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The twin of imechanica in biology and bio-engineering is from MIT !!

Mike Ciavarella's picture

OpenWetWare is an
effort to promote the sharing of information, know-how, and wisdom
among researchers and groups who are working in biology &
biological engineering. Learn more about us.
If you would like edit access, would be interested in helping out, or want your lab website hosted on OpenWetWare, please join us.

http://openwetware.org/index.php?title=Main_Page

 

Maybe some expert here wants to discuss the technology?  Is it Drupal? 

It is certainly more advanced than Imechanica. So we can learn and copy for our next version.  They seem to be trying to do science together already!  See for example:

   

Labs

Labs & Groups
From around the world

   

Courses

Courses
Host & view classes

   

Protocols

Protocols
Share techniques & more

   

Blogs

Blogs
Read OWW blogs

 The technology is maybe Wikimedia: Eric wouldknow...

About OpenWetWare

and mediawiki?   But certainly the page has been visited 1/2 million times. How many times has imechanica?  What is this OpenWetWare?

 

Comments

Athough i had not a positve attitute about it at first, i found it very useful and interesting in many aspects, but forum of imechanica is much nicer.

Zhigang Suo's picture

OpenWetWare is powered by Mediawiki, the same open-source wiki engine that also powers Wikipedia.  As discussed in the proposal to NSF, we did consider using Mediawiki to run part of iMechanica.  We eventually settled on using Drupal alone to run iMechanica.  If one is familiar with how Wikipedia works, one should have a rough idea of the relative strength and weakness between Mediawiki and Drupal.

  • If we'd like to use Mediawiki, how are we going to use it? 
  • How many people would be interetsed in a WikiMechanica? 
  • Of these people, how many feel their needs are unmet by Wikipedia?  Why?

P.S.  Teng has reported some statistics of iMechanica in January 2008.

wikipedia in its present form is good. only a link is needed to relate a topic in wikipedia to an imechanica discussion! have any body in IMECHANICA started a topic in wikipedia?. actually any topic in wikipedia is a dynamic review paper itself.

Zhigang Suo's picture

I've tried to contribute in my small way to Wikipedia but tend to run out of time to leave the articles in a state that satisfies me.  You can see a list of my recent edits at

 http://en.wikipedia.org/wiki/Special:Contributions/Bbanerje

At present the best I've been able to do is to add a "Needs expert attention" to articles that are incomplete or significantly inaccurate (after correcting whatever I can).  An example is the articles on the J-integral.

Also, very few mechanicians have biographies on Wikipedia.  I've added a couple of lines on Jim Rice (and would love to see pages on Clifford Truesdell and Walter Noll and Rodney Hill).  (Note that Jim Rice's page was deleted in the past after it was discovered that much of the content had been taken from a copyrighted source.)

And I always keep in mind Tagore's song

"If no one comes after hearing your call, go alone ..." 

-- Biswajit 

Not for advertising papers.But to find a way to make wikipedia a resource of complete review papers. it may not be bad for authors to experience Adding their own papers to reviews in wikipedia. but every author may find it impossible  because the current topics are too general for our papers,

wikipedia has started to build this information tree with up todown approach (from gerneral topics to specific  ones). but it may not be bad for researchers to experience building it  with down to up  (approach), start specific topics related to our papers and adding our papers to them. then others will use this special topics in the structure of more general topics and this two side of tree will reach together one time. Just like Nanotech nology .if it is not possible to use wikipedia for that we should try to build another wiki- which can build it from down to up

At the end we will have a great science tree that can be used for many regards. evaluation of the work of others with something with more information than single numbers!. and also to find out our place in current world of scince, or positioning ourself in more applied places. also find out others who work similar things and contact them. 

 

BEST REGARDS.

ROOZBEH SANAEI. CELLULAR AND MOLECULAR BIOENGINEERING, NATIONAL UNIVERSITY OF SINGAPORE

 

Zhigang Suo's picture

The slogan of Wikipedia has been "the free encyclopedia that anyone can edit."  The basic approach was discussed once again recently in an article by Jimmy Wales, the founder of Wikipedia.  Wiki might be useful for purposes other than building an encylopedia.  One can also limit who is allowed to edit.  It is really easy to set up a wiki engine.  The difficulty has been to set up a wiki engine, and evolve a cause that a lot of people are willing to spend time on it.

