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Pymerase Docs - FAQ
Pymerase Docs - FAQ
Brandon King & Diane Trout
Copyright © California Institute of Technology
Version 0.1.6 May 2, 2003
Contents 1 FAQ - General
1.1 How do you pronounce Pymerase?
1.2 Why the name 'Pymerase'?
1.3 Where was Pymerase originally developed?
1.4 What is the Wold Lab?
1.5 Who originally developed Pymerase?
1.6 What was the original purpose of Pymerase?
1.7 What License is Pymerase distributed under?
1.8 Does Pymerase support all versions of ArgoUML and/or XMI?
2 FAQ - Bin
2.1 General
2.1.1 How do I run Pymerase?
2.2 Pymweb
2.2.1 What is Pymweb?
3 FAQ - Input Modules
3.1 parseGenexSchemaXML
3.1.1 Does the parseGenexSchemaXML input module only parse the GeneX project schema?
3.2 parseXMI
3.2.1 What happend to Jython?
3.2.2 Does parseXMI support all versions of XMI?
4 FAQ - Output Modules
4.1 General
4.1.1 What modules do hope to include in the future?
4.2 CreateDBAPI
4.2.1 What does CreateDBAPI do?
4.3 CreateSQL
4.3.1 What does CreateSQL do?
4.4 CreateGraphvizUML
4.4.1 What does CreateGraphvizUML do?
4.4.2 How can I create a postscript from my generated .dot file?
5 FAQ - Glosary
5.1 What does API stand for and what does it mean?
6 FAQ - Contributing to Pymerase
6.1 Can I contribute to Pymerase?
6.2 What ways can I contribute?
6.3 How can I help fund development and how will it help?
1 FAQ - General
1.1 How do you pronounce Pymerase?
Pie mer ase - The Py in Pymerase
comes from Py in Python and the merase comes from the word
Polymerase. See section 1.2 for more information.
1.2 Why the name 'Pymerase'?
Pymerase is the combination of 'Python', the primary language Pymerase
is written in, and 'Polymerase'. Polymerase, in short, is a molecule
which copies/converts DNA into RNA. We figured that Pymerase had
similar functionality in that it took table.dtd XML (DNA) files and
converted them into other things, such as SQL statements (RNA) which
is then used to create a database (Protein).
1.3 Where was Pymerase originally developed?
Pymerase was originally developed in the Wold Lab at the California
Institute of Technology (Caltech).
1.4 What is the Wold Lab?
The Wold Lab, run by Barbara Wold, is a Bioinformatics / Biology Lab at the
California Institute of Technology. The Lab consists of both
biologists and computational members. For more information visit
http://woldlab.caltech.edu/.
1.5 Who originally developed Pymerase?
Diane Trout and Brandon King originally developed Pymerase in the Wold
Lab at Caltech. Barbara Wold is the principal investigator in charge of
the project at Caltech, along with collaborator Eric Mjolsness of
UC Irvine.
1.6 What was the original purpose of Pymerase?
The original purpose of Pymerase was to generate a Python Database API
for the GeneX Microarray Gene Expression Database. As development
progressed Pymerase was made more generic to support other projects
defined in UML such as Sigmoid and MAGE.
1.7 What License is Pymerase distributed under?
Pymerase is distributed under the MIT license which can be found in
the source code of Pymerase or on the web at
http://www.opensource.org/licenses/
1.8 Does Pymerase support all versions of ArgoUML and/or
XMI?
Please see section 3.2.2 for more information.
2 FAQ - Bin
2.1 General
2.1.1 How do I run Pymerase?
There is a document called "Pymerase Docs - Running Pymerase" which
you should find useful. It covers four ways in which you can run
Pymerase. These include, in python, command line, GUI, and web
interfaces.
2.2 Pymweb
2.2.1 What is Pymweb?
Pymweb is web front end for running Pymerase. It's useful if you would
like to maintain one installation of Pymerase or if you would like to
expose Pymerase to a number of users.
3 FAQ - Input Modules
3.1 parseGenexSchemaXML
3.1.1 Does the parseGenexSchemaXML input module only
parse the GeneX project schema?
