Tips On How To Set Up A Virtual Online Workbench For Bioinformatics

Question

[Jarretinha]

Greetings again,

I want to build a virtual workbench on a bunch of Linux servers (VM allowed) for a medical community. I'm thinking in a solution in the spirit of the Taverna project (server version). Every user shoud be able to construct its own online virtual workflow from a set of in-house tools, submit and retrive data, etc.

The data are somewhat sigilous. Applications will be critical in a near future. So, I can't use elsewhere servers/services.

The most important point is: the community is large and the bioinformaticians are very few. If we could set up a customizable online service for common tasks (alignment, phylogeny, GO annotation retrieval, etc.) our life would be so much happier (and we could focus on bioinformatics research again) !!!

I aware only of Taverna and Plone4Bio. Is there other server-like virtual benches? Did someone already test them? Extensively?

Answer 1

[Pierre Lindenbaum]

Some workflow engines. Some of them (like Mobyle or Galaxy) are hosted on a web server.

• Mobyle
• Galaxy
• Orange
• KNime
• Wildfire
• Ugene
• Kepler

...

[Jarretinha]

Kepler project has the right spirit! I just forgot to say that it shoud be online. Have you ever tested it?

Answer 2

[User 59]

Plenty of people have tried this before for other communities

CARMEN for neuroinformatics: http://carmen.org.uk

BIRN (Biomedical Informatics Reseatch Network) http://www.birncommunity.org/

NUGO (via the NuGO Black Box or NBX) http://www.nugo.org/nbx

This is not a trivial problem and can be attacked with varying levels of complexity. You would do well to look at how other people have attempted to solve the problem. It's not just an issue of providing the services, or a workflow handler, but also opens up serious consideration of how you provide authentication and security for data and resources.

[Jarretinha]

I'm aware of the nontriviality of such an endeavour. But, as we have legal difficulties to hire qualified people, this is our best bet. Hard time fo find some examples of the architecture of such a service. Right now I just need to provide a prototype of the workbench. Thinking about Zope/Plone or Django/Plone to produce the interface/front end.

[User 59]

I should confess I am a member of the CARMEN project and that we ended up building a system from scratch for this without managing to deploy a single reused component people might recognise from Pierre's list.. I was not in charge of the architecture details. We do use Plone as the CMS associated with the project, but not as a front end to the workflow/data/services portal.

[User 59]

I am a member of the CARMEN project and the work package in charge of architecture looked at a number of the solutions above for services and workflow management. Unfortunately it was impossible to integrate these tools with what we wanted to do with the project and a so a fully home-grown solution was developed. Including a web based workflow editor. We do use Plone as the CMS associated with the project, but not as a front end to the workflow/data/services portal

[Jarretinha]

What was the problem with zope/plone?