Chamber of Commerce Visit

August 31st, 2009 by Accelrys Team

The San Diego East County Chamber of Commerce hosted a meeting between company officials from San Diego based Accelrys, Inc. and Congressman Duncan Hunter on Thursday, August 27th.

Congressman Hunter and his Chief of Staff, Rick Terrazas met with Max Carnecchia, Dr. Frank Brown and Rob Walker to receive an overview of how Accelrys provides tools that enable new drug and material discovery as well as provide enterprise data management/registration solutions for a multitude of disparate data sources. Additionally, we were able to showcase our proud involvement with the San Diego Science Fair, an annual event that promotes science and engineering education in the US.

Congressman Hunter sits on the House Armed Forces Committee and the Committee for Education and Labor; he is a keen supporter of San Diego-based business and technology. As a result of this meeting, Accelrys has been invited to visit his staff in  Washington, DC for a follow on visit.

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Stimulating Scientific Innovation

August 28th, 2009 by Robert Walker

You are probably wondering why a scientific informatics software company is addressing the issue of The American Recovery and Reinvestment Act (ARRA). I will respond to that question with two answers; first Accelrys has a group devoted to government programs and second, we believe in and have a long history of promoting innovation that drives the discovery process in science and engineering application.

ARRA, also known as the stimulus bill or spending package, is the most historically significant infusion of government funding since the Great Depression with the key objectives of investing in American infrastructure and stimulating the economy by encouraging innovation and boosting employment.

As summarized from www.recovery.gov, the key goals of stimulus spending is to:

  • Create jobs with 90% of the estimated three to four million jobs going to the private sector
  • Implement technology toward computerizing health records with the goal of reducing errors and health care costs
  • Increase capacity by reviving the renewable energy industry
  • Reward energy efficiency through numerous weatherization incentives
  • Increase college affordability by funding shortfalls in student aid programs
  • Invest in American infrastructure concentrating on major transportation projects
  • Provide tax credits for those that need them

The entire stimulus package is estimated to cost $787B over seven years with a large portion of the outlay to occur in government FY 2010 (48%). Approximately $280B will be administered by the state and local governments over the seven year period with the focus in 2009 on healthcare, education and labor. Spending will be phased in FY 2010 and 2011 to shift to longer term economic growth opportunities to include energy, science and technology.

Having supported a government acquisition program office for five years, I know two things. First, it takes a lot of effort to spend this kind of money. Requirements have to be prioritized, sourced and resourced. Next, funding documents have to be prepared, reviewed and ultimately approved. Finally, the ARRA has imposed some significant reporting requirements that make the funding process pale in comparison. The level of effort alone WILL RESULT in creating jobs. I have heard that some agencies have had to bring some financial analysts out of retirement to accommodate this additional workload!

Second, those that currently hold contracts with the agencies that are on the receiving end of the spending are going to do well. It is a lot easier to put money on an existing contract vehicle then it is to let a new contract. To let a new contract takes time because of the solicitation process and rules for competitive procurement. This is time the agencies do not have as they are required to meet spending benchmarks. I view this as being an unfortunate consequence and goes against the intent of the ARRA to promote innovation.

With that said there are truths that are self evident. America is still a country of opportunity and never, ever bet against the American people when it comes to innovation and the advancement of technology.  Regardless of your views on the ARRA, this unprecedented event in American history presents a significant opportunity to really do some good with all the great technology that we know is out there. The key is knowing where to look and who to partner with.

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Next Generation Sequencing—Pass the Pipeline, Please

August 25th, 2009 by Nancy Miller Latimer, M.S.

The drug discovery landscape has morphed into a larger playing field.  Move over small molecule; make room for biologics, diagnostics, biomarkers, and translational research–all key players as medicine gets personal and the division between research and the clinic narrows.  The “one drug, many people” paradigm now has a sibling “one person – just the right drug” paradigm.   Deep sequencing is a technology that figures prominently in the new birth.

As large pharma scrambles to figure out what the new landscape will mean for them, they (1) have reorganized along therapeutic lines with translational research and biomarker departments and (2) have placed their orders for or taken delivery of the next generation of sequencers. And this is not just pharma that is interested.  Biotech, academic and commercial core sequencing facilities, and government research organizations worldwide are actively acquiring the next generation of sequencers—no one wants to be left out.  Obama has pumped billions of dollars into US research.  At some point, sizable chunks will find their way into sequencing facilities[1].

The deep sequencing technologies have moved very fast, while the price of sequencing a human genome has plummeted.  It is no surprise that this inverse relationship is fueling sequencer sales and some anxiety about analyzing all those reads.  The price of sequencing a human genome will soon be under $1K.  “…the much-discussed goal of the $1,000 genome could be attained in two or three years. That is the cost, experts have long predicted, at which genome sequencing could start to become a routine part of medical practice.”[2] An intense desire for an unprecedented “look” into the genome, coupled with analytic inexperience, has created an unmet need in the marketplace.  Hardware vendors are keen to make NGS[3] data analysis as user-friendly as possible, setting the stage for a perfect Pipeline Pilot application.

