Pipeline Pilot 7.5 Component Update 4 is nearing completion. This update includes the new Pipeline Pilot Chemistry Cartridge, which forms part of the expanded Cheminformatics Collection. Also in Component Update 4, the updated List Management and Query Services system is set to wow with an enhanced form designer, improvements to make it easier to use, and the ability to use protocol-based reporting and analysis tools directly from a form and the new favorites bar.
I’ve been working on the Pipeline Pilot Chemistry Cartridge and its associated Pipeline Pilot Components. The Pipeline Pilot Chemistry Cartridge is a new Oracle Data Cartridge built using the Pipeline Pilot Chemistry Toolkit. In the weeks leading up to the recent Accelrys European User Group meeting, I was busy timing the creation of a 123 million compound database using a beta version of the Pipeline Pilot Chemistry Cartridge. I never quite made it to my goal of 1 billion compounds in time for the User Group meeting, but in the coming weeks I hope to be able to update you on my attempt to index 1 billion compounds using the actual release version and to provide pointers for indexing your own chemical data.
Among the forward-looking technologies previewed at the European User Group Meeting in Barcelona last month was next generation sequencing. Richard Carter of Oxford Nanopore Technologies overviewed the impressive growth of this technology, which by many accounts is not just outpacing Moore's Law, but making Moore's Law look like it's flatlined! With throughput now doubling every five months or so, bioinformaticians and scientists to find better ways to integrate next generation sequencing data into their existing workflows.
In the video below, Richard provides more information on his talk, which described how Oxford Nanopore Technologies is using the Pipeline Pilot Next Generation Sequencing Collection to translate work from many of the prominent next-generation sequencing publications within Pipeline through relatively trivial protocols.
"What Pipeline Pilot gives us is a platform," Richard says. "I as a bioinformatician can write the protocols and roll that out to the bench scientists so that they can start asking their scientific questions of the data instead of asking the bioinformaticians to solve those problems for them. It's all about empowering your bench scientists. At the moment, next generation sequencing technology is an elite tool. If we can bring that to the masses, so much the better, and especially we believe at Oxford Nanopore Technlogies the combination of simple technology that we're introducing with the benefits and simplicity of Pipeline Pilot will really spread the use of next generation sequencing."
If you aren’t able to join us in Spain for what’s shaping up to be the most heavily attended European User Group Meeting in Accelrys’ history, follow us at #EUGM10 on Twitter. It’s the next best thing to being there, and if you’re the first to correctly tweet the answer to a question about information posted to the feed each day of the conference, you’ll win a Flip HD camcorder.
The view outside the conference rooms
The agenda features three days of proven best practices, product demos, expert user presentations, and one-on-one interaction with Accelrys executives, industry keynote speakers, fellow colleagues, Accelrys partners, and product experts. Accelrys executives will kick off the meeting by outlining the company’s new shared vision, integration plans, and product roadmap. Another highlight of the first day is a keynote address by Joseph Cesarone of Abbott titled Experiences in Collaborative Development and Deployment of a Registration System for Biologics. Abbott was a key partner in a special interest group (SIG) that assisted in the design and development of the Accelrys Biological Registration system and was the first partner to deploy the system in September 2009.
Three parallel conference tracks will feature 37 customer presentations, and we hope to post interviews with some of the presenters during the meeting and in the weeks immediately following. We’ve designated experts to tweet from the sessions to broadcast information on the meeting both to attendees who want to know what’s happening in the other rooms and to anyone who is unable to attend the meeting. We also have a fun competition that we’ll be running where we’ll be giving away a Flip HD camcorder each day. Look for a tweet from @Accelrys asking a question about information given in one of the tweets that day. If you’re the first to tweet the correct answer, you’ll win the Flip camcorder! You don’t need to be present to win, but you can only be a winner once.
We look forward to “seeing” you, either at the conference or online!
What do energy materials and pharmaceuticals research have in common? They both stand to benefit from the major improvements in quantum tools now available Materials Studio 5.5.
Supporting the energy and functional materials field is a new method in Materials Studio’s DMol3 that’s all about light-- excited states, UV/Vis spectra, and non-linear optical properties. The measurement of these properties is essential in the design of new energy efficient lighting as well as alternative energy generation, such as photovoltaics. DMol3 optical properties are based on time-dependent density functional theory (TD-DFT) . Some of you may know, or perhaps vaguely remember, that the Schroedinger equation is time dependent, so that’s the one that is basically solved here, rather than the usual static approximation. As you can imagine, this can be costly, but I am happy to say that the implementation is actually quite fast (keeping computing costs down) and accurate (making experimentation faster and more efficient).
