This the the first issue of our monthly newsletter! If you have any news you would like to share with the rest of the community, don't hesitate to let us know :)
 

This is our second issue of the monthly newsletter! If you have any news you would like to share with the rest of the community, don't hesitate to let us know :)

We hope that during these times you and your loved ones are safe and healthy!

Many of us are using new tools, approaches, and environments to continue engaging our students in high quality instruction while maintaining social distance.
Join us for a Q&A session with a panel of experienced online instructors to trouble-shoot issues and barriers you and your students are encountering and potential solutions and work-arounds.

This session of Online with LSE will feature a discussion with educators who have experience teaching online and working with faculty to transition to online instruction.

Panelists
Andrew Bouwma, Instructor in Biology at Oregon State University, experienced online course designer and instructor, including award-winning online lab instruction
Cynthia Brame, Associate Director of the Vanderbilt University Center for Teaching and Senior Lecturer in Biological Sciences, who has experience working with faculty to transition to online instruction
Jim Hewlett, Professor at Finger Lakes Community College and experienced online course designer and instructor
Erika Offerdahl, Associate Professor of Molecular Biosciences and experienced online course designer and instructor

"The Academic Data Science Alliance is working with partners to pull together data and data science resources related to the COVID-19 pandemic. This is a living list of resources and we welcome additions, suggestions, and collaborations. Please send additions, corrections, comments, and suggestions to us using this feedback form.

Please keep suggestions limited to research and data resources, avoiding opinion pieces and teaching resources. 

Note that the resources listed here are provided as-is. Use your professional judgement and best practices to vet these resources before you use them for research and scientific communications."

A PBS Newshour: Student Reporting Labs Interview 

"West Ranch High School student reporter Madi Marks interviews University of Pittsburgh professor and epidemiologist Dr. Wilbert Van Panhuis on how he's collecting data on the coronavirus and how to combat it for our #SRLAsks series."

Quick intro to epidemiology and modeling and a peek into career pathways in this area.

Min, A., Ashcroft, J., Monroy, J., Wolf, V., Lee, C., Horton, J., Ehrmann, R., Rodriguez, B. 2019

The Remotely Accessible Instruments in Nanotechnology (RAIN) Network is a conglomerate of nineteen community colleges, four-year universities and high school sites that aims to enhance STEM learning by bringing advanced technologies to K-12 education. RAIN provides free remote access to instruments such as Scanning Electron, Atomic Force and Transmission E ectron Microscopes, as well as Energy Dispersive and Infrared Spectroscopy.

Jared Ashcroft and William Miller

RAIN has been developing science labs that can be used in conjunction with remote access instruments to expose K-12 classes to modern experimentation that will help fulfill requirements of NGSS. Currently, RAIN has access to seven experiments that can utilize with remote access available on its website (www.nano4me.org/remoteaccess).

Ashcroft, J.M., Min, A., Bojanini, I., Hacopian, M., Schroeder, K., Cakmak, A.O., Rodriguez, B. 2018. Journal of Laboratory Chemical Education

In a series of activities/labs, designed in a building block approach, whereas each subsequent lab builds into the next, students will explore the reactivity and production of oxygen in various biological and chemical systems.  Use of remote access technology to a Scanning Electron Microscope (SEM) with elemental analysis capabilities allows students to investigate their oxygen reaction via formation of iron oxide.

With the emergence of online conferencing tools and the flexibility required for effectively working remotely, more and more meetings are being held online. Organizers generally have the goal that everyone who attends their meetings can fully participate and access information. Using a handful of strategies, this goal can be met.

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

Video from Nova on how the tests work.

• International Society for Computational Biology (ISCB)
• Online
• ISCB education pages

Our Vision is to see high quality computational biology education and training accessible to all interested communities across the world, and instilled in all life science-related educational programs.

Our Mission is to promote worldwide education and training in computational biology by providing guidance and support for educational resources and community activities.

The information contained within this section covers two general areas:

1. World-wide educational and training resources for all levels from novices to advanced practitioners of computational biology
   • Online Courses in Bioinformatics
2. Resources that enhance learning and preparation geared towards a career in computational biology
   • Articles on Bioinformatics Education

In addition to the content generated by ISCB Education, we also solicit and collect input and information from the larger computational biology community to be made available through these pages.

• The Jackson Laboratory
• The Jackson Laboratory, ME
• The Jackson Laboratory education and learning resources

The Genomic Education team at The Jackson Laboratory is committed to creating diverse and inclusive educational programs where all students, employees and visitors feel valued and are empowered to participate in our mission to improve human health though genomics research, scientific resources and education. We believe human diversity is an essential ingredient for empowering the global biomedical community, and therefore our programs should reflect, embrace and celebrate the diversity of our world ... JAX's programs for high school and undergraduate students and teachers predate the founding of the Jackson Laboratory by six years. Including our flagship Summer Student Program, JAX offers opportunities for academic year research, teacher professional development, and the Maine State Science Fair.

Courses are designed to impart knowledge through intensive lectures, hands-on training and informal interactions. Workshops offer extensive hands-on training, teaching participants how to perform specific techniques, interspersed with lectures or seminars.

• Global Organisation for Bioinformatics Learning, Education & Training
• Online
• GOBLET training portal

This portal allows you to browse our course pages and training materials, to download content of interest and/or to upload course pages and training materials.

NOTE: this page has not been updated for more than 4 months.

• Galaxy Training Network
• Online
• Galaxy Training web site

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:

• Introduction to Galaxy Analyses
• Assembly
• Computational Chemistry
• Ecology
• Epigenetics
• Genome Annotation
• Imaging
• Metabolomics
• Metagenomics
• Proteomics
• Sequence Analysis
• Statistics and Machine Learning
• Transcriptomics
• Variant Analysis
• Visualisation

Events with Galaxy-related content (includes virtual events)

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

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).

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.

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

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.

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

Use of synthetic biology approaches in cancer treatment.