Indeed, iMechanica can easily become a wiki engine if we so choose.  We can let users edit posts initiated by other users.  Right now, this editing function is only available to the moderators.  But do we want to turn iMechanica into a wiki, or even partly a wiki?  What are the cost and benefit?  I'm curious to learn people's thoughts.

Mike Ciavarella's picture

Zhigang

  as you seem to suggest already, we could "test" wiki as part of imechanica.

This is what for example my italian friend wants to do in this site

http://www.mappacervelli.org/

where he plans to collect all the italian scientists in the world.  One section of that is wiki

http://wiki.mappacervelli.org/index.php?title=Pagina_principale

I notice most of this is in italian, maybe I can ask him to join the discussion?  He is really expert of all this.

 Mike

 

michele ciavarella
www.micheleciavarella.it

 

Mike Ciavarella's picture

Zhigang

I suspect the problem with imechanica is that it is too polite!

When I posted my agressive posts, they were n.1 for many weeks (and ultimately I had to remove them).

So the problem is that imechanica is too polite.

I guess you need to make a choice, between the NSF people who are ultraconservative and killed your proposal saying it was over-ambitious and "could not work", see also A "Supreme Court" for peer review of papers and proposals

and a more radical approach.

Most blogs become popular when there is really radical choice. http://en.wikipedia.org/wiki/Leadership

Maybe we have to wait some more.  But you are both in the board of IJSS and in Imechanica.  These two are a little extremes.  I made my choice.  Now your turn!

It is mainly your energy that needs to go more seriously into this to

  • convince some sufficient number of core people to start this (not even wikipedia started from scratch, there was a previous project)
  • convince senior people to do at least one abstract to start each theme (like guest editors)
  • find out systems to make sure the result goes into papers - since you are in IJSS (while I am no longer), maybe you can talk to IJSS editors to have 1 paper from Imechanica each issue 

 

See also

A collection of "this cannot work" statements

 

Mike Ciavarella's picture

Ages ago, (beginning) of april, I posted

And I am sure many other discussions exist before, including

    But Zhigang knows that, in the next generation of imechanica, while our community expands, we need some sort of wikipedia capability.  Of course, one can argue that for that function there is already wikipedia itself. 

    Also, probably as long as imechanica were small, it could NOT have the strength to write more than few review papers, if even.  But apparently the imechanica community is not enough even to write in wikipedia itself. I need to study wikipedia more to tell you the distribution of articles, but I have the impression that they are not for the latest technologies (?), or anyway since they are only volonteers who write, there must be a correlation between volonteering and subjects.

    There must be subjects which are very popular and of general interest, and these will be covered. On personal web pages, either is the person himself, or a devoted "fan".  For example, I checked Huajian Gao's wikipedia entry.

    It was Markus Buhler to start.  Markus is a very active MIT professor now, formerly student of Huajian --- so my suspect confirmed

    http://en.wikipedia.org/w/index.php?title=Huajian_Gao&action=history

    All the later corrections were done by others and were small.

    But then remember what are the weakness of wikipedia, they cover easily some subjects, less so others.  For example, when there was the 5 bomb attack in London in 2005, within few second a wikipedia maniac had written a short report (before the journalists had), and within few hours, hundreds of people had contributed to about 14 pages accurate report, matched by none of the existing classically financed journals.

    I have to conclude that, as long as the reward for academics is to write papers useful in the  "Citation index" there is not enough energy put in either imechanica or wikipedia. A few proposals to make this easy from one end

    1) Talk to isi Thompson to have Imechanica or Wikipedia (or special sections of them) in the citation index --- who is the author however, the complete list of contributors?

