README.md

# DEEP Computational Metadata

## Identification
This repository can be cited in publications using the following DOI:

[DOI: 10.17617/1.2W](http://doi.org/10.17617/1.2W "https://github.molgen.mpg.de/DEEP/comp-metadata")

Also consider citing the corresponding publication listed [below](#Reference).

## Process documentation
In DEEP, standardized computational analysis pipelines are documented in form of so-called *Process* specifications.
A *Process* document lists required input and reference files, specifies the output generated by the pipeline and
provides a step-by-step description of the computational analysis.
*Processes* are in XML format and are rendered into a readable form when opened in a standard web browser
(assuming an active internet connection). They are lightweight enough to be send via e-mail to collaboration partners.

[Proceed to Process documentation](docs/process.md)

## Creating new *Process* documents


## Analysis documentation
Each run of a standardized pipeline produces an *Analysis* metadata document at the end. These are simple tab-separated
text files listing all input, output and reference files as well as non-default parameters in form of *key-value*
entries. Whereas a *Process* document has to be manually created and describes an analysis pipeline in generic form,
an *Analysis* metadata file is created automatically. Consequently, these files are not accessible via this repository.

## Reference
See the corresponding publication in Oxford Database for details:

["A general concept for consistent documentation of computational analyses", *Database* 2015](https://dx.doi.org/10.1093/database/bav050)

The [supplemental material](publication/) is also available in this repository. Please note that this material is just kept for reference, and is considered outdated. Please **do not use it** to create new *Process* documents.