At our annual RSC evening event (#PistoiaRSC, registration:, to be held on February 11th 2015 from 6-10pm at the Royal Society of Chemistry in London, UK, we want to shine a spotlight on our extensive community of Contributing Members. We want to ask: What keeps you up at night?

Our members and friends are a diverse collection of pharma companies, technology vendors, life science businesses, publishers, small and medium sized businesses, academics, consultants, and interested individuals. With such a large group it can be hard to make everyone’s voice heard. With the introduction of IP3, our platform for gathering ideas and tracking their progress as they turn into Pistoia Alliance projects, it has become easier for all of our members to have their say. In the run-up to our RSC event we want to make it even easier.

We are encouraging all our friends and members to join our @pistoiaalliance Twitter campaign #PistoiaRSC #UpAtNight. Tell us what your problems are that you feel the Pistoia Alliance might be able to address; they could be technical challenges, strategic questions, informatics hurdles, or something else. If you don’t use Twitter, email us instead: [email protected]

We’ll use IP3 to collate the responses for a special debate at our RSC event. Everyone who submits an idea is encouraged to attend the event, even if they are not a Pistoia Alliance member, and during the debate we’ll run a live vote among the audience to pick their favourite ideas. The people behind the most popular suggestions will have the chance to pitch to the audience and convince them to set up a Pistoia-funded project to address their needs.

We really hope you’ll join in the conversation and tell us what keeps you #UpAtNight, and we look forward to meeting you all in person at the RSC. Keep track of the event using our app:

Tweets will appear in this feed:

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By Claire Bellamy, HELM project manager

The Pistoia Alliance HELM project started almost two years ago in December 2012 when David Klatte proposed that the Pistoia Alliance help open source a technology first developed for internal use at Pfizer. That technology was HELM and it enabled the representation of complex macromolecules. The Pistoia Alliance membership enthusiastically embraced the idea and the HELM project was born.

The first phase of HELM had the following objectives:

  • Make the internal Pfizer code independent of internal Pfizer systems and making it available to the wider community free of charge.
  • Set up a community to govern the standard and manage enhancements and further development work.
  • Promote the standard and encourage adoption.

Although the original project plan scheduled the code to be available in Q4 2013, the project exceeded all expectations and released the code well ahead of schedule in May 2013, having only used a small fraction of the original budget. Particular thanks go to ChemAxon who provided the development resource, and Sergio Rotstein (Pfizer) who took over from David as project lead, but it was the time, expertise and effort from a very large number of companies which enabled such a lot of work to be completed in a short period of time.

Instead of closing the project at this stage the steering committee decided to continue and use the remaining funds to extend HELM and continue to encourage adoption. Further technical developments ensued:

  • xHELM – an exchangeable format that includes monomer definitions in the notation.
  • Search prototype from Cambridge University.

In parallel, others got involved:

  • EBI started converting ChEMBL structures to HELM format.
  • Roche extended the HELM editor to recognise and display antibody domains.

And at the time of writing we have a growing list of companies who are using HELM, have active projects to use HELM or are involved with the project and have supplied funds:

  • Vendors: ChemAxon, Biovia, BioMax, Next Move, Sciligence, BioChemFusion, Arxspan, eMolecules, ACD Labs
  • Pharma: BMS, GSK, Lundbeck, Merck, Novartis, Pfizer, Roche

Just to encourage the team even more, we won a BioIT World Best Practices Award for 2014!

Our heartfelt thanks go to the many people and organisations who contributed to the project. We have thoroughly enjoyed working with you and appreciate everything you have done.

Having achieved far more than we expected, the initial phase of HELM is at a close, but such a successful standard does not and should not stand still. The new project OpenHELM intends to build on the foundations and address key extensions identified by HELM adopters. There is more to come and we look forward to an exciting future.

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by Peter Boogaard, Analysome project leader

The Analysome concept was initiated by the U-BIOPRED team and supported by the Pistoia Alliance. Although developed as a pre-project assessment exercise, the outputs delivered by the Pistoia Alliance provided many of the benefits of a full-scale project and included the creation of a fully functional prototype.

U-BIOPRED is a project run by the Innovative Medicines Initiative (IMI) organisation, Europe’s largest public-private partnership. IMI aims to improve the drug development process by supporting more efficient discovery and development of better and safer medicines for patients. Within IMI, the U-BIOPRED project is aimed at speeding up the development of better treatments for patients with severe asthma.

