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alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.

alphafold

Open source code for AlphaFold.

antismash

antiSMASH

big-scape

Similarity networks of biosynthetic gene clusters

bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

boltzmann

Simulation software for biochemical systems that use mass action kinetics based on maximum entropy production.

caffe2

Caffe2 is a lightweight, modular, and scalable deep learning framework.

ccms-sps

conda-build

Commands and tools for building conda packages

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deepdist

Distributed Deep Learning on Spark

demos

deseq2

Differential gene expression analysis based on the negative binomial distribution

doubledutch

doubledutchapi

genui-gui

GenUI frontend application. It provides a GUI to the GenUI REST API web services.

glmnet

:exclamation: This is a read-only mirror of the CRAN R package repository. glmnet — Lasso and Elastic-Net Regularized Generalized Linear Models. Homepage: https://glmnet.stanford.edu, https://dx.doi.org/10.18637/jss.v033.i01, https://dx.doi.org/10.18637/jss.v039.i05

guacamol

Benchmarks for generative chemistry

lace

Building SuperTranscripts: A linear representation of transcriptome data

libsbol

C++ implementation of SBOL 2.2.0.

paintomics3

Integrative visualization of multiple omic datasets onto KEGG pathways.

pdb-redo-builder

Docker files to create an image you can use to build pdb-redo executables that run on older OS's like CentOS

protter

a customizable protein feature visualization tool

singularities

soymeta

Large scale meta-analysis of soybean

spark

Mirror of Apache Spark

synbiohub

Web application enabling users and software to browse, upload, and share synthetic biology designs

synbiohub-docker

tellurium

Python Environment for Modeling and Simulating Biological Systems