No. It's called parseGenexSchemaXML to give credit to the GeneX
project for coming up with the file format used for this particular
input module and the schema of the GeneX 2.x project. The format can
be used to make any number of schemas using it. Special thanks goes to
Jason Stewart of OpenInformatics.org for the original design of this
XML format.
3.2 parseXMI
3.2.1 What happend to Jython?
parseXMI use to use a Java xmi parser which prevented parseXMI from
running under Python. Now parseXMI is using SMW, which is a python xmi
parser, so we no longer need Jython. We are no longer supporting
Jython as we would like to use Python v2.2 features. Jython is
currently (5/2/2003) at v2.1.
3.2.2 Does parseXMI support all versions of
XMI?
No. Unfortunately, the XMI standard is still developing rapidly, so
different versions of XMI can become incompatible with previous
versions. Supporting XMI was difficult in the first place as it's a
complicated standard.
I will have to compile a list and post it to the Pymerase website as
soon as I figure out which versions of ArgoUML, Poseidon, and the SMW
UML programs are compatible with parseXMI.
If you want to know more information on which versions of ArgoUML
export the version of XMI that Pymerase can read, please e-mail the
mailing list pymerase-devel at lists.sourceforge.net.
4 FAQ - Output Modules
4.1 General
4.1.1 What modules do hope to include in the future?
In the future we hope to include many more output modules. One of the
output modules we hope to develop is the generation of a C++ API which
then could be swig wrapped to allow many different languages like,
Python, Perl, and Java to use the same generate API.
4.2 CreateDBAPI
4.2.1 What does CreateDBAPI do?
CreateDBAPI generates a Python Database API for a given
schema. Currently the generated DBAPI is only compatible with
PostgreSQL databases. With some work, it could be ported to other
Relational Database Management Systems such as MySQL or Oracle.
4.3 CreateSQL
4.3.1 What does CreateSQL do?
CreateSQL generates a file containing SQL statements for the creation
of a PostgreSQL database for a given schema.
4.4 CreateGraphvizUML
4.4.1 What does CreateGraphvizUML do?
CreateGraphvizUML creates a .dot file which describes the
relationships of objects in your schema. This file can then be used by
the Graphviz program 'dot' to generate a UML like diagram of your
schema. This is great if you are using the Table.dtd format used by
Pymerase.
4.4.2 How can I create a postscript from my generated
.dot file?
You can use the command 'dot -Tps -o fileName.ps fileName.dot' to
generate a postscript file. See the man page for dot for more options.
5 FAQ - Glosary
5.1 What does API stand for and what does it mean?
API - Application Programming Interface
An API provides set of standard building blocks for programmers to use
to make custom applications which interface to a particular resource.
6 FAQ - Contributing to Pymerase
6.1 Can I contribute to Pymerase?
Yes, anyone with the will to help may contribute to the Pymerase
project. Be it with programming skills, documentation, examples, money
or good old moral support, we could use all the help we can get. If
you would like contribute in any way please send an e-mail to
pymerase-devel at lists.sourceforge.net or contact on of the current
developers.
6.2 What ways can I contribute?
Pymerase as an open source project services from the support of the
Open Source community. Any help is welcome. Becoming a programmer
is probably the most obvious way to help, but is not the only way one
can contribute.
Here is just a small list of things one can do to help:
- writing documentation
- testing code
- creating examples
- updating the web site
- contributing expertise
- contributing ideas
- funding development
Please send e-mail to the mailing list pymerase-devel at
lists.sourceforge.net if you would like to contribute in any way.
6.3 How can I help fund development and how will it help?
If you would like to help fund the Pymerase project or other projects
in the Wold Lab please contact Barbara Wold or send an e-mail to
pymerase-devel at lists.sourceforge.net. You can find out more about
the Wold Lab in section 1.4
Additional funding for Pymerase would help in many ways. First of all,
Diane and myself (Brandon) also work on other projects in the Wold
Lab, so not all of our time goes into the project. Funding would help
with the continuing development by providing more time for us to work
on the project or the hiring of more programmers to work on the
project.
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Last Modified: Friday, 21-Mar-2003 02:43:07 UTC
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