SmartPlanet: Open Source Tree of Life

SmartPlanet

smartplanet logoQ&A: Tiffani Williams, computer scientist, on creating an open source tree of life

By | July 29, 2013

Tiffani Williams
Tiffani Williams

The Open Tree of Life project culls years’ worth of segmented scientific research in an effort to create a current, open source version of our knowledge on thousands of plant and animal species. Tiffani Williams, a computer scientist at Texas A&M University who is working on the project, said the Open Tree of Life will eventually be a Wikipedia-like living document for scientists and the community to edit and use for research.

I spoke recently with Williams about the segmented nature of the tree of life, the challenges of the project and how an open tree of life could impact science in schools. Below are excerpts from our interview.

What is the tree of life and why should people care about it?

One way I explain the tree of life is to think about it from the human perspective. A lot of us are interested in understanding our family tree. We want to know about our grandparents and great-great grandparents and down the line. Part of that is this whole notion of where we fit in the world. Who are we? That’s certainly one aspect of a family tree. But there’s another aspect too. For example, when you go to the doctor, they’ll ask you about your family history. High blood pressure and heart disease [in your family] can be signs that you might be impacted, as well. We as human beings have this notion of appreciating our family history. All the tree of life does is take that to another level. Instead of thinking of a family in terms of your human ancestors, the tree of life is the world’s ancestry, which includes all of the world’s organisms. It’s still thought of as a family tree, but the context is a lot more broad.

Continue reading “SmartPlanet: Open Source Tree of Life”

Jean Lievens: Commons Framework

Architecture
Jean Lievens
Jean Lievens

Our future depends on our commons and each of us as commoners. We all have a mutual responsibility to name, claim, protect and equitably manage what belongs to all of us for today and future generations. Here we will discuss the framework underlying that system in greater detail so you can learn how to understand and animate the commons in your own field or community.

Commons Framework

 

Robin Good: Argument Curation and Critical Thinking Skilss

Knowledge
Robin Good
Robin Good

Ashley Hutchinson has an excellent article on the NWP site, illustrating how content curation can be effectively used to move students from passively memorizing information that they have no interest into, to become active investigators of a topic to uncover its different facets and critical evaluators of the same in light of their own values. 

Her key goal was to find a way to make “research” something fun to do for her students. 

I wanted students to be able to funnel their interests into a more authentic academic experience so that they could learn about what they want to learn about and become empowered as researchers, both casually and formally. 

To do that, I needed to remix their idea of what research is, transform it from something boring and arbitrary into something rich and useful.

When I don't know something, I look it up…  So I called this an “argument curation” project, and not just to sound fancy; they were actually identifying arguments and curating resources that helped inform those arguments.” 

The beauty of this approach is that students need to check and research the different aspects of a story, to see it through and to develop their own viewpoint relative to it.  And here is the a good example of how this can be achieved: 

Continue reading “Robin Good: Argument Curation and Critical Thinking Skilss”

Stephen E. Arnold: Metadata for Documents

Advanced Cyber/IO, Data
Stephen E. Arnold
Stephen E. Arnold

Metadata for Documents

Posted: 19 Jul 2013 06:37 PM PDT

We read numbers about the amount of time wasted on searching for documents all the time, and they are not pretty. When we stumbled upon Document Cloud, we could not help but wonder if this type of service will help with the productivity and efficiency issues that are currently all too common.

The homepage takes potential users through the steps of what using Document Cloud is like. First, users will have access to more information about their documents. Secondly, annotations and highlighting sections are functionalities that can be done with ease.

Finally, sharing work is possible:

Continue reading “Stephen E. Arnold: Metadata for Documents”

Richard Stallman: Challenge Ubuntu — For $32 Million Why NOT Open Source?

Software
Richard Stallman
Richard Stallman

Ubuntu is aiming to raise $32 million in crowdfunding to fund Ubuntu Edge, a mobile computer that can dual-boot between Android and Ubuntu GNU/Linux.

Will Ubuntu Edge commit to using only free software? If the project succeeds and has $32 million available to spend, this is surely possible, but there is no indication in any of the promotional materials that this is part of the plan.

