It’s been a long time since I was actively involved in scientific research – that was during my Ph.D., post-doc and early career. But I can still remember one of the most challenging tasks was getting to the library at least once a week to go through the new journals, find the relevant and interesting articles, and make copies to read “soon”. And that was after getting through the large backlog of journals which had already resulted in a large pile of papers that silently mocked me as they sat there, day after day, collecting dust on a corner of my desk. And then there’s all the articles I had already read and filed, with their siren calls of “come back to me, there’s important information in here that would explain that new result…”. Electronic abstracting services were just becoming available (yes, I know I’m dating myself here), which streamlined the process a bit, but also meant access to more journals than our library subscribed to, only adding to the work! Consider then this chart showing the increase in PubMed journal articles year over year (almost a million articles published last year!). PubMed serves primarily life sciences, but you’ll see a similar pattern with other scientific and technology document sources.
So how can anyone possibly keep up to date with relevant published literature in the face of the growing mountain of articles? Specifically, with a finite amount of reading time, how can researchers find the most relevant papers to read? Well, that problem has been solved by Ian Stott from Unilever who has developed an application that “knows” what journal articles are relevant to you, and delivers them right to your email inbox! Not only that, but the app continually learns and adapts to your interests, based on your preferences. This app, which was recently presented by Ian in a webinar entitled “Informatics-Led Literature Service: Keeping up with the Data Deluge” (find the recording here), was built using the Accelrys Enterprise Platform and Pipeline Pilot, and in particular, features components from the Documents and Text Collection. Using out-of-the-box components and other standard tools, Ian built the app and has deployed it to his colleagues at Unilever. We had a record-breaking attendance at the webinar, with many questions, proving the point that this is a major problem facing researchers.
Several attendees asked whether the same learning technique could be applied to patents, and other documents. It certainly can! And since the app is built using Pipeline Pilot and the underlying platform, it is easy to apply it to other document types, or even have it process multiple types simultaneously. The Documents and Text Collection provides out-of-the-box connectors for PubMed and both US and WO patents. Connectors to commercial document databases can also be created.
One concern that some attendees raised was that if you rely on a learning approach such as this, as opposed to a more manual search, what might you be missing out on? Well, although Ian didn’t present this in the webinar, the statistical modeling techniques that he used allows those kinds of analyses to be performed, and the results will vary by document type and the extent of training that individual users undertake. Of course, any researcher can, and probably should, use a combination of methods to find key research articles.
So what do you think about using modeling techniques such as this to try and manage the “data deluge”? Do you have alternative strategies? What about actually extracting information out of the papers? Can that be automated as well, rather than having to read the papers? That’s a whole other discussion!
In any event, maybe with tools as good as this one that Ian developed, I might be tempted to try my hand at research again…do they still use mouth pipettes?
Open innovation, as defined by H.W. Chesbrough, calls for good ideas to come from both inside and outside a company. Clearly R&D organizations see the value in this advice. Contract research has surged even during the global recession, with one source noting it accounted for 29% of the $74 billion drug development budget in 2008.
But it’s not just in life sciences that contract research has become essential. Critical scientific challenges in a range of industries—chemical, automotive, aerospace, microelectronics, and consumer packaged goods—require new ways of pooling knowledge to better understand how systems fundamentally work. For example, you can see how contract research helped Johnson Matthey discover new fuel cell catalysts by downloading this webinar recording.
In the embed below, Lalitha Subramanian, senior director, fellow, and Accelrys blogger, explains how the Accelrys contract research team works with R&D organizations to extend their internal R&D capabilities. Subramanian will be kicking off a webinar series on contract research on September 15 with an intro to Accelrys contract research. A customer presentation by Roger Avakian of PolyOne Corporation follows on September 28, and on October 7 Johan Carlsson, a member of the Accelrys contract research team, will give an application oriented talk on graphene multiscale simulations. Click here to register or learn more about this webinar series.
According to Gabriel Weatherhead, lead systems engineer at Millennium: The Takeda Oncology Company, the real value of Symyx Notebook is that it offers an overall platform that lets R&D informatics teams give scientists what they want. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc.]
Building applications that scientists will like and use is at the core of research IT’s mission, but that challenge was amplified at Millennium when it chose to implement an ELN across 10 different biological departments. The workflows and requirements ranged widely, Gabe explained. “Some scientists wanted a blank page that they could fill with information, others wanted stuff pulled in automatically off instruments and fields calculated automatically. Symyx Notebook provides an overall platform where you can build in hooks or just deliver something simple out of the box—whatever it is that scientists want.”
