OpenWetWare talk:Steering committee/NSF BDI Grant/Draft

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Contents

What's missing

  • References
  • A mention of the Berkeley SB class run on the site
  • How well does the proposed activity broaden the participation of underrepresented groups (e.g., gender, ethnicity, disability, geographic, etc.)? (in Broader Impacts)
  1. Do we have any users in far-flung places that we could show benefit from the digital community? i.e cost of conference travel from Alaska is expensive, but with OWW XXX can create collaborations accross the country much easier...
  2. Do we have any disabled users that we know of who find traditional communication methods a challenge, but find that a digital community allows them to participate fully? --Johncumbers 21:28, 2 July 2006 (EDT)

long term sustainability

Sri Kosuri 02:53, 24 June 2006 (EDT):Is there somewhere to put development of tools to help with long-term sustainability... ie., tools that make less work of administration... e.g., user management system

tables and figures

Please post possible tables and figures that make sense in this document.

  1. Syntheticbiology.org
    • picture of site, description of information on it, and dewikify.
  2. Table on Extensions we have made or incorporated
    • name, description, importance

Extensions

The custom extensions developed for OpenWetWare were suggested by and developed from within the community. As a result, each one meets a very specific request from researchers. We intend to preserve the direct link between community needs and software development, in order for new technologies to prove useful to community members. However, dedicated software developers will enable us to respond to many more user requests and to pursue some of our backlog of extension ideas.

Citation Manager An extension that allows simple citations and creation of bibliographies. One can link to PubMed or by ISBN number to a reference, and citations and links are automatically added to the document.
Show/Hide A simple extension allowing users to simply hide excess information, which viewers can expand if they choose to get more detail.
Automatic linking to published documents using DOI, or other biological databases such as the Registry for Standard Biological Parts.
Filtered Changes A common way to track current activity on the site is by looking at the Recent Changes of other users. However, as the site has grown, this has been a cumbersome way to track what is going on as we normally have several hundred edits a day. This extension developed by members allows you to filter those recent changes by laboratory, group, and other useful criteria.
SideBar Customization Allows individual users to customize their navigation bars to allow easier navigation with the larger site of OpenWetWare.
Wiki Import Allows importing of separate wikis into OpenWetWare to facilitate merging of disparate wikis. We have used this tool as other’s have used wiki software, but slowly move to OpenWetWare for its added features.
Dewikify A tool that allows automatic dewikification of wiki pages. This allows groups to use the site as a distributed content mangement system for websites. For example, http://openwetware.org is dynamically generated from http://openwetware.org/wiki/Synthetic_Biology. Many individual laboratories and groups use this feature as their public website from OWW.
User Management System A custom tool that allows simplified user request handling. In the past, administrators strictly relied on emails from new users that wanted an account. This system provided a means for automatic processing, and greatly increased our efficiency at handling the many users that apply for an account each day.

(Need to do a better job making the existing tools flow with the other stuff, also probably want a shorter list and to have it in paragraph form).

cut sections to be used elsewhere?

Case Study 2: Current Research Information

Generating new research ideas and improving existing ones often depends on communication with others scientists. This communication typically occurs at retreats and conferences where researchers have time to interact and talk informally. However, outside that arena, it is often difficult to assess the state of current research of a particular group or individual. Laboratory websites are often outdated or contain minimal information about the ongoing work of individual researchers. Conference posters and abstracts, research expertise, and basic contact information are often unavailable, even when there is no need to keep such information confidential.

One of the reasons could be that expertise in developing, maintaining, and updating laboratory websites requires technical expertise on someone’s part. Even when a laboratory has such support, often there is only one person that is responsible for updating this information. This barrier to putting information prevents individuals from posting information they would like to see public, but do not get the chance to. Individuals on OpenWetWare can post research talks, posters, papers, documents, protocols, etc., without having to go through a bottleneck. I just realized this overlapped with Jason, I’ll change it

Reusuability of teaching materials

MIT OpenCourseWare pioneered the mission of making institutional course materials freely available. That experiment has been a wildly popular success. Educators, students and independent learners from around the world use MIT OpenCourseWare materials. OpenWetWare takes the next logical step in this mission by making materials not only freely available but also freely reusable. Instead of providing static PDFs of handouts (which are designed to be difficult to copy), OpenWetWare provides the text and images itself. It goes further and gives others the tools to expand and adapt the content to their own educational needs. This is a key advantage of the wiki platform over existing online tools for the purpose of curriculum development. Since all OpenWetWare content including courses are dual-licensed under the widely accepted Creative Commons Attribution-Sharealike 2.5 license and the GNU Free Documentation License, anyone may freely reuse the material as long as they too permit reuse under the same license eliminating worry about copyright issues.

