Free, open-source software enables innovation with popular but tricky lab technique

February 11, 2009

(PhysOrg.com) -- When scientists need to detect and analyze DNA, or traces of a bioweapon or maybe an environmental contaminant, there's a good chance they'll turn to a lab technique called electrophoresis—or one of its many cousins. The versatile process is so pervasive that scientists published research employing it at a pace exceeding one paper every hour in 2007. But even though electrophoresis is used for routine experiments, such as gene sequencing or clinical analysis, it can be fiendishly difficult to create new experiment variations because the technique can be intricate and subtle.

To wash away the difficulty, Stanford engineers have released free, open-source software that can greatly ease experimental design and troubleshooting, smoothing the way for new medical and chemical discoveries. Spresso, available for download at microfluidics.stanford.edu , is like a double shot of caffeine for researchers seeking to do experiments that no one has done before.

"The software provides a new tool for designing complex electrophoresis problems and optimizing them," says mechanical engineering Associate Professor Juan Santiago, a senior author on a paper describing Spresso, published last month in the Journal of Chromatography A. Mechanical engineering and aeronautics and astronautics Professor Sanjiva Lele is a co-author. "The algorithm is about 75 times faster than current state-of-the-art tools and the open-source feature means it can be adapted to new problems," Santiago said.

That 75-fold faster performance, enabled by numerical algorithms unique to Spresso, can mean the difference between waiting overnight for a result and getting it in a few minutes, says Moran Bercovici, an aeronautics and astronautics doctoral student and first author on the paper. Spresso allows scientists to iterate through experimental variations much faster than they could by going into the lab and relying on trial and error.

Electrophoresis simply refers to putting a charged molecule, such as DNA or an explosive compound, into a medium such as a liquid and using an electric field to move it past a detector. What is not so simple, however, is the behavior that results from simultaneous interactions with electric fields, chemical reactions and the other phenomena at play. Among the advances Spresso makes over other software programs is the ability to account for dispersion effects, which can lower the concentration of a target chemical to the point where it becomes unresolvable.

Using the software, researchers can quickly and accurately predict how their experiments will run using a database of more than 400 chemical species, electric field and flow control methods, and other variables, Bercovici said. They also can use the software to troubleshoot and refine their experiments.

Bercovici and mechanical engineering graduate student Robert D. Chambers have used Spresso to design electrophoresis experiments, including a related process called "isotachophoresis," in which they were able to successfully but indirectly detect particularly stealthy toxic chemicals by sensing their effect on the surrounding medium.

"Electrophoresis is helping to enable some of the technologies that are on the forefront of science right now, such as genomics and proteomics," said Chambers, referring to the study of the coding for and expression of proteins made by the cells in our bodies. "Using Spresso, people can now better optimize chemical analyses; it is not inconceivable, for example, that these advances may help us sense a cancer marker which was otherwise at too low of a concentration to be detected."

Spresso: microfluidics.stanford.edu/spresso/2008/09/introducing-spresso.html

Provided by Stanford University

Explore further: Promise and peril: a primer on gene editing

Related Stories

Promise and peril: a primer on gene editing

February 1, 2016

Britain's granting of a licence Monday for scientists to alter the genes of embryos for infertility research has thrown the controversial technique under a white-hot spotlight.

Are computers creative?

December 8, 2015

High-tech automation is eliminating jobs like Pac-Man gobbling yellow dots. According to a 2013 study by the Oxford Martin School, 47 percent of U.S. jobs are susceptible to takeover by machines in the coming decades. Whether ...

Shining a light on water-splitting reactions

December 17, 2015

As a youth, Eric Isaacs moved from the Midwest to the West Coast. He went from there to the East Coast for his doctoral studies. But he traveled less than 70 miles for his 2013 practicum.

Sketch-interpreting software

February 19, 2010

(PhysOrg.com) -- Science writers know as well as anyone how much information a diagram can contain. We often labor to express in words what a researcher was able to convey in a single image. But while a drawing can be rich ...

Recommended for you

Intelligent robots threaten millions of jobs

February 14, 2016

Advances in artificial intelligence will soon lead to robots that are capable of nearly everything humans do, threatening tens of millions of jobs in the coming 30 years, experts warned Saturday.

Proto-planet has two masters

February 13, 2016

A Rice University researcher will discuss images that may show the formation of a planet—or a planetary system—around a distant binary star at the annual meeting of the American Association for the Advancement of Science ...

Scientists glimpse Einstein's gravitational waves (Update)

February 11, 2016

In a landmark discovery for physics and astronomy, scientists said Thursday they have glimpsed the first direct evidence of gravitational waves, ripples in the fabric of space-time that Albert Einstein predicted a century ...

Gravitational waves found, black-hole models led the way

February 11, 2016

Gravitational waves were predicted by Einstein's theory of general relativity in 1916, and now, almost exactly 100 years later, the faint ripples across space-time have been found. The advanced Laser Interferometric Gravitational-wave ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.