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| Key Concepts, Desmond User Guide |
The basic ideas underlying software for molecular dynamics simulations, and how the application suite fits into a typical researcher's workflow |
| Introducing GemStone/J | High-level overview of a J2EE application server |
| Scaffold User's Guide | Tutorials for a proteomics application |
| SRXL Satellite Tuner User's Guide | How to install, configure, and operate a PCI Bus board that receives radio signals from a satellite, digitizes them, and transfers them to host memory |
| GeometryExpressions User's Guide | Concepts and tutorials for an educational geometry application |
| Tuning Peformance in GemStone/S | Performance-tuning a large object database and application server |
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Key Concepts © 2008 D. E. Shaw Research. All rights reserved. Reproduced by permission. 328 KB PDF |
Desmond is a suite of collaborating applications for carrying out molecular dynamics simulations, which model the motion of a collection of atoms over time according to the laws of classical physics. This introduction explains the underlying concepts, then describes how Desmond fits into the workflow of a computational chemist. I was initially unfamiliar with molecular dynamics simulations and read quite a bit at the start, before interviewing the developers.
Calendar time: about a week of reading, one day for interviews, and two weeks to write three drafts. Hours billed: about 60 |
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Introducing GemStone/J © 2000-2001 GemStone Systems, Inc. All rights reserved. Reproduced by permission. 80 KB PDF |
To introduce a J2EE application server to new users. I was somewhat familiar with the purpose of the app server, but Java and J2EE were new to me at the time.
Calendar time: one week for interviews, three days to write the first draft, one day to follow up on comments, and one last day to write the second (and last) draft. Hours billed: 82 |
| Scaffold User's Guide
© 2005 Proteome Software, Inc. All rights reserved. Reproduced by permission. 2.9 MB PDF |
Scaffold is an application for identifying proteins from mass spectrometry samples, developed and sold by Proteome Software. In under a month, I learned enough about proteomics to understand the application, helped design five tutorials and then wrote them, along with a brief conceptual overview.
I initially outlined a more conventional user's guide, but the company founder and chief architect opted for a five-task tutorial instead. My concern was that, while such a manual would be an excellent resource for those who run tutorials, not everyone has the time and interest to do so; meanwhile, the tutorial structure buries useful reference information deep within a long narrative. The compromise was to highlight reference information where it appears, by shading it light yellow.
Note The final version of this manual includes some work I did not do. The developer and others produced the final screen shots, the illustration callouts, and a few additional entries in the final table. I didn't have the opportunity to go over the final to fix bad page breaks. |
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SRXL Satellite Tuner Operator's Manual
© 2006 Engineering Design Team, Inc. All rights reserved. Reproduced by permission. 400 KB PDF |
Engineering Design Team makes PCI Bus boards that accept data from a wide variety of sources and get it into the memory of a host computer, where customers can write all sorts of applications to make use of it. The SRXL receives analog radio signals from a satellite, digitizes them, and collaborates with another EDT board to get the results into the host. People writing applications for the SRXL are highly technical; the manual describes custom hardware, firmware, and software.
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GeometryExpressions User's Guide
© 2006 Saltire Software, Inc. All rights reserved. Reproduced by permission. 804 KB PDF |
GeometryExpressions is a nifty application for teaching geometry developed and sold by Saltire Software. In my two weeks on this project, the developer gave me an in-depth demo, after which we collaborated in designing two tutorials. I then wrote the tutorials, plus a brief concepts chapter that covered the basics. Finally, a colleague tested the tutorials and found the bugs, which I fixed.
Note The final version of this manual includes some work I did not do. The developer and others produced the final screen shots, all the worked examples, and, with some guidance, the user interface reference. |
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Tuning Performance
© 2000-2001 by GemStone Systems, Inc. All rights reserved. Reproduced by permission. 264 KB PDF |
This chapter from the GemStone/S System Administrator's Guide describes how to use a performance analysis tool to inspect the complex choreography of bits passing among objects in memory, being copied to disk, or fetched back out. I organized it by known performance bottlenecks. Then I made sure that the performance analysis tool shipped with a set of templates to match, giving the user a coherent set of places to start in a thick combinatorial forest of possibilities.
Note I fear this sample is rough going for the uninitiated -- the terminology is a significant impediment, and we are peering through a magnifying glass, watching the bits scurry here, there, and yonder. For the curious and undaunted, I offer this brief glossary: Stone: the database monitor process
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