O'Really?

December 19, 2006

Taverna 1.5.0

Filed under: Uncategorized — Duncan Hull @ 8:26 pm
Tags: , , , , , ,

Happy Christmas from the myGrid team, who are pleased to announce the release of version 1.5.0 of the Open Source Taverna bioinformatics workflow toolkit [1]. This is now available for download on the Sourceforge site and includes some substantial changes to version 1.4.

IMGP4570Taverna 1.5.0 is a small download, but when first run it will then download and install the required packages which can take some time on slow networks. In the near future there will be a mechanism for downloading a bundle of core packages. There are some significant changes in the underlying architecture of Taverna and how it handles core packages and optional plugins, using a system called Raven, see release notes below.

The documentation is currently being updated and the user documentation should be complete very soon, with the technical documentation following shortly afterwards. The reason for this is to allow the software to be released with some time to spare before the Christmas holidays.

Release notes:

There have been a number of substantial changes in the underlying architecture of Taverna since the previous release. These include:

  • An overhaul of the User Interface (UI), replacing the unpopular Multiple Document Interface with a cleaner and simpler single document UI which can be customised using Perspectives. There are built in perspectives to allow the design and enactment of workflows, and plugins can integrate with the UI by providing perspectives of their own. Together with this, users are able to create their own layouts built from individual components.
  • Taverna now allows for multiple workflows to be open and enacted at the same time.
  • Support for the new BioMart data management system version 0.5, together with backward compatibility for old workflows that used Biomart 0.4.
  • Better provenance generation and browsing support, through a plugin now known as LogBook.
  • Better support for semantic service discovery through the Feta plugin [2].
  • Modulularisation of the Taverna code base.
  • Development and integration of an underlying architecture know as Raven. This allows for Apache Maven like declaration of dependencies which are discovered and incorporated into the Taverna system at runtime. Together with the modularisation of the Taverna code base, Raven gives the benefit that updates can be provided dynamically and incrementally, without the need for monolithic releases as in the past. This allows the provision of updates to bugs, and new features, within a very short timescale if necessary. It also provides plugin developers with a greater degree of autonomy and independance from the core Taverna code base.
  • Improved and more advanced plugin management with the ability to provide immediate updates, and for plugin providers to publish their plugins via xml descriptions.
  • Numerous bug-fixes including the removal of a number of memory leaks.

JIRA generated release notes and bug status reports can be found here and here

References

  1. Peer-reviewed publications about the Taverna workbench in PubMed
  2. Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery
  3. BioMoby extensions to the Taverna workflow management and enactment software

December 1, 2006

NAR Web Server Issue: Walking in a Webby Wonderland

Filed under: Uncategorized — Duncan Hull @ 3:18 pm
Tags: , , , , , , ,

WonderlandHave you recently built a bioinformatics web application useful to the wider community that you’d like to tell the world about? Are you also looking to score brownie points for a rigourously peer-reviewed publication that stands a reasonable chance of being well cited? If that’s you, then you have one month from today (December 1st) to sort your code out, and get your abstract in, for the fifth annual Nucleic Acids Research (NAR) Web Server issue published by Oxford University Press (OUP) in 2007. All articles in this issue are published under an open access model.

As regular visitors to nodalpoint will already know, every year NAR publishes two special issues: one on databases (annually in January since 1993) and the other on web servers (annually in July since 2003). Authors interested in pre-submitting abstracts for the 2007 Web Server Issue should read the Instructions to Authors for Web Server papers in NAR and send an abstract to Gary Benson at Boston University before December 31st 2006. The deadline for final submission of full articles is January 31st 2007. Gary Benson has taken over this year from previous web server issue editor, Nobel laureate and Ignobel participant, Richard Roberts [1].

One advantage of publishing your application paper in NAR, instead of alternative open access journals like Source Code for Biology and Medicine (SCFBM), is a listing in the bioinformatics links directory [2] and a bigger impact factor [3] of 7.6, if you care about these things. There are of course, disadvantages of publishing with OUP in NAR, like the expensive open access publishing fees of $1185 to $2370 per article which are debateable value-for-money. If you’re living in a ‘List A’ developing country these charges are waived, which makes it tempting to set up a laboratory in Malawi to evade payment…

Anyway, does anyone out there know how OUP prices compare with the complicated Biomed Central membership fees which are presumably required for publication in SCFBM? Another leading open access publisher, the Public Library of Science (PLOS) currently charges from $2000 to $2500 for open access publication. Maybe I’m missing something, but aren’t these charges a lot of money to pay an administrator to shuffle a few bits of paper around and run a web server? Don’t let that put you off submitting your paper though, because in Science and academia you will either publish or perish. This is where the web is your friend because free online web availability substantially increases a paper’s impact.

On a lighter note, and now that the festive season is upon us, I’ll hand over to the Christmas crooner Perry Como to sign off:

♫ Sleigh bells ring, are you listening? In the lane, snow is glistening. A beautiful sight, We’re happy tonight, Walking in a webby wonderland. ♫


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June 28, 2006

Marginal Power

Filed under: Uncategorized — Duncan Hull @ 11:03 pm
Tags: , , , ,

Garage doorLISP Hacker and Painter Paul Graham writes entertaining essays about technology. His latest piece, discusses how important and sometimes lucrative ideas usually come from the “garage” outside rather than the inside, what he calls The Power of the Marginal. His essay rambles a bit in places, but has some interesting observations that are relevant to bioinformatics. For example…

“…if you’re an outsider you should actively seek out contrarian projects. Instead of working on things the eminent have made prestigious, work on things that could steal that prestige.”

Paul did a PhD in Computer Science and has fond memories of being a student which will ring true with anyone who has been there:

“That’s what I remember about grad school: apparently endless supplies of time, which I spent worrying about, but not writing, my dissertation.”

PhDs and obscurity go hand-in-hand and according to this essay, obscurity and marginality is good for you. It doesn’t taste as good as junk food but is allegedly “good for you”. Pauls personal choice of marginality is the relatively obscure language called LISP, and the people I’ve met who use this langugage are either crazy or at the top of their game, sometimes both. Does LISP turn people crazy or are crazy people attracted to the obscurity of LISP?

Either way, Paul Grahams occasionally crazy essays are worth a read if and when you have a moment to spare. Even better, read them when you don’t have the time and are procrastinating writing your PhD thesis or next Bioinformatics paper.

Further reading

  1. Structure and Interpretation of LISP programs
  2. Most grad students are stuck on problems they don’t like
  3. Startups and garages in bioinformatics: The effect of software patents
  4. Garage Genomics and bio-hackers
  5. Lisp as an Alternative to Java by Peter Norvig, Director of Research at Google
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