The CybertoryTM project is brought to you by Attotron Biotechnologies Corporation.
Please send us email if you have questions, comments, or feedback.
Robert M. Horton, PhD
Bob is the Principle Investigator of the Cybertory project. He founded Attotron Biotechnologies in 1997, and currently serves as Director of Research. He received his PhD in Biomedical Sciences in 1991 from the Mayo Graduate School in Rochester, Minnesota, where he studied Molecular Biology in the Department of Immunology. More recently, he finished his master's degree in Computer Science from California State University in Sacramento, earning a diploma signed by Arnold Schwarzenegger.
Bob can pretty much be blamed for any aspect of this project not otherwise credited. He designs the user interfaces, maintains the websites, administers the databases, keeps the application server running, builds data sets, develops exercises, conducts workshops, and stands by to answer your questions. Feel free to browse his CV, or to contact Bob directly if you have questions or comments.
Carl was lead developer of the PCR simulation server, the 'back-end' Java application that does the actual searches of primers against genomic sequences, and manages genotypes of individuals. He now lives in Missouri, where he works as a computer engineer, designing fire alarm and suppression systems.
Long ago (in a college far away), Bill double majored in Biology and Computer Science, before such an unlikely combination was even fashionable. He has worked at several companies, mostly programming in Perl, and sometimes working on what would now be called bioinformatics. On the Cybertory team, Bill developed the Microarray Scan Simulator, his first major Java project. He is currently pursuing a Master's in Nutrition at UC Davis, where he takes courses in statistics and microarray data analysis for fun.
Joe is a C/C++ programmer's programmer, having left school to work as a game developer during the dot com boom. He updated the code of the venerable autoseq base caller so that it now compiles on GCC, and is better optimized for our application. Joe also set up and administered our original development servers, and saved the day on several occasions when the other developer's enthusiasm began to get the better of their Linux administration knowledge. Having (finally!) completed his Computer Science degree at CSU Sacramento, Joe now works at Intel Corporation.
Camille Bodley Troup, PhD
Camille received her Ph.D. in Pharmaceutical Chemistry from UCSF, and has worked for several major biotechnology and pharmaceutical companies, in addition to teaching.
She headed development of the HIV Genotyping exercise; this was a walk down memory lane for her, since she developed a similar assay while working at Applied Biosystems. She has also helped with developing and working the bugs out of other exercises, especially Shotgun Sequencing.
Developing educational software in a field as technical as molecular biology requires teachers and scientists to work in close collaboration with software developers. While such collaborations can be quite rewarding, they can also be quite challenging, especially as the number of key participants and distinct skill sets grows.
To mitigate some of these challenges, we have designed Cybertory as a software platform, where the exercises are embodied in data sets and protocol documentation, but are not built into the software. New exercises using these simulators can be developed by teachers and scientists, without extensive additional software development. Many science instructors, particularly at the university level, have the combination of skills required to develop exercises on this platform. Performing the exercises requires troubleshooting skills similar to those needed in a real laboratory, and teachers with laboratory experience can put it to use guiding their students through the problem-solving process.
This work has been funded by a Small Business Innovation Research (SBIR) grant from the US National Institutes of Health. The purpose of these grants is to support small businesses in developing products deemed desirable by the funding agency. Our commercial products and services are being developed on our sister site, cybertory.com, where we are currently recruiting beta testers. The commercial site builds upon the simulation modules presented here. It adds a "virtual laboratory" interface which connects the various simulations to solutions held in virtual reaction tubes, which are manipulated with a micropipette, and affected by incubations, thermal cycling, enzymes, pH, and so forth. Exercises are incorporated into a course management system (moodle), which provides a full-featured framework for online courses, including quizzes, discussion forums, schedules, and other resources and services that make on-line instruction easier and more effective.
While the commercial site will (eventually) offer paid services, cybertory.org will remain free, both in the sense of not charging money, and in the sense that the code and the documentation on this site are freely available under "copyleft" licenses.
"Open source" means a copyleft arrangement for software. The source code for software is the human-readable set of instructions for how the program should behave, written in a computer language like Java, C, or Perl. If the source code is open, it means you technically have access to read and modify the program. If it is released under an open source license, it gives you the legal right to modify it, and share it with others. The licenses we have applied to our work are described in the next section below.
There are two reasons we have made the reaction simulation modules open-source:
First, they can serve as vehicles for collaboration with academic scientists. If you are a researcher or bioinformatician with an interest in modeling molecular biology reactions, you may find these modules to be useful starting points. You are free to modify, redistribute, and use them in accordance with their open source licenses, which means that the result of your work will also be open source.
Second, these modules have been released to encourage scientists and teachers to create educational resources based upon the simulations. An exercise consists of appropriate starting data (DNA sequences, expression profiles, etc) for specification of "virtual reagents", together with a protocol for an experiment to perform using these "reagents". Third-party exercise developers are not expected to have extensive programming experience. Releasing the open source modules assures prospective exercise developers that the platform for their exercise will always be available for their own use and for distribution to others at no charge.
The commercial platform will be designed so that exercises developed for the open source modules will be easily used there as well. In addition, the commercial platform will include support for more extensive experiments, such as those involving multiple modules working together, or those requiring user data to be stored on the server for multiple sessions.
Web Site Terms
This product is not intended for use in aircraft control systems or for operating nuclear power plants.
Server Software License
Our server-based simulations are available for you to run on your own server, under the terms of the GNU Affero General Public License. This is a 'copyleft' software license specifically designed for server software. If you modify the software and let the public access it on a server, you must release the modified source code under the same terms.
In addition to the software we have developed for the Cybertory project, most of the software used on this site is open source, with the following exceptions:
- The family tree is run in PerlGED, a shareware program. You are expected to pay a registration fee to use that program on your web site. The contents of the family tree are available in GEDCOM format, and should be loadable into other geneology programs, including open source family tree software such as PHPGedView.
Unless otherwise noted, all images and artwork on this site are copyrighted by Attotron Biotechnologies Corporation, and are made available under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 License. Most of the vectored illustrations have been created in Inkscape, an open source SVG-based drawing program. This makes it technically easy for you to save and edit the illustrations, while the Creative Commons license allows you to use either the originals or your modified versions under these same terms.
In brief, you are free to copy, distribute, display, and make derivative works under the following conditions:
Attribution: You must attribute the work to the author (without implying their endorsement of you or your use of the work).
Noncommercial: This license does not permit you to use this work for commercial purposes.
Share Alike: If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one.
For any reuse or distribution, you must make clear to others the license terms of this work. The best way to do this is with a link to the Creative Commons license web page. If you want to use these works under other conditions, get permission from the copyright holder.
This work was funded by NIH SBIR grant 2R44RR013645-02A2 to Attotron Corporation.
These simulators build upon a foundation of open source and public domain software and technologies:
- Ubuntu Linux
- Apache web server
- NCBI Blast
- autoseq base caller (by Reece Hart)
- GNU Compiler Collection (GCC)
- CyberDuck Mac OS X SFTP client.
This work was also greatly facilitated by non open-source software created by commercial entities (including some freeware and shareware):
- Mac S X 10.5 operating system (with built-in TimeMachine backup software. Thank you, thank you!)
- TextEdit text editor (freeware from Bare Bones Technologies)
- Poser (for images of simulated people)
- Graphic Converter image conversion and manipulation program (shareware)
- PerlGED web-based family tree viewer
- VMware Fusion virtual machine host (to run a Linux server on a MacBook for development)