The Third Bit

SourceForge has announced that nominations are open for this year’s Community Choice Awards. This time around, any project can be nominated, not just SF-hosted ones. So please, nominate your favorite open source project Awards will be handed out at OSCON 2008.

Announcements

“The Student Council of the International Society for Computational Biology (ISCB) invites you to attend the 4th ISCB Student Council Symposium. This student-organized event will be held at the Metro Toronto Convention Center in Toronto on July 18th. It will bring together bioinformatics and computational biology students for scientific exchange, networking and career-development. Both undergraduate and graduate students are welcome!”

See http://symposium.iscbsc.org for details — it’s only $60.

Announcements

Source Code for Biology and Medicine is a peer-reviewed journal from BioMed Central devoted to, well, source code for biology and medicine. It’s been around for at least a couple of years; based on a quick scan of four of their most popular papers, they seem to cover everything from getting and installing software to its numerical properties, user interface, and typical applications. This is very cool—but why isn’t there something like this for computer science? All I can think of are Software: Practice & Experience and The Journal of Systems and Software, both of which are one meta removed from SCBM.

Learning, Research, Software Carpentry

Registration is now open—it looks like it’ll be a good hands-on content-ful show.

Announcements

Todd Veldhuizen‘s UbiGraph dynamic graph visualization software is now available. The demos are very cool (though they could use a soundtrack); you should give it a try.

Announcements

Via Dobbs Code Talk (which has a brief summary), a pointer to a Google talk about “How to Protect Your Open Source Project From Poisonous People“.

Uncategorized

The New York Times ran a piece today on the under-representation of women in the sciences—in the Fashion and Style section, of course, because hey, women don’t read the business pages, do they? *sigh*

Later: a friend pointed me at this piece in the Boston Globe, titled “The Freedom to Say No”. Its basic thrust is that women are scarce in STEM (science, technology, engineering, and mathematics) because they’d rather do other things. There’s acknowledgment of “rampant sexism” (the article, quoting a study), but most of the article is based on “men like things, women like people, so self-selection explains the imbalance”. It’s a pity its author appears not to have read Ceci and Williams, or s/he might have realized just how many holes there are in that argument.

Equity

…or maybe even dinner, if you will build a usable table differencing tool.  I have some SQLite database files under version control that I need to merge (updated on my laptop yesterday while flying, not remembering that I’d made some updates on my desktop machine as well).  Ditto spreadsheets: I store all my grades in Excel now, but every once in a while, I have to merge changes made at home with changes made in the office. Both are multi-tabular data (“multi” because there can be many tables in a database, and many worksheets in a spreadsheet); after images, I’d guess tabular is the most common format that people want to put into version control that diff(1) can’t deal with. I can’t promise wealth or fame, but you’d sure be popular.

Uncategorized

I left Toronto for Austin mid-day Wednesday, and got back at midnight last night. Lots happened in the interim, so here’s a linkandthoughtdump (which I bet actually is one word in German):

• Gave a talk about Beautiful Code to the Austin Python Users’ Group Wednesday at Enthought‘s swanky offices. (They’re the kind folks who provide web hosting for the Software Carpentry course.) About 27 people in attendance, and good discussion afterward; was grateful to Travis Vaught and Sergey Fomel for rides from the airport and to the hotel respectively.
• Gave another talk titled “HPC Considered Harmful” at the Texas Advanced Computing Center‘s Second Annual Scientific Software Days. I was a bit nervous about telling people at a supercomputing center that focusing on massive parallelism and peak performance is wrongheaded, but there were a lot of nodding heads.
• I made lots of notes from two other talks that I want to follow up on at some point:
  • Robert van de Geijn’s FLAME system lets you draw matrix operations, then automatically generates the corresponding high-performance code. It’s a great example of a real high-level programming tool for scientists (and yet another special case of what a real extensible programming system would support).
  • Eric Jones (also from Enthought) talked about a tool they’re building that watches changes to variables in Python programs, and automatically generates interactive plots of their values. It sounds simpler and less impressive than it actually is; I’ve asked him to put together a screencast, and I think you’ll be wowed—I was. (Later: Steve Eddings from The Mathworks sent me a link about data linking in MATLAB, complete with a video tutorial.)
• At roughly the same time, half a world away, Diomidis Spinellis presented a study comparing the code quality of Linux, Windows, OpenSolaris, and FreeBSD. Very cool work; wish I’d been at ICSE’08 to ask questions.
• Meanwhile, Dmitri Vassiliev, who is continuing his work on SlashID this summer, has discovered that generated code is next-to-impossible to debug. Not to be a one-note symphony or anything, but I said in that same article about extensible programming systems that the real challenge is not extending notation, but creating extensible debugging tools so that those notations and high-level representations can be fixed when they break. Robert van de Geijn doesn’t think FLAME needs a debugger; respectfully, I disagree.
• Science in the Open has a plea to scientists to make their raw data available, motivated by yet another irreproducible result.
• Kosta Zabashta has posted early thoughts about integrating IRC into DrProject. (Gray on black? Kosta…your design skills rival mine…) I need to tell him that DrProject’s RPC module doesn’t handle tickets because Jeff Balogh is going to replace the entire ticketing system with an extensible one this summer, using his Dojo Form Editor as a front end…
• Elisabeth Hendrickson has thoughts on automating tests for legacy web applications. Students, take note.
• Thanks to Nick Jamil and others, we have instructions for installing DrProject on Windows. Yay!
• Everything old is new again, including Ada and the Bletchley Park Colossus.

And then there’s this:

Thanks again to Sergey Fomel for inviting me down, and for introducing me to the reproducible research community—I’m looking forward to many more discussions.

Beautiful Code, DrProject, Python, Research, Software Carpentry

Some of our summer interns have started blogging about their projects:

• Dojo Form Editor
• DrProject Admin
• DrProject IRC Integration
• DrProject Testing & Documentation
• DrProject Ticketing
• Flare Dataflow Editor
• Hackystat Data Visualization
• Hackystat and Visual Studio
• OpenAFS Console
• OS161 Visualization
• SlashID
• Web-CAT

I’ll add more as I get them.

Learning