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6 Posts authored by: fbrown

It was a great pleasure to announce last month that Accelrys has added HEOS by SCYNEXIS to the new Accelrys Cheminformatics Suite. There has been a lot of buzz since the announcement, including a well-attended webinar. So, I've invited Frederic Bost, director of information services at SCYNEXIS, back to expand on his recent post about HEOS and explain the value it brings to our Cheminformatics Suite.

Fredric Bost.JPGOne of the most significant trends influencing the way drug discovery proceeds is externalization. We've seen the impact directly here at SCYNEXIS, which is why we began building HEOS nine years ago. to facilitate collaborations with our research customers.


Today, research organizations are complementing their unique expertise and moving research programs forward by using externalization to bring valued, skilled partners into select projects. This has fundamentally changed the nature of outsourcing relationships. Once, outsourcing was based on transactions, with a commissioning company telling another company to "make this" or "test that."  Modern partnerships and outsourcing now aim to "discover this" through collaborations that often involve multiple partners playing different roles in different projects from locations around the world.


Most research organizations currently support collaborative research using one of two models. Some trade files via email or an e-room, an option that can be insecure and error prone, requires scientists to mediate and interprest the data exhanged between partners, doesn't occur in real time and simply doesn't scale to projects involving multiple partners. Other organizations opt to open up their internal systems to partners via VPN connections, relying on security settings in their internal systems to keep partners segregated. Most cheminformatics systems can do this, but internal systems have been designed on the assumption that everyone accessing data is an employee entitled to full access rights. Hence, opening up an internal system at best increases risk and requires extra resources to maintain security; at worst, it is time-consuming, expensive and, like the other model, fails to scale given the dynamic nature of collaborative research.


More importantly, both of these current models fail to address IP ownership. Traded files are hard to track, and storing IP from collaborative research alongside internally owned IP in the same system makes it difficult to delineate and separate who owns what when a collaboration ends.


The needs associated with modern collaborative, externalized researchare perfectly suited to cloud computing. HEOS, as we've demonstrated with the Drugs for Neglected Diseases initiative, captures all the data and processes associated with conducting multi-company drug discovery projects and was designed from the ground up to enable multiple companies with different access rights and requirements to collaborate within the system.


The graphic below shows how it works. A primary collaborator can establish any number of secure team areas in the HEOS cloud to manage collaborative research. Within each research area, the primary collaborator partitions access to the data among its partners. Some partners may only have the ability to upload or publish data. Others may be able to download certain data from other team members (such as an analytical lab needing to conduct tests on compounds produced by a medicinal chemistry partner). New partners can be rapidly spun onto projects or spun down when their services are no longer required. Best of all, collaborative IP remains in the collaborative space and can be partitioned among the partners and downloaded into their internal systems when appropriate.


Heos Collaboration.GIF

Above #is a figure showing how it works. A primary collaborator can establish any number of secure team areas in the HEOS cloud to manage collaborative research. Within each project area, the primary collaborator partitions access to the data among its partners. Some partners may only have the ability to upload or publish data. Others may be able to download certain data from other team members (such as an analytical lab needing to conduct tests on compounds produced by a medicinal chemistry partner). New partners can be rapidly spun onto projects or spun down when their services are no longer required. Best of all, collaborative IP remains in the collaborative space and can be partitioned among the partners and downloaded into their internal systems when appropriate.


To those who worry whether they can trust the cloud for managing research data, HEOS has been audited by some of the largest pharma companiesand has survived ethical hacking attack tests (read the HEOS security white paper to find out more). I’d say the cloud is ready for research data—HEOS is a proven technology that has managed millions of compounds and tens of millions of data points.


So, are you and your research partner networks ready for the cloud?

5,237 Views 0 References Permalink Categories: Trend Watch, Cheminformatics, Modeling & Simulation Tags: hosted-informatics, cloud-computing, guest-authors, externalization, research-collaboration

Due to the response to my recent post about how the Hit Explorer Operating System (HEOS) collaborative program is assisting in the treatment of neglected diseases, I've invited Frederic Bost, director of information services at SCYNEXIS, to talk a little bit more about HEOS and the project. It is with great pleasure that I welcome Fred to our blog!