Hosting classes in turn enriches OpenWetWare.

OpenWetWare has tremendous advantages for classes, especially classes under development and lab classes. However, OpenWetWare itself also benefits from the presence of these courses on the site. First, the course content itself is a great addition to the site. Today, research funding and resources are increasingly focused on biological research. Scientists and engineers from other disciplines are entering biological research in droves. These folks face a steep learning curve when it comes to the lingo, experimental techniques and current state of research in biology. Having content from courses like 20.109 on OpenWetWare provides the kind of comprehensive background, explanation and detail that novices need but that is missing from many general protocol resources.

vandalism

A common concern many have with this approach is that the students might introduce errors or worse, intentionally delete information. In practice, there is little risk of this since (a) all students must login to edit the site and all edits to the site are tracked and (b) wiki software keeps detailed revision histories of every page allowing rapid reversion of incorrect page edits.

sections cut from community

Goal 2: OpenWetWare annotation pages CUT THIS

OpenWetWare could serve as a mechanism for community annotation and discussion of various sources of biological information that are currently accessible online. We would like to enable a simple mechanism for creating an OpenWetWare page about a particular existing web page or information source. For instance, when viewing a protein in PDB clicking on an “OWW-this” bookmark would open an OpenWetWare page that has much of the information about the protein entered dynamically and has created areas for the user to add annotations such as experimental results, etc. (need some help here – what are the other sort of pages that the “OWW-this” link would handle well?)

Also, as we incorporate more semantic web technologies we will build semantic links between disparate information sources, using OpenWetWare annotation pages as community-created bridges between sources. (are we talking about semantic web?)

Goal 3: Semantic Information about Users not a fan of this title

One of the most important aspects of a research community is the ability to seek help for troubleshooting experimental procedures and research plans. We intend to develop technologies that will make OpenWetWare an excellent tool for connecting researchers with possible collaborators or simply with the right person to answer questions for troubleshooting a protocol. By forming semantic links between researchers and protocols, scientific fields, equipment, etc, a future OpenWetWare user will be able to pose the query: “Who should I speak with to find out plate reader protocols of interest to molecular biologists studying ClpX” and receive a short list of relevant contacts. (OK, that’s all for now until I know we actually want stuff like this ;)

education note

we should talk about the other classes as well where it is appropriate... especially in the preliminary results. berkeley class could be used as an example of a fast changing field.. and reuse

web2.0

Collaborative internet technologies have seen great improvement and investment recently, a movement collectively referred to as Web 2.0. Wikis, tagging, and the semantic web are just a few examples of Web 2.0 technologies that are of immediate use to information sharing in science. Wikis offer an easy-to-use, flexible platform for contributing information to a website, removing the “webmaster” bottleneck and democratizing information contribution. Tagging enables a bottom-up approach to information organization. Users are able to “tag” information with relevant keywords leading to more appropriate categorizations. The semantic web is a term describing a suite of powerful technologies that enable the context of data (so called “metadata”) to be associated with the data itself in a machine-readable form. This enables advanced querying of data, as well as more powerful data-mining techniques. OpenWetWare is a wiki that was begun to bring some of these technologies into the service of the scientific community.

discussion

  • RS 08:22, 14 June 2006 (EDT): The background and motivations section might want to also emphasize that biology is at a place where it it attracting a lot of attention from people outside the field. Therefore in some sense, OWW is most useful for those trying to move in to the field who don't have access to the institutional memory of a lab that has been around for 30 years.
    • Sri Kosuri 20:32, 14 June 2006 (EDT): agreed, let's see where it fits in as things shake out.
  • RS 08:22, 14 June 2006 (EDT): We might need to address comparable sites like Nature Protocols and the Cold Spring Harbor site and explain what our site brings to the picture.
    • Sri Kosuri 20:32, 14 June 2006 (EDT): Agreed... there are a couple of ways we should bring this in, and we can talk offline.
  • RS 08:22, 14 June 2006 (EDT): I'll try to include text on these ideas later (if others agree that it is a good idea) ... I just wanted to record them before I forgot.
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