The main objective of the Analysome work carried out by the Pistoia Alliance was to explore whether an analyte search portal needed for U-BIOPRED’s Asthma research could also be used in other disease areas. This Analysome portal enabled scientists to rapidly find available assays for analytes of interest, including those in related biological networks, and allowed assay providers to create a marketing channel for high quality assays. Stakeholder benefits were anticipated to include:

  • FTE saving on finding the right biomarker at the right time with the right quality and the right availability
  • FTE saving on in-house curation of biomarker resources providing vendors a marketplace for their assays
  • Risk mitigation – using appropriately validated & qualified biomarkers minimizes experimental and regulatory risks

Originally only intended to be a desk-based research exercise, the Analysome concept in the hands of the Pistoia Alliance soon led to the creation of a working prototype, which was achieved entirely within the original budget. It was felt that a complex concept such as this could only be truly appreciated if seen in action, and that a prototype or demonstrator would be vital for assessing the potential impact and true value of the project.

The prototype consists of an easy to use web search portal backed by Thomson Reuters’ powerful Cortellis Data Fusion platform. An initial set of analytes were loaded for the purposes of demonstration, including Singleplex Analytes, Southampton Analytes, Assay register, Somalogic serum analyte assays, Soton serum MSe proteomics, and Uniprot. Combined, these analyte sets provide approximately 750,000 data points.

The working prototype ( is hosted at Thomson Reuters Cortellis Labs on behalf of the Pistoia Alliance. A free Cortellis Labs account is required to access it, and on the prototype’s front page there is a link to a video explaining how the Analysome portal works. The prototype is open-source.

The Pistoia Alliance’s assessment work for the Analysome concept is complete. Further development may take place if additional funding becomes available. If you would like to invest in the next stage of this project, or gain access to a copy of the source code for the prototype, then please get in touch by emailing our business development team: [email protected].

Posted in Informatics architectures, Standards & deliverables, The life science cloud | Leave a comment

On February 17th and 18th in Philadelphia, PA, USA, the SmartLab Exchange 2015 conference will be chaired by our very own John Wise, Executive Director of Business Development for UK & Europe. John was invited to chair the two-day event by the organisers and is delighted to be able to take them up on their offer.

With businesses under constant pressure to; increase productivity, cut cost, streamline their organisation, and demonstrate regulatory compliance, lab environments are under more scrutiny than ever before. This along with the challenges of outsourcing, big data and an upsurge in M&A, standardisation and integration is all the more difficult.

It is therefore of key priority for lab informatics professionals to find the right tools in the market that will help them achieve this complex mix of business objectives in the most cost effective manner, to deliver their business maximum value. However finding the right tools that are both efficient and reliable is not an easy task.

As such, for organisations that recognise the need to increase productivity, cut costs, streamline their organisation, and demonstrate regulatory compliance, the SmartLab Exchange provides a platform to benchmark with an exclusive group of senior peers and solution providers capable of helping them define and successfully navigate this new territory.

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By Carmen Nitsche, Executive Director Business Development North America

Today begins a new era for the Pistoia Alliance.  With the launch of the Interactive Project Portfolio Platform (IP3) we are embracing a new level of openness, access, and transparency around the Pistoia Alliance’s idea-to-project process. The platform is open to the public for review, and individuals who wish to contribute need only register to be able to comment on the current idea pool, or vote on the viability of existing ideas, or submit their own ideas regarding collaboratively mitigating pharma industry challenges.

As ideas get submitted, the Pistoia Alliance IP3 team will recruit champions for the ideas, and will begin socializing the ideas among the membership.  Those ideas that generate significant member interest will be invested in by the Alliance to develop preliminary business cases.  We will then turn to the community to solicit funding to advance the ideas into full fledge project with clear deliverables. Funded initiatives will move on to active project status, where they will execute on the planned deliverables.  And all along this path, the background information, business justification, decision points, and day-to-day progress will be documented in the IP3 system for all to see.

We have been working closely with our partner QMarkets to configure their SaaS-based innovation management software to the needs of the Pistoia Alliance.  The new system will allow for free idea exchange along with a rigorous workflow to move ideas through the system.

Please visit to see for yourself what our community can do.  The live system is populated with all Pistoia Alliance projects underway, along with a large selection of new ideas generated at the 2014 Annual Pistoia Alliance Conference in New York City this past June, which require your input and support. We also have a Getting Started module available to help familiarize you with the IP3 system.

We encourage you to join us for the IP3 Launch webinar, which is scheduled for August 20th at 11 EDT/4 pm BST to walk you through the new system and answer your questions.   Please sign up today at If you have any questions, feel free to email the IP3 team at [email protected].

