SMPDB - Small Molecule Pathway Database
An interactive, visual database containing more than 30,000 small molecule pathways found in humans.
YMDB - Yeast Metabolome Database
The Yeast Metabolome Database contains detailed information about the small molecule metabolome of Saccharomyces cerevisiae.
DrugBank
A comprehensive, freely accessible, online database containing information on drugs and drug targets.
HMDB - Human Metabolome Database
The Human Metabolome Database is a comprehensive, freely available electronic database containing detailed information about small molecule metabolites found in …
PathBank
Pathway database for analyzing protein expression and connecting that information to other omics data. Contains 110,000 pathways from 10 model …
RIpred
Retention Index predictor is a web server that uses machine learning to predict the Kovats' Retention Index (RI) of compounds …
RT-Pred
Retention Time Predictor is a web server that takes a submitted structure and uses ML to accurately predict the retention …
PredEI
A bidirectional neural network to predict EI-MS spectra. Outperforms NEIMS with improved parent ion intensity prediction and is able to …
BioTransformer
Predicts "biofeasible" transformation products using ML methods and a large database of chemical constraints. Capable of performing Phase I, Phase …
Euklid
Web-based Eukaryotic genome annotation system. Fast (30 sec – 3 minutes per genome), interactive genome and circos plots. Provides 60-65 …
Evolutionary Algorithm Game AI
Implementation of evolutionary algorithms for game AI behavior, adapted from population genetics methods used in bioinformatics.
FAIR Data Management Toolkit
Tools and guidelines for implementing FAIR data principles in bioinformatics research. Includes metadata schemas, data validation scripts, and repository templates.
R Bioinformatics Starter Kit
Collection of R scripts and tutorials for common bioinformatics tasks. Includes data import, visualization, statistical testing, and pathway analysis examples.
Containerized Workflow Pipeline
A complete Nextflow pipeline for RNA-seq analysis packaged with Docker containers. Includes quality control, alignment, quantification, and differential expression analysis.
Introduction to Genomic Variant Analysis
Comprehensive tutorial covering SNV and indel analysis, including quality control, annotation, and interpretation of genomic variants in disease research.