mrhedmad/handbook

The Handbook contains concise, practical information on a variety of topics.

I'm Luca, and these are my repositories.

I work as a PhD student at the University of Turin, Italy in the Complex Systems for Life Sciences program. I'm a bioinformatician, working with everything genomic and transcriptomic related.

I'm an author and the maintainer for (almost) all packages in my laboratory's organization.

If you want to learn more about me, take a look at my ABOUT page. It contains more information on what I do, as well as my Curriculum Vitae and publication lists.

I really like collaborating with others. If you want to collaborate, check the CONTRIBUTING files in the repository for the project you want to contribute to, or contact me directly!

I administrate bioinfo.ds, a bioniformatics-centered community on Discord.

📨 Contact Me

All my contact information lives in my linktree. I strive to keep it up-to-date!

My projects

This is a (possibly incomplete) list of my finished, abandoned (💀) and current (🚧) projects. I look at this when I want to feel good about myself.

🔨 Tools

• Kerblam! and Kerblam usage examples: a Rust tool / project management system that makes your life easier when dealing with data analysis.
• Metasplit: a Python tool to break up (large) CSV files column-wise based on an external metadata file.
• Panid: a Python tool to convert between different IDs (e.g. ensembl, HGNC, etc...).
• Fast Cohen's D: a small Rust tool to calculate Cohen's D.
• BioTEA: a containerized Python tool to analysi microarray expression.

📖 Resources

• 🚧 The Data Stewardship Knowledgebase: an aggregator of links related to data stewardship, open science and data management in general.
• 💀 The Handbook was meant to be the place to go to when looking for code style guides, how-tos and more.
• 🚧 Mimir: a policy to handle data for a research group with little resources in a FAIR way.
• A tiny guide to Make, which converts to this website.
• The code for my blog, which you can read here.
• 💀 The Data Myr specification, the precursor to Mimir.
• Programming notes some notes and exercises on the usage of R.
• The Membrane Transport Protein database, a database of transporters.
• ICT-Bib, a database of papers about transporters.

📦 Libraries

• Bonsai a Python library to handle Tree like data structures. It's very easy to use.

🔬 Data analyses

• 🚧 Transportome Profiler, the main analysis of my PhD thesis.
• 🚧 Data analysis project structure: an analysis on the structure of data analysis projects.
• Turin author network: an analysis of the co-authorship network between the authors of the university of Turin.
• Code used in my Master thesis.

📝 Papers and preprints

• A Typst paper template to jumpstart paper writing in Typst.
• A Latex paper template to jumpstart paper writing in Latex.
• 🚧 Code of the paper for Kerblam!

🛸 Others

• My dotfiles
• Milton: my Discord bot.
• 💀 Chip 8 implementation in Rust (which does not really work).

handbook's Issues

The python script to rebuild the indexes does not sort the index values by name

The title of the page is extracted by the python script (in the PageGobbler, the .title attribute). It should be used to order the lines in the index alphabetically, so that:

• They are easier to read;
• Produce smaller git conflicts.

It should be an easy fix (note that the formatted index_lines have their alphabetical order depend on just the title)!

Setup a pre commit hook to remake the indexes on commit

The Python script to remake the index does not respect nested binders

It currently makes shallow indexes, while nested indexes (perhaps with the content of the README file in each directory) are to be preferred.

The Python script to remake the index does not make working links