INSIGHTS from Pistoia Alliance

Dragons’ Den Roars at Royal Society of Chemistry

Posted on February 21, 2012 by Michael Braxenthaler

This is the second year that the Pistoia Alliance has held a social event for members and non-members in conjunction with the face-to-face meeting of the Board and Operational Team. In planning these events, we’ve tried to come up with formats that stimulate thinking and offer more entertainment than your typical talking head. This year, that meant turning a “learn-ed body”—the Royal Society of Chemistry—into a dragons’ den!

The Dragons’ Den was first launched in Japan, but was turned into an institution by the UK—numerous offshoots around the world were inspired by the UK reality show. In the program, entrepreneurs pitch business ideas to five rich “dragons,” who will invest their own money in promising ideas. At our event, the pitches were delivered by members of the Pistoia Alliance Board, and we gave the audience play money so that they could be the dragons and award their “funds” to the pitch or pitches they liked best.

No one expected reality; pitches were intended more for entertainment, which is probably a good thing given that in at least one case the intended “pitcher” had to designate a stand-in due to uncooperative EuroStar service. But it was interesting to see how each of the pitches ultimately had some grounding in reality. The pitches applied a mix of the hottest technological trends to real issues associated with navigating the cloud, finding new sources of knowledge, and spurring innovation.

Monetized Annotation, a public-private data store designed to encourage pharmas to share data in order to benefit from “crowd-sourced” discovery. Dragon seed funding would be used to provide monetary awards to anyone who provided substantive annotation on a successfully delivered new drug, and the system would be sustained through subscriptions that would give pharmas full access to the system. (Pitched by Ramesh Durvasula and Ingrid Akerblom)
ODDT, Open Drug Discovery Dream Teams intended to pull not just published data, but social sources of data together into a central hub that would serve as “the world’s biggest, open electronic lab notebook.” Dragon seed funding would be used to build the infrastructure, which would be sustained through advertising and subscription services from established publishers. (Pitched by Sean Ekins)
The Cloud Buster Toolkit, a set of tools intended to educate life science organizations about cloud standards for life science and provide a mechanism for organizations to test and validate their cloud-based infrastructures. Seed funding would be used to build the initial system and provide initial fee access; broader access and full hosting services would sustain the system. (Pitched by Alex Drijver and Richard Bolton)
Ontologies For All, which aims to let academics “kick the tires” of an innovative set of ontologies for free in an attempt to engage pharma in standardizing on a single ontology rather than developing their own. Seed funding would be used to provide the ontologies to ALL academic institutions for free; return would be based on a percentage of revenue generated by pharmas adopting the ontologies. (Pitched by Rob Greenwood standing in for Andreas Matern playing the role of Joe Donahue)

The winning entry was Monetized Annotation, but the winner in this case is less important than some of the lessons learned, namely:

Show them the money. The three venture capitalist attendees pointed out that none of the pitches was particularly strong, because none put enough emphasis on the return (a lesson we’ll keep in mind as we develop future business cases for Pistoia projects!).
Death by iPad ≠ Death by PPT. Sean Ekins sketched his entire presentation on an iPad, and while a lack of WiFi meant he wasn’t able to access his “prototype’s” data, the whimsical, off-the-cuff quality of the presentation puts a few more nails in PPT’s coffin. Sean posted his slides on Slideshare, and blogged about his experiences in the Dragons’ Den here and here.
Presentation matters too. Many attendees admitted that the delivery of the presentation had as much to do with their decision to fund a project as the content. The winning presentation did a great job not just at introducing the idea, but defending it under pressure with confidence and enthusiasm.

What do you look for in a business pitch, particularly for something disruptive and innovative?

Posted in Collaboration & community | Tagged annotation, business models, cloud computing, hosted services, innovation, meetings, ontologies, open source, scientific publishing, security, social media | Leave a comment

Sequence Squeeze Heating Up

Posted on February 16, 2012 by Simon Thornber

The Sequence Squeeze Competition has turned into a bit of horse race a month out from the competition end date of 15 March 2012. For those not aware of this competition, the Pistoia Alliance is awarding $15,000 to the developer of the best novel open-source compression algorithm for next-generation sequencing data. Anyone can enter, and we’ve specifically been hoping to get computer scientists and other non-life science coders involved.