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The proposal for the CSCS Expert Community originated from the Pistoia Alliance CSCS Project, which ran from November 2012 – April 2014.  The CSCS Project completed successfully with the delivery of two commercially available Controlled Substance Compliance Services by ChemAxon/Patcore (Compliance-checker) and Scitegrity (CS Squared).The Controlled Substances Compliance Services (CSCS) Expert Community Kick-off meeting was held on the 25th of June 2014. The purpose of the meeting was to recruit members and define the CSCS Expert Community goals.  We had an excellent turnout with over 23 attendees, from a range of pharma and technology companies.

While the CSCS project team were confident in the interpretation of the bulk of the legislation and the implementation of the chemoinformatics and the technology by the CSCS vendors.  The project team felt there were still some key areas of the legislation, which were ambiguous and needed further interpretation.  The CSCS Project team found value in bringing together experts from across the world to identify and review this sometimes ambiguous and often difficult-to-interpret legislation.

During the kick-off meeting the attendees discussed the plan to create the CSCS Expert Community and the initial goals.   The Expert Community has funding for 1 year, in that time it must demonstrate it is sustainable and will deliver tangible benefits to the membership.

CSCS Expert Group

The attendees were then asked to formally sign-up to the CSCS Expert Community by email.

For more detail about the kick-off meeting,  follow this link to the slides and a recording of the meeting.

The next meeting is planned for the 30th of July, if you wish to attend please contact Anne Dunlop

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Having joined the Pistoia Alliance as Executive Director Operations just one week earlier, last week’s annual conference in New York was very much in at the deep end for me. In many respects I was there with the same intention as the majority of the other delegates: to learn more about what the Alliance is, what it has been doing, and what it plans to do next.

The conference took a slightly different format to previous years. The first day was open to the public and started by allowing delegates to hear about innovation-driven projects undertaken by organisations in related fields, such as NYC Bio, Quintiles, the NYC Clinical Data Research Network, the Global Alliance for Genomics and Health, and Deloittes. The idea here was to learn from experiences of others and use their findings as a springboard to the generation of new ideas for Pistoia-led activity.

Supporting these external speakers in the morning session were a selection of existing Pistoia Alliance members presenting projects from their own organisations that demonstrated significant innovation in life sciences R&D. BMS, ChemAxon, Infosys, Oracle and J&J all contributed a brief presentation each that shone a light on exactly the kind of pre-competitive internal innovations that Pistoia aims to encourage its members to share with each other so that the whole industry may benefit. Whether these idea-sharing presentations lead to a light bulb moment in one other member’s head or a fully blown Pistoia-led project that reaches out to the entire community, it will have helped.

The afternoon saw a review of current Pistoia projects and those currently in early stages of discussion, followed by round-table discussions around a number of subjects. For my part I led a discussion on generating new project ideas that resulted in at least two new project suggestions. As Pistoia is rolling out its new IP3 platform for managing the lifecycle of project ideas we will enter these new projects into it in due course.

Once in IP3 all projects are open for public discussion by the wider community, allowing Pistoia to gauge opinion and suitability for progression into funded activities. These new ideas will be joined by all existing project ideas and a selection of historic projects to set it all in context. We hope to have this IP3 system in production and fully populated by mid-Summer.

The second day, restricted to members only, saw a more in-depth discussion of Pistoia’s ongoing remit, goals, and specific projects – particularly HELM and CSCS which are both completing their initial phase and have delivered some impressive results. As part of this day a short session was held on the idea of sharing internally developed software directly between members via a kind of in-house bartering market, which is a concept I am particularly interested in and keen to see delivered.

During a core members meeting in the afternoon, at least ten further project ideas were developed and lined up for submission to IP3. This wealth of new project ideas – resulting in a pipeline almost triple the size it was before the event – is a significant step forward for Pistoia as it continues to work on its Next Chapter Initiative.

The Alliance is keen to scale up on the projects it delivers and the audience it can reach, and the injection of a large number of new ideas – and a significant increase in the support of these projects via the direct involvement of members at the meeting – is a big step forward. It is now my job to ensure that when these projects reach the production stage they are delivered on time, to budget, and that their deliverables meet the deservedly high expectations of success.

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Cast your mind back to the nineteen seventies.  Think Glam Rock, Morecambe and Wise, Watney’s Red Barrel, the Ford Capri, endless strikes and every man sporting long hair, a dodgy tie and enormous sideburns.

Paul HadlandIn those turbulent times, many pharmaceutical companies were still managing some of their R&D information systems on paper.  Those that had moved to computer-based systems were tied to the mainframe, with little or no interactive access.  All updates and queries were performed in batch mode – apart from online searches of external systems, which were carried out mostly on teletypes.

