taskSavannah Administration - Tasks: task #8364, Submission of Annotathon

 
 

task #8364: Submission of Annotathon

Submitter:  Pascal Hingamp <hingamp>
Submitted:  Fri 27 Jun 2008 05:19:32 PM UTC
   
 
Should Start On:  Fri 27 Jun 2008 12:00:00 AM UTC Should be Finished on:  Mon 07 Jul 2008 12:00:00 AM UTC
Category:  Project Approval Priority:  * 5 - Normal
Status:  Cancelled Privacy:  Public
Assigned to:  stevenr Open/Closed:  Closed
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Sun 07 Sep 2008 11:23:54 AM UTC, comment #3: 

OK, Thanks for letting us know, sorry we lost you.

Regards,

Steven

Steven Robson <stevenr>
Mon 01 Sep 2008 06:36:52 AM UTC, comment #2: 

Hi Steve!

Many thanks for your follow up. However, because I needed an immediate code repository for our publication, I used launchpad and included the launchpad URL in the published article. Since it will be impractical to have two repositories and the launchpad site has been made public, I guess this means we should abandon the Savannah registration. I looked for some mean of suspending the procedure on the Savannah web site but did not find it.

I hope I didn't waste too much of your time, and wish GNU and non-GNU free software ever more success!
Regards,
Pascal

Pascal Hingamp <hingamp>
Mon 25 Aug 2008 05:52:21 PM UTC, comment #1: 

Hi,

Firstly, I'm sorry for the delay in getting to your submission.

I'm evaluating the project you submitted for approval in Savannah.

Please include a (perhaps temporary) URL pointing to the source code. Alternatively, you can forward the code to me by email or attach it to this tracker. The URL you provided is broken.

We wish to review your source code, even if it is not functional, to catch potential legal issues early.

For example, to release your program properly under the GNU GPL you must include a copyright notice and permission-to-copy statements at the beginning of every  copyrightable file, usually any file more than 10 lines long.  This is explained in http://www.gnu.org/licenses/gpl-howto.html.  Our review would help catch potential omissions such as these.

Note that sending code to our repositories is a release, since the code will then be publicly available through anonymous access.

To help us better keep track of your registration, please use the tracker's web interface following the link below. Do not reply directly, the registration process is not driven by e-mail, and we will not receive such replies.

Regards.

Steven Robson <stevenr>
Fri 27 Jun 2008 05:19:32 PM UTC, original submission:  

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves or discards the registration.


Registration Administration


While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific Group Administration page, accessible only to site administrators, effectively logged as site administrators (superuser):



Registration Details


  • Name: Annotathon
  • System Name:  annotathon
  • Type: non-GNU software & documentation
  • License: GNU General Public License v3 or later





Description:

The project concerns an Internet teaching environment dedicated to bioinformatics. It consists in PHP scripts and a MySQL database. Here is the abstract of a manuscript sent for publication:
"We have taken advantage of the increasing amount of metagenomic data publicly available to develop a teaching environment in which undergraduate students are given the opportunity to “turn data into knowledge”. Called Annotathon, this internet teaching platform fosters team work and guides apprentice annotators through each step of in silico analyses, from ORF identification to functional and phylogenetic classification. Generating raw results is an integral part of the exercise, but heavy emphasis is put on their interpretation and critical assessment. The online format is ideally suited for student involvement outside class, whilst allowing instructors to provide annotators with continuous feedback. An iterative evaluation cycle allows students to respond to constructive criticism and produce enhanced versions of their annotations. A student exit survey shows that, although challenging, the study of as yet non-annotated  sequences is a major incentive for 75% of participants. The success of this approach relies on the following: i) Learning by doing: bioinformatics is best introduced by first hand experience; theoretical considerations are easier to grasp once truly familiar with the tools. ii) Learning by repetition: successively analysing several sequences gives the students the opportunity to experience a wide range of situations, e.g. “twilight zone” similarities, or “garbage in, garbage out” phylogenetic tree reconstructions.
iii) Learning from constructive criticism: giving students the opportunity to correct themselves results in noticeable progression over time. 502 students have taken part in the Annotathon over the past three years, analysing a total 2.3 Mb of ocean microbial DNA, representing 9500 hours of cumulative annotation. Interestingly, student hand crafted annotations are in very close agreement with those obtained by automatic annotation pipelines.
Based on these observations, we call on our colleagues to consider joining an initiative to create a worldwide “grid of undergraduate annotators”. Tentatively, as more teams join in, this could lead to an educative annotation community with room for scientific contribution. The open source online Annotathon environment (http://annotathon.univ-mrs.fr) is offered as a basis for this collaborative initiative.  "


Other Software Required:

PHP Mail/mime, Net/GeoIP, Math/Stats PEAR libraries: BSD Style, LGPL 2.1 & PHP licences
http://pear.php.net/

MySQL GPL License
http://www.mysql.com/about/legal/licensing/

JpGraph: released under a dual license. QPL 1.0 (Qt Free Licensee) For non-commercial, open-source or educational use
http://www.aditus.nu/jpgraph/jpdownload.php



Tarball URL:

http://annotathon.univ-mrs.fr/Annotathon_1.0.tar.gz


Pascal Hingamp <hingamp>

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

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  • -email is unavailable- added by stevenr (Posted a comment)
  • -email is unavailable- added by hingamp (Submitted the item)
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    Follow 4 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2008-09-07 stevenr StatusNeed Info Cancelled
        Open/ClosedOpen Closed
    2008-08-25 stevenr StatusNone Need Info
        Assigned toNone stevenr

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