Our group has started a project called the Scriptome to provide experimental biologists with tools for exploring and manipulating biological data. (I mentioned it in an exploratory email to the list a couple months ago.) We're not targeting the complicated bioinformatics tools that EMBOSS, Bioperl, etc. provide. Rather, we want to help bench biologists to "eyeball", filter, format, and analyze the many large files they get from those and other programs. While these tasks may be trivial for a programmer, not every bench biologist has the time or inclination to become a programmer - especially those who do computational analysis only occasionally. http://cgr.harvard.edu/cbg/scriptome has an alpha version. There's a (small) set of tools up, including a "Fetch" tool that uses Bioperl. You might also want to look at the Principles & FAQ pages where we talk about the thinking behind the project & the particular solution we chose. We taught a debut 3-hour session to two groups of five biologists in the last few weeks, showing them how to find and use the tools. Newbies were excited that they could filter files in five minutes, instead of five hours of hand-editing. People who knew a bit of Perl appreciated that the tools were not "black box"; they could tweak the tools to be more useful, while learning more Perl on the side. Of course, it remains to be seen how many people use The Scriptome after the class is over. We're currently using an extremely lightweight interface to allow quick tool development, and to free occasional users from needing to learn & remember yet another "intuitive" GUI. We may want to change that (e.g., a lite version of Catherine Letondal's Pise http://www.pasteur.fr/recherche/unites/sis/Pise/ ? SeWeR?), but any change in interface requires wrestling with some frustrating pluses & minuses. For example, the current interface requires no install whatsoever for almost all the tools, just Perl on Unix. This project struggles with big questions: teaching programming skills to non-programmers, optimizing human-computer interface, and understanding biologists' (changing) needs. But even if we can't solve all of these problems, I believe this project can help to address an unmet need for a large group of scientists. We invite submissions of new tools (optionally including code) or "protocols" (series of tools) to be added to the site. I'd also be happy to get advice and feedback about the project in general. Thanks for listening, - Amir Karger Computational Biology Group Bauer Center for Genomics Research Harvard University