ALife data standards tools
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Overview
This is a repository which will contain tools designed to work with the ALife community data standards.
The tools here fall broadly into two categories, which define the organization of this repository:
- (1) converters
- (2) everything else (tools)
Tools
The tools directory contains tools that work with files in the standards format. Tools are usually scripts or programs that perform analyses, visualizations, or intermediate data processing.
Currently, each tool in the tools directory is contained within a folder with a readme that describes the tool and the tool itself. This way of organizing tools may, however, become unwieldy in the future and is thus subject to change (suggestions are welcome!).
Converters
Data conversion tools translate data files from non-standard file formats to a standards-compliant file format and vice versa. Data conversion tools can be found in the converters directory.
Within the converters directory, for each system that we have a conversion script/program for, there is a directory associated with that particular system. Each system-specific directory should contain a readme that gives a high-level description (at least a sentence or two; e.g., system X does digital evolution) of the system and, if possible, references to a publication that describes the system. Please create an issue for inadequate readmes!
Conversion tools should follow the following naming scheme: [standard data type]_[system]2std
or [standard data type]_std2[system] (e.g., genome_mabe2std.py, phylogeny_avida2std.py).
Again, in the future we may find this naming scheme to be inadequate; suggestions
for changes are welcome!
Other tools
Web apps
Tools in this category cannot be housed in this repository because they are set up as web applications. However, they have been tested on the latest version of the standards and found to work. If you run into issues using a web app with standard-compliant data (e.g., the tool is down or out of data), file an issue.
- Phylogeny visualizer
- Description: Upload a standards-compliant phylogeny file and this website will draw a tree based on it. If you have additional fields in your data, you can color the nodes based on them.
Third-party tools
This section contains links to tools that the standards maintainers have not yet vetted.