Search Results for "bioinformatics with python cookbook"
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Showing 82 open source projects for "bioinformatics with python cookbook"
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Llama Cookbook
Solve end to end problems using Llama model family
The Llama Cookbook is the official Meta LLaMA guide for inference, fine‑tuning, RAG, and multi-step use-cases. It offers recipes, code samples, and integration examples across provider platforms (WhatsApp, SQL, long context workflows), enabling developers to quickly harness LLaMA models -
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E2B Cookbook
Examples of using E2B
E2B Cookbook is an open-source collection of example projects, guides, and reference implementations demonstrating how to build applications using the E2B platform. The repository acts as a practical learning resource for developers who want to integrate AI agents with secure cloud execution environments that allow large language models to run code and interact with tools. The examples illustrate how developers can build AI workflows capable of performing tasks such as data analysis, code... -
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ai-cookbook
Examples and tutorials to help developers build AI systems
ai-cookbook is an open-source repository that provides practical tutorials, code examples, and reusable snippets designed to help developers build real-world artificial intelligence applications quickly. The project focuses on delivering hands-on engineering guidance rather than theoretical explanations, allowing developers to copy, adapt, and integrate working code directly into their own systems. The repository contains examples that demonstrate how to build AI workflows using modern tools... -
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OpenAI Cookbook
Examples and guides for using the OpenAI API
openai-cookbook is a repository containing example code, tutorials, and guidance for how to build real applications on top of the OpenAI API. It covers a wide range of use cases: prompt engineering, embeddings and semantic search, fine-tuning, agent architectures, function calling, working with images, chat workflows, and more. The content is primarily in Python (notebooks, scripts), but the conceptual guidance is applicable across languages. -
Connect with customers in one appDialpad Connect is an AI-powered unified communications platform that combines voice, video, and messaging to enhance team collaboration and customer interactions. It features real-time call transcription, automated call summaries, and AI-generated action items to help users stay focused during conversations. The platform integrates seamlessly with popular business apps like Salesforce, Zendesk, Microsoft Teams, and Google Workspace to streamline workflows. Designed for businesses of all sizes, Dialpad Connect delivers enterprise-grade reliability with 100% uptime SLA and robust disaster recovery. Security and privacy are core priorities, meeting standards like GDPR, HIPAA, and SOC 2 compliance. Dialpad Connect helps companies elevate customer experiences while boosting team productivity.
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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
AWS ParallelCluster is an AWS supported Open Source cluster management tool that makes it easy for you to deploy and manage High Performance Computing (HPC) clusters in the AWS cloud. Built on the Open Source CfnCluster project, AWS ParallelCluster enables you to quickly build an HPC compute environment in AWS. It automatically sets up the required compute resources and a shared filesystem and offers a variety of batch schedulers such as AWS Batch and Slurm. AWS ParallelCluster facilitates... -
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Granite TSFM
Foundation Models for Time Series
...The repository focuses on end-to-end workflows: loading data, building datasets, fine-tuning forecasters, running evaluations, and serving models. It documents the currently supported Python versions and points users to where the core TSFM models are hosted and how to wire up service components. Issues and examples in the tracker illustrate common tasks such as slicing inference windows or using pipeline helpers that return pandas DataFrames, grounding the library in day-to-day time-series operations. The ecosystem around TSFM also includes a community cookbook of “recipes” that showcase capabilities and patterns. ... -
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Codon
A high-performance, zero-overhead, extensible Python compiler
Codon is a high-performance Python compiler that compiles Python code to native machine code without any runtime overhead. Typical speedups over Python are on the order of 100x or more, on a single thread. Codon supports native multithreading which can lead to speedups many times higher still. The Codon framework is fully modular and extensible, allowing for the seamless integration of new modules, compiler optimizations, domain-specific languages and so on. -
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AlphaFold 3
AlphaFold 3 inference pipeline
AlphaFold 3, developed by Google DeepMind, is an advanced deep learning system for predicting biomolecular structures and interactions with exceptional accuracy. This repository provides the complete inference pipeline for running AlphaFold 3, though access to the model parameters is restricted and must be obtained directly from Google under specific terms of use. The system is designed for scientific research applications in structural biology, biochemistry, and bioinformatics, enabling... -
