Doyen is a GPL Cooperative Effort
Axiom | Doyen@MathAction | Mailing List
The Doyen project is a cooperative effort of the Center for
Algorithms and Interactive Scientific Software (CAISS) and
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
- 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:
axiom commands here
and if you wish to invoke REDUCE you would use:
reduce commands here
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
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:
ScienceSoftware commands here
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
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
It can also be customized to schools or businesses. This gives
a direct, immediate distribution path for scientific work to a
very wide audience.