OpenOffice Framework Project

These notes relate to one of Marty Brandon's research projects. I am posting posting the ideas and development notes related to this project in the hope that it will stimulate and aid related research, result in useful feedback, or lead to fruitful collaborations. Please email your comments.

This was an experimental project that is now closed due to lack of time. Open Office still seems like a useful platform for developing a bioinformatics suite. Maybe explore this in the future. Compare the relative benefits of a system developed using Perl libraries, database, and Foswiki.

Description

OpenOffice is a highly extendable work environment that could be very useful for certain types of analyses. It offers the ability to make database connections, macros, and several language bindings. Several CMEM tools are being developed in OO Basic, a connection has been made to the CMEM Web database, and we are exploring how it might best be used to supplement the existing informatics structure.

Projects Using OO

mitocurator

GUI tool for managing the spreadsheets which are the source of data stored in MITOMAP. More info at the data curation project page.

haplogrid

A list of mtDNA alleles is submitted in a spreadsheet and a grid is generated which shows the number of sequences in each haplogroup that have a particular allele. A connection to the mito database is used to get the current list of haplogroups and their frequencies. Takes a few minutes to run.

DNA Compression

Set of basic functions for implementing part of a DNA compression project. The functions are probably too specific for anything else, but may be useful examples. More info is at the DNA Compression project page.

Freezer Database

Open Office forms used to provide a user interface to a set of tables in the CMEM Web database which stores information about biological samples. More info at the freezer database project page.

Gene Map Analysis

OO BASIC script for extracting SNP markers from a spreadsheet produced by the Gene Map assay.

Notebook

7/7/2009 - Have decided to focus more on web-based applications. OpenOffice provides a nice development environment and might be a very good core for a bioinformatics platform, but just not enough time, and our information projects are more web-centric. Will focus on mitocurator, and a small supporting library of functions that might be implemented for little jobs on an ad hoc basis.

1/25/2009 - Exporting modules as extensions seems to be the best way for sharing code. Extensions are created by exporting a library, which means that I will export two libraries, "Utilities" and "Projects" to share with those in the lab. The Projects library will contain modules used by on a few persons, but keeping track of only a couple libraries will simplify distribution. The easiest thing would seem to be a simple version number along with posting them on CMEM Web. Since the most popular application will be the freezer interface, they will be posted there.

1/21/2009 - Reorganized libraries and sent Leo code for Gene Map Analysis. Keep standard modules in the "Utilities" library and project-specific code in modules stored in the "Project" library. Copy modules to a specific document for distribution.

11/1/2008 - Can be a bit tricky trying to share the macros. OO stores has three separate categories: system wide, individual user, or document specific. Storing them in the document seems to be the easiest, but to share a standard library to someone else's collection of user scripts export the library and then import them as a BASIC file.