Find open-source science resources

This tool estimates the completeness of KEGG pathway modules from the presence or absence of KEGG orthologues (KOs)

RAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.

Databank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.

linkset-automation is a set of tools to automatically generates CyTargetLinker linksets from different resources, starting with WikiPathways.

Generates pre-miRNA and mature miRNA count tables from read alignments to pre-miRNA sequences and a gff file, both downloaded from mirBase. Produces also read coverage plots of pre-miRNAs.

blue-crab is a tool to convert from ONT POD5 format to the community maintained SLOW5/BLOW5 format. Lossless nanopore pod5 s/blow5 file conversion.

SMBGC Annotation using Neural Networks Trained on Interpro Signatures

RFantibody is a pipeline for structure-based de novo antibody and nanobody design, integrating backbone design with RFdiffusion, sequence design with ProteinMPNN, and structure prediction with RoseTTAFold2. It provides a comprehensive toolset for generating and filtering high-quality antibody designs.

CebraEM is a bioinformatics tool for analyzing and processing large-scale imaging data, providing a pipeline for segmentation, annotation, and analysis with support for both Linux and Windows environments. It includes modules for core functionality, annotation, and network analysis, requiring specific dependencies and a conda environment for execution.

Efficient foundation model and benchmark for multi-species genome understanding with context-aware nucleotide representations, improving upon DNABERT for diverse genomic task transfer learning (UIUC MAGICS Lab, 484+ stars)

The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.

The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.

Short Python script (using Biopython library functions) to extract sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given by a column of a tabular file. The output order follows that of the tabular file, and if there are duplicates in the tabular file, there will be duplicates in the output sequence file.

Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime.

SEACR: Sparse Enrichment Analysis for CUT&RUN

Subvolume processing scripts with the TOM toolbox is a collection of scripts form a pipeline for subvolume alignment and averaging of electron cryo-tomography data.

A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities.

thromboSeq is a bioinformatics tool designed for the analysis of thrombosis-related sequencing data, providing functionalities for variant calling, annotation, and functional interpretation. It streamlines the processing of high-throughput sequencing data to identify genetic variants associated with thrombotic disorders.

Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

RxDock is a fast and versatile open-source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and binding mode prediction studies.

Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly

Simple test framework for Nextflow pipelines