Accelrys has been investing in a pipelining solution for NGS for over a year now.  Pipeline Pilot is an integration backbone for many hard-working scientific “collections” and third party applications.  Many IT and domain scientists are “hooked” on Pipeline Pilot to deploy robust and easily modified “protocols”.  I know from firsthand experience about the Pipeline Pilot “addiction”.  Oh, and if you aren’t aware, Pipeline Pilot is not just about chemistry anymore.  Complementing our released collections for Imaging, Sequence Analysis, Gene Expression, Plate Data Analytics, and Mass Spec for Proteomics, we look forward to releasing on our first version of our NGS Collection.   You can expect the same drag and drop functionality that you have come to expect and enjoy with the other Pipeline Pilot Collections.

In our first version of our NGS collection, we are making choices about which use cases to support. I am in the process of collecting input from our customers and those awaiting this new product—but I’d like to hear from you, too.  Do your plans for NGS analysis include cloud computing?  If you would like to participate in this survey, please send your name and contact information to me at nlatimer@accelrys.com.  Also, if you are interested in being an alpha or beta tester, let me know!

[1] http://blogs.wsj.com/health/2009/07/08/genetist-francis-collins-nominated-to-head-nih/

[2] http://www.nytimes.com/2009/08/11/science/11gene.html?_r=1&hp

[3] NGS stands for Next Generation Sequencing

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A Man with 5 Rules

August 12th, 2009 by Nancy Miller Latimer, M.S.

Chatting with Christopher Lipinski at Drug Discovery & Development Week

Some ten years ago, I first “met” the Lipinski rules in a software project.  That was my last direct “hands-on” encounter with chemistry.  At Accelrys I am the senior product manager for the Biosciences and Analytics Collections for Pipeline Pilot.  Think genomics, proteomics, sequencing, and ontologies and not chemistry!  This week I was at the DDDW show in Boston – don’t think “booth babe”.

The conference was not as busy this year as it had been in the past and it was the afternoon of the last day.  A distinguished gentleman walked up to our booth wearing a name tag of “Christopher A. Lipinski,” happy to see a fellow booth dweller.   Half in jest I asked if he might be the man with 5 rules.  Turns out he was and, boy, I was in for an intellectual treat.   That Lipinski filter came to life in a new way over the next hour or so.  I was spell bound by Dr. Lipinski’s breadth of knowledge, passion for science, and his out of the box thinking.  What I didn’t anticipate were his insights into the importance of chemistry for the biomarker and translational research space.

He was saying some really awesome things so I started writing them down.    It was hard to focus on note taking because Dr. Lipinski is an excellent speaker and very animated.  Below are a few items that I am willing to share in no particular order:

  • Translational research must have good chemistry married to good biology.
  • Your company (Accelrys) combines chemistry and biology in one software application.  If biologists are using your software to look at high throughput screening (assay) data that has associated chemical structures, they could better filter out results for poor compounds.
  • When faced with people problems (like chemistry—biology conflicts) versus technical problems—the people problems are always much more difficult to solve.
  • The people side is the most important.
  • NIH is making good strides in the dialog between chemists and biologists.
  • As soon as the biologist has an assay for a small molecule they should probe/stress test the assay with compounds known historically to cause assay problems.
  • In software for the (bench) biologist – it needs to be dead easy.  Too many peer-reviewed publications have great biology but rotten chemistry.
  • Biologically active compounds are tightly clustered in chemical space.  It is always best to look for new activity in areas of chemical space where you previously found activity.
  • It takes 10 years to “mature” a medicinal chemist.  He then becomes an expert in pattern recognition even if he can’t articulate why certain structures look better than others
  • Areas of interest
    • Stem cell (non-embryonic source)  derived screening application
    • Many previously proprietary databases are now in the public domain  (See PMID:  17897036).  These provide a great starting point for the discovery of drugs for rare diseases.

Dr Lipinski’s long and prestigious career in medicinal chemistry, assay development, computational chemistry, and now in consulting, lecturing, and as an expert witness does not look anything like retirement.  That is good news for me.

Dr. Lipinski is shown here with his rapt audience.

Dr. Lipinski is shown here with his rapt audience.

Note: Lipinski’s total number of rules actually equals 4.  His rules are known as the “Rule of Five” because each of them incorporates the number 5 in some way.  For all you literalists out there, “5 Rules” should be interpreted in this way.

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Overlaps and Crossovers at the European User Group Meeting

August 11th, 2009 by Gerhard Goldbeck-Wood, PhD

We announced the European User Group meeting a few days ago. Check out the UGM webpages, and especially the themes.  I am excited that we’ll have users from all product and application areas together, including:

• Materials Studio

• Discovery Studio and Platform

• Training sessions and the lot.

We’re in different tracks, but I expect to see some interesting overlaps/crossovers.  For example, we’ll discuss the high throughput methods in materials to the platform, along with what we can learn from the collaborative environments and custom solutions in the Discovery Studio field for other areas such as Materials.

Also, I’ll be hosting the Annual meeting of the Nanotech Consortium on the Tuesday/Wednesday of that week, where we’ll discuss the latest, especially in the field of kinetic modelling of reactions. Take a look at my previous post on that subject.

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