Dr. Bost.JPGThank you Frank, it's great to have this opportunity to talk to your readers.  We couldn't think of a better case for the HEOS® cloud-based collaborative platform than what we've seen with the committed scientific community engaged in Drugs for Neglected Diseases initiative (DNDi). The project is grand in scope and comprises scientists spread over five continents representing different cultures, disciplines, processes and companies. In this way, it's a macrocosmic example of what happens in industrial pharma research.


Collaboration requires all team members -- from different physical locations, disciplines and cultures -- to interact equally and as needed regardless of their physical location, disciplinary background or expertise. We've set out to develop a platform that invites all scientists involved in a project to contribute any information that might be beneficial to the team, especially if these scientists don't have the opportunity to interact frequently face-to-face. HEOS ensures that scientists can share whatever they deem relevant; be it a data point,  comment on another's work, an annotation, a document, a link from the web or a Pipeline Pilot protocol. The science or the data should never be compromised by external factors. For that reason, we embrace the motto of the DNDi -- and extend it: The Best Science (and the best supporting software) for the Most Neglected.


What does true collaboration look like? Here's an example from the DNDi project:  The non-profit organization started a research program against an endemic disease by collecting small compounds sets from volunteer large pharmaceutical and biotech companies. Assays were run by an expert screening company in Europe. While several of the programs proved to be dead ends, one showed promise. The non-profit organization hired an integrated drug discovery contract research organization (CRO) to produce additional analogs using high-throughput screening. Using HEOS, the biotech that provided the initial compounds was able to continue to manage the project while the CRO for high-throughput screening confirmed the most promising hits and leads. The managing biotech was also able to track in vivo studies performed by a US university.


As the program moved along, several ADME, safety and pharmacokinetic teams got involved in the project. Several peer organizations were also consulted on certain decisions. All these efforts successfully delivered a compound ready for the clinic that is today showing great promise in treating a disease for which a new treatment hasn't been produced in decades.


Managing this type of program, whether in a non-profit setting or an industrial one, demands flexible, rich features that can accommodate the needs of each partner at each stage of research while capturing data, keeping it secure and consolidating it so that it is available in real-time to authorized team members when they need it. Data must also be curated, validated and harmonized according to the rules that the project team has established and provided in a common language that enables scientists to compare results, whatever their origin. And because of the power of embedded Accelrys tools, HEOS can also provide the scientific analysis tools necessary to support the team in its decision process. All of these capabilities enable scientists to compare results and make decisions as a team.


It's been fascinating and rewarding to serve this community of passionate scientists fighting against endemic diseases. Together they have participated in an evolution, creating an agile networking environment that combines competencies and science from many places to achieve a common goal. HEOS has quite simply helped the DNDi's virtual teams function as if the world were much smaller than it really is.

1,301 Views 0 References Permalink Categories: Trend Watch Tags: pipeline-pilot, data-mining, cloud-computing, cheminformatics, neglected-diseases, knowledge-discovery, collaboration

In my last blog, I talked about how improved global collaboration in the Cloud is not only improving Neglected Diseases research but also the "exuberance quotient" of science. Today our current economic woes tied to the sovereign debt crisis have got me thinking about the darker cloud hovering over researchers today, one that may very well threaten "exuberant" science in the months ahead, especially in university labs.


There’s no way you can look at today’s economic situation and postulate that government funding of scientific research in academic labs is going anywhere but down. It stands to reason that this will drive changes in behavior and requirements for Academia to find funding alternatives for their research.


First, university labs will need new ways to collaborate externally, not only with colleagues at other institutions but with those at the many commercial companies that will likely end up funding more and more academic research as government sources dry up. Second, they will need viable channels for commercializing the technology they develop, so that new applications, protocols and processes emerging from university labs become readily available to the wider scientific community (while also providing a return revenue stream supporting university research). Last but not least, with university researchers under increasing pressure to publish results, secure patents and acquire grants in the face of shrinking budgets and resources, they need simplified access to affordable software and services -- and we just took steps towards that end with our recently announced academic program.


