Science and Spotfire®: Customizing the way you interact with data

Photo Credit: Matteo Bagnoli via Compfight cc

Since partnering with TIBCO Software, Inc. in September 2012, PerkinElmer Informatics has been researching and developing solutions to increase the efficacy of using the TIBCO Spotfire® software program with customized scientific informatics applications.

The TIBCO Spotfire software program is a powerful data visualization platform that is used across various industries to revolutionize the way data is analyzed, interpreted and accessed. In scientific research, the TIBCO Spotfire program enhances and complements the use of scientific informatics tools by eliminating the need for back-end programming language to be coded in the informatics system by an IT department.

In addition, the TIBCO Spotfire program allows for data to convene in one centralized, accessible location, without the need for manual copying and pasting of data sets. This centralized process eliminates the risk of transcription errors and joins multiple data sets together for contextual analysis.

Furthermore, data presentation is facilitated in a much more attractive and comprehensive manner. The TIBCO Spotfire platform allows researchers to create dynamic dashboard reports that allow reviewers to interact and manipulate published data, a drastically more scientifically-relevant method than the use of traditional static, 2D reports.

Best yet, the TIBCO Spotfire software platform is highly customizable – and looking ahead to what’s to come in 2013, we’re excited to be planning several scientific applications that will engage the TIBCO Spotfire software program to increase scientific intelligence. The applications, which will work by being installed on top of the TIBCO Spotfire software platform, are being developed based off the recommendations and wish lists of scientific researchers who already use PKI Informatics solutions to improve their data collection and analysis.

Learn more about the TIBCO Spotfire software platform by clicking here.

Ethical recommendations: Whole genome sequencing and privacy

Photo Credit: The Moonstone Archive via Compfight cc

As we have discussed in recent blog posts, whole genome sequencing is sure to be an imminent component of future health care, yet measures need to be taken to assure personal privacy of genetic data.

In October 2012, the Presidential Commission for the Study of Bioethical Issues made twelve recommendations regarding regulation of genetic data related to whole genome sequencing, in a report titled “Privacy and Progress”.

Here’s our recap of the recommendations:

  1. Clear guidelines and policies should be created to protect individuals from being disadvantaged or discriminated against based upon genetic findings. Individuals should also be able to opt for their genetic data to be provided to persons or entities of their choosing.
  2. Federal and state governments should establish baseline laws and regulations that will protect individuals from having their whole genome sequenced without explicit consent.
  3. Providers of whole genome sequencing should adhere to professional ethical guidelines and take measures to avoid the intentional or unintentional misuse genetic data, and should be held accountable to laws and guidelines.
  4. Genetic data should not be able to be re-identified, and should not be made available to law enforcement or defense without consent, except in the case of highly special circumstances.
  5. The most effective methods of ensuring privacy protection should be communicated and shared across the industry.
  6. Ironclad consent practices should be put in place and participants should be informed about who will have access to their genetic information throughout and after the sequencing process.
  7. Consent forms should include a summary of whole genome sequencing services, explain how genetic data will be used, explain how data may be used in the future, explain benefits, risks and unknown risks, and explain what information the individual can expect to receive from his or her genetic data.
  8. Participants should be made aware that additional, unintended findings will likely be found during the whole genome sequencing process.
  9. Guidelines for dealing with incidental findings should be established, and efforts should be made to establish individuals’ preferences for learning about such incidental findings.
  10. Data privacy and protection should be ironclad yet data communication should flow between researchers and healthcare providers to facilitate personalized, genomic medicine.
  11. Policy makers should act to endorse the benefits of whole genome sequencing to encourage the public to participate in genetic research.
  12. Scientific advancements generated from whole genome sequencing should be used to benefit the greatest number of people possible.

You can read the full October 2012 commission report here.

DNA Anonymity, Part II: What privacy can we expect in the future?

