Monitoring
Environmental Microbiomes
(MEM)

19-24 May 2024, Durango, CO

About The Workshop

About MEM Workshop

MEM aims to increase the number of Indigenous/Native American students and folks from marginalized communities (low income, disabled, etc.) in data science and scientific computing by studying environmental microbiomes. This workshop is designed to incorporate Indigenous values and approaches when conducting scientific research. Our workshop has an elder-in-residence to facilitate discussions and provide support during the workshop. Read our open access publication: "Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework."

Studying microbial systems enables researchers to understand the interactions in natural environments to gain insight into environmental microbiome dynamics. MEM utilizes microbiome research to study mining impacts to the San Juan Watershed alongside the context of "environmental and social (in)justice perspectives." (reference) In Southwest Colorado, there is over 100 years of mining that have impacted the San Juan Watershed.

In this week-long workshop, participants will gain hands-on computational experience to explore the presence of bacteria in environmental samples affected by mining contamination downstream of the Gold King Mine and Red & Bonita Mine near Silverton, CO.

This experience will introduce participants to sequencing technologies, current computational biology tools and data science methods to investigate the hidden world of microbial communities!

Housing and all meals will be arranged and paid by the workshop. Students will receive stipends for their time.

For more information about the history of MEM workshops.

Where

Fort Lewis College, Durango, CO

"We acknowledge the land that Fort Lewis College is situated upon is the ancestral land and territory of the Nuuchiu (Ute) people who were forcibly removed by the United States Government. We also acknowledge that this land is connected to the communal and ceremonial spaces of the Jicarilla Abache (Apache), Pueblos of New Mexico, Hopi Sinom (Hopi), and Diné (Navajo) Nations. It is important to acknowledge this setting because the narratives of the lands in this region have long been told from dominant perspectives, without full recognition of the original land stewards who continue to inhabit and connect with this land. Thank you for your attention and respect in acknowledging this important legacy. "

For more information about FLC Land Acknowledgment.

When

Sunday to Friday
19-24 May 2024

Workshop Organizers

The workshop organizers are also the hosts, instructors and teaching assistants from Fort Lewis College and University of Colorado. Click on the individual below to learn more about who will be teaching at the workshop.

Speaker photo Joslynn Lee

Joslynn Lee, PhD

Instructor and co-host

Speaker photo Jen Lowell

Jennifer Lowell, PhD

Instructor and co-host

Speaker photo Larry Hunter

Larry Hunter, PhD

Instructor

Speaker photo Brook Santangelo

Brook Santangelo

Teaching Assistant

Speaker photo Clyde Benally

Clyde Benally

Elder-in-residence

Speaker 6

TBD

Non autem dicta

Workshop Schedule

We will have participants arrive Sunday evening and depart Friday afternoon. There will be travel to samples collection sites and the surrounding area of Durango, CO.

The focus of this workshop is to learn about the various data science methods to analyze environmental microbiomes. For more information about the data science projects. See this site for details on the project.
There will be an introduction to computing (command line), this workshop is for beginners! We hope that you learn and gain experience on scientific computing, algorithms and software.

Tentative schedule of events. Day 2 is a field trip to Silverton, CO. Days 3-6 will be on the Fort Lewis College campus.

Arrival

Participants check-in to dorms

Joslynn Lee

Welcome Dinner Joslynn Lee

Overview of the workshop and meet each other

Hubert Hirthe

Evening Social TA

Get to meet each over dessert and games.

Brenden Legros

Breakfast Dorm

Food, juice and coffee served.

meeting

Opening Session Joslynn Lee

Opening Blessing and overview of the day.

bus

Field Trip Joslynn Lee

Departure to sample collection sites in Silverton, CO.

lunch

Lunch Silverton, CO

Food and drink from local restaurant.

field trip

Visit Mine Sites Silverton, CO

See areas affected by mining.

bus

Return to Fort Lewis College Campus

dinner

Dinner

Food and drink from local restaurant.

food

Breakfast Dorm

Food, juice and coffee served.

