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

Rossen Apostolov rossen.apostolov at cbr.su.se
Wed Sep 30 12:04:32 CEST 2009

Hi Mark and David,

I agree with the points you make. The change was rather abrupt but in 
the long term I believe the dekiwiki will be a much better and useful 

The dekiwiki has been initially developed on top of mediawiki with the  
aim to make it more user friendly to modify content, e.g. using a 
WYSIWYG editor etc. It has very powerful scripting capabilities (using 
dekiscript) and a lot of useful extensions that make it possible to 
mash-up all sorts of content. You can easily embed videos and RSS feeds, 
view PDF/DOC/XLS/PS/RTF documets, SVG images or interface with 
tweeter/linkedin/skype(?) etc.
It is basically mediawiki on steroids!

Not that all of this is needed for this website but providing a rich 
platform will give the Gromacs community much more flexibility in 
sharing knowledge and experience. Tutorial videos, RSS feeds to sites of 
interest, current weather in Stockholm, etc. can enrich the site by a lot.

>> 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.
In fact, dekiwiki can be very easily set up as a graph/free-form style 
wiki. One just has to disable the navigation pane, one click away. Then 
you have only one page from which you can access the rest of the site. 
Also, in a wiki way, if you try to access a non-existing page you are 
automatically presented with the editor to add new page to the top level.

Hyperlinks to other pages on the site are also relative as in a standard 
wiki, so even if you rename a page or move it to a different level in 
the tree (if you are using one) all links pointing to it will be able to 
find it.
>> 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 can easily remove the left pane and leave only a flat graph structure 
if that's better. It wasn't easy to categories all the info from the 
previous site but there is some inherent hierarchy in the type of 
content we have on the site.

It is possible to combine both styles. How about keeping the tree and 
put easily "categorizable" content into the appropriate level? Then, 
have a top level "Others" (or something like that) where you can dump 
any page that doesn't fit the structure, and include link to it from 
another place.

Same would hold for levels like "How-tos" and "Programming Guide". They 
can have 100s of sub-pages but you don't need to scroll down to find 
something. Put a new page there along with a link to it at some other 

Last but not least, there is a search form:)

>> 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,
I think it's more of a feature than a bug. For example, by going down 
just 3 sub-levels you'll start using up lots of screen space if you keep 
all the indentations. Same holds for cropping long lists of sub-pages 
which are at the same level. But I will look at that and see what can be 
> and the excessive amount of menus which apparently are difficult to 
> change. 
By modifying the skin you can remove most of the elements and leave it 
pretty bare by default and display certain elements as needed, e.g. only 
Contributors would see the "Edit Page" etc. icons. I will work on that also.
> 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.
Again, I can make the site to look and behave like the old wiki, but I'm 
not sure this is a good idea.


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