 Photo Credit: DaveFayram via Compfight cc

Despite the recent findings that have shown individuals donating genetic information are not guaranteed anonymity due to lack of regulation over the use of genetic information, all signs indicate that widespread whole genome sequencing will be the norm in the not-so-distant future. 

As whole genome sequencing continues to become a larger component of medical progress, federal regulations will inevitably be established to regulate and protect the privacy of individuals’ genetic information.

In October 2012, the Presidential Commission for the Study of Bioethical Issues made strong recommendations regarding whole genome sequencing, a tell-tale sign that it's on the horizon of becoming increasing common. The commission addressed concerns over the competing interests of personal privacy and the improvement of medicine when it comes to the use and protection of genetic data collected through sequencing.

Not only did the commission issue recommendations for regulation, but it publicly acknowledged the importance that whole genome sequencing will play in health research and medical progress. And, most importantly, the commission stated that the main benefactors of widespread whole genome sequencing will be members of the public through improved health treatment and disease prevention.

Yet, the commission also acknowledged that changes in federal regulation need to occur in order to establish the necessary public trust to ensure that individuals will be willing to submit to genetic sequencing. State regulations need to be addressed as well, since current state regulations vary widely.

It is likely only be a matter of time before state and federal regulations are put in place to protect the use of genetic data, which will secure individual privacy while paving the way for the maintenance and informatic analysis of large-scale genetic databases to discover breakthroughs in the practice of medicine.

In our next blog post, we will be breaking down the recommendations put forth by the Presidential Commission for the Study of Bioethical Issues on the subject of regulating the use and protection of genetic information.

You can read the full October 2012 commission report, titled "Privacy and Progress", by clicking here.

DNA Anonymity, Part I: Current state and concern

Photo Credit: JohnGoode via Compfight cc

The past few days have seen a flurry of controversial conversation following news reports that an online search engine was used to identify anonymous DNA donors. The news reports followed the January 17 release of a paper titled,“Identifying Personal Genomes by Surname Inference,” published in Science magazine.

The revelation that anonymous DNA donors could be re-identified sparked commentary about the privacy issues inherent to the collection of DNA databases. Within the past year, proponents of personalized healthcare have seen great achievements in genomics, with genetic sequencing kits on trajectory to become available over the counter, and with several companies already offering genetic sequencing services to the public commercially.

And with the rise of informatics' ability to interpret scientific data with increasing efficacy, researchers have naturally become excited about the potential advantages of creating genetic databases comprised of DNA sequences from vast numbers of people – because with high volumes of diverse genetic information readily available for analysis, personalized and effective disease treatment and prevention solutions become achievable.

This revelation about the non-guaranteed anonymity is not novel. Individuals who donate genetic information are informed that their anonymity is not 100% guaranteed, and the findings published in the recent Science article aren’t the first time an online search process was used to identify an anonymous donor. 

For example, in 2005, a news story swept the internet that a 15-year-old boy had correctly identified and then contacted his biological father, an anonymous sperm donor. The teenager used an online genealogical DNA service and an online birth date and birth name registry to pinpoint his father’s identity.

But if the regulation of large, widespread DNA databases becomes routine in the future of medical progress, would we ever find ourselves in a world akin to the fictitious, futuristic society of the 1997 sci-fi movie Gattaca?

The answer: highly unlikely.

Why? Stay tuned for a second blog post, "DNA Anonymity, Part II: What privacy can we expect in the future?", that will discuss what Americans can expect in terms of federal regulation concerning personal privacy and anonymity as genetic sequencing will likely become a routine part of future disease prevention and treatment.

Informatics for a greener tomorow: guidelines and solutions


PerkinElmer Informatics offers several laboratory solutions designed to allow

for adherence to the Twelve Principles of Green Chemistry set for by the ACS.

Established by the American Chemical Society Green Chemistry roundtable, these principles outline the methodologies scientific organizations and individual researchers can adhere to in order to conduct lab processes with minimal impact upon human and environmental health.