There are many more applications DMol3, for example materials for holographic discs, which have simply amazing storage capacity. Another application area which I find intriguing is in life sciences, for example helping to understand vision better, so I’ll be interested to see where DMol3 optical properties will be used next.
Talking about life sciences, another new quantum feature I am really excited about could have big implications for the development of drug molecule candidates into dosage forms. The crystallization and polymorphism of drug molecules needs to be well understood, and modelling has been used for a while to support that work. Polymorph prediction remains tricky however, for a number of reasons. Sampling all the possible structures is a tall order, particularly if the molecules are flexible, as many new drug molecules are. Also, it may not be sufficient to consider the thermodynamics of the structures, as crystallization kinetics can play a major role.
However, these considerations are in a way academic if one cannot even optimize structures and rank them by energy with high accuracy. One of the key reasons why this has been so difficult is that both classical and quantum methods have significant shortcomings in this type of application. The force-fields used in classical methods either neglect or at best approximate electronic effects such as polarization, which are often important in drug crystals. Density functional quantum methods on the other hand do that well, but are less effective at capturing more long range, dispersion interactions. Now in Materials Studio 5.5, DMol3 and CASTEP have dispersion correction terms to overcome this issue. With some pioneering work in the literature that demonstrated the power of combining density functional and dispersion methods, I look forward to many great applications of this technology.
Fermi surface of Yttrium, a rare-earth material used in lasers, displays etc
Using regular adhesive tape they managed to obtain a flake of carbon with a thickness of just one atom. This at a time when many believed it was impossible for such thin crystalline materials to be stable.
All of us in materials science at Accelrys congratulate Geim and Novoselov on their achievement. Would it be pompous to refer to our webinar Thursday on graphene as the “Nobel Webinar”? Probably. Nevertheless, we hope you’ll attend to see the role modelling and simulation have played in helping us understand this extraordinary material.
Dr Johan Carlsson, Accelrys Contract Research Scientist
The final presentation in our recent contract research webinar series features work on graphene, which has been described recently as the “ultimate” material for next-generation nanoelectronics development. I asked Johan Carlsson from the Accelrys contract research team to provide some background on this nanomaterial. Attend the webinar to see how simulation methods have helped and are helping unravel some of graphene’s secrets.
Graphene is one of the most interesting nano-materials at the moment [1,2]. With all the hype, it might seem as though graphene is a completely new material discovered just recently. And in a sense this is correct.
When I started to work on carbon materials some eight years ago, graphene was just an imaginary model system. Back then the excitement about the fullerenes was being replaced by what I call the “nanohype.” All the fashionable forms of carbon suddenly needed to have names including the buzzword “nano.” So we had nanohorns, nanofoams, nanoporous carbon, and, of course, nanotubes.
These fashion changes indicate the cyclic nature of carbon science. During the last 25 years, a new form of carbon has been discovered every five to six years. The fullerenes were discovered in 1985 , the nanotubes in 1991 , and, in 1998, graphynes were predicted . That same year, thin graphite layers were grown on top of SiC wafers—what might today be referred to as the first few layers of graphene . However, it took another cycle of carbon science before the graphene hype really took off, when researchers at the University of Manchester managed to extract individual graphene sheets from a graphite crystal in 2004 . It’s actually about time for another carbon allotrope to emerge on the scene. Graphanes (graphene sheets fully saturated by hydrogens) have potential, but they are not strictly pure carbon structures . We’ll have to see if some other new carbon material will emerge soon.
Yet while humans have only discovered the potential of graphene recently, graphene sheets have always been available in nature as two-dimensional layers that are the building blocks of graphite. They’ve just not been accessible, as individual graphene sheets have been very difficult to isolate. The barrier to graphene synthesis was perhaps more mental than technical, as the method that finally succeeded was incredibly simple. The reseachers in Manchester had the ingenious idea to use adhesive scotch tape to lift off the graphene sheets from a graphite crystal!  Of course, this method didn’t scale industrially, and since this breakthrough a number of alternative methods have been quickly developed.
