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Ken Aiello’s Dissertation Defense

  • Posted on: 8 November 2018
  • By: admin


On November 7, 2018, Ken Aiello successfully defended his dissertation titled “Systematic Analysis of the Factors Contributing to the Variation and Change of the Microbiome Concept.” He will continue his research as a postdoctoral researcher in the Global Biosocial Complexity Initiative. The Laubichler Lab congratulates Dr. Aiello on a job well done!

Want to know what Aiello’s dissertation is about? Read the abstract!

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THE COMPUTATIONAL ANTHROPOCENE

  • Posted on: 5 November 2018
  • By: admin

Mankind finds itself in the Anthropocene, the current geological epoch generally accepted by scholars and denoted by one species, our own, ascending to the role of major driver on Earth. The term Anthropocene was first-coined in the eponymous article by Paul Crutzen and Eugene Stoermer in the IGBP Global Newsletter [1]. Later, Crutzen argues in "Geology of Mankind" [2] that human effects on the global ecosystem have accelerated and are now the primary influence on the global ecosystem. This human-domination over nature necessitates a new epochal designation; in contrast to the previous epoch, the Holocene, that designated the post-glacial geological period proposed by Sir Charles Lyell in Principles of Geology [3] in 1833 and adopted in 1885 by the International Geological Congress (IGC). Read the story here.

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Tutorial: Generating and Visualizing Topic Models with Tethne and MALLET

  • Posted on: 17 December 2017
  • By: admin

Tethne provides a variety of methods for working with text corpora and the output of modeling tools like MALLET. This tutorial focuses on parsing, modeling, and visualizing a Latent Dirichlet Allocation topic model, using data from the JSTOR Data-for-Research portal.

In this tutorial, we will use Tethne to prepare a JSTOR DfR corpus for topic modeling in MALLET, and then use the results to generate a semantic network like the one shown above.

In this visualization, words are connected if they are associated with the same topic; the heavier the edge, the more strongly those words are associated with that topic. Each topic is represented by a different color. The size of each word indicates the structural importance (betweenness centrality) of that word in the semantic network.

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The Data Mining and Analytics Team

  • Posted on: 30 August 2017
  • By: admin

The Data Mining and Analytics Team focuses on extracting the dynamics of complex systems from real-world data.

We build unique and innovative data systems that capture in unprecedented detail the processes that lead to important scientific innovation. Combining expertise in data wrangling, network science, and advanced statistical modeling, we push at the interdisciplinary boundaries of the life sciences, medicine, clinical research, data science, and digital humanities.

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DH2017 Pre-Conference Workshop Outcomes

  • Posted on: 28 August 2017
  • By: admin

Published: August 28, 2017

On 7 August 2017, the Digital Innovation Group together with the Max Planck Institute for the History of Science hosted a pre-conference workshop at the Digital Humanities Conference 2017 in Montréal.

The workshop called 'Let’s Develop an Infrastructure for Historical Research Tools' focused on collaboration and integration of digital humanities software and tools.

New Publication in Biomedical Research

  • Posted on: 28 August 2017
  • By: admin

Published: August 28, 2017

On March 30th, 2017, Manfred Laubichler, Julia Damerow and Erik Pierson published a paper titled The diversity of experimental organisms in biomedical research may be influenced by biomedical funding.

Contrary to concerns of some critics, we present evidence that biomedical research is not dominated by a small handful of model organisms. An exhaustive analysis of research literature suggests that the diversity of experimental organisms in biomedical research has increased substantially since 1975. . .

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Software Development & Trans-disciplinary Training

  • Posted on: 28 August 2017
  • By: admin

Published: August 28, 2017

Julia Damerow, Manfred Laubichler, and Erik Pierson collaborated on a paper titled Software development & trans-disciplinary training at the interface of digital humanities and computer science.

The computational turn in the humanities has precipitated the need for sustainable software development projects that are specifically focused on humanities research problems, and the need for graduate and undergraduate training models that address the trans-disciplinary nature of computational humanities research.

Austria’s Ahead-of-Its-Time Institute That Was Lost to Nazis

Manfred Laubichler was interviewed for an article by Chelsea Wald about the Biologische Versuchsanstalt in Vienna, published in the recent issue of Nautilus. From the article:

In 1911, Popular Science Monthly published an enthusiastic description of a young, private experimental-biology institute in Vienna, lauding its “remarkable scientific productivity resulting from only eight years of research.”

An early air-conditioning system used to control air temperatures at the Vivarium

The author, zoologist Charles Lincoln Edwards, attributed the success of the Biologische Versuchsanstalt (Insitute of Experimental Biology) to its many advanced experimental devices. The institute, popularly known as the Vivarium, boasted a wide range of terrariums, which housed hundreds of organisms, from glow-worms to kangaroos, at strictly controlled temperatures, humidity, pressure, and light levels. That wasn’t always easy—the Vivarium had to adopt or invent many cutting-edge technologies, including an early air-conditioning system. It was “a pioneer in the use of the carbonic-acid cooling machine for maintaining a cold environment,” wrote Edwards. With the help of circulating salt water and a condenser, four rooms were kept at temperatures ranging from 5°C to 20°C.

The idea of using various apparatuses to control the living conditions of plants and animals for study was new; before that, scientists mainly observed their subjects in nature. At the Vivarium, the focus was on raising many generations under the same conditions in order to probe questions of heredity and development—a unique approach at the time, and one that many consider a precursor to today’s research on evolutionary developmental biology, or “evo-devo.”

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