[gmx-users] Mailing List Search on the new website

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 30 08:45:35 CEST 2009

Mark Abraham wrote:
> Rossen Apostolov wrote:
>> Hi,
>> It is now possible to search the mailing list archives from the new
>> website: http://www.gromacs.org/Support/Mailing_Lists/Search . There is
>> a link to it at the "Quick Links" section on the front page also.
>> Currently:
>>    * Only the [gmx-users] mailng list is being indexed.
>>    * The index is updated every 2 hours.
>>    * The search input is not parsed, rather search is done only for the
>> exact string.
>>    * The results are displayed in descending order of the date. You can
>> change the sorting by clicking on the column names.
>>    * For some postings, the contents section in the table is empty but
>> following the link will display the full contents.
>>    * It is likely that the interface will be implemented into the
>> website differently.
> That's great. Hopefully we'll get more content and functionality soon too!
>> Also, almost all of the information from the old wiki/www sites is now
>> transfered and incorporated, although many pages contain broken links to
>> them. They will be fixed one by one, but everyone is welcome to update
>> them when you come across such.
> I would have approached this process differently. The MediaWiki content 
> was intrinsically free-form, and now we're apparently trying to shoehorn 
> it into something hierarchical. This process converts hundreds of links 
> that are now defunct because they were created as relative links to 
> targets in a free-form database, and have now been automatically 
> converted to what look like hard links to non-existent targets. The 
> correct targets are presumably placed somewhere in a fairly arbitrary 
> hierarchy (e.g. what's the difference between "Best Practices" and 
> "How-tos"?), which anyone wanting to spend the time to fix now has to 
> memorise. These categories existed in the previous wiki, but nobody 
> adding content or links was forced to use or know them. That's a big 
> change in philosophy.
> I've spent a lot of time over years creating and maintaining a large 
> slab of this content (with other notable contributions from quite a few 
> people - Dallas Warren in particular) and feel that this new imported 
> format greatly reduces the utility of the information. While some 
> curated hierarchical indexes are good things for helping to find 
> content, I think preserving the underlying lack of hierarchy is a much 
> better approach to preserving the usefulness of the content. The 
> alternative is appointing a curator and having them spend lots of time 
> organizing and fixing links. Given the slow rate of transition of 
> GROMACS web content from old to new forms, I think we should be very 
> keen not to make more centralized work, and to preserve the goodwill of 
> previous "external" volunteers :-)
> I'd much rather see the Documentation section 
> (http://www.gromacs.org/Documentation) have links to
> * the paper manuals,
> * either a compatible Wiki, or a flat wiki-style import of the previous 
> wiki (so that automated link conversion can just work - even if it's 
> done with a simple perl script!),
> * some new and updated index pages for that previous wiki,
> * and if necessary, any other non-wiki content.

Dear Mark,

you raise many good points. A lot of the strong points of the simple 
wiki have been lost in the transition, I guess we have been misled by 
the wiki in the name Dekiwiki. Dekiwiki has some important advantages 
over mediawiki, like security (apparently the oldwiki was abused by 
spammers recently, this is why it was shutdown), and the ease for adding 
images and documents (mdp files :)). Whether dekiwki was the right 
choice for the job I am not sure. Overall it is easy to conclude that 
the move was done too hastily, seeing that the new website is still not 
anywhere close as informative as the two previous websites were.

Rossen has done a lot of hard work on the website (e.g. the mailing list 
search), but there are some fundamental flaws like the lack of 
indentation in the menu structure, and the excessive amount of menus 
which apparently are difficult to change. You correctly identify the 
most important point that is missing: the self-organization that is 
inherent in the mediawiki format. I wonder whether it is impossible to 
get that functionality on dekiwiki (without that, one can not call it a 
wiki really...).

The goodwill of external volunteers is another point that should not be 
overlooked. GROMACS is by now a community effort with many developers 
and contributor, big and small, scattered around the globe. To make the 
new website a success we do need many contributors, and we should try 
not to alienate contributors by such abrupt changes.

> Cheers,
> Mark
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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