From Reads to Function Workshop at ISME19

From Reads to Function Workshop at ISME19

A Workshop on an Accessible Metagenomics Toolkit for Decoding Microbial Contributions to Biogeochemical Cycles

Welcome!

Here you will find the agenda and resources for the From Reads to Function Workshop at ISME19 in Cape Town on August 16 and 17.

Workshop Agenda

Agendas for each day are listed below. Reminder that the Hybrid Sessions (with webinar components) are only in the morning from 9:00-12:00 local time South Africa.

Day 1 - Friday August 16th

Reads to Metagenome-Assembled Genomes (MAGs)

South Africa Local Time – Activity / Topic (Lead)

Day 1 Slide Decks

Day 1 Recordings

7:45 Travel to Workshop – provided by ISME
8:45 Who is all here?! (Dow)
9:00 Virtual attendees join – Hybrid Session
9:00 Introduction to Workshop and GROW (Borton)
9:20 Introduction to KBase (Allen)
9:50 Break for 10 min
10:00 Introduction to multi-omics methods (Wrighton)
10:25 Assembly QA/QC to Binning (Allen)
10:50 Taxonomic Assessment of Communities (Allen)
11:10 Metagenome-Assembled Genomes (Allen)
11:40 Review and Q&A (Allen)
12:00 End Hybrid Session
           Lunch Break
13:00 Workshop Only – Working Session
13:00 Reads to MAGs workflow in KBase (Allen)
14:15 Break for 15 min
14:30 Reads to MAGs workflow in KBase – continued (Allen)
16:00 Report out, recap, and next steps (Allen)
17:00 Depart to hotels
17:30 Networking Event (CoSMic)

Day 2 - Saturday August 17

MAGs to Function and Metadata Standards

South Africa Local Time – Activity / Topic (Lead) – Activity / Topic (Lead)

Day 2 Slide Decks

Day 2 Recordings

7:45 Travel to Workshop provided by ISME
8:30 Review analyses from Day 1 (Allen)
9:00 Virtual attendees join – Hybrid Session
9:00 Microbial Genome Annotation (Borton)
9:30 Metabolism with DRAM (Ellenbogen)
10:00 Break for 15 min
10:15 National Microbiome Data Collaborative (NMDC) and sample metadata (Skoog, Pham, Oduwole)
10:50 DRAM outputs (Borton)
11:00 Publishing with KBase (Dow)
11:30 Q&A, survey (All)
12:00 End Hybrid Session
           Lunch Break
13:00 Workshop Only – Working Session
13:00 NMDC sample metadata demonstration (Skoog, Pham, Oduwole)
14:15 Break for 15 min
14:30 Interpreting DRAM (Borton)
16:00 Report out and recap (Borton)
16:45 Close out and survey (Wood-Charlson)
17:00 Depart to hotels

Resources & Helpful Links

Project Paper – in review at Nature
MA Borton, BB McGivern, KR Willi, BJ Woodcroft, AC Mosier, DM Singleton, T Bambakidis, A Pelly, F Liu, JN Edirisinghe, JP Faria, I Leleiwi, RA Daly, AE Goldman, MJ Wilkins, EK Hall, C Pennacchio, S Roux, EA Eloe-Fadrosh, SP Good, MB Sullivan, CS Henry, EM Wood-Charlson, MRV Ross, CS Miller, BC Crump, JC Stegen, KC Wrighton. A functional microbiome catalog crowdsourced from North American rivers. (2023) bioRxiv 2023.07.22.550117; doi: https://doi.org/10.1101/2023.07.22.550117

KBase GROWdb US River Systems Narrativehttps://doi.org/10.25982/109073.30/1895615 

GROW Org in KBasehttps://legacy.narrative.kbase.us/#org/grow

NMDC GROWdb – https://data.microbiomedata.org/details/study/nmdc:sty-11-5tgfr349

Reading Materials

Workshop Notes

Workshop Activities

About our participants

Sunburst chart visually representing virtual and in-person participants and their countries. Participants from over 50 countries joined the workshop, including 25 individuals who received an Africa Travel Grant from ISME to attend in-person.

 

 

 

 

 

 

Folks also took a Microbe Personality Quiz! Check out the total diversity of our microbial community.

Pie chart representating the microbial community of all workshop participants.

And we compared between our sampling sites – virtual and in-person.

Pie charts comparing the representative microbial communities between virtual and in-person participants.

Take the quiz to find out what microbe you are!

Check out the workshop and networking in action

People

Colorado State Microbiome Network
Mikayla Borton – Workshop Lead and Microbial Ecosystems Lab co-PI
Jared Ellenbogen – Postdoctoral Researcher, Wrighton Lab
Emily Bechtold – Postdoctoral Researcher, Wilkins Lab
Kelly Wrighton – Microbial Ecosystems Lab PI

KBase
Ben Allen – KBase Outreach Lead
Ellen Dow – KBase Educators Program Lead
Elisha Wood-Charlson – KBase User Engagement Lead

NMDC Ambassadors
Iyanu Oduwole – University of Tennessee – Knoxville
Emilie Skoog – University of California – San Diego, Scripps
Kent Pham – University of Kentucky