Missing alumni

Every time there’s a class reunion, the class officers send out a list of people from the group who they’ve lost touch with. Well, I have my own list of people that disappeared from my life, who I wonder what happened to.

For instance, Lavinia, a cute girl from my kindergarten class. Her family moved to Phoenix. I don’t even know her last name.

In elementary school it was Pam Hartley. We really liked each other in second grade, but she never returned to school after that. I guess she only moved one town over, but I never saw or heard from her again.

At the top of my list is Ellen Rubin. A year ahead of me in school, she went up to high school, but by the time I got there her family had moved. I’ve often searched, but never found her.

Speaking of junior high school, there was my music teacher, Miss Lerer. She was a porky little thing when I had her, but between one year and the next she lost a ton of weight and turned cute. Alas, I recently saw her obituary. Several of my old teachers have died, including a couple of the best teachers and best people. But I wonder what my old teachers Miss Ciannavei and Mrs. Gelpke, both of whom I think are still living, are up to nowadays.

High school friend Paula Nahabedian’s family moved away. Sue Wald is out there somewhere, and I owe her an apology. Virginia Peters. Alda Glover. Where are they now?

Even college friends have disappeared: Glori Feinstein, Lori Oshansky, Abby Hacker, Alma Souza, Cindy Goozh … And from the beach, Maya Laurinaitis and Beetle Donati, and the folks with whom I did summer theatre.

I wonder what become of the folks with whom I attended Phillips Academy’s Short Term Institutes. I wonder where my old BESGL friends are.

And old work friends, and friends of friends – Peter Paige, Brenda Ortiz, Chet Shuman, and everyone from H&S; Judy Reardon, Bob Jordan, Gwen Wharton, Susan Boulanger, and many other old Globe friends; and Christine and Debbie from Long Island. All of them live in the pre-social networking era. All of them are lost to me now.

I hope you’re all well. I miss you. I think of you more than you might expect.

Lee needs work

After a year of posting a daily blog entry for my employer, I’m going a little stir-crazy with nothing productive to do. If you’ve visited my site recently you’ll notice a new look – I put in a new WordPress theme, and added an archive sidebar. Might as well keep the place looking fresh, even if there’s not much new content.

For reproducible research, go to Madagascar

Reproducible research is, or should be, a tenet of any scientific endeavor. In today’s world, it means integrating results of published computational experiments with software and the data necessary for reproducing the experiments. Madagascar, an open source software package for scientific analysis of large digital datasets such as those occurring in geophysics, focuses on promoting reproducible research. Madagascar is used primarily by exploration geophysicists, but it can be employed for other scientific applications as well.

Madagascar comes from the Stanford Exploration Project. With the help of his students, including Madagascar project leader Sergey Fomel, geophysicist Jon Claerbout created an environment for reproducible computational experiments at his lab there. The environment worked at Stanford but was too complicated and clumsy to be shared with other groups, Fomel says. In addition, published results quickly lost reproducibility because nobody maintained them. “During my Ph.D. studies at Stanford in the late 1990s, I was inspired by the free and open source software movement and decided that the proper way to promote reproducible research was by turning it into an open source project,” Fomel says. “I started working on Madagascar (previously named Regularly Sampled Format) in 2003. The project got publicly released under the GPL in 2006. Since then, around 25 people have joined the community and contributed to development.

“We use C in the number-crunching part of Madagascar for optimal efficiency and for staying close to the hardware. We provide APIs for users who want to develop scientific codes in other languages, including C++, Fortran, Matlab, Python, and Java. We use Python for gluing the number-crunching code together into data processing workflows and for integrating them with publications. SCons, a Python-based open source replacement for make, provides a particularly useful environment. Python is a clean and easy-to-learn scripting language, which seems perfect for the task.”

Fomel says he released the software as open source because the open source philosophy matches the thinking behind reproducible research. “Reproducible research is a way of communicating computational results in a scientifically meaningful way so that other people could reproduce, verify, and extend them. Open source software works on the same principle. It is a natural match.

“SourceForge.net was attractive for us because it has the reputation for hosting famous open source projects and because it provides all the necessary tools for organizing an open source community: the Subversion server, the file server, mailing lists, etc. However, we miss the Compile Farm feature, which was useful for testing installation on different platforms and was one of the original attractions.”

Madagascar reached a big milestone last week with its release of version 1.0. “We had a particular goal for 1.0,” Fomel says, “which was a system for automatic testing. Once a computational result is archived in a reproducible form, it serves as a regression test for further development. We wanted a system for running such tests automatically. When a system like that was developed (in a community effort, with invaluable contributions from Joe Dellinger, Jim Jennings, and Nick Vlad), we could release 1.0.”

But this version is just one milestone for the project, Fomel says. “The collection of reproducible research papers will expand. We hope to diversify from geophysics to other scientific fields that work with large multidimensional data. There will be better tools for large-scale parallel computations and better documentation for existing tools. We have been doing two releases per year, which seems to catch major improvements, but that rate might accelerate.

“We could definitely use some help. New scientific applications, graphical user interfaces, better visualization, a cleaner Python framework are some of the areas where someone could contribute. The best way to get in touch is by writing to the mailing lists for users or developers.”