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Galaxy Training Materials

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This web site is a gateway for lessons, tutorial, and examples of using Galaxy for genomics education and analysis. Among other things, links to tutorials for the following subjects are provided:

Events with Galaxy-related content (includes virtual events)

Galaxy Event Horizon (list of upcoming and past events)
Galaxy Events Google Calendar

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Wilson Leung onto Faculty Training Workshops in Genomics
@ 7:02 pm on 02 Apr 2020

Assignment for Coronavirus dianostic kit design

Design_a_diagnostic_kit_for_SARS-CoV-2.pdf 105 KB
MT020880.1_genbank_table.txt 1 KB
2019-nCoV_qPCR.pdf 1 MB
https://genome.ucsc.edu/cgi-bin/hgPcr link
https://www.ncbi.nlm.nih.gov/tools/primer-blast/ link

The homework assigned through the files follows a presentation on qPCR. The goal of the assignment is for the students to get primer pairs that do not bind to human DNA or the SARS Coronavirus that caused the 2003 epidemic. It is easy to assess through Primer-Blast or the UCSC in-silico PCR tool (links provided above).

PCR primer design

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Nik Tsotakos onto Coronavirus
@ 10:13 am on 02 Apr 2020

In-classroom activity for genome alignment of different strains of viruses in the Coronaviridae family

6.2_MEGA_workshop.pdf 174 KB
https://www.viprbrc.org/brc/home.spg?decorator=vipr link
Coronavirus_genome_alignments.pdf 916 KB

This is an activity that took place in an Advanced Genetics class that meets in a computer lab. The activity aims to construct a phylogenetic tree of different Coronaviruses, including a few strains of SARS-CoV2. The sequences were pulled from the Virus Pathogen Database and Genbank. Since the activity initially took place in mid-February, there are a lot more available sequences in the databases, while at least one of the sequences included has been retracted. The homework in the end is another application of the skillset the students acquired through the activity, and can be modified based on the course's objectives.

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Nik Tsotakos onto Coronavirus
@ 10:03 am on 02 Apr 2020

Cases from the National Center for Case Study Teaching in Science

Uploaded image Screen_Shot_2020-04-01_at_10.45.54_AM.png

https://sciencecases.lib.buffalo.edu/ link

NCCSTS requires a $25 annual subscription for individuals. Materials are peer reviewed, and include student handouts and teacher materials. We are sharing information about recent cases published on COVID19 from this organization:

"COVID-19: Where Did You Come From, Where Did You Go?” by authors from North Carolina State University: Stefanie H. Chen, Carlos C. Goller, and Melissa C. Srougi

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1125&id=1125

"Put to the Test: RT-PCR and Antibody Detection Diagnostic Tools for COVID-19 ” by a team of authors from Brandeis University: Melissa S. Kosinski-Collins, Lindsay Mehrmanesh, Jessie Cuomo and Kene N. Piasta.

Fatally Flawed? Early Genetic Testing for the COVID-19 Virus” by Amy C. Groth, Department of Biology, Eastern Connecticut State University

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1123&id=1123

“Social Distancing in the Midst of COVID-19” is by Jason C. Cochrane, Science Department, Mountain Vista High School, Highlands Ranch, CO.

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1113&id=1113

“Pandemic Pandemonium: Why Can’t We Just Treat COVID-19?” by a team of authors from Brandeis University: Melissa S. Kosinski-Collins, Lindsay Mehrmanesh, Jessie Cuomo and Kene N. Piasta.

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1114&id=1114

"Coronavirus Quandaries for Patients with Cardiovascular Disease” by Janine Bartholomew, Department of Biology, Carlow University, Pittsburgh, PA

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1121&id=1121

“Where’s the Evidence? Confronting Public Panic About COVID-19” by Laura Pickell, Department of Biology, Cégep Heritage College, Gatineau, QC, Canada

https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1120&id=1120

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Kristin Jenkins onto COVID-19/Public Health
@ 10:46 am on 01 Apr 2020

Teaching Effectively Online from CIRTL

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https://www.youtube.com/playlist?list=PLJSYKbO0r9fnAlJ68JhrFqpciFrxMYq4O link

The CIRTL Network is providing various trainings to assist in the sudden transition to online learning as campuses close to slow the spread of COVID-19. These trainings are offered both as synchronous online workshops and in recorded modules on YouTube.