And yet, even then, pharmaceutical companies were actively collaborating on an IT project that they believed would be of mutual benefit.

In the early seventies, ICI Plant Protection produced an index of 20,000 organic chemicals from a dozen or so supplier catalogues. Paper copies of this index were shown to a meeting of the UK chapter of the Chemical Notation Association (now the Chemical Structure Association), and an inter-company project was launched with the aim of producing a database of all organic chemical suppliers’ catalogues.  The name of the project was CAOCI: the Commercially Available Organic Chemicals Index.

Coding into Wisswesser Line Notation (WLN – a predecessor of SMILES) and punching (on to 80-column punch cards – the preferred input format) were carried out by UK and US R&D Information staff in six pharmaceutical companies: ICI, Wellcome, Glaxo, Boots,

Pfizer and Beecham.  ICI co-ordinated and consolidated the system using their internally developed software, CROSSBOW, and within 18 months produced printouts of Molecular Formula and WLN KWIC indexes which were easily decipherable by trained information scientists and some adventurous chemists – such folk existed, even then.

ICI sold the CROSSBOW system to its collaborators, who now had a standard product for substructure searching using bit, string and connection table searches – not so different from what is done today.  With CAOCI, they also had most organic chemical supplier catalogues on a single searchable database.

CAOCI went from strength to strength, suppliers began to get much more involved and it went on to be managed (along with CROSSBOW and other ICI database systems) by Fraser-Williams Scientific Systems. Later on, it was renamed the Fine Chemicals Directory, and after a couple of changes in ownership, became the Available Chemicals Directory (ACD).

ACD is still with us today, and is now owned by Accelrys. (For details please contact Keith Taylor ([email protected]).

So the principles underlying PISTOIA have a firm foundation, and there is a strong precedent for collaboration across the industry leading to enduring value.

Just ask any R&D chemist!

Now, here are some questions to (hopefully) stimulate discussion:

  • Are there any other examples of long-lived, successful collaborations?
  • Is today’s environment more hostile or more open to such initiatives?
  • What role should commercial partners play in cross-industry collaborations?
  • If CAOCI was launched from scratch today, what would it look like, and how would it operate?


S. Barrie Walker: J. Chem. Inf. Comput. Sci., 1983, 23 (1), pp 3–5

(Paul Hadland started working on CAOCI in 1978 and has been involved with Pharmaceuticals R&D ever since.)

Posted in Cheminformatics, Collaboration & community, Standards & deliverables | 2 Comments

We don’t suffer a lack of ideas for potential Pistoia Alliance projects. The trick is getting a critical mass (including people and funds) behind an idea to turn it into an active project driving toward a solution. With the latest round of portfolio projects, we worked with David Seemungal of Cubase Consulting to conduct an indicative valuation of the various proposed activities. I asked David to explain the methodology, which we plan to employ as a way of calibrating expectations around future proposed activities.

My first exposure to the Pistoia Alliance was at the Dragons’ Den meeting in London, where I served as one of the dragons listening to the pitches and determining whether to invest in any of the proposals. Frankly, I ended up holding onto my play money, because none of the proposals were clear about their long-term value and the return investors would see on their investment. That’s not to say the projects didn’t have value—they just weren’t making that value clear in the pitch. So it’s been rewarding to be working with the Alliance to help put some quantitative measures of value onto its activities.

Assessing value is a bit easier for my firm, Cubase Consulting, which is primarily concerned with drugs or diagnostics, where you can track things like future sales. Pistoia Alliance efforts are “virtual” projects aimed at “softer” things like time savings, where the value is seen in freeing people’s time to work on other tasks. We defined value as having five components:

  • Cost: Savings in annual operating costs
  • Productivity: Organization is able to achieve more output at the same cost
  • Time to decision: Organization is able to make a go/no go decision more quickly at the same cost
  • Quality: Organization is able to deliver higher quality output at the same cost
  • Risk reduction: Able to comply with regulatory environment and avoid penalties

The first step in performing the valuation is to determine how these components factor in each project. The result is a “valuation tapestry” that assesses whether each component is a large (red), medium (orange), or low (yellow) component of the project’s value, as shown in Figure 1. So looking at the controlled substance compliance effort (first row in the table), the largest component of the value of this project is in risk reduction, whereas a project like tranSMART (last row in the table) spans most of the other four components.

Table showing the relative values of new Pistoia Alliance projects.

Figure 1: The valuation tapestry for proposed new Pistoia Alliance projects.