This new academic paradigm and resulting wish list become much more achievable when university researchers deploy their technology on a scientific informatics platform that’s already widely used in the commercial world. This provides a built-in installed base and ready market for workflows and protocols. A widely deployed platform with the ability to capture a protocol as a set of XML definitions enables scientists working in the same environment to replicate an experiment or calculation with drag-and-drop simplicity and precision. If you start with the same data set, you end with the same results. Experiments are more reproducible, academic papers more credible and, most importantly, non-experts can advance their research using robust, expert workflows.


Academic researchers drive innovation that impacts the larger scientific community, but getting the innovation out there is still a challenge. In this regard, an industry-standard platform can also serve as the basis for an innovative new marketplace, a kind of scientific application exchange, where academics and their partners can expose their breakthrough technologies to a wider audience—and even charge a fee for using them. In the present economy, this new channel could provide much needed additional funding and a feedback loop for academic groups, enabling them to continue their vital research.


What are your thoughts on surviving—and perhaps even thriving—in today’s down economy?

690 Views 0 References Permalink Categories: Executive Insights, Trend Watch Tags: discovery_studio, pipeline-pilot, materials-studio, innovation, cloud-computing, academic-research-funding

Neglected Diseases like malaria, Chagas, schistosomiasis and human African trypanosomiasis (sleeping sickness) affect millions of people in the developing world. Drugs currently used to treat these diseases are of limited availability and efficacy. They’re also costly, often based on old molecules and some have severe toxic effects. Even more worrying, drug resistance is emerging in several infectious diseases.The bottom line is: A coordinated, global campaign investigating therapeutics for Neglected Diseases is a critical imperative.  


When SCYNEXIS approached us to donate software licenses and be a part of the cure, the Accelrys executive team readily agreed, and I’m so happy and quite proud to be with an organization that’s a part of this worthy effort.


A collaboration involving Accelrys, SCYNEXIS and Tibco Software is now providing a way for scientists around the world to work together on Neglected Diseases. It’s already helping to change the way science is done today and also creating the possibility for new economic opportunities for under-resourced labs in developing countries. 


The scientific collaboration consists of SCYNEXIS’ SaaS-based platform for drug discovery—the Hit Explorer Operating System (HEOS®) —which is providing hosted data for several not-for-profit, public-private partnerships (PPPs) that are leading the charge against Neglected Diseases. Accelrys’ contribution includes: Pipeline Pilot for moving data around, running calculations and assembling reports, while our chemical registration software builds the chemical registry. Completing the system, Tibco Spotfire Analytics provides visual analysis tools enabling scientists to interact with their data in real-time. The collaborations are truly global in nature and HEOS® allows real-time sharing of data.



Our Neglected Diseases collaboration has resulted in at least two “Eureka!” moments for me. First, I’m intrigued by the geographical distribution of the scientists using the system. Thanks to the hosted HEOS® platform, Principal Investigators (PIs) in Brazil, Ivory Coast, the Philippines, South Africa, Zimbabwe and many other countries have come together in a vibrant virtual research community. Like other social and professional networks today, this virtual community is empowering isolated researchers as never before, making them part of a larger team, much like big pharma. The hosted system is also increasing the importance of these researchers’ work by making it widely available to their colleagues around the world. A participating researcher recently told me: “My molecules matter, now that they’re part of the larger collection. So what if I only contribute a few… one of them could be a winner someday, which means my work is important now.”


The other thing I find interesting is the remarkably diverse chemistry that is emerging from the project. With so many disparate molecules from so many different places now available for testing against screens, it’s easier for scientists to “jump the chasm” when assessing activity because they’re not locked into only a couple of series.fig2.png The number of coumpounds, data points and disease targets are growing every year (see figure).


One of the major benefits of a global project like this is really untainted perspective, providing the ability to move beyond fixed ideas and preconceptions to fresh insights. The far-flung researchers now contributing to the HEOS® database bring an unabashed passion to their search for answers. Let’s face it; the diseases they’re researching are endemic to their locality, often touching neighbors, friends and family. When motivated scientists are empowered to make a difference, everything becomes possible — everything from important scientific breakthroughs resulting from better sharing of data to improved viability for the labs providing the data. For example, hosted environments like HEOS® can simplify the process of registering molecules in industry-standard sourcing databases like the Available Chemicals Directory. Under-resourced labs in economically challenged regions can become more sustainable by selling the molecules they discover.