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MedgeClaw
Open-source AI research assistant for biomedicine
MedgeClaw is a specialized AI-powered research assistant tailored for biomedical and scientific workflows, built on top of OpenClaw and Claude Code architectures. It integrates a large library of domain-specific skills, enabling it to perform complex analyses in areas such as genomics, drug discovery, and clinical research. The system connects conversational interfaces with computational environments, allowing users to initiate research tasks through messaging platforms while the backend... -
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LLaMA Models
Utilities intended for use with Llama models
This repository serves as the central hub for the Llama foundation model family, consolidating model cards, licenses and use policies, and utilities that support inference and fine-tuning across releases. It ties together other stack components (like safety tooling and developer SDKs) and provides canonical references for model variants and their intended usage. The project’s issues and releases reflect an actively used coordination point for the ecosystem, where guidance, utilities, and... -
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audioFlux
A library for audio and music analysis, feature extraction
A library for audio and music analysis, and feature extraction. Can be used for deep learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. audioflux is a deep learning tool library for audio and music analysis, feature extraction. It supports dozens of time-frequency analysis transformation methods and hundreds of corresponding time-domain and frequency-domain feature combinations. It can be provided to deep learning networks for training and is used to... -
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DGL
Python package built to ease deep learning on graph
Build your models with PyTorch, TensorFlow or Apache MXNet. Fast and memory-efficient message passing primitives for training Graph Neural Networks. Scale to giant graphs via multi-GPU acceleration and distributed training infrastructure. DGL empowers a variety of domain-specific projects including DGL-KE for learning large-scale knowledge graph embeddings, DGL-LifeSci for bioinformatics and cheminformatics, and many others. We are keen to bringing graphs closer to deep learning researchers.... -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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Fastq-Fasta Converter
A bioinformatics tool that converts Fastq into Fasta
Fastq-Fasta Converter is a desktop application that converts Fastq files into Fasta files. -
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Armadillo
fast C++ library for linear algebra & scientific computing
* Fast C++ library for linear algebra (matrix maths) and scientific computing * Easy to use functions and syntax, deliberately similar to Matlab / Octave * Uses template meta-programming techniques to increase efficiency * Provides user-friendly wrappers for OpenBLAS, Intel MKL, LAPACK, ATLAS, ARPACK, SuperLU and FFTW libraries * Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. * Downloads:... -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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DataPrep
Python-based data preprocessing tool
DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal... -
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A... -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Python codes can be supported upon request. Article: Gemi: PCR primers prediction from multiple alignments Comparative and functional genomics 2012;2012:783138 DOI: https://doi.org/10.1155/2012/783138 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 PMCID: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535827/ -
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Parallel and Distributed Process System
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of the Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author Computational Neuroscience: Large-scale neural population dynamics, brain-inspired... -
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LLM Cookbook
LLM Introduction Tutorial for Developers, Chinese version
LLM Cookbook is an open-source learning repository designed to help developers understand how to build applications powered by large language models through practical examples and translated course material. The project adapts and reproduces content from widely known LLM developer courses and reorganizes it into a structured learning path tailored for developers who want to build real AI applications. It covers the essential topics required to start working with LLM APIs and frameworks,... -
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LaTeX Cookbook
A comprehensive LaTeX template with examples for theses, books, etc.
This repo contains a LaTeX document, usable as a cookbook (different "recipes" to achieve various things in LaTeX) as well as a template. The resulting PDF covers LaTeX-specific topics and instructions on compiling the LaTeX source. -
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Code Cookbook
Reusable code patterns which you can use as reference or copy
Reusable code patterns which you can use as reference or copy to your project. Achieve small or large tasks using recipes that contain steps, scripts, and config files. -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome...