As of 6 February, 38 entries had been submitted. Interestingly, many of the submissions so far are from repeat entrants trying to better their previous efforts and outdo other competitors. The Sequence Squeeze leaderboard shows all the details—take a look! The game is definitely on!

The fact is, whichever coder wins the $15,000 cash prize, the real winners will be those struggling with compressing next-generation sequencing data. The best entry (by compression ratio) as of 6 February had improved the baseline (Zip) by 50%, and the competition between individual entrants has definitely improved the quality of the entries over time.

Eagle Genomics, which is running the competition on behalf of the Pistoia Alliance, posted an informative entry last week about questions entrants have had about judging criteria. We are thrilled to have judges from the three major global sequencing centers (BGI, Broad, and Wellcome) serving on the Sequence Squeeze judging panel in addition to the Alliance’s own Nick Lynch. We’re confident in their ability to fairly adjudicate the subjective elements of the competition, which are based on the robustness and utility of the code.

At any rate, it’s exciting to see such a response at this stage of the competition, particularly given the complexity of the task we’ve set for the competitors. All of us at Pistoia—and the broader life science community—look forward seeing the contest play out over its final four weeks. May the best coder win!

Posted in Bioinformatics, Sequencing & omics | Tagged compression algorithms, next-generation sequencing, open source, sequence squeeze | Leave a comment

Nick Lynch Receives First Pistoia Alliance Leadership Award

Posted on February 14, 2012 by Michael Braxenthaler

Last week saw the third annual face-to-face meeting of the Pistoia Alliance Board and Operational Team. We’ll have more to say in future entries about some of the happenings at and outcomes of that meeting, but today I want to highlight that this was the third such meeting in what is now the Alliance’s fifth year since being conceived over dinner at a conference in Pistoia, Italy. And much of the credit for the Alliance becoming a hub for precompetitive collaboration in our industry goes to Nick Lynch, Pistoia Alliance founder and immediate Alliance past president (he stepped down from the presidency this fall).

Nick Lynch receives Pistoia Alliance Leadership Award

Michael Braxenthaler, Pistoia Alliance president, presents Nick Lynch, past president of the Alliance, with the Pistoia Alliance Leadership Award.

Following up Nick as Pistoia Alliance president has been difficult, because as president Nick not only did so much for the Alliance, but did all of it with enthusiasm, wit, and patience. Nick was always available for questions and always willing to put himself forward on the Alliance’s behalf. His dedication and leadership shaped this group into a thriving organization, and he did it all while juggling his responsibilities at AZ and his personal obligations with panache and good grace. And Nick continues to be a driving force in the Alliance, serving in the highly visible role of external liaison on the Alliance Operational Team.

So I was delighted at an intimate dinner at the Marriott Marble Arch on the first day of the face-to-face meeting to present Nick with the first Pistoia Alliance Leadership Award. The text of the award reads as follows:

The Pistoia Alliance Leadership Award was presented to Dr Nick Lynch in February 2012 by decision of the Pistoia Alliance Board. The mission of the Pistoia Alliance is “lowering the barriers to innovation by improving interoperability of R&D business processes through precompetitive collaboration.” This Pistoia Alliance Leadership Award is made in formal and grateful recognition of the effective leadership Dr Lynch has displayed in co-founding and developing the Pistoia Alliance from a concept to a functioning, global non-profit organisation. Dr Lynch’s achievement is due to his energy and domain knowledge, his widespread cross-industry network of colleagues, peers and industry leaders, and his ability to inspire them to work together in an open-innovation, precompetitive framework to further the mission of the Pistoia Alliance.

Congratulations, Nick, for a well-deserved honor!

Posted in Alliance news & milestones | Tagged awards, membership | Leave a comment

Kicking Off New Working Groups

Posted on January 12, 2012 by John Wise

Two teleconferences are planned for the next fortnight aiming to kick off working groups on two topics emanating from the highly fruitful Information Ecosystem Workshop that the Pistoia Alliance held last October in Hannover.

Registration is open for the first teleconference, to be held on Wednesday, 18 January 2012, on Topic #31 from the meeting—Biomarker Exchange Standards. Sandor Szalma, head of external innovation, R&D IT at Janssen R&D, has kindly agreed to head up this discussion. I asked him to elaborate on how this topic has developed, and here are his responses. I’ll publish more information on the other teleconference addressing Canonical Models for Large Molecules (Topic #7 from the meeting) in a future entry, but in the meantime, you can learn more and register for that event too.