    2)  insist on h-index first, which stops increased profits by publishers, so that they have to reduce their size (Elsevier alone has 7000 employers), their commercial power, and reduce number of journals. Then, later we are in a position to suggest them to change: for example, sponsor and fund imechanica

    3) ask publishers after 2 or even before, to "publish" papers produced by wikipedia or by imechanica in normal journals

    4) assuming wikipedia is one system, and imechanica another, find a new one intermediate between them --- or that permits an easy transition from one to the other.  For example, launch initiatives in imechanica that later could be put into wikipedia.  I need to study the Harvard new system, but if Zhigang Suo can explain, Harvard people now can post their papers to the Harvard collection, and later submit to a journal.

    5) how can imechanica expand more?  I discussed this, and I have few ideas that I am slowly trying to realize in practise.  The "get-together" at conferences, some marketing, eventually I would suggest Suo to have "sponsors" for the project --- the first I can think of is Elsevier.   I think the commercial "users" should need to pay for posting.   Since Elsevier is a profit organization, when they organize a conference, publish  a journal,  or even  publish a book, they do it for profit.  If we contribute to this, we NEED to get advertissment charges.

    This is only a few ideas. The discussion  should continue, in a wikipedia style!

    I suggest to continue to "study" scientifically wikipedia, and see patterns and try to criticize,to improve in imechanica.

    Finally, let me signal that Elsevier and the other publishers are TRYING hard to innovate in this.  You may have notice that ScienceDirect now has some functionality like "vote" --- our competition with them is only just started.

    I am not sure if the US panorama, but in Europe I found 2 large projects connected to Liquidpublication, both in Trento, one with Elsevier in, and one with Springer in.  They are both from the Information Engineering community.

    So probably Imechanica was not funded because reviewers in mechanics are not experts of Informatics.  But there are certainly Informatics projects about this also in US?   Or anyway, do you all contribute and follow the development of the LiquidPUB projects?  My collegues (Fabio Casati) have told me they are interested to open a forum on imechanica, if you like...

     

    mike

     

     

    In fact Science 1.0 and Science 2.0 can live toghether, both of them have advantages and disadvantages.

    Mike Ciavarella's picture

    I see you would like to see review papers first into imechanica or wikipedia.

    You may be right.

    I also suggested the ISI thompson citation index system, and the present impact factor classification, is hard to cancel in a second, at least UNTIL we don't have an equivalent and serious and generally agreed system to rank quality.

    Anyway, I agree we need to move step by step.

    In telephones, wiki-like collaborative efforts have worked: skype.  This expanded from 100.000 to 100.000 millions in 2 years!  And was sold to Ebay for 2US$ billions!

    In research, we need to think about what will come first. Research, papers, or review papers.  I don't know.

    From NSF call for proposals 2007 I read

    http://www.nsf.gov/pubs/2007/nsf07558/nsf07558.htm

    Initial engineering-focused VOs (EVOs) have demonstrated the potential
    for this approach.  Examples of EVOs involving significant engineering
    communities are the George E. Brown Jr. Network for Earthquake Engineering Simulation (NEES), the Collaborative Large-scale Engineering Analysis Network for Environmental Research (now called the WATERS network), the National Nanofabrication Users Network, and the Network for Computational Nanotechnology and its nanoHUB.org portal. 

     

    For you to prove you are rigth we need to start from review papers, simply you have to demonstrate that you are capable to convince enough people to do it!  I would keep thinking.

    Having a general index system for web 2.0 is very beneficial.

     

    Mike Ciavarella's picture

    There is a wiki section of Open New Ware

    http://openwetware.org/wiki/Materials

    Is it going far?  Maybe they are just starting.  There is around any other project using WIKI except wikipedia itself?

    And what about my other ideas to use imechanica as a place to start wiki entries later to be posted, or perhaps to be sent as paper to normal journals of the Harvard collection?  Maybe I should write 1 idea per post, or people don't respond to 10!

     
    Putting shareworks in wiki-source is beneficial for those who dont know imechanica.

     

     

     

    Mike Ciavarella's picture

    Rousing Success
    In principle, says PLoS ONE's
    Surridge, scientists should find the transition to Web 2.0 perfectly
    natural. After all, since the time of Galileo and Newton, scientists
    have built up their knowledge about the world by "crowd-sourcing" the
    contributions of many researchers and then refining that knowledge
    through open debate. "Web 2.0 fits so perfectly with the way science
    works, it's not whether the transition will happen but how fast," he
    says.

