Academic Computing Blog

Wolfram Workbench is the state-of-the-art integrated development environment that makes it easier to build and maintain software solutions written with Mathematica technologies.

Wolfram Workbench is currently available as a prerelease exclusively at UVM as part of our subscription to Wolfram’s Premier Service. All Mathematica users at UVM can download a free copy now for any work machine on which they’ve installed Mathematica through the site license.

Key features in Workbench enable users to:

* Group files, code, and other Mathematica resources into a single project

* Perform source-code editing with syntax highlighting, error reporting, local variable coloring, and many more options

* Study code as it runs to easily detect and fix any problems * Profile code’s execution and develop and run tests, with an array of insightful reporting methods

* Manage multiple versions of files and access their version histories

* Build and deploy Mathematica packages

For more information about Workbench, visit our website at:
http://www.wolfram.com/workbench

To download Wolfram Workbench, go to:
http://www.wolfram.com/services/premiersupport/

Genomics & Proteomics, a web publicatgion of Reed Business Information, has a cover story on the Open Source Bioinformatics community. The lead paragraphs set the tone …

Source: Protein_molecule, Wikipedia, May 10, 2006

Jeff Bizzaro, MSc, launched the Bioinformatics Organization Inc. (BOI: bioinformatics.org), one of the largest organizations in the field of bioinformatics, to support the goals of BOI embraced the ideals of the open-source movement to combat restrictive, if not elitist, working conditions imposed by the cost of scientific progress rendered proprietary. (For this article “open source” is defined as freely available software, data sets, or computing capacity.)

“When I got into this field in 1995,” says Bizzaro, “software as well as biological data were being patented at an alarming rate. Computational tools could run hundreds of thousands of dollars, requiring institutional licenses that only the better-endowed academic institutions could afford.” Out of this frustration and almost a sense of isolation, the idea of shared bioinformatics resources evolved. “I created an environment—an online community where myself and others, those of us who didn’t have a local group—could meet and share information.”

Sited as examples of the open source movement are a variety of projects:

• ALFRED, the Allele Frequency Database, is a resource for gene frequency data on human populations around the world. http://alfred.med.yale.edu/alfred/
• Coffee Genome Project, CoffeeDNA.net
• EGAD, a protein design program, egad.berkeley.edu/software.php
• IntAct, the European Bioinformatics Institute molecular interaction database, www.ebi.ac.uk/intact
• Rosetta@home, a distributed processing model for protein folding, design, and docking calculations (akin to Seti at Home), boinc.bakerlab.org/rosetta/

Quinn Norton, Coding Tool Is a Text Adventure, Wired News, 02:00 AM Mar, 15, 2006 EST.
http://www.wired.com/news/technology/0,70413-0.html

You’re in a maze of twisty subroutines, all alike.

Now, thanks to a new software-collaboration tool, you and your intrepid party of fellow hackers can navigate your labyrinth of code and slay its dastardly bugs, all in a dungeonlike world similar to an old-school text adventure.

Called playsh, the new tool is a collaborative programming environment based on the multi-user domains, or MUDs, so popular online in the early 1990s.

Trying to do things in playsh is most similar to games like Zork from the 1970s. To go north, you type north. To examine an object, you type look. There are no graphics, just descriptions.

But instead of ducking grues and collecting zorkmids, you’re interacting with whatever program code you’re working on, as well as the data and hardware devices that it uses. “It treats the web and APIs as just more objects and places, and is a platform for writing and sharing your own code to manipulate those objects and places,” says developer Matt Webb, who unveiled the tool at last week’s O’Reilly Emerging Technology Conference in San Diego.

Craig Mundie, Science as a Web Service. XML can supercharge research, Technology Review, March/April 2006.
http://www.technologyreview.com/InfoTech/wtr_16461,258,p1.html

Although my roots before joining Microsoft were in supercomputing, I believe that “extreme computing” and adding gigaflops (billions of floating-point operations per second) are no longer the optimal solutions to most scientific and technical problems. Today, scientists and engineers can buy or build 10-gigaflop desktop computers for around $5,000, and within the next several years, we will see similar supercomputing power at the chip level.

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