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bioLegato is a programmable graphic interface capable of handling a wide range of data types. bioLegato is:

bioLegato takes its initial inspiration from Steven Smith's GDE interface.

BioLegato internal menu format ideas
Unknown future TODO
Current version TODO List

PCD - Pythonesque Command Definition

PCDEdit - Graphical PCD editor

PCDEdit is a graphical editor that allows the BIRCH administrator to create and modify PCD menus. It should currently be considered an experimental application.

Semi-automated Add-Ons

Creation of the BioPCD language has drastically simplified the process of adding a program to a local copy of BioLegato. However, it still requires enough steps that would be daunting to most biologists. The architecture of BIRCH and BioLegato lends itself to automating almost all of these parts. This project would create a BioLegato Add-On wizard that would take as its starting point any 3rd party package that was installed on the user's system. The wizard would walk the user through the process of selecting files and directories for executables, documentation and ancillary data files (eg. scoring matrices, alternative genetic codes, lists of restriction enzyme recognition sequences). The wizard would create the appropriate environment variables and file paths, and a sample menu that suggests input file filters, program parameters, and viewers for displaying output. Finally, the wizard would let the user edit the menus and shell commands, until a working menu was achieved. The wizard would also have a mechanism for submitting the final menu as a BioLegato Add-On. The Add-On would be vetted and refined by Bit lab staff, and published to our web site, or directly incorporated into a subsequent release of BIRCH.


Table Canvas


Need a full functioned Find built into the table. Find should tell you how many hits were found, automatically select the rows (or cells?), have an next and previous feature. Search by regular expression, ignore case... the usual stuff.


bltable is a bioLegato interface for tabular data.

bltable ToDo List


bldb is a bioLegato interface for data objects. It is intended as a database client.

bldb concept

Migration to github


Although originally written for bioinformatics, BioLegato is potentially useful in many fields. As well, development is currently limited by lack of funding. Therefore, we would like to expand the base of developers so to expand the capabilities of BioLegato, as well as ensuring its ongoing support.

Up to now, BioLegato has been an intrinsic part of the BIRCH system, and this page was the definitive site for planning BioLegato development.


Choice of Java version

We almost certainly need to go with Java8 as the development version. All new operating systems typically have Java17+, and Java11 is probably the most common version in production, there are still many older systems on which Java8 is the default. RHEL 7 reaches End of Life on June 30, 2024.

Conclusion: Current BioLegato development will be in Java8.

Choice of IDE

Must be able to compile using Java8.

Articles comparing IDEs for Java

Apache NetBeans


The most recent Eclipse requires Java11, but you can compile using any version of Java 8 or later.

Oracle JDeveloper


Before committing to any specific way of managing the Git repository, it will be best to create a test Git repo to try things out. Let's make mistakes and learn using a test site, and then do it right with BioLegato.

Migration path

1. Plan layout to make things easy for end users and developers.

2. Implement main page and a few ancillary pages

3. Push the code base to Git and test checkout, modify and push

4. Start with a few easy bug fixes or simple changes to shake down the working process.

Working principles


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