Another big change between the biology implementation completed this year and the chemistry implementation that Millennium started in 2003 was user expectations. “In the age of iPad and Windows 7, users expect more from software,” said Gabe. “They expect things to be streamlined, with shiny buttons. Today’s applications have to do as much of the grunt work as possible behind the scenes. This puts a lot of pressure on the implementation team to provide real value.”
Gabe said that it’s difficult to determine ROI for an application like an ELN. One measure of success for them is that their lab record keeping has been entirely electronic for four years. Productivity-wise, the ability to capture and search information previously bound in paper notebooks—sometimes illegibly—has helped Millennium protect and defend its intellectual property. Additionally, at least 50% of Millennium’s records are cloned from previous records. “The ability to document and set up a reaction has become trivial,” said Gabe, who was himself a scientist at Millennium before moving into research IT. “With the ELN, I could easily set up more experiments than I could work up.”
Gabe was only able to address five of the 145 questions asked by webinar participants, so watch this space—we plan to address some of the most popular questions in future posts.
Over 700 people have registered to attend the webinar we are sponsoring on Thursday, July 22--the largest audience ACS has collected for a webinar since it initiated the series! The webinar features Gabe Weatherhead, lead systems engineer at Millennium: The Takeda Oncology Company, speaking about how his company implemented a Symyx ELN in chemistry and biology. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc.]
Offering insight from the perspective of a Pipeline Pilot and Materials Studio user, Accelrys is pleased to host a posting written by guest blogger Dr. Misbah Sarwar, Research Scientist at Johnson Matthey. Dr. Sarwar recently completed a collaboration project focused on fuel cell catalyst discovery and will share her results in an upcoming webinar. This post provides a sneak peek into her findings...
“In recent years there has been a lot of interest in fuel cells as a ‘green’ power source in the future, particularly for use in cars, which could revolutionize the way we travel. A (Proton Exchange Membrane) fuel cell uses hydrogen as a fuel source and oxygen (from air), which react to produce water and electricity. However, we are still some time away from driving fuel cell cars, as there are many issues that need to be overcome for this technology to become commercially viable. These include improving the stability and reactivity of the catalyst as well as lowering their cost, which can potentially be achieved by alloying, but identifying the correct combinations and ratios of metals is key. This is a huge task as there are potentially thousands of different combinations and one where modeling can play a crucial role.
As part of the iCatDesign project, a three-year collaboration with Accelrys and CMR Fuel Cells funded by the UK Technology Strategy Board, we screened hundreds of metal combinations using plane wave CASTEP calculations.
In terms of stability, understanding the surface composition in the fuel cell environment is key. Predicting activity usually involves calculating barriers to each of the steps in the reaction, which is extremely time consuming and not really suited to a screening approach. Could we avoid these calculations and predict the activity of the catalyst based on adsorption energies or some fundamental surface property? Of course these predictions would have to be validated and alongside the modeling work, an experimental team at JM worked on synthesizing, characterizing and testing the catalysts for stability and activity.
The prospect of setting up the hundreds of calculations, monitoring these and then analyzing the results seemed to us to be quite daunting and it was clear that some automation was required to both set up the calculations and process the results quickly. Using Pipeline Pilot technology (now part of Materials Studio Collection) protocols were developed which processed the calculations and statistical analysis tools developed to establish correlations between materials composition, stability and reactivity. The results are available to all partners through a customized web-interface.
The protocols have been invaluable as data can be processed at the click of a button and customized charts produced in seconds. The timesaving is immense, saving days of endless copying, pasting and manipulating data in spreadsheets, not to mention minimizing human error, leaving us to do the more interesting task of thinking about the science behind the results. I look forward to sharing these results and describing the tools used to obtain them in more detail in the webinar, Fuel Cell Catalyst Discovery with the Materials Studio Collection, on 21st July.”
Looking for tips on how to implement a single ELN across disciplines? Gabriel Weatherhead, lead systems engineer at Millennium: The Takeda Oncology Company, will present an American Chemical Society webinar next Thursday, July 22, describing how his company implemented an ELN from Symyx. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc.]
