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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?

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

Is Academia ready for ELNs?

Posted by Dominic.John Aug 26, 2011

Or put another way--are ELNs ready for Academia? Academia in the past has viewed ELNs as a tool for commercial scientific research and development pointing out complexity, cost and perceived value being barriers to adoption. However, several changes in the industry and academia are driving large ELN adoption. The first and most fundamental change is that vendors are now delivering low cost ELNs that are easy to use, easy to deploy and require little infrastructure.


A case in point is the newly acquired iLabber ELN from Contur that Accelrys recently purchased. iLabber is one of the fastest adopted ELN products in the world. There’s a free personal edition, and you can sign up for a free team edition trial and be running in seconds with a zero footprint Windows and Mac compatible web client, all hosted in the cloud for a low monthly fee. The experience is outstanding. See for yourself at-  


According to the iLabber developers the ELN has been developed on 3 main goals:  They’ll tell you, ease-of-use, ease-of-use and ease-of-use…and they keep a straight face while masticating some Swedish snus between their gums. Evidence of this is that standard training is 1 hour for scientists and 30 minutes for admin. But delivering ease-of-use means also ease-of-access, ease-of-administration and ease-of-deployment--all critical qualities needed to enable academia to deploy and utilize an ELN.


Other changes driving academics to adopt ELNs include economic pressures, distributed research groups and industry funding. With grants becoming harder to attain and fewer, there’s pressure to make the research pennies go further and show higher returns. The new ELNs like iLabber provide a central environment for research groups and academic departments to immediately adopt a collaborative data management environment. Experiment information can be captured, searched and shared electronically within and between sites. Any researcher can see what has been done before, learn and re-use. The result is less experimental repeats, reduced experiment failures and less re-invention allowing grants to go further. Furthermore, brain drain is a common problem with a very transient population of postgraduates, post-doctorate’s, RA’s, PI’s and professors. With an ELN there is a continuity of knowledge that can be rapidly searched, easily read and picked up by current or new academic members. The result is that grants go further, research groups are more productive and the groups get better recognition as a centre of research excellence for further grant awards.


The sources of academic funding are shifting more and more to industry. Commerce is now using academia as an agile and low risk strategy for research ideation and innovation. But with commercial funding comes pressure to adopt commercial infrastructure to protect IP and preserve and transition knowledge to the funding partner. An ELN gives Academia an immediate electronic infrastructure to support industry funding and relationships. In the process of adoption, an ELN also provides a competitive advantage for industry dollars when compared to sites without a data capture environment like an ELN.


Finally, it is more and more common for PIs (Principle Investigators) to be coordinating research across multiple geographically distributed research groups. Traditional paper-based notebooks provide a significant barrier to efficient project management, not to mention, information exchange. Meanwhile, an ELN in the Cloud provides PIs with the ability in real-time, from anywhere in the world, to review, provide feedback, or sign off research being documented in the ELN. For new staff or groups joining a project from anywhere in the world, they can gain instant access to an ELN, thanks to the availability of “elastic” cloud ELNs, and can start leveraging the ELN and the group knowledge within.


So is academia ready? Yes! Is the ELN ready for academia? Yes!  Still skeptical? Check out the testimonies, or try it yourself


….and if you don’t want to try some software why not try some Snus..

802 Views 0 References Permalink Categories: Electronic Lab Notebook, Cheminformatics, Lab Operations & Workflows, Bioinformatics, Data Mining & Knowledge Discovery Tags: notebook, eln, electronic, academic, academia, pi, ilabber, contur

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

We often wonder why the regulatory rules are so stringent for pharmaceuticals. At the end of the day the primary goal is to protect the patient. Today, I read an article that defied belief. A contract research and development organization was caught modifying documents and samples!  There are not only implications for patients who may receive potentially unsafe products but those pharma and biotech companies that have invested may have to re-file, even fail or enter class action law suits in extreme cases. For their financial investors this could send share prices through the floor.


To quote the article “Specifically, in at least 1,900 instances between April 2005 and June 2009, laboratory technicians identified as conducting certain studies were not actually present at [Company Not to be Named by Accelrys] facilities at that time, the FDA said in its May report”


I can't help but wonder if the scientists were still using paper lab notebooks. After all, paper has always been the very foundation of the forger's trade. Moving to an electronic environment documenting samples, experiment ownership and providing data traceability along with not just electronic signatures, but full electronic audit trails, makes falsifying information that much harder.


In the land of paper processes and paper documents anyone with pen and paper can make some subtle changes or create documents and samples at a later date with ease. With an ELN this becomes near impossible to do and importantly, hide, unless the whole company is in on the deal. Falsifying data within an ELN is near impossible. You need to be a scientist, a database wizard and be an expert in IT systems that have been designed to protect billions of dollars from fraudulent activities, for instance, in financial institutions.


I see news like this not only accelerating the use of ELNs, but also resulting in contracting organizations mandating 3rd parties to use more robust and electronic methods to document their day-to-day experiments, instead of a paper based process. In addition, I see that contract research and development companies can gain competitive advantage by demonstrating that they have electronic systems that protect their partners from fraudulent activities that can have massive financial and liability implications.


