sample annotation

relates to discussion with Sebastian and phenotypic data

• data integration interfaces should have an accent
• might involve search interfaces across archives
  • NITRC could be an end-user of search endpoint to discover data

Satra brought up a good concern on why animal beh data could be desired to be restricted - due to ethical concerns like a recent case with primate lab/germany video recordings

https://grants.nih.gov/grants/guide/rfa-files/RFA-MH-22-240.html

Fixup wording

Buggy markdown

Casing

Casing

A

Casing of new sentences in this section

Leads to code on GitHub - I can't submit data there

Leads to code folder not documentation

Broken link.

Hm.. I was told to contribute data there, not clear why some other than precisely mentioned application, please clarify

Here or in that document, point to examples of such applications

might benefit from clarification, like "make your data available for use by pipelines of other researchers", since contribute usually means to share

404s. Forgot .md?

One direction but circular? Not clear

It is a very simplistic example. Would be nice if followed by a reference to some real life useful ones

Uses?

In this list also inconsistent trailing .

Inconsistent trailing .

Asked me to sign in... Even though disconnects from the source, could it point to an included copy?

Mention that it is in JavaScript

Not clear why root access is required. Does coinstac require root to run, why? What if it is a shared system where I have no root, could be used? Alternative ways to install?

Overview of conda principles by presenting some common misconceptions behind it

Thorough review of available (cloud, VM, live) image building tools for Debian. Additional ones (e.g. packer, openstack-debian-images, diskimage-builder) are mentioned in the follow up emails

TACC Scientific Apps -- Docker containers to be used on HPC

FOSS service binding together Jupyter and Kubernetes (to manage docker images) to provide executable Jupyter notebooks.

Collection of pipeline toolkits

A platform to facilitate collection of provenance information about ran analyses. Somewhat similar in idea to https://pythonhosted.org/Sumatra/

Collection of a docker images for bioinformatics. Large part of them (with debian/ prefix) are autogenerated using packages from Debian-Med (NeuroDebian contributes some there) in an image-per-package style

A review (wiki) by CWL project of approaches for "userspace containers" to solve the use case of running pipelines established using more recent (primarily) debian environments on HPC installations. Mentions projects such as proot, fakechroot, psuedo

A system for automating deployment, operations, and scaling of containerized applications originating from Google. It handles scheduling onto nodes in a compute cluster and actively manages workloads to ensure that their state matches the users declared intentions. Although with a primary accent on web services, I think it (or its ideas) could be of good use for managing collections of the execution environments. There is a nice FLOSS weekly podcast https://twit.tv/shows/floss-weekly/episodes/351 which introduces the platform and its abilities.

An umbrella website as a part of the Moore/Sloan Data Science Environment. New York University, the University of California, Berkeley and the University of Washington , pointing to useful resources @NYU/UW/BIDS(Berkeley) and providing news feed with relevant

Approach similar to CDE (http://www.pgbovine.net/cde.html) for wrapping entirety of the execution environment into a redistributable and possibly reusable (? might not grab all dependencies which weren't excercised in particular analysis) bundle

Framework for unified containers construction

Now dominant container management solution