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As someone who uses <a href="http://www.boffosocko.com">my own WordPress site</a> as a research notebook/tool and commonplace book (as well as for owning all of my own data and social posts), I'm <a href="http://boffosocko.com/2016/06/17/hypothes-is-and-the-indieweb/">already loving</a> this plugin and can see some tremendous potential for improvements on both it and on the hypothes.is platform in the future.

While I've played around with other platforms like Genius.com as well, Hypothes.is seems to have a more focused approach to how I prefer to use annotations, highlights, and marginalia on the web. It also has a growing API and related suite of tools which portend more flexibility and growth for the future.

Still, one must be cognizant for how these sometimes "hidden" tools can be used for abuse and bullying on the web: <a href="http://boffosocko.com/2016/04/07/webmentions-for-improving-annotation-and-preventing-bullying-on-the-web/">Webmentions for improving annotation and preventing bullying on the web</a>[http://boffosocko.com/2016/04/07/webmentions-for-improving-annotation-and-preventing-bullying-on-the-web/]

 

Replied to a post on hyp.is :

On the topic of extrapolating where some of this is going, there's also a pending UI issue amongst competing annotation platforms. They're going to need to watch where they put their overlays for annotating/highlighting or they aren't going to work together well. Not to mention other social media plugins that have similar popups for highlighting and sharing.
http://boffosocko.com/wp-content/uploads/2016/04/NewsGenius-vs-Hypothesis.png

 

I recall a few other resources in the same category as this. Here are a few links for meta-coverage on them, which may provide more beneficial than spending hours trying to delve into how to use them:
VidBolt: http://chronicle.com/blogs/profhacker/annotate-video-on-the-fly-a-review-of-vidbolt/56787
Socialbook: http://chronicle.com/blogs/profhacker/using-video-annotation-tools-to-teach-film-analysis/57171

Other tools of interest, which you'll see notes on in the comments to the two above articles:
VideoAnt: http://ant.umn.edu
ULBPodcast: https://github.com/ulbpodcast and http://ezcast.ulb.ac.be (open source code available)
Genius.com: http://boffosocko.com/2014/04/08/rap-genius/ Particularly take a look at http://lit.genius.com/ which is a great tool for classrooms to do small scale shared annotations and close reading with the benefit of full texts (in particular, try looking up the various creation stories, eg: Gilgamesh [http://genius.com/Epic-of-gilgamesh-tablet-1-the-coming-of-enkidu-annotated; Letters of Paul [http://genius.com/Laura-nasrallah-the-pauline-epistles-contents-annotated], which was part of HarvardX religious studies course and is an excellent example of using the platform for education]). There's also http://genius.com/history-genius.