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Accelrys Blog

November 2011

Today at the Materials Research Society meeting in Boston, Cyrus Wadia, the Assistant Director for Clean Energy and Materials Research and Development at the White House Office of Science and Technology Policy challenged the audience to “think as a network” of collaborators, not individual researchers, and to “learn from colleagues” how to better handle large data sets.


The recently publicized presidential initiative for a Materials Genome aims to insert or provide new materials for the production and technology advantage of US industry. This initiative mirrors exactly the focus Accelrys has on integrated multi-scale modeling and laboratory-to-plant optimization. The heart of these initiatives is improving the estimation and management of innovation and design of materials from the nano-scale right up to the process and macro production scale.


As many Accelrys users know, multi-scale modeling where the results of atomistic and micro-scale simulation can be combined with larger scale processes, high throughput screening and testing, and laboratory information yields valuable insights into materials design. The combination of computational and real analytical instruments alongside the organization of laboratory data allows the use of models at all length scales and can be considered as driving the innovation cycle of many companies.


The MGI initiative clearly recognizes this function and the idea of developing a framework and ontologies where information, models and data can be exchanged at different levels and different time scales. The value of making information, more widely available to the engineer and materials scientist for collaboration will help drive more accurate and systematic materials development and usage. Accelrys is very excited about this initiative and is sure its technology will provide clear aid in the acceleration of the innovation lifecycle of new materials—which is a clearly stated goal of this initiative.


How do you feel about this initiative?

758 Views 0 References Permalink Categories: Trend Watch, Data Mining & Knowledge Discovery, Modeling & Simulation, Materials Informatics Tags: materials, nanotechnology, pipeline-pilot, atomic-scale-modeling, high-throughput, materials-studio, cloud-computing

Transferring paper documentation to a software application is only part of the solution going electronic. Scientists are used to sharing SOPs, paper binders, log books and paper notebooks physically. Labs using paper had well-entrenched physical processes for assigning tasks, then tracking and sharing the insights.  A log book next to an instrument, an SOP on a fume hood, a paper binder of the latest analytic protocols next to the HPLC machine, a notebook of common recipes in the store room or tickets for managing samples. Now move the paper information electronically with an ELN and there’s a great opportunity for collaboration, but a potential risk that scientists get lost in the electronic ethos collaborating with colleagues.



Typically, the innovative scientist uses tools at hand to invent and replace physical processes with electronic process. An explosion of e-mails, sharepoint portals, Excel sheets and shared directories become the norm for tracking and communicating scientist requests and findings. While low cost and resourceful, these homo sapien orchestrated systems are prone to breakdowns and delays, with tasks and information going unchecked and astray.


So what’s the answer? It obviously has to be electronic and importantly needs to work in context to the scientists workflow where they’re orchestrating their work i.e. the Electronic Notebook. The new generation ELNs have now caught on to the added opportunity to drive improved collaboration by delivering integrated task request and management systems within the ELN. The new work request modules enabling collaboration can be configured in 2 ways: fixed workflows for defined tasks and processes or, they can provide the scientist with total flexibility to create ad hoc tasks and then track these tasks. Now from within their ELN scientists can create a task, assign the task to another scientist, associate an experiment or set of samples, and track the task. Those being assigned tasks, when they open their notebooks, will instantly see what’s to do. Once processed, the requested information is all tracked back and linked to the original experiment or sample request. 


Care to see how it's done?

1,075 Views 0 References Permalink Categories: Lab Operations & Workflows, Cheminformatics, Bioinformatics, Electronic Lab Notebook, The IT Perspective Tags: workflow, notebook, eln, collaboration, work, request

Music-ular Dynamics

Posted by stodd Nov 25, 2011

Ever wondered what molecular vibrations would sound like? JC Jones and Andy Shipway in Israel pondered this question and decided to use molecular dynamics to investigate.You can find more information about their project here and listen to the ethereal sounds of a journey along the myelin protein.


I always like to hear about people taking software like Materials Studio and using it to create something completely outside of the original intent. When we introduced MaterialsScript to control parts of Materials Studio, I played my own games around the theme of Winter resulting in the Season's Greetings set of scripts. However, the sort of work linked above takes abstraction to a totally new level!


The question is, what else do you use Materials Studio for that isn't in our user stories?

723 Views 0 References Permalink Categories: Modeling & Simulation Tags: atomic-scale-modeling, materials-studio, computational-chemistry

Biofuel is a leading area of investment and innovation with a high research focus on new and more efficient ways to tame natural and sustainable processes into highly efficient processes to deliver sustainable energy.