Twelve Principles of Green Chemistry:

  1. Prevention: Rather than clean or treat waste after formation, take measures to reduce the creation of waste in the first place.
  2. Atom Economy: Efforts should be made to incorporate process materials into the final product, reducing waste and increasing materials efficiency. Atom Economy = (Mass Weight Product / Sum of Mass Weight of Reactants) x 100.
  3. Less Hazardous Chemical Syntheses: Reduce use and creation of substances that are toxic to human and environmental health.
  4. Designing Safer Chemicals: Substances should be designed to maximize efficacy while reducing toxicity.
  5. Safer Solvents and Auxiliaries: Efforts should be made to avoid use of auxiliary substances, and non-toxic solvents should be selected when using an auxiliary substance is absolutely necessary.
  6. Design for Energy Efficiency: Energy use should be minimized with environmental and economic impacts in mind.
  7. Use of Renewable Feedstocks: Renewable raw materials should be selected whenever possible.
  8. Reduce Derivatives:  To reduce the use of additional reagents or creation of additional waste, use of derivatives should be avoided if possible.
  9. Catalysis: Selective catalytic reagents are superior to stoichiometric reagents.
  10. Design for Degradation: Substances should be designed so that when they are no longer useful or effective, they degrade into innocuous materials that do no accumulate in the environment.
  11. Real-time analysis for Pollution Prevention: Efforts should be made to create real-time, in-process methods to detect and prevent the formation of toxic and bio-accumulative substances.
  12. Inherently Safer chemistry for Accident Prevention: Substances and processes to produce substances should be selected to minimize potential for chemical accidents.

Implementing these methodologies is scalable through an offering of several solutions provided by PerkinElmer Informatics. Here is a sampling of how our products can make a positive, green impact in several areas of laboratory management:


  • Reduce disposal and waste of chemicals through purchasing management
  • Allow Environmental Healthy and Safety (EH&S) reporting and monitoring

E-Notebook for Chemistry:

  • Fully integrated with Inventory
  • Green chemistry configurations available
  • Provide preferred/alternate solvent information

Reaction Genius:

  • Reduce trial and error in synthetic method development
  • Manage and analyze trends of use and performance throughout organization

Method Genius:

  • Reduce trial and error in analytical method development

Learn how you can implement these green chemistry solutions by speaking with our technical support staff who can recommend suitable laboratory informatics by contacting us here.

Sustainable science: reducing the environmental stress of research

Image courtesy of Flickr user huskyte77

The idea of green practices in chemical research may be more well-rounded than you think – it’s not just about creating and choosing chemical compounds that will have the least amount of toxic impact on the environment.

While a big part of green chemistry is to make smart choices about which substances or solvents to use, there are other ways in which scientists can improve the sustainability of their R&D projects. Making economical decisions in research will have a positive effect on the environment through a reduction in wasted materials.

Using minimal materials not only reduces waste at the front end of a research project, but also reduces the amount of energy and resources needed to clean up or remove waste products at the back end of development.

Selecting substances that have longevity of functionality can also help reduce waste. Whenever possible, use raw materials that are renewable and will not put pressure on limited resources.

Looking at research methods with a sustainable eye is becoming more and more important. Scientific consumption of materials has already proven to be putting stress on the earth’s finite supply of naturally-occurring raw materials.

In fact, the United States Department of Energy has deemed that the shortage of certain raw materials is so critical that a special research center has been set up to investigate rare earths. These materials are necessary to the production of technologies that we use every day, such as automobiles and smartphones, and they on course to run out of supply if conservation efforts are not made.

Although it seems like a daunting task for the special research team, each and every scientific organization can do its part by managing its research projects with sustainability in mind. Our E-Notebook customers can take the first steps to becoming more sustainable by learning about simple ELN configurations that will increase atom economy and reduce toxic output. You can read about available configurations in this blog post.

To learn more about the DOE’s initiative to conserve rare earths, read this news story.

