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Mark Miller: A Pioneer in Science Gateway Development and Phylogenetics

Mark MillerScience gateways have emerged as vital platforms that provide researchers with streamlined access to advanced computational resources, enabling them to carry out complex analyses and simulations that were once constrained by the limitations of personal computers. 

Mark Miller, a visionary leader and the owner of the science gateway CIPRES (Cyberinfrastructure for Phylogenetic Research), has played a pivotal role in shaping the landscape of computational biology and phylogenetic studies through his dedicated efforts in developing and maintaining this essential resource. As Mark Miller embarks on a new chapter in his journey, we reflect on his impactful contributions and the transformative role of CIPRES in scientific research.

Unveiling the Tree of Life: Phylogenetics Explored

As one traverses the diverse landscapes of our planet, encountering a myriad of species from the smallest microorganisms to majestic creatures, a fundamental question arises: how are these organisms related to one another? Enter phylogenetics, the science that unravels the intricate branches of the evolutionary tree, revealing the genetic connections that link all life forms on Earth.

The "Tree of Life" concept dates back centuries, with astute observers categorizing species and establishing relationships based on shared characteristics. With Charles Darwin's groundbreaking work in the theory of evolution laid the foundation for modern phylogenetics. This scientific discipline emerged as a systematic approach to mapping the evolutionary relationships between species, akin to plotting the branches and leaves of the Tree of Life.

Early phylogenetic analyses relied on observable traits, which provided valuable insights but could be confounded by convergent evolution, where unrelated organisms develop similar features in response to shared environments. DNA sequencing emerged as a powerful tool to overcome these limitations. By deciphering the "language" encoded within DNA, researchers could compare genetic sequences between species, discerning their relatedness and shedding light on the intricate tapestry of evolution.

The Data Deluge and Analytical Bottlenecks

With advanced DNA sequencing technologies, collecting genetic data has become faster and more affordable. This data deluge presented a new challenge: efficiently analyzing and making sense of the wealth of genetic information. 

Dr. Mark Miller recognized that while data collection had become expedited, data analysis remained a bottleneck in the scientific process. As quoted from Dr. Miller in an article with Scientia in 2019, "As more DNA sequence data has become available, routine analyses that used to run in a day on a laptop now require a week or a month." The complexity of DNA sequence alignment and analysis increased exponentially as datasets grew in size and complexity. Many researchers needed access to the high-performance computing resources required for these demanding analyses, hindering their ability to unlock the secrets encoded within the genetic data.

Enter CIPRES: Accelerating Discovery with Supercomputing

The CIPRES Scientific Gateway, an innovative creation by Dr. Mark Miller and his team, emerged as a solution to these challenges. CIPRES, derived from "Cyber Infrastructure for Phylogenetic RESearch," is a virtual portal to a suite of cutting-edge phylogenetic analysis programs. By harnessing the power of supercomputers, CIPRES empowers researchers to upload their genetic data, select analysis approaches, and obtain results within minutes that would otherwise take hours or weeks on personal computers.

The efficiency of CIPRES is attributed to two key factors. First, it leverages the colossal computing power of computing at the San Diego Supercomputer and other National Science Foundation's funded computing resources, granting researchers access to these advanced systems. Second, CIPRES employs parallel computing techniques, breaking down complex analyses into smaller, manageable tasks that can be processed simultaneously. This approach significantly accelerates the overall analysis process. Using CIPRES, most analyses also run 10–200 times faster - a fantastic outcome.

Empowering Researchers and Transforming Science

CIPRES's impact extends far and wide, transcending geographical boundaries and financial constraints. The gateway provides free access to its computational resources, enabling researchers worldwide, including those with limited funding, to engage in cutting-edge phylogenetic research. The diverse user base of CIPRES ranges from NASA to the Korean National Arboretum, with tens of thousands of researchers benefiting from its capabilities.

By relieving researchers of the technical burdens of software maintenance and computing infrastructure, CIPRES empowers biologists to focus on the essence of their research – the biological questions and discoveries that drive scientific progress. CIPRES makes it easy for biologists to access and use computing resources through a web interface without months of training.

A Glimpse into the Future

While Dr. Miller enters his next life journey in retirement, he has initiated the transformation of CIPRES to continue support for the large CIPRES community. As shared in an article with SDSC on August 4, 2023, “Although my involvement will diminish, CIPRES is actually entering an exciting new phase, and will be offered through the new One Science Place platform, led by Amit Chourasia and Mike Zentner at SDSC,” Dr. Miller said. “Not only will users continue to have access to the current capabilities of CIPRES, they will have a new, more flexible set of tools for studying phylogenetics via the large clusters that ACCESS makes available.” 

Thank you, Dr. Miller, for all of your amazing contributions and creating a space for biologists to illuminate the Tree of Life.


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