Content Management Systems For Bioinformatics Websites

Question

[Khader Shameer]

I am looking for a content management systems for our lab server. It will be nice, if I can integrate the CMS with bioinformatics dbs and apps that we develop. I know about moinmoin, docuwiki and plone and have tried some of the websites implemented in them. Feedback on these CMS from a bioinformatics perspectives are welcome. You may suggest other CMS that you have tried.

[Jarretinha]

Are you trying to build a online workbench and lab notebook?

[Khader Shameer]

No workbench or lab notebook at the moment. I would like to have a quick way to set up the web pages and to provide a uniform interface for the dbs and apps that we are developing.

[Khader Shameer]

Any one tried template-toolkit?

[Jarretinha]

How quick? Out-of-the-box quick?

[Khader Shameer]

I didn't mean that, just tired of vi foo.html way of web development.

Answer 1

[Simon Cockell]

We use Drupal a lot, but our own website is in Wordpress, which is overlooked as a general CMS a lot of the time.

If your lab uses a lot of Python, there is a Django CMS, though last time I investigated it, it was a bit of a pain. It looks like it has changed a lot since then. You could argue that with the powerful templating provided by web frameworks like Django, a CMS isn't really necessary. Just develop apps in your framework of choice, and apply the same templates to all of them.

[Jarretinha]

Django is more of a CMF than a CMS. Of course, you can turn it on a CMS if you like.

[Simon Cockell]

@Jarretinha - that is kind of the point I was making, the link is to django-cms.org (A CMS implemented in Django), not django-project.org.

[Jarretinha]

I was just clarifying the point. Django can be turned into a CMS without creating a whole new product. With other CMF this can really hard (high level of abstraction). DjangoCMS is something in between. I think the distinction CMF/CMS can be quite tricky. That's why a I said "more of" instead of "is". A similar tought can be applied to DjangoCMS. A simple installation of DjangoCMS will give a sort of barebones to a CMS. Even templating will be turned off.

[Khader Shameer]

Thanks Simon & Jarrtinha: Drupal & Wordpress seems to be an interesting option. Any one tried integrating bioinformatics database / servers with these CMS ?

[Jarretinha]

Drupal has some issues with SQL (check bugs & foruns). Wordpress works nicelly with low traffic servers. I've tried smth with these two before sticking to Plone. I would choose Wordpress.

[Tal Galili]

+1 for WordPress (especially with the new wordpress 3.0 release that is going to happen in the next month or so)

[Dror]

If you want python - I would suggest web2py, which is more powerful and easier than django.

Answer 2

[Jarretinha]

Hi there,

-- Edit --

Just received from insideHPC a link to Hubzero. It seems to be the solution for a lot of my problems in a CMSish like sytle !!!!

-- EndEdit --

I'm a strong advocate of CMS for lab sites and lab management as I demonstrated at other posts. My choice was Plone for several reasons:

• Natively secure and has a lot of authentication procedures/protocols;
• Mature software and very well supported;
• OO/Templated underlying architeture (it's kind of OO CMS);
• Totally written in python !!!
• Works over Zope/Django or any other CMF python-compatible.
• Runs everywhere python runs;
• Connects nicely to a wealth of database systems;

Of course, there are some cons:

• Hard to debug;
• Hard to tune for performance;
• Depends on specific python versions (for now, 2.4);
• Time consuming layout/theming customization.
• Support is good only if you had a moderate experience with the CMS;

I've tried to use PHP CMS (Joomla, Wordpress, etc.) but they're not flexible/dynamic enough. PHP can really limit your creativity. There are some Java CMS that are very powerfull like Sakai, tought it was designed for a different purpose. And of course there's Apache Lenya in Java/XML. IMHO Lenya and Plone are the best ones for their language choice, architecture and flexibility. They're somewhat harder to grasp than PHP ones, but totally worth a try.

In terms of real application, I know Plone4Bio. CBMI at harvard uses Lenya. Of course, I've never searched for ir throughly.

[Khader Shameer]

Thanks for this nice account on Plone.

Answer 3

[Nico]

I have tried Joomla to create a website for french students in bioinformatics but we've been hacked couple of times... So we just open a phpBB forum :-/

But Joomla is one of the best cms I used. There is a big community around it and lot's of good plugins / extensions.

[Ian Simpson]

I had a similar hacking experience with Joomla, despite toughening my server before deploying it.

[Nico]

Yes, apparently it is a well known security problem on the template. It seems "easy" to change the first page...

[Neilfws]

Joomla is the only web software I've used that has led to a server hack. Often it's the extensions that cause security problems as opposed to the core. Regardless, I stopped using it a couple of years ago.

[Ian Simpson]

@neilfws agreed !

[Khader Shameer]

I have tried Joomla for a course work related web site. But, I didn't see any bioinfomatics server / dbs with Joomla based interface. Thanks guys for sharing your experience with Joomla.

Answer 4

[Michael Kuhn]

A similar question has been asked by Lars J. Jensen on FriendFeed, where Drupal seems to have gotten the most votes. Depending on how much you do integration with your own databases, you might want to look at a Django-based system. I make most of my database-frontends in Django nowadays (e.g. SIDER).

[Khader Shameer]

Thanks a lot Michael. This looks very interesting.

Answer 5

[Louis Letourneau]

We use atlassian's confluence to track our SOPs, extra documents, etc. It's not a CMS, but to track document history and the like it's very useful.

[Khader Shameer]

Thanks, but am looking for a free resource.

Answer 6

[Fred Fleche]

[?]

[Khader Shameer]

Preference is more for languages like Perl, PHP, Python than Java. Thanks for the links. Wordpress CMS is interesting.

Answer 7

[Dave Lunt]

I've not used it myself but I've seen some good sites, including labs, done with Plone http://plone.org/

Answer 8

[Madelaine Gogol]

We have a MoinMoin wiki that's been good. Plenty of people use and update pages.

Answer 9

[Kurtb]

I'm developing tools in Plone to use in the Labs here at NREL. We're creating some flexible "base" types and workflows to handle generic processes and analysis that can be modified for the particular desires/needs of each individual team's research focus.