Graphene is now a mature material. Perhaps the maturation of graphene has represented the next step in the cyclic carbon evolution? Anyway, the progress in this field has been rich because graphene science straddles two different communities: the nanotube community and the low dimensional semiconductor community. Graphene has been proposed for a variety of applications in diverse fields, including field effect transistors with graphene channels , gas sensors , and solar cells . It’s even attracted interest in life science as an active membrane that can separate different molecules out of a solution .
Interestingly, the progress in graphene science is to a large extent driven by theoretical predictions and results from simulations. Graphene has been the model system of choice for theoretical investigations of sp2-bonded carbon materials. As such it has been the starting point to study graphite, fullerenes and nanotubes. Many properties of graphene were then known from theoretical point of view, before it was possible to perform actual measurements. The electronic structure of graphene for instance is known from theoretical calculations performed more than 60 years ago . Only recently has it been possible to actually measure the bandstructure of individual graphene sheets. Similarly, a substantial amount of our knowledge about the structure and properties of point defects and edges of graphene was first obtained by simulations and later confirmed by experiments. This shows that simulations and experimentation go hand in hand, and theoretical methods will continue to play a major role in the further development of the graphene and other materials.
 A. K. Geim and K.S. Novoselov, Nature Materials 6, 183 (2007).  A. K. Geim,Science 324, 1530 (2009).  H. W. Kroto, J. R. Heath, S. C. O'Brien, R. F. Curl & R. E. Smalley, Nature 318, 162 (1985).  S. Iijima, Nature 354, 56 (1991).  N. Narita, S. Nagai, S. Suzuki, and K. Nakao, Phys. Rev. B 58, 11009 (1998).  I. Forbeaux, J.-M. Themlin, and J.-M. Debever, Phys. Rev. B 58, 16396 (1998).  K.S. Novoselov, A. K. Geim, S. V. Morozov, D. Jiang, Y. Zhang, S. V. Dubonos, I. V. Grigorieva, and A. A. Firsov, Science 306, 666 (2004).  J. O. Sofo, A. S. Chaudhari, and G. D. Barber, Phys Rev. B 75, 153401 (2007).  Yu-Ming Lin, Keith A. Jenkins, Alberto Valdes-Garcia, Joshua P. Small, Damon B. Farmer and Phaedon Avouris, Nano Lett. 9, 422 (2009).  F. Schedin, A. K. Geim, S. V. Morozov, E. W. Hill, P. Blake, M. I. Katsnelson, and K. S. Novoselov, Nature Materials 6, 652 (2007).  X. Wang, L. Zhi, and K. Mullen, Nano Lett. 8, 323 (2008).  S. Garaj, W. Hubbard, A. Reina, J. Kong, D. Branton, and J. A. Golovchenko, Nature 467, 190 (2010).  P. R. Wallace, Phys. Rev. 71, 622 (1947).
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.
Today we announce the first major product release since the merger of Accelrys and Symyx. Fittingly, it’s a product that spans many of the sectors our combined company now touches. The latest 6.5 version of Symyx Notebook by Accelrys delivers improvements supporting chemical process development, production scale-up, and administrative compliance for scientists working in pharmaceuticals, fine chemicals, agrochemicals, and consumer products.
The new functionality in this release is focused specifically on process chemists, who work in areas that are strictly regulated and subject to stringent quality assurance (QA) oversight. The greatest challenge faced by process chemists is identifying, optimizing, and delivering the best process to pilot and manufacturing plants in the shortest time possible while complying effectively and efficiently with regulations and QA mandates.
As described in the press release, the 6.5 version of Symyx Notebook by Accelrys offers an array of new features requested by customers already working in regulated environments. Crucially, the system offers the ability to search experimental data stored in most legacy Symyx notebooks. Such functionality is clearly valuable to those who have these legacy Symyx notebooks. But the underlying API also provides an opportunity to develop a single portal to any ELN data—whether that ELN is from Symyx or another ELN vendor.
Visit www.symyx.com/elnprocess to learn more about how the 6.5 release of Symyx Notebook by Accelrys supports process chemists. Representatives from AstraZeneca and Bristol-Myers Squibb discuss their use of an ELN in process chemistry in a downloadable PDF and a short video recorded at the Symyx Symposium. You’ll also find an informative slideshow describing the release. We also encourage you to check out our sibling blog, Symyx’s Life in the Electronic Lab, which will feature several posts over the coming weeks on ELN use in process chemistry and the 6.5 version of Symyx Notebook by Accelrys.