If you’d like counseling on you can utilize scientific informatics to make your R&D more sustainable, contact our representatives and visit our website.

Green chemistry made easy: simple configurations for ELN

Simple configurations to electronic laboratory notebooks can help chemists

adhere to ACS green chemistry guidelines. Photo courtesy of Flickr user Horia Varlan.

With the New Year upon us, 2013 brings a renewed opportunity to consider how environmental initiatives and green goals can be applied to scientific research. The practice of green chemistry is to conduct chemical research and engineering with the intention to reduce the creation and use of hazardous chemicals.

For chemists, who are responsible for the creation of compounds that make up the materials and medicines that we rely on to live, it may be of interest to learn that there are many green configuration options available for use on electronic laboratory notebooks.

PerkinElmer Informatics offers several green chemistry options on the E-Notebook for chemistry. These configurations are very easy to set up and can help scientists choose the most environmentally and economically friendly substances and solvents. They are implemented without the use of additional code or programming and are compatible with the green chemistry requirements established by the American Chemical Society.


This screenshot shows some E-Notebook green chemistry configurations in action

Solvent replacement: This configuration will prompt you to consider a list of suggested alternate solvents and will allow you to establish your own list of preferred replacements.

Atom economy: A simple configuration will allow for atom economy to be calculated easily within each experiment.

TRI/PBT reporting: An optional tickbox will allow you to find out which substances are included in the Toxic Release Inventory (TRI) and Persisent, Bioaccumulative, Toxic (PBT) chemical databases.

Click here to learn more about our E-Notebook for chemistry. To speak with technical support staff who can help you easily configure your E-Notebook to include these green chemistry tools, please contact us here. We look forward to contributing to your environmentally-friendly successes this year!

Smart data from big data: Free trial of powerful data visualization software


The TIBCO Spotfire® software platform provides users with powerful data visualization tools

Ever get the feeling that when it comes to reviewing data sets, you’re “missing something”? One of the most frustrating experiences a researcher can have is to worry that a data pattern or trend will go unnoticed. 

The analysis of traditional data reports can seem non-scalable and unwieldy – but there is a method available to allow you to interact with data in an intuitive way. Data visualization uses graphical representations of information to allow researchers to manipulate data and uncover trends or outliers that would otherwise be difficult to detect using traditional reporting methods. 

It’s why at PerkinElmer Informatics, we are so excited that we have entered into a strategic relationship with TIBCO Software Inc., enabling us to offer the TIBCO Spotfire® software platform to our customers in certain scientific research and development markets. These markets include R&D; QA; and QC applications in basic and preclinical life sciences; chemical, petrochemical, and environmental sciences; food and beverage; consumer products; and academia.

The TIBCO Spotfire software platform allows scientific researchers in these markets to analyze and understand data in a fundamentally natural and interactive manner, changing the way trends in experimental data sets are recognized.

While data visualization sounds like an attractive solution in theory, it’s hard to ‘visualize’ the benefits of data visualization without having the experience of using the software to delve into information sets.

So we are providing you with the opportunity to take control firsthand and see how the TIBCO Spotfire software platform works from a user’s perspective. We’ve put a fun holiday twist on the experience as well – you can explore data we’ve compiled about Santa’s naughty and nice lists. The software allows you to move through data using pie charts, bar graphs, data plots and graphical representations, with the ability to toggle various selection options to isolate and compare information.

We’ve also created a few questions to challenge your ability to manipulate the data using the visualization methods – if you submit correct answers to all the questions asked, you will be entered to win a free iPad® mini.

Check out the free holiday demo of the TIBCO Spotfire software platform. 

NO PURCHASE NECESSARY. Open to legal residents of the 50 United States (including the District of Columbia) who are at least 18 years of age as of the date of entry. Contest Ends 01/11/2013. Additional rules and restrictions apply. For complete details click here for the Official Rules. Void where prohibited. 