    The OpenWetWare project at MIT is an early success.
    Launched in the spring of 2005 by graduate students working for MIT
    biological engineers Drew Endy and Thomas Knight, who collaborate on
    synthetic biology, the project was originally seen as just a better way
    to keep the two labs' Web sites up to date. OpenWetWare is a wiki--a
    collaborative Web site that can be edited by anyone who has access to
    it; it even uses the same software that underlies the online
    encyclopedia Wikipedia. Students happily started posting pages
    introducing themselves and their research, without having to wait for a
    Webmaster to do it for them.

    But then, users discovered that
    the wiki was also a convenient place to post what they were learning
    about lab techniques: manipulating and analyzing DNA, getting cell
    cultures to grow. “A lot of the 'how-to' gets passed around as lore in
    biology labs, and never makes it into the protocol manuals," says Jason
    Kelly, a graduate student of Endy's who now sits on the OpenWetWare
    steering committee. "But we didn't have that." Most of the students
    came from a background in engineering; theirs was a young lab with
    almost no mentors. So whenever a student or postdoc managed to stumble
    through a new protocol, he or she would write it all down on a wiki
    page before the lessons were forgotten. Others would then add whatever
    new tricks they had learned. This was not altruism, notes
    steering-committee member Reshma Shetty. "The information was actually
    useful to me." But by helping herself, she adds, "that information also
    became available around the world."

    Indeed, Kelly points out,
    "Most of our new users came to us because they'd been searching Google
    for information on a protocol, found it posted on our site, and said
    'Hey!' As more and more labs got on, it became pretty apparent that
    there were lots of other interesting things they could do."

    Classes,
    for example. Instead of making do with a static Web page posted by a
    professor, users began to create dynamically evolving class sites where
    they could post lab results, ask questions, discuss the answers and
    even write collaborative essays. "And all stayed on the site, where it
    made the class better for next year," says Shetty, who has created an
    OpenWetWare template for creating such class sites.

    It may be funny if I say MOST OF OUR PROBLEM IS FROM OUR SEARCH MOTORS and Indexing System. but it is!.

    Mike Ciavarella's picture

    .. you my system to find out things is certainly NOT google search.

     I use google search very seldom these days.

    I read widely in the good literature, nature, newspaper, general topics in economics not only in my specialized field.  I have "google reader" and "google alert" to many topics of interest.  These are much more powerful than simple Google

    For example, this OpenWetWare I found in a reference to a Scientific American article, which I also posted, Science2.0.

    So I suggest you do the same, keep reading broadly.

    there are many forums in biochemistry (and in any other
    topic)

    http://www.scienceforums.net/ 

    http://biowww.net/

    http://www.molecularstation.com

    ... and many others that i dont know!!! i have to send my question to all of them.

    QUAD-FORUM may be a good solution.

     

     


     

    Mike Ciavarella's picture

    Main Page
    Wikimania 2008 Alexandria :: Change the shape of wisdom

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    Wikimania 2008
    Alexandria, Egypt • July 17–19

    Welcome to the official website for Wikimania 2008! Alexandria will be hosting Wikimania 2008 this Summer in the prestigious new Library of Alexandria (Bibliotheca Alexandrina).

    What is Wikimania?

    Wikimania is a regular conference for all Wikimedians who contribute to one of the many Wikimedia Foundation projects. Past conferences have been held in popular cities around the world such as Frankfurt, Germany (Wikimania 2005 website), Boston, USA (Wikimania 2006 website) and Taipei, Taiwan (Wikimania 2007 website). (more...)

    Wikimania 2008 planning


    General details


    Pictures

    Pictures from Alexandria!


    Want to help us?

    • List of advertisements that you can place on your website or personal blog!
    • If you blog about Wikimania, tag with "wikimania2008".
    • You can talk with other people about Wikimania on IRC.


    Coordination

    From Previous Wikimanias

    From previous Wikimanias!

    Taipei, Taiwan (2007) • Boston, USA (2006) • Frankfurt, Germany (2005)

    Alex Schenck: "Raise your hand here if you have edited Wikipedia"
    Larry Pieniazek: "Does that include vandalizing?"