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Kristin Jenkins onto Best Practices for Teaching Online
@ 3:03 pm on 30 Mar 2020

How UDL Can Support Your Transition to Online Teaching

https://docs.google.com/document/d/1IOTE04Mo4kl099Cm3EK6kK_LUfvNxHCeeZ7YQYhPHB0/edit link

Crowd-sourced table of online teaching practices that align to the UDL guidelines specific to the affective network

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Hayley Orndorf onto Accessibility, Inclusivity, and Universal Design
@ 10:25 am on 30 Mar 2020

Options for biocontainment

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Lisa Scheifele onto Biosafety and Biocontainment
@ 12:28 am on 28 Mar 2020

Synthetic Biology and Cancer

Use of synthetic biology approaches in cancer treatment.

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Lisa Scheifele onto Synthetic Biology and Therapeutics
@ 12:24 am on 28 Mar 2020

Review articles on using synthetic biology to produce therapeutics

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Lisa Scheifele onto Synthetic Biology and Therapeutics
@ 12:10 am on 28 Mar 2020

Artemisinin

Using synthetic biology to produce the antimalarial drug artemisinin.

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Lisa Scheifele onto Synthetic Biology and Therapeutics
@ 12:08 am on 28 Mar 2020

Synthetic Bacteria

Synthetic bacterial genomes as created by Craig Venter's research group.

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Lisa Scheifele onto Creating synthetic genomes
@ 11:51 pm on 27 Mar 2020

Synthetic Organisms Simplify Biology

Synthetic_Organisms_Simplify_Biology.pdf 301 KB

Review article from 2019

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Lisa Scheifele onto Creating synthetic genomes
@ 11:41 pm on 27 Mar 2020

A semi-synthetic organism that stores and retrieves increased genetic information

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A_semisynthetic_organism_that.PDF 2 MB

Creation of a semi-synthetic organism whose DNA harbours two additional letters that form a third, unnatural base pair.

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Lisa Scheifele onto Creating synthetic genomes
@ 11:39 pm on 27 Mar 2020

Genome-wide inactivation of Retroviruses

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Demonstration of inactivation of porcine endogenous retroviruses using CRISPR technology to enable porcine-to-human xenotransplantation of organs.

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Lisa Scheifele onto Creating synthetic genomes
@ 11:35 pm on 27 Mar 2020

Synthetic øX174

Uploaded image Definitive_demonstration_by_synthesis_of_genome_annotation_completeness.jpg

Creation of synthetic versions of viral and bacteriophage genomes to understand principles of genome organization and design

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Lisa Scheifele onto Creating synthetic genomes
@ 11:31 pm on 27 Mar 2020

Engineering bacteria for diagnostic and therapeutic applications

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Engineering_bacteria_for_diagn.PDF 774 KB

A review article on designing bacteria for diagnostics and therapeutics

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Lisa Scheifele onto Creating synthetic genomes
@ 11:28 pm on 27 Mar 2020

Total synthesis of Escherichia coli with a recoded genome

Uploaded image 41586_2019_1192_Fig1_HTML.png

A synthetic E. coli genome that has been designed to use only 61 of the 64 available codons. Includes webinar from Genewiz on design and assembly of the genome.

