20161031_134740

Michigan Biological Software Team to compete at iGEM with MICDE support

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MICDE is pleased to announce its support of the Michigan Biological Software Team (MiBioSoft), for its attendance at the 2017 International Genetically Engineered Machine (iGEM) competition in Boston.

Founded in 2014, MiBioSoft is a student-run organization at the University of Michigan that develops software for use in scientific research, with a focus on synthetic biology. It seeks to provide its members with opportunities to not only improve their skills as software designers, but also to improve their communication and management skills by bringing together students from a variety of backgrounds including Biology, Mathematics, Computer Science, and Chemistry.

MiBioSoft competes annually in the software track of the iGEM competition, where research teams from around the world present their results over the course of a three-day conference. During the first two years at the competition, the team was awarded bronze medals. In 2016, MiBioSoft received Best Software Project award as well as a gold medal for their protocol catalog, ProtoCat, in a competition that featured over 300 teams from more than 40 countries, with more than 5,000 participants in total.

About Protocat

Protocat is protocol catalog software developed by MiBioSoft students to address the issue of reproducibility in synthetic biology. Like many innovative ideas, it began because of a problem. Studies have estimated that only 10-25% of published scientific results are reproducible. A 2014 survey conducted by the Michigan Software team confirmed that the repeatability problem exists in synthetic biology, with every scientist surveyed reporting prior struggles with replicating protocols.

ProtoCat 3.0 is a free database of crowd-sourced protocols designed to make existing protocols more repeatable and enable more accurate computational models of biological systems. MiBioSoft believes this can most efficiently be accomplished with a commitment to open source protocols and a broader more active community of digital troubleshooters. ProtoCat 3.0 works to establish such a community by giving anyone with an internet connection or smartphone access to a repository of synthetic biology protocols collected from all over the world. Additionally, ProtoCat 3.0 encourages the development of higher quality, more repeatable protocols by allowing users to document, rate, review, and edit existing methods.

MIDAS announces second round of Data Science Challenge Initiative awards, in health and social science

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Five research projects — three in health and two in social science — have been awarded funding in the second round of the Michigan Institute for Data Science Challenge Initiative program.

The projects will receive funding from MIDAS as part of the Data Science Initiative announced in fall 2015.

The goal of the multiyear MIDAS Challenge Initiatives program is to foster data science projects that have the potential to prompt new partnerships between U-M, federal research agencies and industry. The challenges are focused on four areas: transportation, learning analytics, social science and health science. For more information, visit midas.umich.edu/challenges.

The projects, determined by a competitive submission process, are:

