Notes and observations on software for (mostly) scientific applications.
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Friday, December 06, 2002
GFORGE
Some good news (via Hack the Planet) about GForge, an open source version of SourceForge.
A key piece of open-source infrastructure is back, and not enough people have heard, yet. When VA Software Corp. took Tim Perdue's GPLed SourceForge project proprietary (or rather, took proprietary the only component it owned, the "alexandria" set of glue code), following the v. 2.5 release, development slowed for a number of reasons, including the multiplicity of open-source forks[1] and VA Software's unfulfilled promise of a GPLed alexandria 2.7 release (announced for August 2000 release, but then silently dropped).
As of this past weekend, Tim Perdue is back, with GForge (http://gforge.org/), a greatly cleaned-up successor forked from VA Software's final beta, alexandria 2.61pre4. Tim has removed a great deal of unnecessary code and optimisations specific to sf.net (eliminating dependencies and simplifying installation), cleaned up the user interface, removed the little-used "foundry" feature, and added support for Jabber instant messaging. (It's important to note that gforge.org doesn't itself offer project hosting, but rather the software required to run hosting sites.)
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10:28 AM
Monday, December 02, 2002
FRESHMEAT REVIEW
Recent Freshmeat items of interest:
- CwMtx - A library that provides the matrix and vector operations that are used extensively in engineering and science problems. A special feature of this library is the quaternion class which implements quaternion math. Quaternions are very useful for attitude determination in 3D space because they do not suffer from singularities. Furthermore, successive rotations and transformations of vectors can be accomplished by simple quaternion multiplication.
- Astro::FITS::Header - Tools for reading, modifying and then writing out FITS standard header blocks to FITS and NDF files.
- wlog - A real-time signal analyzer using wavelets.
- duplicity - Encrypted bandwidth-efficient backup using the rsync algorithm.
- Buildtool - A portable build infrastructure that can be used in the development of any kind of program. Basically, it simplifies the build process of a program from user's point of view, by automatically configuring the source code with specific details of the host system; it also makes developer's work easier because all Makefile complexity is hidden and behavior is homogenized.
- Source Navigator - A source code analysis tool. With it, you can edit your source code, display relationships between classes and functions and members, and display call trees. You can also build your projects, either with your own makefile, or by using Source-Navigator's build system to automatically generate a makefile.
10:22 AM
RELATIONAL MODELING OF BIOLOGICAL DATA
One of the many challenges facing the bioinformatics community is representing the hierarchical information structures they work with in relational databases. Aaron Mackey addresses this issue in Relational Modeling of Biological Data: Trees and Graphs. After reviewing publicly available biological data and projects, Mackey gets down to brass tacks:
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While these projects have rich public Web sites for browsing and downloading the data, none of them provide the means to compute on the data, to relate your own data to theirs, or to query across the disparate resources. Fortunately, all of these data sources can be freely obtained by ftp or anonymous cvs for integration into a local, custom-made relational database. But how does one represent hierarchical data in a relational database? And, more importantly, how can one make efficient use of such data?
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10:08 AM
AXIOM/ALDOR
The AXIOM symbolic algebra system is no longer available as a commercial product from NAG. The good news is that NAG is apparently working on an open source release. Already available is Aldor, the standalone library compiler for AXIOM. The Axiom site hosts a mailing list for those interested in the project. It also contains an interesting document called the Rosetta, which shows how to perform the same actions in all of the currently available symbolic algebra systems.
9:48 AM
LISPING AT JPL
A friend sends notice of Lisping at JPL by Erann Gat, a highly personal tale of the decline and fall of the use of Lisp at NASA's JPL. Here's the really grim part:
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Now, you might expect that with a track record like that, with one technological success afte another, that NASA would be rushing to embrace Lisp. And you would, of course, be wrong.
The New Millennium missions were supposed to be the flagships for NASA's new "better, faster, and cheaper" philosophy, which meant that we were given a budget that was impossibly small, and a schedule that was impossibly tight. When the inevitable schedule and budget overruns began the project needed a scapegoat. The crucial turning point was a major review with about 200 people attending, including many of JPL's top managers. At one point the software integration engineer was giving his presentation and listing all of the things that were going wrong. Someone (I don't know who) interrupted him and asked if he could change only one thing to make things better what would it be. His answer was: get rid of Lisp.
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9:39 AM
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