What problem is driving this topic?

Pharmaceutical and biotech companies increasingly rely on a network of collaborators—academic labs, specialty service providers, CROs, and other pharma and biotech companies—to bring drug ideas through research and development stages and ultimately to market. As these networks get more complex, so does the management of data and metadata. Currently, data exchange among these networks relies on primitive vehicles such as moving around Word docs, PDFs, and Excel spreadsheets, with no standards to promote effective exchange.

What is this group’s aim?

The initial aim of the Biomarker Exchange Standards workgroup will be to develop requirements and use cases to foster the eventual development and adoption of data and metadata exchange standards for biomarker assays in order to facilitate collaboration.

Who should be involved?

Since many assays in the biomarker domain are similar to (or even the same as) assays in the target validation domain, deliverables from this working group will also have relevance here. Target validation experts should therefore be involved in this project, along with members of screening, target identification and toxicity workstreams. Right now, representatives from AstraZeneca, Bayer, Boehringer-Ingelheim, GSK, Janssen, Merck, Merck-Serono, Roche, and Sanofi have contributed to discussions and are planning to attend the teleconference.

What challenges do you plan to address?

We’ll look into secure, real-time data exchange; IP protection and infringement; process and data harmonization; and the lack of standard data formats and regulatory guidelines around collaboration and networking.

Posted in Collaboration & community, Standards & deliverables | Tagged assays, biology domain, biomarker exchange, collaboration, CROs, externalization, standards, target validation, webinars | Leave a comment

Vocabulary Standards: Helping Scientists Talk the Same Talk

Posted on December 11, 2011 by Lee Harland

In every day discussions we take for granted that we have a reference terminology (in my case, the English dictionary) that provides definitions and usage of the concepts necessary to describe a certain “fact.” But even humans get confused by overlapping terms. Take the buffalo sentence:

Buffalo buffalo Buffalo buffalo buffalo buffalo Buffalo buffalo.

This sentence uses three different valid definitions of the word “buffalo,” so that it is parsed as “THE buffalo FROM Buffalo THAT ARE buffaloED BY buffalo FROM Buffalo, buffalo (verb) OTHER buffalo FROM Buffalo.”

*whew*

We in life science frequently confuse words and meanings. Does a document tagged as “muscle wasting” refer to the indication, a side effect, or the name of an internal research team? Does “SNP” refer to sodium-nitroprusside or single nucleotide polymorphism? And if you think this is confusing for humans, it’s worse for computers. All these overlapping terms can mean data is misinterpreted or, worse, completely missing in areas where it is relevant.

Members of the Pistoia Alliance, including major pharma, academia, and content providers, have together written a paper that summarises the current state and issues around basic biomedical vocabularies. How we identify the “things” that constitute scientific endeavours—from projects to hypotheses to experimental results—is critical to enabling data to be accurately stored and reused. This isn’t a new topic, but has become much more relevant recently. As everyone is aware, our sector is moving to many more fluid business models, where contract research organisations, academic groups, and non-profit agencies intermingle with industry participants in a complex and variable matrix of interactions.

We argue in our paper that while different companies have invested in internal vocabulary work, internally focused approaches do not tackle the wider need to ensure that in all future interactions, data will be captured and communicated in a way that all team members understand. Indeed, as the paper points out, we’re already seeing the negative consequences when global research collaborators fail to speak a “common language.” Precompetitive collaboration to develop such standards fits perfectly with the need for universal languages to describe science.

Will the publication of this paper change things over night? No. Our only aim was to reassess the issue in light of practical business considerations and argue for the need to take a fresh look at the problem. However, as with any new advance, there will be difficulties and questions. How do we do this? How do we resolve conflicts? Who is responsible? Such questions will only be addressed through pilot projects and continued exploration of issues around shared vocabularies. We think that the Pistoia Alliance is uniquely positioned to handle this work, but we need concrete funding proposals and members willing to invest time and resources to make this happen.

I’ve discussed this issue a little more over on my company’s blog, but the question is what Pistoia members think. What ideas do you have to give this initiative life?

