GEM Lab

GEM Lab

Bringing geochemistry, microbiology, and engineering together!

Teaching

BIOL 598A: Applied Bioinformatics

Class, Colorado School of Mines, BIOL, 2018

BIOL598A: Overview

Throughout both natural and engineered systems, microorganisms are ever-present. Modern tools of DNA and RNA sequencing enable us to explore ecosystems to an unprecedented depth; however, these sequencing techniques also require an understanding of computation and data processing to decipher what microorganisms might be in an environment, and what they are doing. Applied Bioinformatics will instruct students on topics in bioinformatics and microbial ecology, giving both biologists and engineers an introduction to DNA sequencing technologies, the bioinformatic tools needed to analyze these data, and the confidence to process large datasets. The course will enable students to produce publication quality graphics in R and explore the topic of reproducible research. Statistical concepts in biological and non-biological systems within R will also be discussed. Finally, the course will expose students to high-performance and cloud computing, using microbiological datasets as case studies.

CEEN 573 - RECLAMATION OF DISTURBED LANDS

Class, Colorado School of Mines, CEEN, 2018

CEEN573 Instructor: John R. Spear

Basic principles and practices in reclaiming disturbed lands are considered in this course, which includes an overview of present legal requirements for reclamation and basic elements of the reclamation planning process. Reclamation methods, including recontouring, erosion control, soil preparation, plant establishment, seed mixtures, nursery stock, and wildlife habitat rehabilitation, will be examined. Practitioners in the field will discuss their experiences. Prerequisite: none. 3 hours lecture; 3 semester hours.

CEEN 560 - MOLECULAR MICROBIAL ECOLOGY AND THE ENVIRONMENT

Class, Colorado School of Mines, CEEN, 2018

CEEN560 Instructor: John R. Spear

This course explores the diversity of microbiota in a few of the countless environments of our planet. Topics include microbial ecology (from a molecular perspective), microbial metabolism, pathogens, extreme environments, engineered systems, oxidation / reduction of metals, bioremediation of both organics and inorganics, microbial diversity, phylogenetics, analytical tools and bioinformatics. The course has an integrated laboratory component for applied molecular microbial ecology to learn microscopy, DNA extraction, PCR, gel electrophoresis, cloning, sequencing, data analysis and bioinformatic applications. Prerequisite: College Biology and/or CHGC562, CHGC563 or equivalent and enrollment in the ESE graduate program. 3 hours lecture, some field trips; 3 semester hours.

CEEN 301 - FUNDAMENTALS OF ENVIRONMENTAL SCIENCE AND ENGINEERING I

Class, Colorado School of Mines, CEEN, 2018

CEEN301 Instructor Josh O. Sharp

This course introduces fundamentals of environmental science & engineering as applied to water resource management and environmental problem solving. Topics include environmental regulation, toxicology, material balance, applications in environmental chemistry, hydrology, water quality management, water supply and treatment, and wastewater treatment and reuse. Topical discussions will address major sources and concerns in measurement, practice and underlying theory in the field of environmental engineering. The course also includes field trips to local water and wastewater treatment facilities to integrate theory with practice. Prerequisites: CHGN122, PHGN100. 3 hours lecture; 3 semester hours.