arXiv subjects

Alva Couch

Publications and source records attributed to Alva Couch.

3 recordsLinked to original sources

arXiv2026

MEDFORD in a Box: Improvements and Future Directions for a Metadata Description Language

Scientific research metadata is vital to ensure the validity, reusability, and cost-effectiveness of research efforts. The MEDFORD metadata language was previously introduced to simplify the process of writing and maintaining metadata for non-programmers. However, barriers to entry and usability remain, including limited automatic validation, difficulty of data transport, and user unfamiliarity with text file editing. To address these issues, we introduce MEDFORD-in-a-Box (MIAB), a documentation ecosystem to facilitate researcher adoption and earlier metadata capture. MIAB contains many improvements, including an updated MEDFORD parser with expanded validation routines and BagIt export capability. MIAB also includes an improved VS Code extension that supports these changes through a visual IDE. By simplifying metadata generation, this new tool supports the creation of correct, consistent, and reusable metadata, ultimately improving research reproducibility.

cs.DL↗

arXiv2022

MEDFORD: A human and machine readable metadata markup language

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.

cs.DL↗

arXiv2021

On system rollback and totalised fields

In system operations it is commonly assumed that arbitrary changes to a system can be reversed or `rolled back', when errors of judgement and procedure occur. We point out that this view is flawed and provide an alternative approach to determining the outcome of changes. Convergent operators are fixed-point generators that stem from the basic properties of multiplication by zero. They are capable of yielding a repeated and predictable outcome even in an incompletely specified or `open' system. We formulate such `convergent operators' for configuration change in the language of groups and rings and show that, in this form, the problem of convergent reversibility becomes equivalent to the `division by zero' problem. Hence, we discuss how recent work by Bergstra and Tucker on zero-totalised fields helps to clear up long-standing confusion about the options for `rollback' in change management.

cs.DC↗