Hi Heidi,
Thanks for sharing and starting this thread.
I actually created a new topic in my Open Source Software Development
class last spring that went really well and students had a lot of
positive feedback about it. I titled it "Open Efforts regarding COVID 19".
It happened about a month after we went remote and in the midst of NYC
outbreak. The assignment was very open and intentionally not specific:
- research open efforts in the area of COVID-19 pandemic
- add links to the resources you find to the wiki page in the course
organization
- be ready to discuss your findings in class on Monday, Apr. 13
I explained that they are not limited to software projects but they
should look for anything that is open in nature.
The collection of links that students created is attached.
During the next class and a half we went over the list and students
spent about 2-3 minutes talking about the project/effort that they
found. Some of these generated further discussion. We kept notes in a
shared etherpad, but unfortunately, I let it expire before I got the
copy of the notes ;(
Then we spent some time talking about categories of these efforts:
hardware vs. data vs. software, large organizations vs. small or
individuals, existing projects working on a new cause vs. brand new
efforts that started to deal with a new situation, projects that are
specific to the locality vs. more generally applicable ones (at that
point the students were dispersed all over the world), etc.
There were also some critical comments about why there are so many
efforts for data visualization and what the value is that they bring to
the table, or about safety of an open sourced "make your own test at
home" instructions.
Students were very impressed seeing the range of efforts they found and
seeing how open source projects can quickly spring up to respond to a
crisis. I think for a lot of the students who had sick family members
and who were displaced due to the outbreak in NYC this was a way to see
relevance of what they were part of to what was going on. None of my
students ended up working on COVID-19 related projects during the class
(for several reasons), but I think this was a valuable lesson and
definitely the most active class discussion that we had in the course of
the entire semester.
Here are a few blog posts from that week with comments on the discussion:
https://nyu-ossd-s20.github.io/Jen-Lopez-weekly/week11/
https://nyu-ossd-s20.github.io/mattfan00-weekly/week11/
https://nyu-ossd-s20.github.io/niniack-weekly/week-12/
https://nyu-ossd-s20.github.io/hkajs-weekly/week11/
https://nyu-ossd-s20.github.io/pmets-weekly/week11/
https://nyu-ossd-s20.github.io/evading1998-weekly/week12/
---
In the fall, I am back to teaching my Data Structure class. I usually
use an open data set for the coding projects. This year it will most
likely be COVID-19 related, but I do not have any specific one yet.
Hope everybody is staying safe!
Best,
Joanna
----------------------------------------------------
Joanna Klukowska, PhD
Clinical Assistant Professor
Department of Computer Science
Courant Institute of Mathematical Sciences, NYU
Warren Weaver Hall, Room 423
joann...@cs.nyu.edu
http://cs.nyu.edu/~joannakl/
Office hours (Spring 2020):
Monday 12:30-2:30pm, Thursday 11:00am-12:00pm
----------------------------------------------------
On 7/12/20 3:13 PM, Heidi Ellis wrote:
Hi Folks,
I have been thinking about my fall classes and HFOSS and thought I'd
share my thoughts. As the summer progresses, I’m finding a new rhythm
to preparing my fall classes. It is clear that even though my
institution is hoping to hold the majority of classes in person, I
need to be able to take all of my classes online at any moment. And
yes, the does mean that class preparation is at least doubled.
I have been focusing on my Software Engineering course which is a
fairly standard coverage of Requirements, Design, Test, etc. In my
case, I am setting students up for their Capstone class which meets in
the spring term. In Capstone, students will be contributing to the
Bear Necessities Market
<https://librefoodpantry.org/#/projects/BEAR-Necessities-Market/>
which is an HFOSS application to support the food pantry located on
Western New England University’s campus. BNM is one of several food
pantry applications being developed by instructors within the Libre
Food Pantry <https://librefoodpantry.org/#/education/> community. In
my Software Engineering course, we use BNM to investigate real-world
requirements, design, test and more. We also learn the environment of
a real HFOSS project so that students are able to make code
contribution in the Capstone course.
As I’ve been thinking about how to best support learning, I realized
that, due to COVID-19, the BNM will Likely need to implement some form
of a visit schedule in order to support social distancing as our
pantry has very limited space. I can see lots of ways that I can bring
this into my classroom and I’m excited at the possibilities the
provides for students to solve problems that are of critical
immediacy! What are you all doing? Please share your ideas!