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.”
On July 1, 2010, the merger between Accelrys, Inc. and Symyx Technologies, Inc. was completed. Both of our teams are excited to come together as the leading scientific informatics software company. Our combined solutions enable customers to improve scientific performance by creating more open, flexible and agile environments, streamlining workflows, reducing operating costs and increasing the potential for innovation.
The full press release explains more about the merger, as does this page on our website. The team leading the transition is committed to supporting the investment you have made in products from both of our companies. Max Carnecchia will continue on as Accelrys CEO and Isy Goldwasser, CEO of Symyx, will continue as an advisor through the transition. The balance of our management team includes members from both companies. Customers should continue to request help from the respective Symyx and Accelrys technical support teams via existing phone, email or website portals.
We know you have questions. In addition to the links above, we have created a new area in the Accelrys Online Community called The Headquarters. This group is open to customers and partners of Accelrys and Symyx, and we encourage you to join the discussion with our team members.
We look forward to hearing your thoughts on this exciting development!
After many months of development, and lots of testing, the Materials Studio Collection for Pipeline Pilot is finally airborne. We are all really excited, of course, by this great new software solution, but equally excited by starting out on a journey with a somewhat unknown destination.
Which reminds me of my ‘ash cloud’ flight. I was on one of the first planes to set off from the US back to Europe after the volcano eruption disruption in mid April. Leaving LA while all UK airports were still closed, we knew we were heading east, but the final destination was to some extent unknown. Checking the in-flight route map throughout the journey became much more interesting...
So, what direction is the Materials Studio Collection (MSC) taking you, and what are your likely destinations? In a way, all the MSC does is make key modeling and simulations tools from Materials Studio available within the Pipeline Pilot environment. Maybe not a big deal, if you think of a single task such as a Geometry Optimisation.
However, if instead you consider collaborating in the organization on some more complex task, such as designing a new fuel cell catalyst, things get a little more interesting. Take for example one of the rate limiting steps in fuel cell performance: the reaction which reduces oxygen from the air so that it can react on with Hydrogen to form water. The R&D team will want to consider a chart of the energetic (and kinetics) of the reaction steps for a range of different fuel cell catalysts at various operating voltages.
To come up with such a chart (as shown here), you would need to build, optimize, simulate, and analyze a range of systems, and finally collate the results. With the Materials Studio Collection and Pipeline Pilot, protocols can quickly be constructed with graphical scripting to take care of that, and the whole process is automated; results stored, and retrieved easily and reports for the team created dynamically. In fact, all of the above has already been demonstrated in a collaborative project called iCatDesign, with support of the UK’s Technology Strategy Board. Dr. Misbah Sarwar will discuss this project in more detail in her upcoming webinar on July 21st, Fuel Cell Catalyst Discovery with the Materials Studio Collection.
So, the direction of the journey is clear, taking us to more automation, increased productivity, improved collaboration, but there are many interesting destinations in that direction.
Taking the above example of creating protocols that generate property charts a bit further, the MSC could transform the way in which the research organization, and even engineers, access and utilize information generated from molecular modeling. The iCatDesign project created a database which can be inspected and constantly updated. With the MSC, you can deploy materials calculations, and embed these into a range of environments, such as web portals, electronic notebooks, materials databases, or even product life-cycle management (PLM) systems. Equally, scientists working across Life and Materials Science applications now have a single environment with tools from across the scientific spectrum. Keep checking that in-flight route map...
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.
Check out this presentation on SlideShare to learn more about four key bioactivity databases. The presentation provides general information on what each database contains, information about what questions they can answer, and details about how they help scientists. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc. Symyx Bioactivity Databases are now Accelrys Bioactivity Databases.]
Wondering what to make of Wendy Warr's comments on the All New DiscoveryGate? Take it for a test drive yourself. The Beta2 version of the All New DiscoveryGate is available now. If you'd like to become a tester, comment here and I'll get you hooked up.
Symyx Symposium has ended, but continue to watch this space for reviews, summaries, and interviews. Folks are calling this Symposium the best in Symyx's history. The content was compelling, networking time was abundant, and the venue was simply stunning. As proof, we give you these two videos that we filmed the first day. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc.]
Below, attendees gather for the first general session Wednesday.
And here, Bruce Pharr, vice president of marketing, and Isy Goldwasser, CEO, welcome attendees to the event.