Isn't Android already free software? In theory, yes, but in practice, no. To work on actual hardware, Android ends up relying on device drivers that are either outright proprietary or use proprietary firmware blobs. All commonly available Android devices also come with proprietary software applications installed.

This is why today we announced a fundraising partnership with the Replicant project, which produces a version of Android that runs on existing devices without proprietary system software.

Isn't Ubuntu already always committed to free software? No. Ubuntu's default GNU/Linux distribution includes nonfree drivers, and its software marketplace promotes proprietary programs.

But, we don't want to make assumptions about what Ubuntu Edge will or won't be. We and many other free software supporters excited about the possibility of a GNU/Linux mobile device would like to hear official confirmation:

  1. Will the Ubuntu Edge versions of both Android and Ubuntu contain or rely on any proprietary software or proprietary firmware?
  2. Will the Ubuntu Edge include any Digital Restrictions Management (DRM) software?
  3. Will the device's bootloader be free software?
  4. Will the device have Restricted Boot, or will users be able to replace the operating system with a free one of their choice?
  5. Will Ubuntu Edge include F-Droid, the free software Android application repository, as part of a commitment to promote and recommend only free software?

Ubuntu in the past has said they are forced to make temporary compromises in software freedom in order to have their operating system work on the computers people own and speed adoption of free software. But in this case, Ubuntu would have the chance to dictate the design of the hardware themselves. Software freedom should be the foundation of that design. There is no reason for compromise.

Conveniently, Canonical founder Mark Shuttleworth is doing an AMA on Reddit starting at 12:30 EDT, so maybe we will get some answers.

Robin Good: EdShelf for Best Educational Apps

Education
Robin Good
Robin Good

EdShelf is a free web service which allows you to curate, review, rate and organize your favorite educational apps as well as to find and discover the ideal ones for your kids or for the next class you need to teach. Ed apps can be organized into collections which can be further filtered thanks to tags and categories. You can search for tools as well as browse curated categories, most recent additions and popular ones. To keep the quality of new apps included in EdShelf and to protect itself from spam, while you can add at any time a new app and add it to your collections, for any new app added the EdShelf curation team will then review it for inclusion in the general EdShelf database and if accepted, it will add more detailed info to it including video clips, and other relevant info. Here's the official rundown: “edshelf is a directory of tools for education. You can search and filter for specific tools, rate and review tools you've used, access your tools with a single sign-on, receive recommended and featured tools, create collections of tools, and share your collections with friends and colleagues.” My comment: Crowdsourced curation focusing on a very fast-growing and much in-demand niche: educational apps and tools. Simple to use. Excellent tool for finding relevant apps for different educational uses. Intercepts a specific need. Promising. Free to use. More info: https://edshelf.com/ FAQ: https://edshelf.com/faq Reviews: https://edshelf.com/press *Added to Curation for Education section of Content Curation Tools Supermap

Patrick Meier: Crowd-Sourcing CPR — There’s an App for That + Next Step Is Local to Global Range of Gifts Table

Crowd-Sourcing, Governance, Innovation, Mobile, P2P / Panarchy, Resilience
Patrick Meier
Patrick Meier

Crowdsourcing Life-Saving Assistance

Disaster responders cannot be everywhere at the same time, but the crowd is always there. The same is true for health care professionals such as critical care paramedics who work with an ambulance service. Paramedics cannot be posted everywhere. Can crowdsourcing help? This was the question posed to me by my colleague Mark who overseas the ambulance personnel for a major city.

. . . . . . .

Click on Image to Enlarge
Click on Image to Enlarge

So why not develop a dedicated smartphone app to alert bystanders when someone nearby is suffering from a Sudden Cardiac Arrest? This is what Mark was getting at when we started this conversation back in April. Well it just so happens that such an app does exist. The PulsePoint mobile app “alerts CPR-trained bystanders to someone nearby having a sudden cardiac arrest that may require CPR. The app is activated by the local public safety communications center simultaneous with the dispatch of local fire and EMS resources” (4).

Read full post.

Continue reading “Patrick Meier: Crowd-Sourcing CPR — There's an App for That + Next Step Is Local to Global Range of Gifts Table”