Heidi
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1. Inventor open sources ventilator design - [link](https://www.cbc.ca/news/canada/london/pandemic-ventilator-design-covid19-1.5511412)
2. Next Strain: uses public pathogen genome data to track the evolution of COVID-19 and other pathogens in real time - [link](https://nextstrain.org/)
3. World Health Organization app for helping people cope with and mitigate the spread of COVID-19 - [link](https://github.com/WorldHealthOrganization/app)
4. Website answering any questions about coronavirus by drawing upon trusted resources - [website](https://covid.deepset.ai/home) and [repo](https://github.com/deepset-ai/COVID-QA)
5. An consolidation of open source resources for fighting covid-19 on Github -
[link](https://github.blog/2020-03-23-open-collaboration-on-covid-19/)
5. [COVID-19 Open-Source Helpdesk](https://discourse.covid-oss-help.org/): a place for those fighting the COVID-19 pandemic to get help from the open-source scientific computing community.
6. [2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE](https://github.com/CSSEGISandData/COVID-19) - Repository that contains data about COVID 19 in the world.
7. [US infected and testing data](https://covidtracking.com/data) - Data of US testing and infection rate
8. [Opentrons](https://opentrons.com/) - Opentron has an open source lab automation platform. Their product can automate up to 2400 tests per day. [Link to repository](https://github.com/Opentrons/opentrons)
9. [Chai Open qPCR](https://www.chaibio.com/openqpcr) - Rapid testing of swabs from surfaces to see if covid virus is there. [Link to repository](https://github.com/chaibio/chaipcr)
10. [NYS Statewide COVID-19 Testing Data](https://health.data.ny.gov/Health/New-York-State-Statewide-COVID-19-Testing/xdss-u53e) - Data of NYS testing since the first confirmed case in NY (March 1st). The dataset is updated daily and is provided by the New York State Department of Health.
11. [Predict COVID-19](https://predictcovid.com/) - An interactive tool to compare the number of COVID-19 cases between different countries to understand how the epidemic might progress in the coming days.
12. [OHIF viewer](https://github.com/OHIF/Viewers) - web-based, medical imaging viewer.
13. [Open PCR](https://openpcr.org/) - DIY PCR kit to test whether someone has COVID-19
14. [Safepaths](http://safepaths.mit.edu/) An open-source app that uses location data to let you know if you have crossed paths with an individual later diagnosed as positive
15. [Folding@Home](//foldingathome.org/start-folding/) - Donate your computing power for protein folding simulation
16. [FoldIt](//fold.it/) - An online puzzle game where you need to design proteins that could cure COVID (or other diseases)
17. [The COVID Tracking Project](https://covidtracking.com/) - The COVID Tracking Project collects and publishes the most complete testing data available for US states and territories.
18. [Real-time COVID-19 visualization](https://github.com/localeai/covid19-live-visualization) - Maps that track the number of cases help us visualize the relative scale and spread of COVID-19.
19. [CoronaTab](https://github.com/PotentialWeb/CoronaTab) - Free & open source platform for COVID-19 data. It's a rest API and encourages contributions such as adding data to their json file.
20. [Awesome Coronavirus](https://github.com/soroushchehresa/awesome-coronavirus) - An open source resource list of other projects related to the coronavirus. Includes datasets/API/maps/other general projects related to the virus.
21. [CHIME](https://github.com/CodeForPhilly/chime/) - An Application that lets hospitals and public health officials understand hospital capacity needs in relation to COVID-19.
22. [Pocket PCR](http://gaudi.ch/PocketPCR/) - A device that can be used to activate biological reactions. The device could be used to facilitate environmental testing of COVID-19
23. [COVID-19-API](https://ainize.ai/laeyoung/wuhan-coronavirus-api) - An API to automatically retrieve the latest as well some of the old COVID19 data.
24. [OpenCoronavirus](https://github.com/open-coronavirus/open-coronavirus) - A digital solution for monitoring, diagnosing and containing SARS-CoV-2 infection that allows quarantine measures to be applied in a controlled manner at focal points or hotspots, thus minimizing the general quarantine of the population, reducing the overload of health systems, and at the same time facilitating the progressive resumption of daily activity in the shortest possible time.
25. [nCoV2019 dataset](https://github.com/beoutbreakprepared/nCoV2019) - An open dataset created by an institute at the University of Washington. It contains various types of data based on individual patients, such as symptom onset time, to help calculate different important metrics and trends.
26. [covidNet](https://github.com/lindawangg/COVID-Net) - An open source initiative to use AI models to detect Covid-19 automatically from CT scans. Based on [this study](https://arxiv.org/pdf/2003.09871v2.pdf).
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