resbazaz/weekly_projects

Suggest projects to work on at the weekly ResBazAZ Hacky Hour and Coffee & Code meetings

weekly_projects's Issues

Data visualization (various)

• Literate Visualization: Theory, software and examples
  
• Processing

Capturing and processing system activity information using `sar`

Open source, self-hosted replacement for Zoom

Why?

• Zoom iOS App Sends Data to Facebook Even if You Don’t Have a Facebook Account
• Working From Home? Zoom Tells Your Boss If You're Not Paying Attention

Why not?

• 🤷‍♂
• 😅

How?

Jitsi? It's rated highly.

• https://jitsi.org/jitsi-meet/
• https://jitsi.org/news/new-tutorial-installing-jitsi-meet-on-your-own-linux-server/
• https://github.com/jitsi/jitsi-meet/blob/master/doc/quick-install.md

Or just use https://meet.jit.si/

Profiling Python applications using PyCharm

myAPI - matching wishes and requests in a general way

(code is not actually in this repo - should I link it here?)

Scraping and processing data from websites using Python & Beautiful Soup

Use the `drive` command line tool to back up files to Google Drive

drive is a tiny program to pull or push Google Drive files.

drive was originally developed by Burcu Dogan while working on the Google Drive team. Since she is very busy and no longer able to maintain it, I took over drive on Thursday, 1st January 2015. This repository contains the latest version of the code.

See https://github.com/odeke-em/drive

link OSF to Rstudio

I'm having an issue with keyring function. When I set the key by using this code: key_set("osf"), it works fine. However, when I try to get the key key_get("osf"), I get the following error message

Error in b_macos_get(self, private, service, username, keyring) :
keyring error (macOS Keychain), cannot get password: An internal error has occurred.

I'm not sure how to solve this issue.

Provisioning launched Atmosphere instances using Ansible

Script to do checksum comparisons between Remote and Local

I'd like to have a script that would allow me to connect to a remote server and compare checksums of files in a remote directory and a certain local directory. My hope is that this would be most useful for confirming that all files have been properly transferred.

Webhooks/events/notifications in HPC PBS scripts

POCs

• 1. Example simple bash script/PBS script which does a callback via curl to a URL. This URL could be Slack, Zapier, IFTTT, etc.
• 2.a. Example of using file watching (entr) to check for a new PBS script in a directory and then submitting it
• 2.b. Example of using file watching (entr) to check for some pattern in a file and then triggering a web hook
• 3. Example of using Python do to some of this instead of using bash
• 4. Example of using psutil in the background to watch resource usage over time and post to Plotly/Google Sheets, etc.

Co-Citation networks and graph databases

Using `archivemount` to mount tar(.gz) files

archivemount is a FUSE-based file system for Unix variants, including Linux. Its purpose is to mount archives (e.g. tar, tar.gz, etc.) to a mount point where it can be read from or written to as with any other file system. This makes accessing the contents of the archive, which may be compressed, transparent to other programs, without decompressing them.

See https://en.wikipedia.org/wiki/Archivemount

This is especially useful in situations where you have many small files.

Advisor Watcher

Need to talk to your advisor? But they are hard to track down?

Use a strategically placed Raspberry Pi and a web camera with motion detection software to alert you when their door opens.

Continuous Integration On Github

I would like to learn continuous integration on GitHub.

Atmosphere GUI Containers

Buzzwords: containers, Docker, Singularity, dependency hell

Problem: Images are limited to having 10 GB installs. Generally this isn't a problem, but with tools that require databases to run (e.g. Trinotate https://trinotate.github.io/) it can be a problem. Also, updating images and then re-imaging can be problematic for myriad reasons.

Background: Atmosphere has several images with Docker installed (https://atmo.cyverse.org/application/images/1457). There are many Docker containers that have been created for bioinformatics research with single tools installed in them (e.g. biocontainers https://github.com/BioContainers/containers).

Proposed idea: Leverage boot scripts on images with docker installed to automatically bring in a container with a tool. Then all someone has to do is update the underlying image and point at the container boot script with the analysis tool of interest.

Potential pitfalls:

1. Boot scripts cause the image to take forever to finish (user perception issue).

Python stream processors and functional programming for DNA analysis

Benefits:

• Easier to verify the correctness of your code
• Straightforward path to speeding up your processing workflow by parallelizing on multiple CPU cores and/or computers

Use Google Drive as storage for `git-annex` and `git-lfs`

Might be possible to use this: https://github.com/odeke-em/drive

Build text-based Xiangqi game in Python

MATLAB neural network code

Using the GUI in MATLAB R2018b, I developed a time series neural network (NARX) and generated a function (weights, parameters, etc.) based on the model results. The next step is to test the model performance on new data but that step can only be done from the command line. I checked the MATLAB help forum and someone asked the same question at https://www.mathworks.com/matlabcentral/answers/309156-how-can-i-use-neural-network-function-generated-by-matlab-i-use-r2015a?s_tid=answers_rc1-3_p3_MLT but my MATLAB coding background is too limited to make use of the reply. Can someone help me with the code needed to apply my model to new data?

Interesting links for reproducible research

• https://github.com/everware/everware

Run Matlab programs as part of command line workflows