Build A Genome Network: Collections

Miami (OH) University: Synthetic Biology: design principles and applications in medicine and industry

MBI450.pdf 540 KB

A lecture-only synthetic biology course

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Lisa Scheifele onto Syllabi
@ 12:25 pm on 05 Aug 2023

Lab results

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 7:19 pm on 13 Oct 2020

Build-a-Genome Session 3

Network_Biology_BUGGS_Soma_Class3.pptx 28 MB
Build-a-Genome_Session_392.mp4 204 MB
Build-a-Genome_Class_5_Oct_92020_190.pptx 4 MB

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 9:22 pm on 11 Oct 2020

BUGSS Build-a-Genome Membership Application

Build-a-Genome_Membership_Application.docx 135 KB

This application is for attendees of the 2020 Build-a-Genome course who want a 6-month BUGSS membership to keep working on the project!

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 8:38 pm on 09 Oct 2020

Build-a-Genome Session 2

Build-a-Genome_Class_3_Oct_22020_1.pptx 6 MB
Build-a-Genome_session_2.mp4 156 MB
Network_Biology_BUGGS_Soma_Class2.pptx 3 MB

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 8:41 pm on 04 Oct 2020

Course outline

BUGSS_2020_Build-a-Genome_course.docx 15 KB

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 8:24 pm on 04 Oct 2020

Lab Sessions

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 11:35 pm on 27 Sep 2020

Build-a-Genome Session 1

Introduction_to_Synthetic_Biology.pptx 11 MB
Build-a-Genome_2020_Session_1.mp4 327 MB
Network_Biology_BUGGS_Soma_Class1.pptx 23 MB

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Lisa Scheifele onto BAG at BUGSS lab 2020
@ 11:35 pm on 27 Sep 2020

Intro to Synthetic Biology

Pierce_SynthBio_syllabus_spring2019.pdf 151 KB

This course is for first year students and is intended to teach them how to think like a scientist and get them excited about biology. By no means is it a comprehensive Synthetic Biology course; rather, students explore basic molecular biology in the first third of the course, work through actual synthetic biology research in the second third, and apply their knowledge of this field to ethical issues in the last third.

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Dan Pierce onto Syllabi
@ 4:30 pm on 11 Aug 2020

Conservation Biology and Ethics in Synthetic Biology

This contains teaching material - powerpoints and handouts that can be adapted for lectures and/or discussion groups.

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Fran Sandmeier onto Ethics in synthetic biology
@ 4:32 pm on 30 Jul 2020

Conservation Biology and Ethics in Synthetic Biology

https://qubeshub.org/publications/2026/1 external link

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Fran Sandmeier onto Ethics in synthetic biology
@ 4:24 pm on 30 Jul 2020

Colorado State University - Pueblo Population Genetics

350_Syllabus_fs_Fall_2019.docx 25 KB

An ethics case study is included in the course material.

Ethics in Synthetic Biology

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Fran Sandmeier onto Syllabi
@ 3:00 pm on 30 Jul 2020

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Genome_Res.-2016-Shen-36-49.pdf 913 KB

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Lisa Scheifele onto The Scramble System
@ 10:19 pm on 28 Jul 2020

SCRaMbLEing of a Synthetic Yeast Chromosome with Clustered Essential Genes Reveals Synthetic Lethal Interactions

acssynbio.0c00059.pdf 2 MB

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Lisa Scheifele onto The Scramble System
@ 10:16 pm on 28 Jul 2020

SCRaMbLE generates evolved yeasts with increased alkali tolerance

Ma.pdf 5 MB

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Lisa Scheifele onto The Scramble System
@ 10:11 pm on 28 Jul 2020

Nature Communications 2018 Yeast 2.0 Collection

https://www.nature.com/collections/dhppvlvxxb/content/scramble external link

A collection of 9 papers all describing improvements and applications of the Scramble system

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Lisa Scheifele onto The Scramble System
@ 9:53 pm on 28 Jul 2020

Genomic epidemiology of novel coronavirus

https://nextstrain.org/ncov external link

A phylogeny shows evolutionary relationships of hCoV-19 (or SARS-CoV-2) viruses from the ongoing novel coronavirus COVID-19 pandemic

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Lisa Scheifele onto Coronavirus
@ 3:07 pm on 05 Apr 2020

How coronavirus tests work

How_Coronavirus_Tests_Work_I_NOVA_I_PBS.mp4 44 MB

Video from Nova on how the tests work.

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Lisa Scheifele onto Coronavirus
@ 3:27 pm on 04 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 external link
https://www.ncbi.nlm.nih.gov/tools/primer-blast/ external 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 external 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