# Doyen is a GPL Cooperative Effort

The Doyen project is a cooperative effort of the Center for Algorithms and Interactive Scientific Software (CAISS) and Red Hat.

Doyen is a Science Platform. It features a Live CD that contains free and open source science software and a Wiki user interface that runs on a laptop. It also features a host-based Wiki that allows drag-and-drop movement of literate programs. These literate programs contain both Latex and program source code and are automatically expanded into documentation, compiled, and added into the local system.

# IDEA 1: Rosetta, a collection of CA systems

Rosetta is a collection of free and open source computer algebra systems. There are, at this time, approximately 100 such packages.

The idea was to collect these systems onto a CD and distribute them as part of the free conference materials. Due to space limitations the CD had to be customized to the conference. The systems included on the CD for any given conference were chosen to support the papers which were presented.

# IDEA 2: Knoppix, a Live CD

The Live CD, of which Knoppix is the most famous, is a CD which contains a Linux system which can be booted on any computer.

The Live CD is arranged so it does not use the hard drives on the machine but works directly from a compressed file system on the CD. This compressed file system allows the CD to hold 2.3 Gigabytes of data. Thus it is possible to boot a computer which normally runs Windows and have a fully functional Linux system. Removing the CD and rebooting will bring back the natively installed operating system. Note that it is possible to install a full, new copy of the operating system on the hard drive if desired.

# IDEA 3: Quantian, Free Quantitative Software

Quantian is a combination of the two previous ideas, except that it specializes the selected software to be quantitative software.

When you boot a Quantian Live CD you have the following packages:
• R, a statistics package
• bioperl, biopython
• blast2, clustalw, emboss, hmmer
• Octave
• Maxima, Pari/GP, GAP, GiNaC, YaCaS, Axiom
• GSL, the GNU Scientific Library

# IDEA 4: Wiki, a User Modifiable Website

A Wiki is a website which any user can modify. Wikipedia is the most famous example.

Axiom has a Wiki website as its home page. Pages on this website can be written using Latex. When changes to the page are saved the Latex program is used to render the page. Since most of the scientific community is familiar with Latex they do not need to learn a separate Wiki language.

Another crucial feature is that it is possible to embed commands for computer algebra systems inline with the text. Thus if you wish to invoke an Axiom command you would use:
\begin{axiom}
axiom commands here
\end{axiom}

and if you wish to invoke REDUCE you would use:
\begin{reduce}
reduce commands here
\end{reduce}


# IDEA 5: Combine Rosetta and Quantian

Now we begin to combine ideas. The combination of the Rosetta idea and the Quantian idea gives us a bootable CD for computer algebra.

In fact, the idea can be extended to any area of science. We could make a specialized CD for physics, chemistry, biology, etc. by collecting free and open source software packages that are useful for those sciences.

# IDEA 6: Combine Wiki and Laptop

In order to provide a common front-end to the various systems we layer a local Wiki on top of the scientific software.

This allows scientists to write papers in Latex which can invoke the various pieces of software inline. If we extend the inline idea to invoke various science software packages we are able to do:
\begin{ScienceSoftware}
ScienceSoftware commands here
\end{ScienceSoftware}


# IDEA 7: Literate Programming

Literate programs allow a person to distribute a single document which contains both the theory and the source code for implementing the theory.

Scientists can collaborate using the online and offline Wiki to write papers using Latex and a variety of scientific software. The Wiki pages contain not only the scientific paper, they contain the software and working examples. These papers become a permanent record of the research and, since they include the code, become the basis of further research work.

# IDEA 8: Drag and Drop

Once a literate program exists on the Wiki it can be dragged from the online version onto the local version running on a user's laptop.

The online Wiki contains a literate program. We can automatically extract the Latex form of the paper and render it into several formats. We can also automatically extract the source code, compile it, and load it into the local wiki environment on a laptop.

# IDEA 9: Doyen Platform

The Doyen platform consists of two parts, an online Wiki and a laptop environment which can be booted from a live CD.

As an example suppose that you write a paper on the online Wiki and present it at a science conference. While presenting the paper you mention that it is available online and give the URL.

Members of the audience have all recieved the Doyen CD as part of their free conference materials. Any member of the audience can boot the CD, visit the URL, drag and drop your paper onto the local Wiki. The paper is formatted, the code is compiled and added to the local environment. The audience member can now run your examples and experiment with your code while your talk proceeds.

# IDEA 10: Doyen Conference Distribution

Red Hat will provide distribution services at various conferences as part of the free conference materials.

The Doyen CD can be customized to a wide range of scientific conferences. It can also be customized to schools or businesses. This gives a direct, immediate distribution path for scientific work to a very wide audience.