The Neglected Diseases project demonstrates that scientific data can be stored securely and shared globally on a thin client. However, the real takeaway message is more compelling than this technical accomplishment. The real value is: Improved global collaboration in the cloud is empowering researchers in developing regions by making their work available to—and important to—the wider research community. This is not only changing the way we do science; it’s increasing the exuberance quotient of science for many of us.


What’s your vision for scientific collaboration in the cloud?

1,242 Views 1 References Permalink Categories: Data Mining & Knowledge Discovery, Trend Watch Tags: visualization, simulation, pipeline-pilot, computational-chemistry, cloud-computing, neglected-diseases
Biology is undergoing a revolution and is becoming a more analytical science with the advent of omics, high content screening, next generation sequencing, and other methods.  These methods lead to the more in-depth understanding of systems biology and the discovery of new biomarkers.  This greater understanding can be used to fill-in our knowledge about pathways, to the point of building mathematical models of the multiple processes involved in any response to stimuli. All of this taken together should increase the odds of success by having better information to base decisions on.

The other area in biology that has great opportunities is in the use of biologics as drug entities. These drug entities range in complexity from antibodies, vaccines, siRNA, etc.  The value to the marketplace is in the hundreds of billions of dollars and intellectual property (IP) protection is essential.  Some of the largest patent infringement cases ever awarded are around biologics.

In the process of building-out of these analytical biology systems, and the biologics as drug entities, there are many biological innovations and inventions.  For example, new stem cell lines, antibody generation as a tool or as a drug entity, plasmids, algae strains, etc.  There is also a lot more inventory, reagents and data to track today than ever before. The best way to track data across multiple sources is the use of a consistent and meaningful key. The way this is handled in the chemical space is to use a registration system to uniquely identify an entity and give the entity a unique integer that represents the entity in every data system.  Until recently, the biologist might track a bar code for a cell line or antibody in their notebook, and a possible location for this entity in a lab-based, simple inventory system.  However, this type of system only tells the same researcher where the cell line is, not uniquely what it is.  In order for the entire company to benefit from the inventory, and protect their IP, there is the need for describing the biological entity uniquely.  This is a rather new concept for biologist which needs to be carefully considered moving forward to better protect IP, manage expensive reagents,  implement safety systems and most importantly, to ensure the query and aggregation of data.  All of this has been implemented in chemistry and shown to be of great value, now it is biology’s turn.

Does your organization have a Biological Registration system?  How could such a system add value to your organization?
526 Views 1 References Permalink Categories: Bioinformatics, Executive Insights Tags: biomarkers, biologics, antibodies, biological-registration, cell-line
Accelrys has recently concluded a series of meetings with a specially convened Biological Registration Special Interest Group , (SIG), formed between several major pharmaceutical companies and Accelrys.  The objective of this forum was to understand some of the critical market and product requirements needed in order to build a state-of-the-art Biologics Registration system.

The success of the SIG can be attributed to the customer members being very open towards one another, in spite of being competitors, and the tremendous diligence each company put into specifying user requirements.   This open and collaborative approach to software development has become an innovative way to introduce first of a kind technology into the market.

First of a kind software is usually developed as a bespoke project for a single company and then modified over time to meet the needs of the wider market.  This can create disadvantages for early adopters as the product functionality evolves and improves with subsequent releases.    This situation can be avoided by getting a wider set of requirements through a collaborative SIG formed of a diverse and representative sample of interested parties.

The  ability to capture and prioritize a wider set of requirements through leading companies discussing and debating the relative merits and benefits of proposed features, is a more efficient and effective way of understanding market requirements than more traditional methods.  The approach also  enables the development team to capture feedback and more rapidly create a product that should be attractive to the wider market.  The anticipated result is the timely delivery of a product that is well positioned to capture both broad interest and market share.

Have you innovated through collaborative work groups?  If so, we would welcome the chance to learn from your experience.
463 Views 0 References Permalink Categories: Bioinformatics, Executive Insights Tags: consortia, biologics, biological-registration