Gabe will review how Millennium rolled out the system in chemistry and, most recently, in biology. Discussion points will include
The key business drivers and benefits of implementing a single ELN platform
Challenges associated with electronically managing biological versus chemical data
Reasons why Millennium’s legal team advocated strongly for an ELN
Strategies Millennium employed to select an ELN and achieve buy-in from scientists
The inherently complex nature of cell lines, plasmids, proteins, antibodies and vaccines makes a biological registration system challenging. Yet such systems are needed so that researchers and companies can track these entities and their relationships, creating critical intellectual property positions as well as connections to past research and manufacturing processes.
Patterned on the services of registration systems for chemical entities, which are well-known and entrenched in the drug discovery process, the Accelrys Biological Registration system is an "intelligent" solution for registering, associating, searching and retrieving data for entities such as siRNA, plasmids, cell lines, proteins, antibodies, vaccines and future biological entities.
Join us on Wednesday, May 26 for our live webinar, “Intro to Accelrys Biological Registration,” the first in a series on biological registration. To register or learn more, please click here.
Remember A Company That Cannot Be Named that conducted the study described here? It implemented a suite of different systems that tightened the timeline between discovering a compound and collecting data to inform next-step decisions. But where does the credit go? Is the transformation due to the specific systems companies purchase, or the way companies choose to implement the systems they’ve chosen?
We think it’s the latter. I mean, honestly, pharma now has more tools than ever to choose from to expedite just about any task an R&D scientist needs to do. What’s challenging is integrating all these information sources so that they benefit the entire organization rather than one group of scientists. In fact, the lack of a well-thought out strategy for implementing informatics can actually inhibit R&D productivity by creating silos that make it hard to find information or create comprehensive reports to inform decisions.
Increasingly, we are seeing companies provide a self-service information buffet to scientists. The whole idea is to provide an environment that’s not limited by what’s on the menu or the speed of service—an environment that puts scientists in control rather than expecting them to always consume the same mass-produced, out-of-the-box burger.
How might such an information buffet look? Here’s one enticing smorgasbord. The screen below shows a dashboard for viewing stability study results for different formulations. Scientists select data of interest from multiple experiments, and Isentris assembles various charts on the fly. Bar charts indicate the relative composition of the formulations. The line charts illustrate the stability of micelles as the surfactant in each formulation destabilizes.
We’d love to hear which analogy best fits the way you are providing information to researchers. Do your scientists prefer to grab information from buffets, fast-food joints, or sit-down restaurants—and how do these approaches affect how you purchase and implement informatics? And to get a taste of an Isentris informatics buffet, check out this 10 minute video demonstration.
During 2009, we touted Symyx Notebook's strength at connecting scientists in different disciplines across the enterprise. Three Webinars presented at the end of the year give you a chance to verify these claims yourself. Check out recordings highlighting Symyx Notebook's utility at transforming enterprise R&D, as well as specific workflows for analytical chemistry and biology.
A list of other recorded webinars can be found here covering such topics as collaborating in Isentris, getting started with DiscoveryGate, and intelligent structure editing in Symyx Draw. Holler, too, if there are other learning sessions you’d like to see offered in the coming months, and I'll pass on your thoughts to our webinar team.
A webinar on Thursday, January 14, will highlight the new functionality in the all new DiscoveryGate. Titled “Keeping IT Simple,” the webinar focuses on DiscoveryGate’s new search, filter, and reporting options to speed synthesis design and planning.
Power users and research IT administrators can learn about transitioning from legacy ISIS installations to Isentris in a webinar on Tuesday, January 26. The webinar explores not just benefits of transitioning, but showcases two new packages Symyx has developed to ease the transition.
To register for either webinar or view recordings of past webinars, visit the Symyx events page.
This Wednesday, join Dr. Agnes Derecskei-Kovacs, Principal Scientist at Millennium Inorganic Chemicals, to hear how her team, consisting of both experimentalists and modelers, helped increase the company’s R&D efficiency in the search for improved catalysts. This live webinar, Catalysis Applications in Industry, will use case studies to illustrate the team’s theoretical and experimental approaches as they are applied to solve real life industrial problems. Agnes will explain how rapid developments in molecular modeling are enabling the enhancement and acceleration of catalyst design at Millennium Inorganic Chemicals.
We recently launched the latest version of Materials Studio and will be holding a 5-part webinar series led by leading researchers and Accelrys scientists. The first in the series kicks off Wednesday, November 4th at 8am PST with an overview of the new features and enhancements. Join us for this informative session and have your questions answered in real-time by Stephen Todd, Senior Product Manager of Materials Studio.
Future webinars will include customer case studies and deep dives into new functionalities found in CASTEP and Amorphous Cell.