BioLegato

From Bioinformatics.Org Wiki

Jump to: navigation, search

Click here to go back to: Bioinformatics


bioLegato DEVELOPERS WIKI

Contents

Description

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
Changelog

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.

BioLegato_-_Semi-automated_Add-Ons

Table Canvas

Find

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

bltable is a bioLegato interface for tabular data.

bltable ToDo List

bldb

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

bldb concept

Migration to github

Rationale

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.

Goals

Testing

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.

Links

Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox