Sustainable science: Earth Day tips for a green laboratory


Photo Credit: Dominic's pics via Compfight cc

So much scientific research goes into discovering methods to increase energy creation and efficiency while minimizing environmental impact, but ironically laboratories themselves use up extremely high amounts of energy to maintain operation. This Earth Day, let's review several pointers to help make your laboratory more sustainable and environmentally friendly.

On average, research laboratories use four or five times more energy than office buildings. It’s not surprising given the amount of equipment and technology that laboratories employ. Devices like fumigators, exhaust devices and containment systems, heating and cooling equipment, building ventilation systems and back-up generator and emergency power units all draw heavy energy usage. In addition, laboratories are subject to around-the-clock operation as scientists need 24/7 access to carry out their experiments.

Research facilities hoping to increase energy efficiency and sustainability can decrease electricity usage through simple steps like remembering to power off equipment that is not in use, disconnecting seldom-used equipment and remembering to turn off lights whenever a room is unoccupied.

More aggressive energy conservation efforts can be taken to optimize water usage by selecting low-flow faucets and water retention systems. Natural sunlight can be captured through rooftop and building-side photovoltaic panels so that laboratories can generate self-sustaining electricity. Airflow systems use a lot of energy to provide heating and cooling throughout laboratories; special window treatments and roofing can be used to leverage natural sunlight. Changes can be made to the heating and cooling system to reduce energy waste. PerkinElmer’s Santa Clara data center implemented an airflow optimization project that reduced annual energy usage by 69,000 kilowatt hours through the elimination of unnecessary overcooling.           

Laboratory employees should also maintain careful inventory records to avoid over-purchasing which can contribute to waste. Once products are ordered, stock chemicals and reagents should be used in the chronological order in which they were purchased. The purchasing of recycled products should be encouraged whenever possible, and supply managers should select vendors that participate in equipment buy-back programs. Inventory management can be achieved through diligent record keeping, but laboratory managers are also wise to invest in inventory management software that will help make automated, real-time decisions about the quantity and frequency of ordering new materials.

Laboratories can also opt to participate in organizations such as the Carbon Disclosure Project and the EPA’s Green Power Partnership to promote and contribute to the awareness of sustainable practices.

You can read more about specific ways to establish more environmentally-friendly, energy-efficient and sustainable laboratory practices here:

Green chemistry made easy: Simple ELN configurations

Sustainable science: Reducing the environmental stress of research

Informatics for a greener tomorrow: Guidelines and solutions

It’s basic biology: How data visualization is improving translational medicine

 Photo Credit: JohnGoode via Compfight cc

For researchers and practitioners of translational and personalized medicine, implementing effective diagnosis and treatment methods is all about bringing together novel and diverse data and being able to draw meaningful insights from that information.

It’s been well established that not all patients will respond the same way to the same drugs, but the challenge is figuring out exactly which factors impact a drug’s efficacy within an individual’s body. The only way to flush out patterns and correlations among patient populations is to compare mass amounts of diverse data. Even after carrying out data reductions, all these data sets are still different types of data – the solution is finding a tool that is capable of bringing all of this information together and integrating it in a coordinated fashion.

The end goal is that from this data integration, insights can then be revealed. While software programs can perform the heavy lifting parts of data crunching and analysis, it still requires a human operator to explore and identify potential areas of correlation. Data mining of patient populations cannot be done without a scientist first asking: how, why, what, when, who?

Biologically, humans are well wired for exceptional visual analysis. Our optic nerve can transfer incoming visual data to our brains as fast as an Ethernet connection. Once received in the brain, evolution has honed our abilities to distinguish shapes, edges, and boundaries, and to identify patterns from that visual data – all almost instantaneously.

When it comes to working with data sets, it’s our pattern matching ability that makes data visualization such an effective analysis tool. As data is portrayed visually, we can quickly distinguish differences in shapes and patterns between sets much more quickly than we would be able to do by looking at numbers alone.  Visualization gives meaning and context to data that would otherwise be vast compilations of numbers, facts and measurements.

For many scientists in the clinical and life sciences market, the TIBCO Spotfire® data visualization software platform has already been a helpful tool for understanding data. Many users have already implemented their own best practices strategies for using visual analysis tactics in data mining. However, through our exclusive agreement with TIBCO, Inc., our Informatics team is now focused on developing software templates and add-ons that will cater specifically to the life sciences industry.

Over the next several years, as data visualization becomes a best practices standard for analysis of data in clinical and life sciences research, one of the biggest changes we can hope to see will be the advent of the application of next generation sequencing in the clinic. When it comes to understanding diseases like cancer, scientists will be able to diagnose types of cancer instead of locations of cancer, narrowing down treatment options that are most likely to be effective against a certain cancer’s type.  Visualization software will be used return better diagnoses, to recommend more specific therapies, and to even provide guidance for illness prevention.

To learn more about data visualization and Spotfire, consider attending our Dr. Spotfire Day on May 6in San Jose, California.

Our guide to ACS Dallas: ChemDraw® + SciFinder®, collaborating in the cloud, and why Spotfire® matters

SciFinder® and ChemDraw® have united to empower scientists.

We've entered the homestretch of the countdown to ACS Dallas, the 247th American Chemical Society National Meeting and Exposition, which is to be held March 16-20 in Dallas, Texas. The PerkinElmer Informatics team is not only excited to attend, but also to present the latest product developments that we've been working on this year. Here's a preview of what you can expect to see and hear from PKI Informatics at ACS Dallas:

ChemDraw® + SciFinder®

Our Informatics team is thrilled to preview our integration of SciFinder® into ChemBioDraw Ultra®, which we've been developing in collaboration with Chemical Abstracts Service, the provider of SciFinder. We'll be presenting the integration and demonstrating its capabilities in the ACS Village at 3:00pm on Monday, March 17, and 11:00AM on Tuesday, March 18. Attend a session to see how you can get answers sooner and increase your productivity now that our scientific drawing program has united with the world's largest database of scientific and chemical information.

ChemDraw for iPad®

Our ChemDraw for iPad® app has been a big hit, earning an honorable mention from The Scientist magazine for the Top Ten Innovations of 2013. Join Dr. Layne Morsch of the University of Illinois Springfield on Tuesday, March 18, at 8:55am in the Hyatt Regency Dallas Reunion Ballroom G to learn how ChemDraw is fostering increased engagement in organic chemistry education.

Collaborating in the cloud

Register to preview the next big thing in science on Monday, March 17, from 12:30-3:00pm in the Dallas Convention Center, room D220, when our team will demonstrate how simplicity and cloud technology will redefine electronic laboratory notebooks with the launch of our new collaborative science platform. Or attend a 5:00pm session on Tuesday, March 18, in the Omni Dallas Hotel, Deep Ellum A, to hear directly from one of our beta users.

Why Spotfire® Matters

Come see why the TIBCO Spotfire® data visualization and analysis platform (example pictured above) "matters" in rheology, nanoscience, and renewable resources research. If you have ever struggled to uncover trends and patterns from a sea of data, we will show you how to unlock insights through the power of visualization software. Hear Dr. Josh Bishop speak on Monday, March 17, at 2:15pm in Omni Dallas Hotel, Deep Ellum A, on optimizing catalyst development by using Spotfire to mine ELN-based structured test results and chemical property data.

Visit us throughout ACS Dallas in booth #1508 to learn more about any of these products and to meet our team. We are looking forward to seeing you in Dallas!

Spotlight on science: Study reveals the brain's white matter "scaffold" of connections

 Image credit: USC Institute of Neurology and Informatics

Neuroscientists have introduced new terminology to describe the brain’s connective neural pathways after completing a study that used social network models to analyze the brain’s communication network. Researchers at USC Institute for Neurology and Informatics are now calling the brain’s network of white matter a “scaffold” of connections through which the brain operates.

“We coined the term white matter ‘scaffold’ because this network defines the information architecture which supports brain function,” researcher John Darrell Van Horn was quoted as saying in USC’s press release on the study. Van Horn was a senior author on the article describing the study, which was published in Frontiers in Human Neuroscience on February 11.

While the potential consequences of brain injuries to gray matter are better known, it is not yet well understood just how injuries to white matter affect the brain’s network properties.

To study the effects, USC researchers used MRI data from 110 individuals to analyze simulations of brain injury to white matter pathways. The results were then analyzed through comparison to social network models, which document how large networks of social ties are affected by individual damaged relationships. Researchers specifically focused on understanding how strong the connections between neurons are, revealing instances in which certain connections demonstrated higher sensitivity to injury and instances in which damage to one connection led to a catastrophic ripple effect, resulting in disconnection of a large number of communication pathways.

By using the application of a social network model to analyze the effects of simulated brain injury, the USC Neurology and Informatics team was able to observe connective damage within the context of a larger communications network. The results of the study help to explain why brain injuries have been so unpredictable until this point – such as when some people experience severe brain trauma but can make a full recovery, while others suffer a seemingly small injury but experience irreversible and life-altering loss of brain functions.

The results of this study on the white matter "scaffold" have big implications for the diagnosis and treatment of degenerative neurological diseases and traumatic brain injuries, and contribute to a worldwide effort led by the Human Connectome Project and the Laboratory of Neuro Imaging at USC to map all 100 billion neurons and 1,000 trillion connections in the human brain.

Upgrade: E-Notebook 2014 packs a punch with new features

Navigation Pane in E-Notebook 2014

Launched in late 2013, the newest version of PerkinElmer’s electronic laboratory notebook, E-Notebook 2014, has upgraded the E-Notebook experience to provide even more seamless integration with TIBCO Spotfire® software and the Datalytix query tool, and to provide the most user-friendly solution for planning, capturing, recording and analyzing scientific data.

Already the most widely used electronic laboratory notebook, the new version of E-Notebook will offer a significantly improved user experience, features modernizations and attractive appearance to researchers in pharmaceutical, biotech, chemical, food/flavor/fragrance, and petrochemical industries, as well as academic and government institutions. A well-tailored upgrade toolkit means that migrating to E-Notebook 2014 will accommodate existing customizations.

Key highlights from the new E-Notebook 2014 include an improved interface appearance and usability, enhanced integration with registration and inventory workflows, and upgraded core components to provide a faster, more robust and adaptable platform.

A brand new drag and drop feature drastically reduces the number of required mouse clicks while allowing users to search, find and drag files right into their experiment, which are sorted automatically into organized document sections. The drag and drop capabilities extend even further to allow for moving entire experiments from folder to folder, copying experiment data between ELNs, and quick and easy rearrangements of experiment sections.

Another new feature allows for faster data filtering through new tables that sort, group and filter information before automatically saving experiment settings for future convenience. Experiment information is now available in new reading modes that enable users to pick whether they want to view data as tabs and sections or as a scrolling document, all the while being able to collapse or expand sections to maintain an organized screen.

Other new features include inline or external editing options, structured data management built into specific experiments or tests, a comprehensive data mapping wizard, cross-experiment searches across multiple E-Notebooks.

The new and improved upgrade kit has a specialized diagnostic tool that pinpoints customizations that exist within older E-Notebook versions to allow for a comprehensive migration process that reduces the time and cost of an upgrade.

For biology researchers, a new BioAnalytical module has been specially designed to run on E-Notebook 2014 as well as earlier E-Notebook versions. Read about the new BioAnalytical module here: BioAnalytical Module for E-Notebook 2014.

Read a full-length white paper with detailed statistics and screenshots to learn more about E-Notebook 2014: Why Upgrade?

Cancer vaccine clinical trials: Dana-Farber has new findings using Spotfire®

As medical research continues to improve rapidly with the advance of scientific information technology, Dana-Farber has developed a novel analysis method to extract complex data for cancer vaccines from clinical trial repositories. Using TIBCO Spotfire® data visualization and summarization software, Dana-Farber researchers can now work faster and more efficiently to understand data and make decisions that are instrumental in bettering future cancer vaccine trials.

When it comes to discovering meaningful correlations and relationships across cancer vaccine clinical trials, information about trials is fairly accessible. The data is organized into categories and is easily downloaded from data collections that are curated by the website and National Cancer Institute Surveillance. But the data registries are plagued by inconsistency and redundancy, making it difficult for researchers to get a good grasp on analyzing both overview and in-depth trends across available data.

Selected for its easy-to-learn, intuitive user interface and its ability to instantly create search queries or pare down data into relevant subsections, the TIBCO Spotfire platform allowed Dana-Farber researchers to complete an assessment of the cancer vaccine clinical trials market. Using Spotfire, researchers were able to look at the clinical trials from various angles to see clinical trials by timeline, type of cancer, lead institution, patient population, and specific vaccine technology. This allowed the project to reveal previously undetected patterns, trends and biases within cancer vaccine clinical trial data.

Researchers discovered that certain types of cancers, such as bladder, liver, pancreatic, stomach, esophageal and all low-incidence cancers, are lacking in volume of trials in the cancer vaccine field, highlighting areas and opportunities for improved representation of all cancers in future trials.

By using Spotfire to assess the cancer vaccine clinical trials market, Dana-Farber revealed a gap that exists between available data and the ability to properly analyze and extract information from that data. Dana-Farber’s use of Spotfire has now demonstrated that data visualization and summarization software can be used to withdraw important relationships that exist within copious data collections, which specifically in this case can be used to improve and hone future cancer vaccine clinical trials and research efforts.

Interested in learning more about TIBCO Spotfire software? You can read more and watch video demos about the Spotfire data visualization platform and the specific add-ons our PerkinElmer Informatics team is developing with the scientific community in mind: Learn more about TIBCO Spotfire.  

Or click here to read an in-depth white paper detailing Dana-Farber's use of Spotfire to assess the cancer vaccine clinical trials market.

SciFinder® to be integrated into ChemBioDraw software in 2014


The end of 2013 has brought about a big announcement for PerkinElmer Informatics to share with the scientific community. The Informatics team is excited to disclose that it will be partnering with the world’s leading authority for chemical informatics and a division of the American Chemical Society, Chemical Abstracts Services (CAS), to incorporate SciFinder® into the ChemBioDraw software platform.

The CAS team’s sole mission is to locate and curate a collection of every publicly-disclosed chemical substance in the world, making its collection of chemical information the most comprehensive globally. The CAS’ SciFinder tool allows scientists to search for substances, reactions, patents, and journal references with powerful filtering and analysis functions.

ChemBioDraw is the drawing tool used by scientists and students to create publication-ready drawings that allow for research and chemical structure information to be quickly and clearly communicated with colleagues and peers.

Now, beginning in early 2014, the SciFinder solution will be incorporated directly into the ChemBioDraw software platform, streamlining workflow and input for scientists. Instead of going outside of ChemBioDraw to use SciFinder, users can initiate a search for references, substances or reactions inside ChemBioDraw.

With ChemBioDraw software already in use across a wide base of users, integrating SciFinder into the software will allow users to access a more comprehensive collection of chemical information in a more efficient workflow process.

Read the official media alert announcing the partnership between PerkinElmer Informatics and Chemical Abstracts Services by clicking here.

Apple's new iPad Air: Run iOS 7-optimized ChemDraw and Chem3D on faster, lighter iPad

Apple’s latest iPad® design, iPad Air®, will be going on sale Friday, November 1, and is boasting many improved features packaged within a sleeker, lighter design.

Wi-Fi users will see a noticeable increase in internet speed and connectivity thanks to iPad Air’s improved wireless technology and the addition of a second internal antenna.

At one pound, the new iPad Air weighs in at almost a third lighter than its predecessor, and is only five ounces heavier than the newest iPad mini. The 9.7 inch glass screen is backed in aluminum, but still results in a thickness that is just .29 inches. The dimensions of the iPad Air make it the lightest full-size tablet available on the market.

In addition to being the lightest tablet, the iPad Air maintains a huge lead over its competitors in terms of the number of available tablet apps, closing in on half a million with 475,000 available apps.

For scientists who use the ChemDraw® for iPad and Chem3D® for iPad apps, users can expect seamless integration with the new iOS 7 operating system thanks to updates in the latest 2.0 version releases, which can be found in the App Store.

While the apps are now updated to run iOS 7 on all iPad devices, the Air’s touch screen optimization software and services will make it easier to manipulate and create content. The Air’s faster processing and wireless speeds mean that ChemDraw and Chem3D's Flick-To-Share™ collaboration tools will enable users to communicate even faster with the flick of a finger.

The latest versions of the apps utilize Flick-To-Share to allow users to share work in numerous new ways, including social media. Screenshots can now be shared directly via Dropbox, Twitter, Facebook, email, Moxtra and Camera Roll. Chem3D even has the ability to communicate directly to a 3D printer to allow for the fabrication of three-dimensional structures.

Recent international versions of the chemical drawing and structure viewing apps have also been released. ChemDraw for iPad and Chem3D for iPad are now available to Chinese, Japanese and Korean users in their native languages.

Download ChemDraw for iPad ($9.99) and free Chem3D for iPad now!

Novel use of TIBCO Spotfire® unveiled for ELN-based reaction search

 Photo courtesy of Flickr user Horia Varlan.

Since partnering with TIBCO Software Inc. in 2012 to bring data visualization and analysis to scientific industries, the PerkinElmer Informatics team has been working to develop add-ons and methodologies to accelerate scientific research using the TIBCO Spotfire® software platform.

Our team has devised a new way of using the TIBCO Spotfire software platform to dynamically mine reaction data contained within ELN. When reaction data is entered into an ELN, the stoichiometry is calculated and linked to an autotext feature that automatically updates as reagent or product amounts are changed. Solvent, temperature, pressure, atom economy and conditional information are also captured and stored in ELN. But with all of the complex reaction data contained in an ELN system, traditional reaction searching methods can omit relevant information in search results.

In a typical query form, scientists describe a reaction and its parameters which generates a list of search results, ranked in the order in which the system calculates its relevance. The results show experiment name, the reaction, and other metadata for each entry, and by clicking on an entry, a user can go to it and view it in detail.

But using this traditional search method, scientists are dependent on the system’s “best-result” ranking system. The search list doesn’t update when criteria - such as percentage yield – is changed, meaning to modify results, the entire search must be re-run. Furthermore, this list reflects the type of information inherent to an ELN by generating a list of experiments, when reaction information might be more useful when populated in a table of structured data. Finally, there may be data relevant to a reaction search that is housed in other sources, such as an Inventory, Registration, or another ELN. Traditional search methods simply can’t access and compile these various sets of data.

By integrating the TIBCO Spotfire software platform with ELN, reaction searches use dynamic filters to yield interactive visualizations of data presented in hierarchical data tables. Results can be drawn from multiple databases and merged using Information Links or Datalytix. The TIBCO Spotfire software platform is already widely used across chemical and pharmaceutical industries, but it has not yet been used to dynamically mine ELN-based reaction data in this novel manner.

The PerkinElmer Informatics team has tested this reaction-searching method using sample datasets and has proven that TIBCO Spotfire successfully achieves improved search results. Our team is now seeking a partner interested in being an early adopter of this methodology to implement the first real-use case of dynamic reaction searching in ELN using data visualization software.

If you are interested in learning more about whether your laboratory would make a good candidate for the first implementation of this methodology, contact us for more information here.

E-Notebook 2014, extended TIBCO Spotfire® deal announced at 2013 UGM

Clive Higgins, PKI VP of Marketing, Informatics, kicks off the 2013 User Group Meeting with product announcements

BOSTON, Mass. - The PerkinElmer Informatics 2013 User Group Meeting kicked off at 9:30am EST in Waltham, Mass., with the launch of PKI Informatics' newest electronic laboratory notebook version, E-Notebook 2014. In addition, it was announced that PKI Informatics has extended its strategic partnership agreement with TIBCO Software Inc. to offer the TIBCO Spotfire® data visualization software platform to Clinical and Translational/Personal medicine markets.

The announcements were delivered to a global informatics community during the User Group Meeting’s opening talk, given by PKI Vice President of Marketing, Clive Higgins, to an audience of over 200 conference attendees representing 130 organizations from 16 countries. Clive’s presentation, titled “A Year of Transformation”, discussed the sense of momentum felt across the informatics industry, and especially amongst the PKI Informatics team.

The world bioinformatics market will exceed $7.5 billion by 2017, up from less than $2.5 billion in 2011, Clive noted. The important thing, he urged, is that we remember to look at informatics in the context of improving human health.

Informatics plays many roles in the process of progressing global health and medicine, such as accelerating and protecting the discovery process, fostering collaboration, and increasing efficiencies, Clive said. “Our portfolio of informatics solutions spans from personal scientific applications through to data creation, acquisition, storage, management and analytics.”

Improving informatics

The new ELN version, E-Notebook 2014, has a range of improvements that include full integration with Inventory and Registration, canned protocols for numerous biological applications, drastically increased processing speed especially in search functions, and comes as a radically improved upgrade process that greatly reduces the time and cost of upgrading.

The expanded offering of the TIBCO Spotfire software platform comes one year after PKI Informatics first signed an exclusive deal with TIBCO Software to represent Spotfire in the Research market. Over the last 12 months, the Informatics team has invested in developing add-on applications like Lead Discovery and Datalytix, and to create modules that handle Omics and High Content Screening.

Today, the extended partnership allows PKI Informatics to offer TIBCO Spotfire not only to the Research market but also to Clinical and Translational/Personal medicine markets. Additional add-ons will be developed for TIBCO Spotfire that will merge Clinical data with Omics research data coming directly from clinical patients.

“There is tremendous market need for this, and Spotfire is the perfect platform on which to blend this data together,” Clive said. “A key aspect to the extension goes beyond traditional clinical applications to the emerging fields of Translational and Personal medicine.”

Working with a partner, PKI Informatics has already created an application tracking physical clinical samples, routing them for research and then merging together the clinical data with the subsequently gathered Omics research data, which allows for the segmentation of clinical populations based on genotypic and phenotypic research data.

Conference attendees and PKI Informatics team members will celebrate today’s news with a cocktail hour and launch party held this evening, immediately following today’s scheduled presentations at the Westin Boston in Waltham, Mass.