  • Title: Michigan Center for Single-Cell Genomic Data Analysis
    Description: The center will establish methodologies to analyze sparse data collected from single-cell genome sequencing technologies. The center will bring together experts in mathematics, statistics and computer science with biomedical researchers.
    Lead researchers: Jun Li, Department of Human Genetics; Anna Gilbert, Mathematics
    Research team: Laura Balzano, Electrical Engineering and Computer Science; Justin Colacino, Environmental Health Sciences; Johann Gagnon-Bartsch, Statistics; Yuanfang Guan, Computational Medicine and Bioinformatics; Sue Hammoud, Human Genetics; Gil Omenn, Computational Medicine and Bioinformatics; Clay Scott, Electrical Engineering and Computer Science; Roman Vershynin, Mathematics; Max Wicha, Oncology.
  • Title: From Big Data to Vital Insights: Michigan Center for Health Analytics and Medical Prediction (M-CHAMP)
    Description: The center will house a multidisciplinary team that will confront a core methodological problem that currently limits health research — exploiting temporal patterns in longitudinal data for novel discovery and prediction.
    Lead researchers: Brahmajee Nallamothu, Internal Medicine; Ji Zhu, Statistics; Jenna Wiens, Electrical Engineering and Computer Science; Marcelline Harris, Nursing.
    Research team: T. Jack Iwashyna, Internal Medicine; Jeffrey McCullough, Health Management and Policy (SPH); Kayvan Najarian, Computational Medicine and Bioinformatics; Hallie Prescott, Internal Medicine; Andrew Ryan, Health Management and Policy (SPH); Michael Sjoding, Internal Medicine; Karandeep Singh, Learning Health Sciences (Medical School); Kerby Shedden, Statistics; Jeremy Sussman, Internal Medicine; Vinod Vydiswaran, Learning Health Sciences (Medical School); Akbar Waljee, Internal Medicine.
  • Title: Identifying Real-Time Data Predictors of Stress and Depression Using Mobile Technology
    Description: Using an app platform that integrates signals from both mobile phones and wearable sensors, the project will collect data from over 1,000 medical interns to identify the dynamic relationships between mood, sleep and circadian rhythms. These relationships will be utilized to inform the type and timing of personalized data feedback for a mobile micro-randomized intervention trial for depression under stress.
  • Lead researchers: Srijan Sen, Psychiatry; Margit Burmeister, Molecular and Behavioral Neuroscience.
    Research team:  Lawrence An, Internal Medicine; Amy Cochran, Mathematics; Elena Frank, Molecular and Behavioral Neuroscience; Daniel Forger, Mathematics; Thomas Insel (Verily Life Sciences); Susan Murphy, Statistics; Maureen Walton, Psychiatry; Zhou Zhao, Molecular and Behavioral Neuroscience.
  • Title: Computational Approaches for the Construction of Novel Macroeconomic Data
    Description: This project will develop an economic dataset construction system that takes as input economic expertise as well as social media data; will deploy a data construction service that hosts this construction tool; and will use this tool and service to build an “economic datapedia,” a compendium of user-curated economic datasets that are collectively published online.
    Lead researcher: Matthew Shapiro, Department of Economics
    Research team: Michael Cafarella, Computer Science and Engineering; Jia Deng, Electrical Engineering and Computer Science; Margaret Levenstein, Inter-university Consortium for Political and Social Research.
  • Title: A Social Science Collaboration for Research on Communication and Learning based upon Big Data
    Description: This project is a multidisciplinary collaboration meant to introduce social scientists, computer scientists and statisticians to the methods and theories of engaging observational data and the results of structured data collections in two pilot projects in the area of political communication and one investigating parenting issues. The projects involve the integration of geospatial, social media and longitudinal data.
    Lead researchers: Michael Traugott, Center for Political Studies, ISR; Trivellore Raghunathan, Biostatistics
    Research team: Leticia Bode, Communications, Georgetown University; Ceren Budak, U-M School of Information; Pamela Davis-Keane, U-M Psychology, ISR; Jonathan Ladd, Public Policy, Georgetown; Zeina Mneimneh, U-M Survey Research Center; Josh Pasek, U-M Communications; Rebecca Ryan, Public Policy, Georgetown; Lisa Singh, Public Policy, Georgetown; Stuart Soroka, U-M Communications.

For more details, see the press releases on the social science and health science projects.

MIDAS to host faculty meeting on NSF BIGDATA solicitation

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The Michigan Institute for Data Science (MIDAS) will hold a faculty meeting at noon on Thursday, January 19 (Suite 7625, School of Public Health I, 1415 Washington Heights) for the NSF 17-534 “Critical Techniques, Technologies and Methodologies for Advancing Foundations and Applications of Big Data Sciences and Engineering (BIGDATA)” solicitation.

The meeting will include an overview of the NSF solicitation, U-M Data Science Resources (MIDAS, CSCAR, ARC-TS) available to faculty responding to the NSF call, and an opportunity to network with other faculty.

MIDAS has also arranged for Sylvia Spengler, NSF CISE Program Director, to be available at 1:30 pm to answer questions regarding the BIGDATA solicitation.

We invite you to participate in the faculty meeting to share your ideas and interest in responding to this BIGDATA solicitation as well as interact with other faculty looking to respond to this funding mechanism.

For those unable to participate in person, you can join virtually using GoToMeeting:

A box lunch will be provided at the faculty meeting.  Your RSVP (https://goo.gl/forms/OYAuB8mWCOlx3fw73) is appreciated.

ARC Director Sharon Broude Geva elected vice-chair of Coalition for Academic Scientific Computing

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Sharon Broude Geva, the Director of Advanced Research Computing at the University of Michigan, has been elected vice-chair of the Coalition for Academic Scientific Computation (CASC).

Founded in 1989, CASC advocates for the use of advanced computing technology to accelerate scientific discovery for national competitiveness, global security, and economic success. The organization’s members represent 83 institutions of higher education and national labs.

The vice-chair position is one of four elected CASC executive officers. The officers work closely as a team with the director of CASC. The vice-chair also leads CASC meeting program committees, is responsible for recruitment of new members, substitutes for the chair in his or her absences, and assists with moderating CASC meetings.

Geva served as CASC secretary in 2015 and 2016. Her term as vice-chair is effective for the 2017 calendar year.

The other executive officers for 2017 are are Rajendra Bose, Chair, Columbia University; Neil Bright, Secretary, Georgia Institute of Technology; and Andrew Sherman, Treasurer, Yale University. Curt Hillegas of Princeton University is immediate past chair.