Posted in Vocabularies & semantics | Tagged publications, standards, vsi | Leave a comment

Information Ecosystem Workshop Points to the Importance of Standards

Posted on November 23, 2011 by Michael Braxenthaler

It was tremendously gratifying to work with the 36 participants who attended last month’s Information Ecosystem Workshop in Hannover. The discussion was enthusiastic and focused, and efforts are currently underway to prioritize the many ideas (over 30) generated at the meeting into viable project workstreams. You can get an idea of what was discussed at the IES workshop page on our website, which contains links to presentations and notes from the meeting.

One of the key themes at the meeting was standards. Although the Pistoia Alliance focuses on the broader theme of improving business processes, we fully recognize and acknowledge that standards are of critical importance in our industry. The participants at the Information Ecosystem Workshop pointed out several ways that a Pistoia Alliance standards working group could be useful. Such a group could collect together needs and use cases to identify areas where there’s a critical mass calling for a “standard” approach to, for instance, exchanging data between systems or querying systems. Several proposals of this type were raised during the meeting; a standards working group could vet these ideas to determine those most compelling and ubiquitous.

Additionally, a standards working group could monitor and track the work of other standards organizations to determine efforts that already exist or that overlap or complement needs identified by the Pistoia Alliance community. Such activity would enable the Pistoia Alliance to serve as a standards clearinghouse that could signpost ongoing work on particular standards and perhaps even endorse those standards that most effectively meet needs described in Pistoia Alliance use cases.

Finally, if a compelling need is identified and the standards working group finds that no work is occurring externally to develop a standard that meets that need, the group could suggest that a Pistoia Alliance project be initiated to fill the gap.

If you’re interested in following this discussion or participating in a Pistoia Alliance standards working group, email Executive Director John Wise for an invitation to the next meeting of the Information Ecosystem Workshop participants on 1 December. Or leave us a comment and let us know where you think standards are needed to facilitate activities in modern life science R&D.

Posted in Bioinformatics, Standards & deliverables, Workflows & business processes | Tagged externalization, information ecosystem, standards, translational medicine, workshops | Leave a comment

Four IT Themes from Gartner

Posted on November 17, 2011 by Nick Lynch

Robert Mitchell over at Computerworld recently blogged about his takeaways from the Gartner Symposium/ITxpo. He nailed it, I think, raising themes that we’ve definitely noticed here at the Pistoia Alliance. We’re also thrilled he gave us a mention in his post.

Mitchell says that this year, the Gartner talks were all about five things:

The “consumerisation of IT” through mass collaboration
The infusion of social media into enterprise computing
The application of analytics to big data through multiple, shared data repositories
The ascendance of mobile devices in business settings
The cloud as an enabler to all of the above

Mitchell referred to the Pistoia Alliance in unpacking the idea that even the biggest companies can’t deal with big data on their own. Instead, they are replacing separate, independently housed data pools with shared, open access pools co-created and shared by the organisations that need to access the data. Value comes not from the data itself, but from the value organisations are able to extract from that data.

This trend isn’t unique to pharma; the Gartner Symposium covered all areas of IT. But pharma should take pride that the Pistoia Alliance was cited in a general IT forum as an example of what is possible in responding to the tremendous pressures and opportunities that arise from continued IT development.

So here at Pistoia, we’ve not only seen the future, we’re living it. The question, as always, is what we’re going to do now that we’re on this (right) path. Some projects are continuing, like sequence services and its companion project, sequence squeeze. Some, like SESL, proved a concept so that it can be fulfilled by other groups. And other projects are still percolating—it’s been encouraging to see all the ideas floated at the Information Ecosystem Workshop last month.

Where do you think the future lies, and how can the Pistoia Alliance help you realize it?

Posted in Collaboration & community | Tagged cloud computing, innovation, knowledge brokering | Leave a comment

SESL at Bio-ITWorld Europe: What’s the future of knowledge brokering?

Posted on October 17, 2011 by Ian Harrow

I was able to take SESL on a public spin at the Bio-ITWorld meeting last week in Hannover, and it was very well received. As we at the Pistoia Alliance bring this project to a close, it’s clear that we’re in a SESL-is-dead, long-live-SESL situation as we determine the best way to leverage the lessons from this project in other initiatives—very likely the Open PHACTS project sponsored by the IMI.

In my presentation on the SESL pilot on Wednesday, I not only gave an overview of the project, but also exploited the wifi connection to show off the public demonstrator. The demonstrator provides a single point of query for gene or disease information from four publishers and three bioinformatics databases. The simple GUI offers summary results for the queries with links to full text details from the publishers and links to the bioinformatics databases. In other words, it demonstrates that knowledge brokering of primary data sources can be achieved.

