Workshop on Clinical and Environmental Metagenome Analysis CINEMA 2023 materials. Additional materials can be found on our CINEMA 2023 Box folder.
You will need to bring a laptop to actively participate in this course. We can provide user access to our virtual machines during the workshop if needed.
Wifi: RGP Center Guest
PW: RICE*Guest
Gate code: 15B87
- 3 July – Monday
- 4 July – Tuesday
- 5 July - Wednesday
- 6 July – Thursday
- 7 July – Friday
- 8 July – Saturday
- 9 July – Sunday
- Todd Treangen Rice University, Dept. of Computer Science
- Lauren Stadler Rice University, Dept. of Civil and Environmental Engineering
- Todd Treangen Rice University
- Lauren Stadler Rice University
- Jeseth Delgado Vela Howard University, USA
- Sara Vieira-Silva University Medical Center, Johannes Gutenberg University Mainz, Germany
- Alexander Dilthey Institute of Medical Microbiology, University Hospital of Düsseldorf Germany
- Joshua Quick University of Birmingham
- Kristen Curry Rice University
- Ryan Doughty Rice University
- Sonia Villapol Salgado Houston Methodist Research Institut, USA
- Lucie Bittner Sorbonne Université
- Zamin Iqbal EMBL-European Bioinformatics Institute
- Laurent Moulin Eau de Paris
- Nicola Segata University of Trento (Italy) and European Institute of Oncology in Milan (Italy)
All events are held in the Rice Global Paris Center. All times in CEST (UTC+2).
| Time | CINEMA Kickoff |
|---|---|
| 15h30-15h40 | Welcome to Rice Global Paris Center (Dr. Garry White) |
| 15h40-15h55 | Welcome to CINEMA Paris 2023 (Dr. Stadler and Dr. Treangen) |
| 16h00-17h00 | Keynote address (Dr. Nicola Segata) “Large-scale strain-level computational metagenomics of the human microbiome” |
| 17h00-18h00 | Social & Networking |
| Time | Sampling and Sequencing (Instructor: Dr. Quick, Moderator: Dr. Stadler) |
|---|---|
| 9h30-10h30 | lecture part 1 |
| 10h30-11h00 | coffee break |
| 11h00-12h00 | lecture part 2 |
| 12h00-13h30 | lunch/networking |
| 13h30-14h30 | practical session or hands-on demo part 1 |
| 14h30-15h00 | coffee break |
| 15h00-16h00 | practical session or hands-on demo 2 |
| 16h00-17h00 | Lightning presentations |
| 17h00-18h00 | social hour |
| Time | Environmental microbiome analysis (Instructor: Dr. Delgado Vela, Moderator: Dr. Stadler) |
|---|---|
| 9h30-10h30 | lecture part 1 |
| 10h30-11h00 | coffee break |
| 11h00-12h00 | lecture part 2 |
| 12h00-13h30 | lunch/networking |
| 13h30-14h30 | practical session or hands-on demo part 1 |
| 14h30-15h00 | coffee break |
| 15h00-16h00 | practical session or hands-on demo 2 |
| 16h00-17h00 | "Bridging the gap between (meta-)omics and biodiversity perceptions - Can we ignore the "dark" sequences?" (Dr. Lucie Bittner) |
| 17h00-18h00 | CINEMA helpdesk (aka getting ready for Thursday) |
| Time | Clinical microbiome analysis (Instructor: Dr. Vieira-Silva, Moderator: Dr. Treangen) |
|---|---|
| 9h30-10h30 | lecture part 1 |
| 10h30-11h00 | coffee break |
| 11h00-12h00 | lecture part 2 |
| 12h00-13h30 | lunch/networking |
| 13h30-14h30 | practical session or hands-on demo part 1 |
| 14h30-15h00 | coffee break |
| 15h00-16h00 | practical session or hands-on demo 2 |
| 16h00-17h00 | "Changes in the gut microbiome in Alzheimer's disease" (Dr. Sonia Villapol) |
| 17h00-18h00 | social hour |
| Time | Bioinformatics tools and approaches (Instructor: Dr. Dilthey, Moderator: Dr. Treangen) |
|---|---|
| 9h30-10h30 | lecture part 1 |
| 10h30-11h00 | coffee break |
| 11h00-12h00 | lecture part 2 |
| 12h00-13h30 | lunch/networking |
| 13h30-14h30 | practical session or hands-on demo part 1 |
| 14h30-15h00 | coffee break |
| 15h00-16h00 | practical session or hands-on demo 2 |
| 16h00-17h00 | "Using revived 100-year old bacteria and new algorithms to study plasmid evolution" (Dr. Zamin Iqbal) |
| 17h00-18h00 | social hour |
| Time | Putting it all together (bring your own dataset else example data will be provided) |
|---|---|
| 9h30-10h30 | Linux and bioinformatics tips (Kristen and Todd)[first][second] |
| 10h30-12h30 | Analyzing data on your own, session 1 |
| 12h30-13h30 | lunch/networking |
| 13h30-15h30 | Analyzing data on your own (+slide prep for Sunday), session 2 |
| 15h30-16h00 | coffee break |
| 16h00-17h00 | “SARS CoV 2 genome monitoring in wastewater by the French OBEPINE network, deciphering the viral dynamics and VOC evolution” (Dr. Laurent Moulin, Eau de Paris) |
| 19h30-21h00 | CINEMA dinner Restaurant Salon Marais |
| Time | Finale (Moderators: Dr. Stadler, Dr. Treangen) |
|---|---|
| 9h30-11h30 | Participant presentations, 5 minutes per participant, 10 minutes per team |
| 11h30-12h00 | CINEMA recap and closing |