Search Results for "bioinformatics with python cookbook"
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25 projects for "bioinformatics with python cookbook" with 1 filter applied:
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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. -
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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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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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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:... -
Build Securely on Azure with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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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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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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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). -
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for.... -
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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DoCookBook
Cookbook Style Document for DocBook Customizations
This project has been moved to GitHub: https://github.com/tomschr/dbcookbook/ The DoCookBook project aims to create an open source book about DocBook and the DocBook XSL stylesheets written as a cookbook and released under a Creative Commons license. -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.
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A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.
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The dispatcher provides loosely-coupled message passing between Python objects (signal senders and receivers). It began as one of the highest-rated recipes on the Python Cookbook website
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PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.
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E-Cookbook is an electronic cookbook or recipe organizer. It will replace the old tattered cookbook in your kitchen. Easily decide on something to make for dinner, or see what you can make based on the ingredients in your refrigerator.
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openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database
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Disease Gene Profiler (DGP) comprises of a set of (bioinformatics) tools that can be used to identify the genes underlying susceptibility to common multifactorial diseases (such as diabetes, asthma and cancer) using freely available datasources.
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Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
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BlueBook.. The Value of Code. A Zope product to provide a code snippet repository. Provides a "learn by example" environment, and cut&paste type code sharing. It is a "cookbook" in which snippets are "Recipes" that contain code and can be rated.
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Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.
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