I got some extremely positive feedback during my presentation from a number of people, including

Prof. Carole Goble (University of Manchester and Open PHACTS academic leader)
Dr. Etzard Stolte (ex-Roche, now CTO HP Life Sciences)
Dr. Scott Marshall (co-chair WC3 Health and Care Life Sciences interest group)
Dr. Barry Hardy (Open Collaboration pioneer; OpenTox; SAM; Synergy etc.).

And the very next day, Prof. Goble presented on Open PHACTs and recognized publicly how successful the SESL pilot has been and how the thinking and learning from it is helping to shape the Open PHACTS project (22 partners), which has got off to a promising start, now six months into the three-year grant. In fact, throughout the conference, I heard lots of positive feedback about the Pistoia Alliance. Clearly, the community is behind what we’re trying to do, and our ability to deliver lessons and actual proofs of concept, like the SESL public demonstrator and the proofs of concept in sequence services, will only raise our profile and credibility.

In my conversations with people attending Bio-ITWorld and those I spoke to on Monday, after the Pistoia Alliance Information Ecosystem workshop, I noticed that there is a strong community need for better signposting. During my talk, I pointed out the need for the Pistoia Alliance to select judiciously existing initiatives, consortia, and standards to support and endorse in order to help everyone navigate the complex jungle (i.e. ecosystem) in life science R&D. The synergy between SESL and OpenPHACTS illustrates the power of signposting and collaboration.

Are we missing opportunities to work with others to resolve common hurdles to innovation? Let us know where you think “signage” could help you better tackle challenges in your R&D operations.

Posted in Bioinformatics, Literature & information sources, Standards & deliverables, Vocabularies & semantics | Tagged demonstrators, hosted services, knowledge brokering, open phacts, presentations, SESL | Leave a comment

Working with/in the Information Ecosystem

Posted on September 23, 2011 by Michael Braxenthaler

I first used the phrase “information ecosystem” to describe the biopharma informatics environment at the Pistoia Alliance Annual Face-to-Face board meeting last February. It’s a simple concept that’s widely understood now. There are a host of data sources available today, and a cast of players and tools in isolated environments involved in creating, managing, massaging, delivering, and using them. But to be most effective, this environment must be delivered in an interoperable, hosted, secure manner so that scientists can buy target data from commercial providers mined from the literature, connect to public services, and use the best tools for the task, be they open source, commercial, or proprietary.

While the concept is simple, the environment itself is, by definition, rich and complex. We’ll be exploring this ecosystem and how to maximize its utilization to address the big information challenges in life science R&D at a workshop before the Bio-IT World Conference and Expo Europe on October 10. We invite you to learn more about the workshop and, if you’re interested, to attend.

Even if you can’t attend in person, though, we are interested in your help developing use cases to guide discussion at the workshop. We want to avoid “talk shopping” and ensure that we leave the workshop with a clear sense of a path forward including tangible actions and deliverables. Information ecosystem use cases will provide concrete descriptions of what scientists expect and need from this high changeable environment help them solve their problems.

The use cases should address complexities and gaps in the life science information ecosystem that have evolved over the past five to ten years, mostly along three major dimensions:

Translational research: The need to integrate preclinical/molecular and clinical/medical information. (This dimension often has a significant company-internal component, dominated by culture and policy issues; we ask that any submitted use cases think beyond this scope.)
Externalization of R&D processes: The need for collaborative work, which involves moving and sharing mostly proprietary information across institutional borders.
Availability of large volumes of relevant but distributed public information and data: The need to enable seamlessly integrated analysis of public and proprietary information.

Use cases should be high-level, focusing on WHAT problem needs to be addressed, not HOW to address a particular problem. They should also be concise (one page max), as there will not be time to digest large documents during the workshop.

We’ll use the use cases in two ways. First, they’ll guide the breakout group discussion during the morning session of the workshop and help us develop a common understanding of key features and concepts of an information ecosystem that is useful to solving problems presented in the use cases. They will also help focus the roadmap discussions in the afternoon on activities and project proposals that have practical direct impact on life science R&D.

Send us your ideas; we’ll monitor the comments!

Posted in Alliance news & milestones, Bioinformatics, Workflows & business processes | Tagged biology domain, externalization, information ecosystem, translational medicine, workshops | Leave a comment

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