These pre-workshop exercises cover some of the basic functionality in VEuPathDB. Please complete the exercises included in the module prior to the start of the workshop on June 7th. We expect that this module will take 2 - 2.5 hours to complete. The instructors will assume that all attendees have completed these exercises prior to the start of the workshop.
Module pdf files will be linked to the schedule just before the session begins
Instructors: Omar Harb, Jessica Kissinger, Susanne Warrenfeltz, Kathryn Crouch, Mark Hickman, Sam Rund, Gloria I. Giraldo-Calderón, Evelina Basenko, Uli Boehme, David Starns, Sarah Kelly, Beatrice Amos, Mary Ann McDowell, David Roos
Time | Event | Instructor | |
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Monday, June 7th All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/. |
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8:30am | Zoom session opens for discussion | ||
9 - 9:10am | Workshop Introduction | Jessie Kissinger |
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9:10 - 9:15am | Welcome and introductions | Mary Ann McDowell and David Roos | |
9:15 - 9:55am | Introductions | Everyone - Name, organisms of research, geographic location | |
10 - 10:05am | short break | ||
10 - 10:10am | Transcriptomics and Proteomics lecture Trans-and-Prot-lecture-slides.pdf |
Susanne Warrenfeltz |
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10:10am - 12:00pm | Break out rooms for hands on work - transcriptomics and proteomics Transcriptomics.pdf Proteomics.pdf |
12:00 - 12:45pm | Lunch Break |
12:45 - 1:00pm | Gene ontology and enrichment lecture GO-Term-presentation.pdf |
Omar Harb |
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1:00 - 1:30pm | Break out rooms for hands on work - GO enrichment GO-Enrichment.pdf |
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1:30 - 1:50pm | Galaxy/RNAseq lecture RNAseq_lecture.pdf |
Kathryn Crouch |
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1:50 - 3:00pm | Break out rooms for hands on work - RNAseq Galaxy part 1 Galaxy-RNAseq-datasets.pdf Galaxy-RNAseq-instructions.pdf |
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3 - 3:30pm | Optional discussion and question time | ||
Tuesday, June 8th All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/. |
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8:30am | Zoom session opens for discussion | ||
9:00 - 9:10am | Phenotype exercise lecture | Evelina Basenko |
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9:10 - 10:00am | Break out rooms for hands on work - Phenotype Phenotype-Exercise.pdf |
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10:00 - 10:20am | Gene models lecture | David Roos |
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10:20 - 11:30am | Break out rooms for hands on work - Adv. JBrowse gene models Adv-JBrowse-gene-models.pdf |
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11:30am - 12:00pm | Group discussion with some students highlighting what they found | ||
12:00pm | Lunch Break | ||
1:00 - 1:20pm | Lecture RNAseq pipeline output, Fastq and DESeq2 | Mark Hickman |
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1:20 - 3:00pm | Break out rooms for hands on work - RNAseq Galaxy part 2 Galaxy-RNAseq-Part2.pdf |
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3 - 3:30pm | Optional discussion and question time | ||
Wednesday, June 9th All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/. |
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8:30am | Zoom session opens for discussion | ||
9:00 - 9:20am | Orthology lecture | David Roos |
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9:20 - 10:15am | Break out rooms for hands on work - orthology Orthology-module.pdf |
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10:15 - 10:30am | Lecture on variation - SNPs and CNVs Variation-Lecture.pdf |
Kathryn Crouch |
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10:30am - 12:00pm | Break out rooms for hands on work - SNPs and CNVs SNP-and-CNV-module.pdf |
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12:00pm | Lunch Break | ||
1:00pm | Colocation and Introduction to group projects | Omar Harb |
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1:30 - 3:00pm | Break out rooms for hands on work - Group project | ||
3 - 3:30pm | Optional discussion and question time | ||
Thursday, June 10th All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/. |
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8:30am | Zoom session opens for discussion | ||
9:00 - 9:10am | Metabolic pathways lecture Metabolic-pathways-lecture.pdf |
Jessie Kissinger |
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9:10 - 10:00am | Break out rooms for hands on work - Metabolic pathways Metabolic-pathways-module.pdf |
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10:00 - 10:05am | Short break | ||
10:05 - 12pm | Break out rooms for hands on work - Group project | ||
12:00pm | Lunch Break Breakout rooms can stay open for continued group project work |
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1:00 - 2:30pm | Final Project presentations | ||
2:30 - 3:00pm | Workshop wrapup and final thoughts | ||
3 - 3:30pm | Optional discussion and question time |
Quick Links: VEuPathDB | AmoebaDB | CryptoDB | FungiDB | GiardiaDB | HostDB | OrthoMCL DB | MicrosporidiaDB | PiroplasmaDB | PlasmoDB | ToxoDB | TrichDB | TriTrypDB VectorBase