    (See another)

    Retrieved from "http://wikimania2008.wikimedia.org/wiki/Main_Page"

    Category: Main Page

    Mike Ciavarella's picture

    Wikimania 2008: Flagged Revisions with Philipp Birken

    From “Flagged Revisions,” a presentation at Wikimania 2008 by Philip
    Birken. In my opinion, flagged revisions realize the concept of stable
    versions without making the article actually stable. We can get rid of
    protecting articles that are experiencing heavy vandalism if we do
    this, because an edit only updates to the public when it is flagged as
    not-vandalism by a trusted user. However, vandals immediately see the
    results of their edit for an hour, which is just ingenious.

    Everyone meant something different by stable versions, so we called it
    flagged revisions. This gives reader feedback on the quality of the
    articles. Currently, you can make users by default see the most recent
    flagged revision of an article. It enforces the four-eye principle.

    Development of Stable Versions: It is the idea that the article is
    finished. The concept is in printed encyclopedias and Nupedia. Ideas
    early in Meta. Discussed since the beginning. Magnus Manski wrote a
    tool to rate articles - FA, Good, A, B, Start, Stub. We now have
    patrolled edits, active on Wikipedia.

    In June 2006, we started. We asked Jimbo: “What’s up with stable
    versions?” Jimbo said: “You’re right, let’s just do it.” We agreed on
    basic parameters: No voting and 2. Keep it simple. He asked the board
    if they would object. They said they wouldn’t. We hired a contractor to
    implement stable versions. Erik Moeller had become a board member and
    quality was one of his topics. We found Jorg Baach, he did the coding.
    It was put on the SVN under flagged revisions, which stuck. Wikimedia
    France gave 1,000 euro – the first international wiki. People started
    working on it – mailing list wikiquality. Open beta in Feb 2008. Found
    bugs. Now it is stable and on the German Wikipedia.

    People flag and edit or they don’t. You don’t vote on it, you just
    make sure the people who flag are trustworthy. One flag is enough to
    get it approved.

    Ongoing problems:
    • Too few developers
    • No process for giving useful input
    • Developers not present in content creation
    • Not enough competence in design/usability
    • Not enough leadership structure in local projects

    Flagged Revisions
    Two flags: sighed and quality. Editors can flag something as sighed,
    reviewers can flag as quality. If desired, IPs see by default the last
    sighted version instead of the current version. Can do it per wiki or
    per page. Templates and Images are in this. If you flag an article, the
    stable revision incorporates the template and images as they were then.
    If an IP changes a template, that change will not be visible until
    someone flags the template. How to incorporate comments in this system?
    We were told not to think about it.

    Sighed Versions: These are versions that are checked by an editor
    for vandalism. Basic trust – automatic procedure for granting rights,
    and any admin can give it. Misconception is that they are only about
    vandalism. They are about forcing the four-eye principle. An edit has
    to be checked. You guarantee a basic quality for readers: someone
    trustable looked at it. Any edit that is done is logged in the system.
    If an IP corrects a spelling a mistake, hordes of vandal fighters will
    look at it now, but all that needs to look at it is one trusted vandal
    fighter. Now, people concentrate on IPs, but what if you just created
    an account? They won’t have the sighted privilege.

    You can use a box to check the article. Can search for pages without
    any sighted version, or pages where newer unsighted revisions are
    waiting. You see the results of your change, but if you come back an
    hour later, you will see the sighted version. Other people will see the
    sighted version. The vandal sees the results of his vandalism, but no
    one else will. Other people will see that there are new unsighted
    versions and can see them, but will not see it on the main article.
    With Magnus’s tool, you can get intersections with categories. These
    are all the unsighted edits waiting in mathematics. It would take me
    half an hour to look through all the math unsighted revisions.

    Roozbeh Sanaei's picture

    You can start a Wiki-review on contact mechanics, I am going to
    do similar in "protein engineering", Fortunately OpenWetWare is exactly related
    to my subject!

    Mike Ciavarella's picture

    michele ciavarella
    www.micheleciavarella.it

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