiting CDD.  New customers are constantly signing up – equally from both industry and academia.

With a growing user base, we have many more requests for new capabilities to keep us on target.  Frankly, these include more custom requests than we can ever fulfill, but that is a healthy problem to have. And, paid services are always accommodated on time and within budget.  Recently, we’ve even seen customers routinely select CDD over the established vendors in our industry.  They appreciate the simplicity of using CDD to archive and mine drug discovery data, and our unique-to-the-world, secure, cost-effective collaborative capabilities. 
 
We look forward to sharing more positive developments at our 10 year mark!

How many ways are there to communicate how something small can grow to become something much bigger…

Every long journey starts with a single step
Large Oaks from little acorns do grow
And maybe one for our era…  Today the financial sector, tomorrow the auto industry and next week ?

Well, let’s go with the large oaks analogy and talk about how it applies to Collaborative Drug Discovery. We established our company with the intention of making a real difference in the world. With a focus of helping drug discovery scientists around the world by delivering a software environment to archive, mine and collaborate we believe that we can make a real contribution to the process of discovery. We are proud of what we have been able to deliver using a very small team of committed and passionate individuals but we want to deliver more. In order to do so we are expanding our team, expanding our space and, over the next few months, you will see expand our reach in terms of collaborations and projects. In January 2009 we will be moving from our present offices and are now in the process of expanding our team. We are presently looking for a Community Support Professional and a Senior Software Developer as listed on our Jobs page. We are in an exciting phase of growth yet remain focused on our intention of delivering the premier software platform for collaborative drug discovery. Watch this space…