ricomnl Goto Github PK

followers: 38.0 following: 17.0 repos: 94.0 gists: 5.0

Name: ricomnl

Type: User

Company: retro.bio

Bio: I'm interested in computational biology and artificial intelligence.

Twitter: ricomnl

Location: Bay Area

Blog: https://ricomnl.com

Hi there 👋

Currently @ retro.bio. I'm interested in gene regulatory networks, bioelectricity and longevity.

Scientific Software

nf-encyclopedia - A NextFlow pipeline for chromatogram library DIA proteomics workflows

Contributions:

scvi-tools
redun
kb_python
During the bitsinbio hackathon in March '22, I contributed to graphein
EncyclopeDIA - a library search engine comprised of several algorithms for data independent acquisition (DIA) mass spectrometry data analysis: encyclopedia
Gopher - Gene ontology enrichment analysis using protein expression: gopher

Some other stuff I've worked on:

Semantic Podcast Search (using Lex Fridman's AI podcast)
Accompanying code to my blog post Bioinformatics pipeline example from the bottom up: bioinformatics-pipeline-tutorial
Instacart2vec: My bachelor thesis on using word2vec for online grocery recommendations

While participating in the How To Grow (Almost) Anything course on Synthetic Bio:

Opentrons protocol to draw 8x8 digits in 96-well plates: opentron_digits
Protein structure analysis of KLF4 using nglview: protein_structure_analysis | online docs

Fun projects

Tensor Puzzle exercises put together by @srush_nlp
WIP: Nand2Tetris

Twitter: @ricomnl

Website: https://ricomnl.com

ricomnl's Projects

bioinformatics-pipeline-tutorial

A tutorial on how to create bioinformatics pipelines as bash scripts, Makefiles and using tools like Nextflow.

capsule-networks-methods

An implementation of CapsNets with Dynamic Routing using Methods

In this seminar paper I will describe the motivation behind Capsule Networks including its advantages over Convolutional Neural Networks which are the current state-of-the art technique for object detection and image classification.

chess-oracle

chessoracle

chromex

cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cookiecutter-hypermodern-python

Hypermodern Python Cookiecutter

countland

tools in python and R for analyzing biological count data, especially from single cell RNAseq

crx-hotreload-no-page-refresh

Watches for file changes in your Chrome extension's directory. When a change is detected, it reloads the extension and refreshes the active tab (to re-trigger the updated scripts).

cv-tricks.com

Repository for all the tutorials and codes shared at cv-tricks.com

decoupler-py

Python package to infer biological activities from omics data using a collection of methods.

deepdock

Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules

dockingpp

drawio

ee123_bioelectricity

EE123 - Intro to Bioelectricity by Joel Grodstein from Tufts University (https://www.ece.tufts.edu/ee/123/)