Reflecting on a successful 2012 INspiring INnovation North American tour

Vanessa Braunstein of PerkinElmer Informatics demonstrates the benefits of ELN technology

for attendees at the Minneapolis INspiring INnovation event

This past year has been an exciting one as PerkinElmer Inc. celebrated 75 years of business with a continental tour celebrating 75 years of innovation. PKI Informatics has been an important part of the INspiring INnovations tour, which traveled to 15 cities across the United States and Canada, attracting over 1,000 attendees and raising over $14,000 for charity. One-hundred percent of registration fees were donated to local and national charities.

As we traveled across North America, we were privileged to meet with attendees hailing from leading research organizations, academic institutions and scientific corporations, sharing discussions and demonstrations of our product offerings, including electronic laboratory notebooks, LIMS, LimsLink, LES, ChemBioDraw, ChemDraw 3D, Geospiza and the TIBCO Spotfire® software platform.

Leaders in scientific research were invited to give presentations at regional stops along the tour, bringing together experts from a wide variety of fields of science to collaborate and recognize emerging technology and discovery.

In addition to participating in progressive conversations about utilizing scientific tools and software to improve the processes of research and development across scientific disciplines, one of the most rewarding aspects of the INspiring INnovation tour was our ability to give back to communities through charitable contribution. The nearly $15,000 raised by PerkinElmer over the course of the 2012 North American tour allowed us to provide donations to science education and healthcare organizations initiatives.

Our last stop on the tour in Minneapolis saw involvement from representatives from the Mayo Clinic, University of Wisconsin, University of Minnesota, J.R. Watkins Naturals, Bell Pharmaceuticals, Coloplast, Monsanto, and the United States Department of Agriculture.

Charities that benefited from the 2012 INspiring INnovation tour:

·   Society for Science and the Public 

·   Lets Talk Science 

·   The Keystone Center 

·   Students2Science 

·   American Chemical Society

·   North Carolina Science Teachers Association 

·   National 4-H Council 

·   Academy of Science, St. Louis 

·   Arnold Palmer Hospital for Children 

·   St. Jude's Research Hospital 

·   Kitty Andersen Youth Science Center – Science Museum of Minnesota

Read more about the 2012 tour and learn about upcoming destinations for the 2013 INspiring INnovation tour by clicking here.

Leveraging informatics to improve drug therapy

Image courtesy Flickr user Chadou Yama


Informatics is, in many regards, still an emerging technology that continues to push the envelope and challenge the ever-evolving standard of what is considered cutting-edge.

More than ever before, scientists are using informatics technology to consider larger questions that encompass bigger pictures, such as: how can informatics improve the way chemists produce pharmaceutics?

When it comes to drug therapies, scientists understand how and why side effects might potentially affect patients negatively, but there is not yet a go-to strategy for anticipating side effects that a drug will have on an individual patient.

Informatics will change that – commonalities will be found across genetic subtypes to reveal how different genetic make-ups are impacted by specific drug compounds. In the future, pharmacists will consider the patient’s genomic information when prescribing drug treatments, choosing a therapy that will incur the least damage and most benefit.

In a matter of years, this ideal scenario may be a reality. This past week, researchers at The Scripps Research Institute announced that they had developed a chemical toolkit that will revolutionize the way drug compounds are produced.

The new technology will allow chemists to create hundreds of drug compound variants with drastically increased ease and cost effectiveness. Producing so many variants through such a technological advantage will allow pharmaceutical companies to discover and produce a range of the most effective and safe drug compounds faster and more accurately than before.

Many factors need to come together in order for doctors to be able to provide personalize prescriptions based upon individual genomic identities, but the necessary agents to achieve this goal are already in motion. At PerkinElmer Informatics, we look forward to being an integral entity in moving these initiatives toward reality.

Read more about The Scripps Research Institute’s new toolkit here.

Learn how to leverage PerkinElmer Informatics products here.