September 23, 2016

Learning by Doing, Where Doing is Earning Badges

As a member of the OpenWorm Foundation community committee (see previous post), we have been trying to find a means of engaging potential contributors within the context of the various projects. One type of activity is the Badge, a bite-sized [1] learning opportunity that we plan to use as both certifications of competency and concrete goals for the various projects. The OpenWorm Badge System is being spearheaded by Chee-Wai Lee, and is an emerging method in Educational Technology [2]. More details about this will be shared to the community by Chee-Wai in the form of a tutorial at the upcoming OpenWorm Open House.

An example of how semantic data on phenotypes can be extracted from the scientific literature. PICTURE:, BLOGPOST: Phenoscape blog

Each badge is designed to impart a specific skill. The OpenWorm badge system currently covers scientific topics (Muscle Model Builder, Hodgkin-Huxley) and research skills (Literature Mining). My contribution is the Literature Mining (LM) series. Literature mining is a technique used to organize the scientific literature, extract useful metadata (e.g. semantic data) from these sources, and identify secondary datasets for re-analysis [3]. Learning skills in Literature Mining will be useful to a wide range of badge earners, particularly those interested in Bioinformatics and Open Science research. These are skills used extensively in the DevoWorm project, and we will be planning more badges on related topical areas in the future.

The first LM badge is focused on working with the scientific literature, while the second (LMII) badge introduces learners to open-access secondary datasets. The only prerequisite is that you must earn Badge I in order to earn Badge II. Both of these badges recently went live, and you may start working on them immediately.

Example of the badge curriculum for LMI. The badgelist system requires learners to complete each step one at a time, and then request feedback (if applicable) from the Admin (e.g. instructor).

[1] why not "byte-sized", you say? Well, the Literature Mining badges are almost byte-sized (seven requirements apiece), so you could say that we are headed in that direction!

[2] Ferdig, R. and Pytash, K. (2014).  There's a badge for that. Tech and Learning, February 26.

[3] For examples of how Literature Mining can be useful, please see the Nature site for news on literature mining research.

September 6, 2016

Now Announcing the OpenWorm Open House

OpenWorm Browser. Courtesy Christian Grove, WormBase and Caltech.

About two years ago, I announced the start of the DevoWorm project to the OpenWorm community. Now both OpenWorm and DevoWorm have grown up a bit, with the former (OpenWorm) now being a Foundation and the latter (DevoWorm) resulting in multiple publications. Now we will be celebrating all of the projects that make up the OpenWorm Foundation in an Open House format, taking place in cyberspace and tentatively scheduled for October.

Image courtesy Matteo Farinella: These posters are the outcome of an OpenWorm Kickstarter campaign several years ago.

The details of the schedule are still being worked out, but the format is to include both short, 5-minute talks (Ignite-style) and longer tutorials (45-60 minutes, plus questions). The short talks will highlight the various ongoing projects within OpenWorm, while the tutorials will focus on specific methods or procedures employed by the projects. If you happen to be a project leader or major contributor, I have probably already asked you for content. Interested in either contributing content or attending? Please let me know

Dr. Stephen Larson (pre-PhD), discussing the connection between Lt. Data and C. elegans at Ignite San Diego.

I have also been involved in committee work for the OpenWorm foundation. One of the initiatives we are in the process of establishing is the OpenWorm badge system, which is being spearheaded by Dr. Chee-Wai Lee. Currently trendy in the online learning world, this is an experiment in open learning that provides micro-credentials to a global community. Badges are a great way to learn new skills, as well as a means to motivate people's contributions to different projects within OpenWorm. Currently, OpenWorm is offering tutorials on the Hodgkin-Huxley model, the Muscle Model builder, and the Muscle Model explorer. If there are any tutorials you would like to see us offer, or if you think there is a need for a particular skill to be highlighted, please let me know.