cjneely10
University of Southern California class of 2021. Quantitative Biology and Computer Science
DOE Systems Biology KnowledgebasePico Rivera
cjneely10's Stars
hmmlearn/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
steineggerlab/foldmason
Multiple Protein Structure Alignment at Scale with FoldMason
soedinglab/ffindex_soedinglab
elastic/elasticsearch
Free and Open, Distributed, RESTful Search Engine
mpi4py/mpi4py
Python bindings for MPI
moritzbuck/mOTUlizer
Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin
dingp/spin-acme
NVIDIA/NeMo
A scalable generative AI framework built for researchers and developers working on Large Language Models, Multimodal, and Speech AI (Automatic Speech Recognition and Text-to-Speech)
NVIDIA/TensorRT-LLM
TensorRT-LLM provides users with an easy-to-use Python API to define Large Language Models (LLMs) and build TensorRT engines that contain state-of-the-art optimizations to perform inference efficiently on NVIDIA GPUs. TensorRT-LLM also contains components to create Python and C++ runtimes that execute those TensorRT engines.
microsoft/MS-DOS
The original sources of MS-DOS 1.25, 2.0, and 4.0 for reference purposes
monarch-initiative/talisman
LLM-based gene function enrichment tool
cultivarium/GenomeSPOT
Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome
Chainlit/chainlit
Build Conversational AI in minutes ⚡️
snap-stanford/MLAgentBench
nschloe/matplotx
:bar_chart: More styles and useful extensions for Matplotlib
niemasd/TreeCluster
Efficient phylogenetic clustering of viral sequences
promptfoo/promptfoo
Test your prompts, agents, and RAGs. Red teaming, pentesting, and vulnerability scanning for LLMs. Compare performance of GPT, Claude, Gemini, Llama, and more. Simple declarative configs with command line and CI/CD integration.
linkml/linkml
Linked Open Data Modeling Language
mol-evol/panGPT
A Generative Pre-Trained Transformer Package for Pangenomes
helix-editor/helix
A post-modern modal text editor.
stanfordnlp/dspy
DSPy: The framework for programming—not prompting—foundation models
zellij-org/zellij
A terminal workspace with batteries included
nushell/nu_scripts
A place to share Nushell scripts with each other
refresh-bio/kmer-db
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
conda/conda-lock
Lightweight lockfile for conda environments
psf/black
The uncompromising Python code formatter
sourmash-bio/sourmash_plugin_branchwater
fast, multithreaded sourmash operations: search, compare, and gather.
aqlaboratory/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
pylint-dev/astroid
A common base representation of python source code for pylint and other projects
astral-sh/uv
An extremely fast Python package and project manager, written in Rust.