With the growing investment and demand for sustainable energy there are many new research groups springing up. These groups are adopting ELNs for biofuel research in a range of areas, leveraging the ELN to quickly implement electronic lab management to enable scientists to efficiently document information that can be shared and re-used. Importantly the ELN simultaneously captures and secures their IP used to support patent submissions critical to the industry's success and investor’s interest.


The use of the ELN within biofuel research varies significantly; one biofuel research group is investigating hyper-mutation of algae to over express fats, and optimize cell growth and production in bioreactors. The ELN's role here is to capture the biological modifications, the growth dynamics and the variables that effect growth, and the process required for future scale-up and production.


In another example, moving from aquatic bioprocesses to terrestrial bioprocesses, POET Research is focused on creating ethanol from corn starch. With 27 POET biorefineries converting starch to ethanol, optimizing biorefinery processes and improving the conversion of cellulose to ethanol is essential with production of such a large scale.


POET’s number one goal for the ELN was to store experimental data and information electronically, so it could be archived daily and backed up. This would also allow POET researchers to search experiments and collaborate better versus the traditional paper notebook. However, as a green company, POET also had a big initiative to reduce their impact on the environment. A key step towards achieving this was in the deployment of the ELN. It turns out that POET has lots of different instruments in their labs that require paper printouts and paper documentation. The ELN has substantially lowered POET’s paper usage from printing out results. In fact, they also capture more information now, since it’s easier and faster to enter information than with paper notebooks.


Previously, POET’s laboratory procedures used Microsoft Excel and PDFs, which were printed out and pasted into a paper notebook. Now POET is taking paper process and moving it directly into the ELN; in addition to saving paper, it takes out a whole step in the process of documentation. The data is integrated immediately into the ELN experiment and the results can be accessed in real-time from the ELN and any desktop.


Interestingly, when you ask POET what they value about the ELN, POET’s response resonates with similar benefits that others see across industries:

  • Searchability
  • Information capture and re-use
  • Avoiding repeats and re-invention
  • Ability to share experiments
  • Ability to gain insight from others
  • Faster reporting


It’s both interesting and exciting to me that the use of ELNs by the Biofuel industry is yet another example of the ELN’s ability to deliver significant—and sustainable-- improvements to the researcher’s environment, across different industries where paper notebooks are an option. What’s actually more interesting to me is that companies really are seeing the business value of a sustainable approach to achieving their company goals.


Want to give it a try?

733 Views 0 References Permalink Categories: Electronic Lab Notebook, Lab Operations & Workflows Tags: eln, ilabber, contur, biofuels, green, sustainable, poet

When the whole world is going electronic why are many of us still using paper notebooks? Really! When electronic phones came along we jumped from Bakerlite analogue phones to digital in a decade, when mobile phones came along it took another decade, and likewise when smart phones came around it took a decade to move. ELNs have now been in use for over 10 years. So why hasn’t the paper notebook gone the way of the Dodo?


When you look at the reality of paper notebooks I find it surprising that only 154K scientists of the one to two billion scientists globally today have an ELN and the growth is only 25% per year. After all, paper notebooks can’t be shared easily, impossible to search, slow to complete and are an incredibly inefficient scrapbooking exercises. Like the bakerlite phone and the dodo it’s only a matter of time before the extinction of paper.

  paper science.jpg

So what’s holding up the rest of the scientific community? Is it just education about ELNs? Is it fear of change to electronic? Is it that we don’t feel the right ELN is available to support our science? Is it that scientist’s feel they don’t have the resources to deploy, manage and pay for an ELN? Or do people feel there is little value in swapping out paper? If it is any of the above I’d argue that these points are moot now.


Industry reports from Atrium Research in 2011 show an instant 20% accepted productivity gain over paper processes. Today in 60 seconds you can own and be entering data in an ELN whether it’s a Mac or PC. There’s no installation, no hardware, no IT resources and little training required. Every type of scientists and industry is adopting an ELN and being successful with communities from five to thousands of users. ELNs are also being deployed across the enterprise to deliver scientific productivity for every kind of scientist.


Help us out. Why aren’t you moving if you haven't already? How can the ELN software vendors make the paper notebook at your lab a dodo?

1,286 Views 0 References Permalink Categories: Cheminformatics, Lab Operations & Workflows, The IT Perspective, Electronic Lab Notebook, Bioinformatics Tags: chemistry, biology, notebook, eln, ip