Search Results for "biology"
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Showing 273 open source projects for "biology"
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Awesome Network Analysis
A curated list of awesome network analysis resources
awesome-network-analysis is a curated list of resources focused on network and graph analysis, including libraries, frameworks, visualization tools, datasets, and academic papers. It covers multiple programming languages and domains like sociology, biology, and computer science. This repository serves as a central reference for researchers, analysts, and developers working with network data. -
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DeepChem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, etc
...All tutorials are designed to be run on Google collab (or locally if you prefer). Tutorials are arranged in a suggested learning sequence that will take you from beginner to proficient at molecular machine learning and computational biology more broadly. -
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CTK
CLIP Tool Kit (CTK)
CTK (CLIP Tool Kit) is a computational biology toolkit implemented in Perl, designed for analyzing CLIP sequencing data. It offers a streamlined pipeline from raw reads through peak calling and motif discovery. -
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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. The use of these result in beautiful, visually complex and accurate representations. -
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AlphaFold 3
AlphaFold 3 inference pipeline
...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 accurate modeling of proteins, ligands, and covalent modifications. Users can perform local predictions via Docker containers, integrating AlphaFold 3’s inference process with provided JSON input configurations. The software includes flexible options for running both data preprocessing and GPU-accelerated inference, allowing users to adapt to available computational resources. -
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CellTypist
A tool for semi-automatic cell type classification, harmonization
...Harmonization, match and harmonize cell types defined by independent datasets. integration, integrate cell and cell types with supervision from harmonization. CellTypist recapitulates cell type structure and biology of independent datasets. Regularised linear models with Stochastic Gradient Descent provide a fast and accurate prediction. Scalable and flexible. Python-based implementation is easy to integrate into existing pipelines. A community-driven encyclopedia for cell types. -
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Catalyst.jl
Chemical reaction network and systems biology interface
Catalyst.jl is a symbolic modeling package for analysis and high-performance simulation of chemical reaction networks. Catalyst defines symbolic ReactionSystems, which can be created programmatically or easily specified using Catalyst's domain-specific language (DSL). Leveraging ModelingToolkit and Symbolics.jl, Catalyst enables large-scale simulations through auto-vectorization and parallelism. Symbolic ReactionSystems can be used to generate ModelingToolkit-based models, allowing the easy... -
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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Protenix
A trainable PyTorch reproduction of AlphaFold 3
Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as “Protenix-Mini,” offering a trade-off between speed/compute cost and predictive accuracy — making structure prediction accessible even in resource-constrained environments. ... -
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Tellurium
Model, simulate, and analyze biochemical systems using one tool.
Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support.">
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TomoJ
ImageJ plugin to perform Electron Tomography
...TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL). registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. ... -
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...Until that paper is formally published, please cite our earlier work instead: Zhang Z, Xie PL, Guo YL, Zhou WB, Liu EY, Yu Y. 2022. Easy353: A tool to get Angiosperms353 genes for phylogenomic research. Molecular Biology and Evolution 39(12): msac261. Xie PL, Guo YL, Teng Y, Zhou WB, Yu Y. 2024. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Molecular Ecology Resources e139.
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
...Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337">
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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
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matcik svg editor
svg editor: Easily create documents for math, physics, chemistry...
Easily create documents for math, physics, chemistry, biology and other sciences... Book, exam and activity preparation program Easily import application vectors such as geogebra, chart, mathlive, ckeditor, desmos, into your document, or import vectors from pdf files into your document, save and rearrange your file. if you want You can use the documents you have prepared on your website or convert them to pdf. -
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MetaboReport
Metabolomics Data Analysis and Reporting Tool
Metabolomics, as an essential tool in systems biology, is now widely accessible to researchers of all levels. Yet challenges remain in data analysis and result interpretation. To address these challenges, we introduced MetaboReport, a versatile and interactive web app that simplifies metabolomics experiment design, data preprocessing, exploration, statistical analysis, visualization, and reporting. -
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AngClust
AngClust: Angle-based feature clustering for time series
Citation: Aimin Li, Siqi Xiong, Junhuai Li, Saurav Mallik, Yajun Liu, Rong Fei, Hongfang Zhou, Guangming Liu. AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles. January 2022. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. DOI: 10.1109/TCBB.2022.3192306 Full text: https://ieeexplore.ieee.org/document/9833353/ https://pubmed.ncbi.nlm.nih.gov/35853049/ Highlights * We proposed a novel clustering algorithm based on angular features for short-term gene expression profiles. * We defined three indicators to identify significant clusters: (i) the fluctuation degree of expression levels, (ii) homogeneity, and (iii) the degree of clustering while the clusters are functionally significant... -
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this address: https://plateeditor.sourceforge.io - The source code is also available on GitHub, visit: https://github.com/vindelorme/PlateEditor More information about the source code and the API are available there (the wiki is still under construction, thanks for your patience!) ... -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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DEVS-Suite Simulator
Component, CA, and CCA models; superdense time, DB repo, testing, etc.
Integrated component-based and cellular automata (CA) Parallel DEVS simulator: https://acims.asu.edu/devs-suite/ OFFERS: 1) synchronized execution & animation, 2) run-time linear/superdense I/O & state trajectories, 3) Action Level Real-Time modeling & simulation, 4) model checking, 5) ABM, 6) CA & composable CA playback, 7) KIB interaction modeling, 8) hierarchical model libraries, 9) Black-Box testing & debugging, 10) PostgreSQL repository, 11) FMU (OpenModelica), 12) OSATE (AADL) with domain-specific models: NoC; SW/HW co-design, Service-Oriented Computing, cancer biology, Dynamic Structure, SOA DEVS, MIPS32 processors, and computer networks for education. Version: 7.0 [Jan `23], 6.1 [Apr. `21], 6 [Sep. `20] , 5 [Jul. `19], 4 [Mar. `18], 3 [Apr. `15], 2.1 [Feb. `09], 2 [`03] See CoSMoSim: https://acims.asu.edu/software/cosmos : hierarchical visual modeling, database model repository, families of models, statecharts, partial-code generation for XML/DEVS-Suite model -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN.
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ARES
Antibiotic Resistance Evolution Simulator
...These genes can be located in the plasmid, in conjugative elements or in the chromosome; ii) plasmids and conjugative elements transferring genes between bacterial cells; iii) bacterial cells; iv) individual microbiotas where bacterial species coexist; v) hosts containing the microbiotic ensembles; vi) environment(s) where the hosts are contained. Our model facilitates the simultaneous analysis of several features of interest in the prediction of the rules governing the multi-level evolutionary biology of antibiotic resistance, according to a set of pre-established rules. The input of ARES can be prepared with the ARES xml generator server: http://gydb.org/ares. -
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SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.