Morning Meeting Joslynn Lee

Overview of the day

16S rRNA data analysis

Introduction to 16S rRNA amplicon sequencing method

lunch

Lunch

Box lunch and drink from local restaurant.

computer

16S rRNA data analysis

Exploring the 16S rRNA amplicon dataset

dinner

Dinner + Guest Speaker Speaker TBD

Food and drink from local restaurant.

breakfast

Breakfast Dorm

Food, juice and coffee served.

meeting

Morning Meeting Joslynn Lee

Overview of the day

beaker

MinION Sequencing

Introduction to MinION sequencing

lunch

Lunch + Speaker

Box lunch and drink from local restaurant.

computer

16S rRNA data analysis

Wrapping up the 16S rRNA amplicon dataset

dinner

Dinner + Hike

Box food and drink from local restaurant and exploring a local campus trail.

breakfast

Breakfast Dorm

Food, juice and coffee served.

meeting

Morning Meeting Joslynn Lee

Overview of the day

computer

Data Science - Antibiotic Resistance Genes (ARGs)

Exploring a dataset to identify ARS using data science methods

lunch

Lunch

Box lunch and drink from local restaurant.

computer

Data Science - Antibiotic Resistance Genes (ARGs)

Exploring a dataset to identify ARS using data science methods

dinner

Dinner + Guest Speaker Speaker TBD

Food and drink from local restaurant. Guest speaker is a previous GSLI/MEM participant.

breakfast

Breakfast Dorm

Food, juice and coffee served.

computer

Data Science - Antibiotic Resistance Genes (ARGs)

Exploring a dataset to identify ARS using data science methods

lunch

Lunch + Hike

Box lunch and drink from local restaurant.

computer

Work on presentations

Prepare a presentation on what you've learned!

dinner

Dinner + Presentations Speaker TBD

Food and drink from local restaurants.

Event Venue

The organizers will be holding the event on the beautiful Fort Lewis College campus.



We acknowledge the land that Fort Lewis College is situated upon is the ancestral land and territory of the Nuuchiu (Ute) people who were forcibly removed by the United States Government. We also acknowledge that this land is connected to the communal and ceremonial spaces of the Jicarilla Abache (Apache), Pueblos of New Mexico, Hopi Sinom (Hopi), and Diné (Navajo) Nations.

Fort Lewis College Campus

Located in Southwest Colorado, Durango is located between snowcapped peaks and high desert. The campus sits on top a mesa and gets 300 days of sunshine. Surrounding the campus are 300 miles of trails and the Animas River runs through the town.

Location

Participants stay at a hotel near the Fort Lewis College campus located in Durango, CO.

Housing

Housing Common Area

Access to laundry, TV, small kitchen

Housing Bedroom

Housing Bedroom

Bed, linens and bathroom

Sponsors

F.A.Q

  • Must be a current undergraduate student majoring in science or science education, and/or be currently in a science internship and have a GPA of 2.5. Students from groups underrepresented in science are encouraged to apply. American Indians and Alaska Natives students will be given priority but no one will be excluded from consideration based on their ethnic background.

  • We will provide money (post-workshop) to reimburse for travel costs. Participants can drive themselves, there is free parking, or get dropped off.

  • Participants will be staying in a hotel with a shared space but own room. They will need to be 18.

  • We cover all food and housing. We can discuss off-campus stays on a case-by-case basis. The workshop goes from 8AM to 6PM. We do build in activities in the evening for participants to build community.

Apply

DEADLINE : April 15th 2024

Link to: FLYER

Prepare documents the following documents for this application:
1. Statement of Interest (one page limit, word or PDF format): Describe your educational and career plans and how this workshop experience will benefit you.

2. Resume (acceptable in Word or PDF format)

3. Most recent college transcript(s) (unofficial is acceptable in Word or PDF format)

4. Select a Reference (Workshop organizers will contact them via phone) Name / phone number / email of a science faculty or science staff member who will serve as a reference.

Please follow the link to apply: https://forms.gle/4FQqLEEH1R41sqAM9