Assigning numbers to the values required us to make some assumptions. First, we had to come up with some measures of how many scientists at what levels would be impacted within organizations. We made some rough estimates about how head counts in global R&D are typically apportioned between discovery, development, and operations and admin, as well as how external costa and alliances compare to internal payrolls and administrative costs. Second, we then looked specifically at discovery scientists and technicians and broke out their typical daily duties as percentages. These numbers were in turn related back to the head count estimates determined in the first step.

Our valuation methodology then implemented a rather simple algorithm.

A = [Current prevalence of issue] x [Current resolution method] x [Current resolution resources]

B = [Current prevalence of issue] x [Proposed resolution method] x [Proposed resolution resources]

A – B = resources saved through adoption of Pistoia Alliance solution

For simplicity, we assumed each project had an implementation cost of $0.5 million incurred in 2013, with benefits from projects commencing in 2014. We also assumed a rather high private equity discount rate of 25% and a valuation period of five years. We based all valuations on the net present value (NPV), which is essentially the sum of all future cash flows over that five year period.

This kind of quantitation of ROI adds an important dimension to assessing the value of pursuing projects that can be taken together with other, softer reasons to determine which projects to carry forward. Of course, value, like beauty, is often in the eye of the beholder. What do you think of our methodology? And does your organization attach quantitative measures of ROI to determine which projects you should undertake?

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The Pistoia Alliance is partnering with the TM Forum (a non-profit ndustry association focused on enabling service provider agility and innovation) to explore the use of mobile apps in life science R&D. An initial meeting was held at the TM Forum headquarters in Morristown, New Jersey on 26 Oct 2012. The Pistoia Alliance “App Strategy” team shared its vision for the creation of a vibrant mobile community for life science researchers that would foster innovative thinking among researchers and accelerate research breakthroughs globally. Supporting mobile apps in this space will necessitate back-end cloud environments to support data-sharing, information navigation, and high-performance computation to enable desired workflows—elements that are firmly in the wheelhouse of TM Forum member companies.

The focus of the meeting was information sharing—to learn from each other and share perspectives. Invited speakers covered a wide range of topics relevant to the mobile app world. Speakers from the Pistoia Alliance community covered chemistry, biology/bioinformatics, translational medicine, and health IT, while TM Forum covered all things “cloud” including standards, security and computer systems validation, app store models, and novel visualization capabilities.

Chemistry is one area that already has seen some app development, and current mobile app functionality was reviewed, including advanced cheminformatics tools, access to public databases like ChemSpider, and novel ways to foster collaboration and data sharing via apps like ODDT and data appification (such as TB Mobile, which makes available a set of molecules with activity against mycobacterium tuberculosis and known targets in CDD). The Pistoia members described some of the current limitations in mobile apps for chemistry, in particular the difficulty involved in scaling up app capabilities in terms of data size. Mobile apps are making excellent progress in providing functionality for working on small data sets, but working with large data collections will require a new cloud-based infrastructure. It was indeed striking to see that in general biology mobile apps were not as prevalent as chemistry apps, though Life Technologies has collected a few examples.

Another topic covered by several groups was the use of cloud environments to power compute-intensive tasks and support workflows in gene sequencing and genomics. This was predicted to become increasingly routine in both life sciences research and clinical environments. An intriguing discussion covered how, and even whether, mobile apps could actually enhance work in these areas capabilities. In the healthcare domain, crowd sourcing approaches are being used extensively to transform how doctors and patients interact with each other and with their data. Moving from complex static web pages to simplified app designs that make complex information easy to understand has led to accelerated adoption in healthcare and provides a useful framework to emulate as we move to harness the power of apps to both simplify and transform life science R&D. Further, the emerging use of open source platforms such as tranSMART (an effort that the Pistoia Alliance is championing) drives the need for cloud-based data-sharing environments that apps could leverage to drive communication and data analysis.

Many presentations discussed the differentiating features of mobile apps (due to their design) that might make them compelling to life scientists. The camera standard on mobile platforms is a powerful differentiator, and the group brainstormed on what that capability could do to transform thinking. One novel app using the camera could potentially be used to render static pages into 3D models of a molecule or a protein, or even a pathway analysis view. QR codes or other visual recognition modalities might also be useful—could pointing the camera at an instrument bring information on that instrument (such as when it was last used or calibrated) directly to the user?

It was enlightening to hear such a diverse set of opinions from the audience at this meeting. The Pistoia Alliance App Strategy team is now working on developing potential projects we could do in partnership with the TM Forum. We welcome input for this ongoing discussion.

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