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Lisa Scheifele onto Creating synthetic genomes
@ 11:25 pm on 27 Mar 2020

Technological challenges and milestones for writing genomes

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Technological_challenges_for_writing_genomes.pdf 208 KB

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Lisa Scheifele onto Creating synthetic genomes
@ 11:01 pm on 27 Mar 2020

Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

Synthetic_Generation_of_Influenza_Vaccine_Viruses_for_Rapid_Response_to_Pandemics.pdf 453 KB

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Lisa Scheifele onto Creating synthetic genomes
@ 10:59 pm on 27 Mar 2020

Synthetic Reconstruction of Zoonotic and Early Human Severe Acute Respiratory Syndrome Coronavirus Isolates That Produce Fatal Disease in Aged Mice

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Synthetic_Reconstruction_of_Zoonotic_and_Early_Human_Severe_Acute_Respiratory_Syndrome_Coronavirus_Isolates_That_Produce_Fatal_Disease_in_Aged_Mice.pdf 1 MB

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Lisa Scheifele onto Coronavirus
@ 10:35 pm on 27 Mar 2020

Standard and AEGIS nicking molecular beacons detect amplicons fromthe Middle East respiratory syndrome coronavirus

Standard_and_AEGIS_nicking_molecular_beacons_detect_amplicons_from_the_Middle_East_respiratory_syndrome_coronavirus.pdf 2 MB

Use of synthetic biology to improve the signal-to-noise ratio in coronavirus diagnostics

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Lisa Scheifele onto Coronavirus
@ 10:31 pm on 27 Mar 2020

Should scientists infect healthy people with the coronavirus to test vaccines?

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Should_scientists_infect_healthy_people_with_the_coronavirus_to_test_vaccines.pdf 960 KB

Perspectives article discussing important ethical dilemmas in developing coronavirus vaccines.

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Lisa Scheifele onto Coronavirus
@ 10:26 pm on 27 Mar 2020

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Rapid_reconstruction_of_SARS-CoV-2_using_a_synthetic_genomics_platform.pdf 3 MB

Use of synthetic genomics to clone and synthesize the Covid-19 genome. Preprint from Biorxiv.

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Lisa Scheifele onto Coronavirus
@ 10:15 pm on 27 Mar 2020

Race to find COVID-19 treatments accelerates

Race_to_find_COVID-19_treatments_accelerates.pdf 1 MB

Review article on different potential treatment strategies and where in the viral life cycle intervention is possible.

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Lisa Scheifele onto Coronavirus
@ 10:10 pm on 27 Mar 2020

Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium

Mechanisms_of_Zoonotic_Severe_Acute_Respiratory_Syndrome_Coronavirus_Host_Range_Expansion_in_Human_Airway_Epithelium.pdf 967 KB

Using synthetic biology, the authors engineered the spike protein (S) from an animal strain and used in vitro evolution to understand how it could adapt to replicate well in human cells.

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Lisa Scheifele onto Coronavirus
@ 10:06 pm on 27 Mar 2020

Galaxy Training Materials

Events with Galaxy-related content (includes virtual events)

Assignment for Coronavirus dianostic kit design

In-classroom activity for genome alignment of different strains of viruses in the Coronaviridae family

Cases from the National Center for Case Study Teaching in Science

Teaching Effectively Online from CIRTL

How UDL Can Support Your Transition to Online Teaching

Options for biocontainment

Synthetic Biology and Cancer

Review articles on using synthetic biology to produce therapeutics

Artemisinin

Synthetic Bacteria

Synthetic Organisms Simplify Biology

A semi-synthetic organism that stores and retrieves increased genetic information

Genome-wide inactivation of Retroviruses

Synthetic øX174

Engineering bacteria for diagnostic and therapeutic applications

Total synthesis of Escherichia coli with a recoded genome

Technological challenges and milestones for writing genomes

Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

Synthetic Reconstruction of Zoonotic and Early Human Severe Acute Respiratory Syndrome Coronavirus Isolates That Produce Fatal Disease in Aged Mice

Standard and AEGIS nicking molecular beacons detect amplicons fromthe Middle East respiratory syndrome coronavirus

Should scientists infect healthy people with the coronavirus to test vaccines?

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Race to find COVID-19 treatments accelerates

Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium

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