What do you think?

713 Views 0 References Permalink Categories: Executive Insights, Lab Operations & Workflows, Bioinformatics, Electronic Lab Notebook, Cheminformatics, The IT Perspective, Data Mining & Knowledge Discovery Tags: data, notebook, eln, fda, samples, faked

The pending passage of the America Invents Act will transition the United States from a first-to-invent to a first-to-file patent process in sync with the rest of the world. It's no longer important to provide evidence how far back you first generated the idea for the patent and this has implications on the use of the ELN in the research laboratory, as well as, in the use of paper notebooks. The question is, how will this change the way we use and invest in ELNs?


Intellectual Property (IP) protection in a first-to-file patent environment is only a small part of the ELN’s role in today's electronic lab. To quote a scientists using the Accelrys ELN, “when everything else is electronic, an ELN makes a lot of sense.”  It is generally recognized that ELNs increase productivity by up to 20% by enabling scientists to document experiments, find and re-use information and collaborate more efficiently. Backing this up is the adoption of ELNs in the Development or CMC space in pharma. Large adoption and use of the Accelrys ELN in an environment where the focus is on process efficiency and compliance demonstrates that an ELN has an important role even in an environment where IP protection is of less importance.


With a first-to-file patent process ELNs will continue to play a very important role enabling organizations to save time in the patent process. Paper notebooks under the new patent process will be a significant barrier for first-to-file as information is difficult to locate, extract, process and re-use in a timely manner.  Meanwhile, ELNs streamline and  accelerate the assembly and submittal of patent dossiers by providing better traceability, searchability and reporting of information within and across collaborating teams. For these reasons scientific organizations will continue to adopt ELNs at a high rate even with the patent law changes coming.


Do you agree? How do you think a first-to-file process will change how we use paper notebooks and ELNs in the lab? 

885 Views 0 References Permalink Categories: Executive Insights, The IT Perspective, Bioinformatics, Electronic Lab Notebook, Trend Watch, Materials Informatics, Data Mining & Knowledge Discovery, Cheminformatics, Lab Operations & Workflows Tags: notebook, eln, patent, ip-protection

Do We Really Need Solar Power?

Posted by gxf Aug 4, 2011

Ok, before you start with the hate mail, the answer to this rhetorical question is YES. Photovoltaic solar currently provides only a small percent of our electrical needs, but it grew 53% in 2009. And advances like these printed panels mean that it's going to become less expensive and more widespread.


So why the provocative question? I recently saw a couple of postings where people ask "Hey, why don't we put solar panel on electric and hybrid cars to make them even more efficient?" I found an answer to this question from as early as 2008 in the Washington Times - and this analysis was probably carried out even earlier: the energy from solar panel is a drop in the bucketcompared to the needs of a commercial vehicle. The question bugged me enough that I thought I'd go through the analysis again in detail for folks. The bottom line: you need 70 m2 worth of panels to drive 60 km/h.


There's a terrific analysis of vehicle power consumption by Hideaki Horie in Lithium Ion Rechargeable Batteries: Materials, Technology, and New Applications, edited by Kazunori Ozawa. The force required to overcome rolling friction and air resistance in a vehicle is

F = mTg M + 0.5 rCD A V2


  • mT is the coefficient of friction, ~0.025
  • g is the acceleration of gravity, ~9.8 m/s2
  • M is vehicle mass, ~1500 kg
  • ris the density of air, ~1.29 g/cc
  • CD is the drag coefficient, ~0.35
  • A is the exposed vehicle area, ~2 m2
  • V is the velocity, taken here as 60 km/hr = 16.7 m/s

Power consumption, P, is force times velocity,

  • P = F * V

Put this all together and you get a requirement of about 8 kW to drive a vehicle at 60 km/h.


300px-Solar_Car_Tokai_Challenger.jpgHow does this compare to solar? TLC tells us that a home solar panel produces 70 mW/in2, or 110 W/m2. Hence you need over 70 m2worth of solar panels to drive at 60km/h. I haven't measured the surface area of my Prius, but it's definitely less than that.


Am I being negative? Not at all. I just want people to think critically about alternative energy. The same TLC site calculates that 26 m2of solar panels will meet the needs of a typical home, and that's quite feasible to put on a house or in a back yard. How about using those panels to charge your car battery? Driving the car at 60 km/h for 1 hour consumes 29 MJ of energy. 26 m2worth of solar panels will generate 10 MJ/h, so you'd need to charge for 3 hours to drive that far. This approach might actually work for small, efficient cars (think low M, A, and CD) on short trips.


What can we do to make solar power more relevant? As a scientist, I am fascinated by potential new photovoltaic technology like GaAs nanopillars or carbon nanotubes. As a concerned scientist, I can write my elected representatives and urge them to continue funding research like that. But as a consumer, I'll do more for the environment if I take the train to work than if I put solar panels on my car.

887 Views 0 References Permalink Categories: Materials Informatics Tags: alternative-energy, solar-energy